diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5734b025910a9243ad0f9cdb799e2306066d9534..a5fee0b08f51801b05da44724d98512d8840f73f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -51,6 +51,7 @@ option(COMPILE_TESTS "whether unit tests should be compiled by default" OFF)
option(ENABLE_STATIC "whether static libraries should be compiled" OFF)
option(UBUNTU_LAYOUT "whether Debian/Ubuntu's lib and libexec directory layout should be used" OFF)
option(HIDDEN_VISIBILITY "on gcc, use -fvisibility=hidden" OFF)
+option(ENABLE_MM "whether openmm support is added" OFF)
if (CXX)
set(CMAKE_CXX_COMPILER ${CXX})
@@ -234,6 +235,10 @@ if(USE_NUMPY)
find_package(Numpy REQUIRED)
endif()
+if(ENABLE_MM)
+ find_package(OpenMM REQUIRED)
+endif()
+
if (ENABLE_IMG)
find_package(FFTW REQUIRED)
find_package(TIFF REQUIRED)
@@ -290,6 +295,7 @@ include_directories(${Boost_INCLUDE_DIRS}
${EIGEN2_INCLUDE_DIRS}
${TIFF_INCLUDE_DIR}
${PNG_INCLUDE_DIRS}
+ ${OPEN_MM_INCLUDE_DIRS}
)
if(USE_NUMPY)
include_directories(${PYTHON_NUMPY_INCLUDE_DIR})
diff --git a/cmake_support/FindOpenMM.cmake b/cmake_support/FindOpenMM.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..3c0890e392d343190b4abc376f81be5bdba19826
--- /dev/null
+++ b/cmake_support/FindOpenMM.cmake
@@ -0,0 +1,22 @@
+# Try to find OpenMM
+#
+# Once done this will define
+# - Find OpenMM
+# Find the native OpenMM includes and library
+#
+# OpenMM_INCLUDE_DIRS - OpenMM include dirs.
+# OpenMM_LIBRARIES - List of libraries when using OpenMM.
+# OpenMM_FOUND - True if OpenMM found.
+
+find_path (OPEN_MM_INCLUDE_DIR OpenMM.h)
+find_library (OPEN_MM_LIBRARY NAMES OpenMM)
+
+set(OPEN_MM_LIBRARIES ${OPEN_MM_LIBRARY})
+set(OPEN_MM_INCLUDE_DIRS ${OPEN_MM_INCLUDE_DIR})
+
+# handle the QUIETLY and REQUIRED arguments and set OpenMM_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (OpenMM DEFAULT_MSG OPEN_MM_LIBRARY OPEN_MM_INCLUDE_DIR)
+
+mark_as_advanced (OPEN_MM_LIBRARY OPEN_MM_INCLUDE_DIR)
diff --git a/modules/mol/CMakeLists.txt b/modules/mol/CMakeLists.txt
index d417b44124dae1b87b844ec98109a7856b796e32..ac68189a49e54e7d4512519f238c88c4a30b6762 100644
--- a/modules/mol/CMakeLists.txt
+++ b/modules/mol/CMakeLists.txt
@@ -1,2 +1,5 @@
add_subdirectory(base)
add_subdirectory(alg)
+if (ENABLE_MM)
+ add_subdirectory(mm)
+endif()
diff --git a/modules/mol/mm/CMakeLists.txt b/modules/mol/mm/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4468b05a8c86e042baeebb9b56f19468d9f2e4b5
--- /dev/null
+++ b/modules/mol/mm/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_subdirectory(src)
+add_subdirectory(pymod)
+add_subdirectory(tests)
diff --git a/modules/mol/mm/examples/1AKI.pdb b/modules/mol/mm/examples/1AKI.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..0a32657dd9011a3213a5809e94e0c56f10150611
--- /dev/null
+++ b/modules/mol/mm/examples/1AKI.pdb
@@ -0,0 +1,1358 @@
+HEADER HYDROLASE 19-MAY-97 1AKI
+TITLE THE STRUCTURE OF THE ORTHORHOMBIC FORM OF HEN EGG-WHITE
+TITLE 2 LYSOZYME AT 1.5 ANGSTROMS RESOLUTION
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: LYSOZYME;
+COMPND 3 CHAIN: A;
+COMPND 4 EC: 3.2.1.17
+SOURCE MOL_ID: 1;
+SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
+SOURCE 3 ORGANISM_COMMON: CHICKEN;
+SOURCE 4 ORGANISM_TAXID: 9031;
+SOURCE 5 CELL: EGG
+KEYWDS HYDROLASE, GLYCOSIDASE
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.CARTER,J.HE,J.R.RUBLE,B.WRIGHT
+REVDAT 2 24-FEB-09 1AKI 1 VERSN
+REVDAT 1 19-NOV-97 1AKI 0
+JRNL AUTH P.J.ARTYMIUK,C.C.F.BLAKE,D.W.RICE,K.S.WILSON
+JRNL TITL THE STRUCTURES OF THE MONOCLINIC AND ORTHORHOMBIC
+JRNL TITL 2 FORMS OF HEN EGG-WHITE LYSOZYME AT 6 ANGSTROMS
+JRNL TITL 3 RESOLUTION
+JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 38 778 1982
+JRNL REFN ISSN 0108-7681
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : GPRLSA, X-PLOR
+REMARK 3 AUTHORS : FUREY
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
+REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1
+REMARK 3 NUMBER OF REFLECTIONS : 16327
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : NULL
+REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
+REMARK 3 R VALUE (WORKING + TEST SET) : NULL
+REMARK 3 R VALUE (WORKING SET) : 0.212
+REMARK 3 FREE R VALUE : NULL
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
+REMARK 3 FREE R VALUE TEST SET COUNT : NULL
+REMARK 3
+REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
+REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
+REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
+REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
+REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
+REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
+REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 1001
+REMARK 3 NUCLEIC ACID ATOMS : 0
+REMARK 3 HETEROGEN ATOMS : 0
+REMARK 3 SOLVENT ATOMS : 78
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : NULL
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : NULL
+REMARK 3 B22 (A**2) : NULL
+REMARK 3 B33 (A**2) : NULL
+REMARK 3 B12 (A**2) : NULL
+REMARK 3 B13 (A**2) : NULL
+REMARK 3 B23 (A**2) : NULL
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
+REMARK 3 ESD FROM SIGMAA (A) : NULL
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.00
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
+REMARK 3 BOND LENGTH (A) : 0.009 ; 0.010
+REMARK 3 ANGLE DISTANCE (A) : 0.003 ; 0.025
+REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.024 ; 0.020
+REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
+REMARK 3
+REMARK 3 PLANE RESTRAINT (A) : 0.033 ; 0.030
+REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.212 ; 0.200
+REMARK 3
+REMARK 3 NON-BONDED CONTACT RESTRAINTS.
+REMARK 3 SINGLE TORSION (A) : 0.183 ; 0.300
+REMARK 3 MULTIPLE TORSION (A) : 0.159 ; 0.300
+REMARK 3 H-BOND (X...Y) (A) : 0.299 ; 0.300
+REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
+REMARK 3
+REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
+REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
+REMARK 3 PLANAR (DEGREES) : 7.900 ; 5.000
+REMARK 3 STAGGERED (DEGREES) : 17.800; 15.000
+REMARK 3 TRANSVERSE (DEGREES) : 18.900; 15.000
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 2.500 ; 3.000
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.900 ; 4.000
+REMARK 3 SIDE-CHAIN BOND (A**2) : 3.200 ; 4.000
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 3.000
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 1AKI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : NOV-95
+REMARK 200 TEMPERATURE (KELVIN) : 298
+REMARK 200 PH : 4.48
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : N
+REMARK 200 RADIATION SOURCE : ROTATING ANODE
+REMARK 200 BEAMLINE : NULL
+REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
+REMARK 200 MONOCHROMATOR : GRAPHITE(002)
+REMARK 200 OPTICS : NULL
+REMARK 200
+REMARK 200 DETECTOR TYPE : IMAGE PLATE
+REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU
+REMARK 200 DATA SCALING SOFTWARE : BIOTEX
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20571
+REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
+REMARK 200 RESOLUTION RANGE LOW (A) : 15.000
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1
+REMARK 200 DATA REDUNDANCY : 3.100
+REMARK 200 R MERGE (I) : 0.04400
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
+REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
+REMARK 200 DATA REDUNDANCY IN SHELL : NULL
+REMARK 200 R MERGE FOR SHELL (I) : NULL
+REMARK 200 R SYM FOR SHELL (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: NULL
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
+REMARK 200 SOFTWARE USED: X-PLOR
+REMARK 200 STARTING MODEL: PDB ENTRY 2LZH
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 42.84
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.48
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X+1/2,-Y,Z+1/2
+REMARK 290 3555 -X,Y+1/2,-Z+1/2
+REMARK 290 4555 X+1/2,-Y+1/2,-Z
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.53100
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.25850
+REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.22550
+REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.25850
+REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.53100
+REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.22550
+REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
+REMARK 500 NH2 ARG A 45 NH2 ARG A 68 2.16
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
+REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
+REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
+REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
+REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
+REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
+REMARK 500
+REMARK 500 DISTANCE CUTOFF:
+REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
+REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
+REMARK 500 OD1 ASN A 19 ND2 ASN A 39 1556 2.09
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES
+REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
+REMARK 500 ARG A 21 CD - NE - CZ ANGL. DEV. = 13.6 DEGREES
+REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES
+REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES
+REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES
+REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES
+REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES
+REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES
+REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES
+REMARK 500 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES
+REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 8.6 DEGREES
+REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES
+REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES
+REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: PLANAR GROUPS
+REMARK 500
+REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
+REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
+REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
+REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
+REMARK 500 AN RMSD GREATER THAN THIS VALUE
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI RMS TYPE
+REMARK 500 ARG A 14 0.12 SIDE_CHAIN
+REMARK 500 ARG A 21 0.21 SIDE_CHAIN
+REMARK 500 ARG A 68 0.15 SIDE_CHAIN
+REMARK 500 ARG A 73 0.25 SIDE_CHAIN
+REMARK 500 ARG A 112 0.15 SIDE_CHAIN
+REMARK 500 ARG A 114 0.13 SIDE_CHAIN
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
+REMARK 500
+REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
+REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER
+REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
+REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
+REMARK 500 I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI ANGLE
+REMARK 500 ARG A 128 10.17
+REMARK 500
+REMARK 500 REMARK: NULL
+DBREF 1AKI A 1 129 UNP P00698 LYSC_CHICK 19 147
+SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
+SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
+SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
+SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
+SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
+SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
+SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
+SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
+SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
+SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
+FORMUL 2 HOH *78(H2 O)
+HELIX 1 1 ARG A 5 ARG A 14 1 10
+HELIX 2 2 TYR A 20 GLY A 22 5 3
+HELIX 3 3 LEU A 25 SER A 36 1 12
+HELIX 4 4 CYS A 80 LEU A 84 5 5
+HELIX 5 5 THR A 89 ASP A 101 1 13
+HELIX 6 6 GLY A 104 ALA A 107 5 4
+HELIX 7 7 VAL A 109 ARG A 114 1 6
+HELIX 8 8 VAL A 120 TRP A 123 5 4
+SHEET 1 A 2 THR A 43 ARG A 45 0
+SHEET 2 A 2 THR A 51 TYR A 53 -1 N ASP A 52 O ASN A 44
+SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.97
+SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.00
+SSBOND 3 CYS A 64 CYS A 80 1555 1555 1.99
+SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02
+CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 21 21 21 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.016931 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.014609 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.032769 0.00000
+ATOM 1 N LYS A 1 35.365 22.342 -11.980 1.00 22.28 N
+ATOM 2 CA LYS A 1 35.892 21.073 -11.427 1.00 21.12 C
+ATOM 3 C LYS A 1 34.741 20.264 -10.844 1.00 16.85 C
+ATOM 4 O LYS A 1 33.945 20.813 -10.081 1.00 18.94 O
+ATOM 5 CB LYS A 1 36.872 21.435 -10.306 1.00 20.78 C
+ATOM 6 CG LYS A 1 37.453 20.248 -9.565 1.00 18.47 C
+ATOM 7 CD LYS A 1 38.688 20.649 -8.775 1.00 20.32 C
+ATOM 8 CE LYS A 1 39.057 19.508 -7.837 1.00 24.76 C
+ATOM 9 NZ LYS A 1 40.423 19.771 -7.299 1.00 28.27 N
+ATOM 10 N VAL A 2 34.739 18.961 -11.042 1.00 19.96 N
+ATOM 11 CA VAL A 2 33.903 17.998 -10.333 1.00 18.10 C
+ATOM 12 C VAL A 2 34.800 17.312 -9.294 1.00 19.39 C
+ATOM 13 O VAL A 2 35.759 16.605 -9.665 1.00 22.14 O
+ATOM 14 CB VAL A 2 33.140 17.034 -11.232 1.00 16.81 C
+ATOM 15 CG1 VAL A 2 32.251 16.084 -10.434 1.00 21.92 C
+ATOM 16 CG2 VAL A 2 32.294 17.714 -12.290 1.00 19.46 C
+ATOM 17 N PHE A 3 34.491 17.546 -8.038 1.00 19.89 N
+ATOM 18 CA PHE A 3 35.185 16.903 -6.918 1.00 17.43 C
+ATOM 19 C PHE A 3 34.742 15.441 -6.771 1.00 15.70 C
+ATOM 20 O PHE A 3 33.525 15.162 -6.862 1.00 18.52 O
+ATOM 21 CB PHE A 3 34.967 17.632 -5.594 1.00 17.94 C
+ATOM 22 CG PHE A 3 35.944 18.737 -5.375 1.00 16.78 C
+ATOM 23 CD1 PHE A 3 35.666 20.050 -5.798 1.00 15.97 C
+ATOM 24 CD2 PHE A 3 37.000 18.557 -4.473 1.00 19.95 C
+ATOM 25 CE1 PHE A 3 36.577 21.076 -5.568 1.00 17.32 C
+ATOM 26 CE2 PHE A 3 37.869 19.589 -4.157 1.00 17.65 C
+ATOM 27 CZ PHE A 3 37.636 20.873 -4.666 1.00 17.91 C
+ATOM 28 N GLY A 4 35.724 14.639 -6.331 1.00 16.79 N
+ATOM 29 CA GLY A 4 35.366 13.280 -5.870 1.00 16.34 C
+ATOM 30 C GLY A 4 34.924 13.420 -4.415 1.00 11.91 C
+ATOM 31 O GLY A 4 35.303 14.403 -3.781 1.00 16.23 O
+ATOM 32 N ARG A 5 34.053 12.538 -3.973 1.00 14.65 N
+ATOM 33 CA ARG A 5 33.565 12.538 -2.588 1.00 15.91 C
+ATOM 34 C ARG A 5 34.665 12.734 -1.556 1.00 15.38 C
+ATOM 35 O ARG A 5 34.669 13.651 -0.704 1.00 13.15 O
+ATOM 36 CB ARG A 5 32.765 11.262 -2.331 1.00 17.38 C
+ATOM 37 CG ARG A 5 32.213 11.203 -0.920 1.00 13.79 C
+ATOM 38 CD ARG A 5 31.375 10.001 -0.722 1.00 15.84 C
+ATOM 39 NE ARG A 5 32.059 8.749 -0.958 1.00 18.74 N
+ATOM 40 CZ ARG A 5 32.733 8.011 -0.097 1.00 15.19 C
+ATOM 41 NH1 ARG A 5 32.836 8.332 1.187 1.00 17.50 N
+ATOM 42 NH2 ARG A 5 33.245 6.836 -0.526 1.00 23.44 N
+ATOM 43 N CYS A 6 35.674 11.853 -1.612 1.00 14.07 N
+ATOM 44 CA CYS A 6 36.781 11.870 -0.654 1.00 14.62 C
+ATOM 45 C CYS A 6 37.747 13.050 -0.777 1.00 10.99 C
+ATOM 46 O CYS A 6 38.148 13.609 0.264 1.00 16.34 O
+ATOM 47 CB CYS A 6 37.491 10.532 -0.621 1.00 16.90 C
+ATOM 48 SG CYS A 6 36.540 9.205 0.140 1.00 18.61 S
+ATOM 49 N GLU A 7 37.861 13.481 -2.019 1.00 14.24 N
+ATOM 50 CA GLU A 7 38.685 14.686 -2.311 1.00 13.83 C
+ATOM 51 C GLU A 7 38.049 15.926 -1.658 1.00 14.86 C
+ATOM 52 O GLU A 7 38.744 16.729 -1.011 1.00 15.01 O
+ATOM 53 CB GLU A 7 38.784 14.846 -3.818 1.00 14.85 C
+ATOM 54 CG GLU A 7 39.540 16.051 -4.379 1.00 18.50 C
+ATOM 55 CD GLU A 7 39.576 16.242 -5.870 1.00 20.16 C
+ATOM 56 OE1 GLU A 7 38.672 15.644 -6.491 1.00 26.20 O
+ATOM 57 OE2 GLU A 7 40.415 16.953 -6.381 1.00 25.49 O
+ATOM 58 N LEU A 8 36.743 16.049 -1.819 1.00 15.18 N
+ATOM 59 CA LEU A 8 35.964 17.158 -1.255 1.00 12.72 C
+ATOM 60 C LEU A 8 36.051 17.132 0.266 1.00 9.45 C
+ATOM 61 O LEU A 8 36.159 18.166 0.920 1.00 13.45 O
+ATOM 62 CB LEU A 8 34.528 17.172 -1.811 1.00 14.31 C
+ATOM 63 CG LEU A 8 33.718 18.354 -1.305 1.00 15.95 C
+ATOM 64 CD1 LEU A 8 34.297 19.656 -1.841 1.00 16.56 C
+ATOM 65 CD2 LEU A 8 32.246 18.143 -1.596 1.00 15.88 C
+ATOM 66 N ALA A 9 35.754 15.980 0.828 1.00 14.24 N
+ATOM 67 CA ALA A 9 35.838 15.757 2.284 1.00 13.25 C
+ATOM 68 C ALA A 9 37.144 16.314 2.840 1.00 12.89 C
+ATOM 69 O ALA A 9 37.151 16.978 3.897 1.00 14.78 O
+ATOM 70 CB ALA A 9 35.656 14.287 2.623 1.00 13.89 C
+ATOM 71 N ALA A 10 38.272 15.983 2.204 1.00 12.54 N
+ATOM 72 CA ALA A 10 39.610 16.431 2.616 1.00 16.58 C
+ATOM 73 C ALA A 10 39.736 17.944 2.459 1.00 15.35 C
+ATOM 74 O ALA A 10 40.193 18.499 3.469 1.00 17.40 O
+ATOM 75 CB ALA A 10 40.708 15.706 1.842 1.00 15.49 C
+ATOM 76 N ALA A 11 39.227 18.519 1.385 1.00 13.54 N
+ATOM 77 CA ALA A 11 39.264 19.982 1.223 1.00 15.23 C
+ATOM 78 C ALA A 11 38.491 20.702 2.321 1.00 15.68 C
+ATOM 79 O ALA A 11 38.946 21.658 2.953 1.00 16.87 O
+ATOM 80 CB ALA A 11 38.869 20.421 -0.175 1.00 14.12 C
+ATOM 81 N MET A 12 37.288 20.214 2.590 1.00 15.47 N
+ATOM 82 CA MET A 12 36.398 20.781 3.612 1.00 13.69 C
+ATOM 83 C MET A 12 36.990 20.715 5.007 1.00 12.55 C
+ATOM 84 O MET A 12 36.906 21.637 5.840 1.00 17.69 O
+ATOM 85 CB MET A 12 34.993 20.213 3.515 1.00 11.18 C
+ATOM 86 CG MET A 12 34.320 20.724 2.265 1.00 15.06 C
+ATOM 87 SD MET A 12 32.634 19.986 2.235 1.00 17.81 S
+ATOM 88 CE MET A 12 31.788 21.135 1.138 1.00 18.08 C
+ATOM 89 N LYS A 13 37.688 19.628 5.314 1.00 12.42 N
+ATOM 90 CA LYS A 13 38.387 19.385 6.579 1.00 14.58 C
+ATOM 91 C LYS A 13 39.460 20.467 6.731 1.00 14.55 C
+ATOM 92 O LYS A 13 39.507 21.137 7.776 1.00 16.49 O
+ATOM 93 CB LYS A 13 38.934 17.952 6.572 1.00 15.36 C
+ATOM 94 CG LYS A 13 39.742 17.555 7.798 1.00 20.46 C
+ATOM 95 CD LYS A 13 38.973 16.777 8.834 1.00 23.53 C
+ATOM 96 CE LYS A 13 39.293 15.305 8.751 1.00 26.37 C
+ATOM 97 NZ LYS A 13 38.077 14.461 8.946 1.00 30.88 N
+ATOM 98 N ARG A 14 40.267 20.629 5.688 1.00 18.91 N
+ATOM 99 CA ARG A 14 41.387 21.577 5.713 1.00 17.66 C
+ATOM 100 C ARG A 14 40.927 23.017 5.881 1.00 16.78 C
+ATOM 101 O ARG A 14 41.557 23.834 6.584 1.00 20.06 O
+ATOM 102 CB ARG A 14 42.388 21.351 4.601 1.00 20.89 C
+ATOM 103 CG ARG A 14 42.173 22.079 3.289 1.00 25.07 C
+ATOM 104 CD ARG A 14 43.444 22.075 2.490 1.00 23.98 C
+ATOM 105 NE ARG A 14 43.687 20.710 2.012 1.00 31.92 N
+ATOM 106 CZ ARG A 14 43.098 20.255 0.892 1.00 26.04 C
+ATOM 107 NH1 ARG A 14 42.695 21.186 0.018 1.00 33.46 N
+ATOM 108 NH2 ARG A 14 42.949 18.957 0.689 1.00 25.91 N
+ATOM 109 N HIE A 15 39.681 23.247 5.463 1.00 17.84 N
+ATOM 110 CA HIE A 15 39.075 24.591 5.526 1.00 15.99 C
+ATOM 111 C HIE A 15 38.310 24.861 6.814 1.00 17.70 C
+ATOM 112 O HIE A 15 37.608 25.875 6.952 1.00 22.68 O
+ATOM 113 CB HIE A 15 38.223 24.918 4.285 1.00 19.19 C
+ATOM 114 CG HIE A 15 39.085 25.388 3.171 1.00 20.14 C
+ATOM 115 ND1 HIE A 15 39.457 24.635 2.091 1.00 24.53 N
+ATOM 116 CD2 HIE A 15 39.739 26.570 2.993 1.00 24.44 C
+ATOM 117 CE1 HIE A 15 40.211 25.312 1.258 1.00 20.68 C
+ATOM 118 NE2 HIE A 15 40.524 26.419 1.889 1.00 27.34 N
+ATOM 119 N GLY A 16 38.296 23.927 7.720 1.00 17.50 N
+ATOM 120 CA GLY A 16 37.765 24.025 9.072 1.00 18.71 C
+ATOM 121 C GLY A 16 36.264 23.799 9.210 1.00 18.40 C
+ATOM 122 O GLY A 16 35.646 24.400 10.127 1.00 21.57 O
+ATOM 123 N LEU A 17 35.665 23.073 8.274 1.00 17.56 N
+ATOM 124 CA LEU A 17 34.238 22.795 8.298 1.00 15.38 C
+ATOM 125 C LEU A 17 33.845 21.682 9.266 1.00 18.28 C
+ATOM 126 O LEU A 17 32.643 21.594 9.552 1.00 18.24 O
+ATOM 127 CB LEU A 17 33.648 22.647 6.901 1.00 15.02 C
+ATOM 128 CG LEU A 17 33.451 23.889 6.060 1.00 16.08 C
+ATOM 129 CD1 LEU A 17 32.933 23.420 4.705 1.00 13.83 C
+ATOM 130 CD2 LEU A 17 32.556 24.946 6.679 1.00 18.60 C
+ATOM 131 N ASP A 18 34.785 20.814 9.605 1.00 16.36 N
+ATOM 132 CA ASP A 18 34.492 19.722 10.526 1.00 16.25 C
+ATOM 133 C ASP A 18 34.015 20.222 11.901 1.00 17.32 C
+ATOM 134 O ASP A 18 34.826 20.778 12.658 1.00 20.27 O
+ATOM 135 CB ASP A 18 35.557 18.633 10.598 1.00 19.37 C
+ATOM 136 CG ASP A 18 35.017 17.408 11.311 1.00 20.25 C
+ATOM 137 OD1 ASP A 18 33.805 17.154 11.455 1.00 21.00 O
+ATOM 138 OD2 ASP A 18 35.925 16.603 11.662 1.00 27.06 O
+ATOM 139 N ASN A 19 32.746 19.990 12.205 1.00 18.55 N
+ATOM 140 CA ASN A 19 32.123 20.431 13.448 1.00 17.19 C
+ATOM 141 C ASN A 19 31.854 21.941 13.497 1.00 16.61 C
+ATOM 142 O ASN A 19 31.426 22.398 14.573 1.00 18.56 O
+ATOM 143 CB ASN A 19 32.767 20.004 14.770 1.00 18.92 C
+ATOM 144 CG ASN A 19 32.162 20.512 16.064 1.00 24.64 C
+ATOM 145 OD1 ASN A 19 30.967 20.273 16.355 1.00 32.53 O
+ATOM 146 ND2 ASN A 19 32.847 21.361 16.852 1.00 24.14 N
+ATOM 147 N TYR A 20 31.969 22.650 12.406 1.00 16.84 N
+ATOM 148 CA TYR A 20 31.707 24.099 12.411 1.00 15.54 C
+ATOM 149 C TYR A 20 30.231 24.343 12.759 1.00 15.81 C
+ATOM 150 O TYR A 20 29.288 23.874 12.118 1.00 16.89 O
+ATOM 151 CB TYR A 20 32.070 24.736 11.066 1.00 18.16 C
+ATOM 152 CG TYR A 20 32.061 26.250 11.144 1.00 20.28 C
+ATOM 153 CD1 TYR A 20 33.141 26.886 11.760 1.00 21.42 C
+ATOM 154 CD2 TYR A 20 30.979 27.004 10.691 1.00 20.44 C
+ATOM 155 CE1 TYR A 20 33.206 28.277 11.794 1.00 22.24 C
+ATOM 156 CE2 TYR A 20 31.018 28.399 10.779 1.00 21.36 C
+ATOM 157 CZ TYR A 20 32.102 29.017 11.383 1.00 19.38 C
+ATOM 158 OH TYR A 20 32.136 30.371 11.525 1.00 26.77 O
+ATOM 159 N ARG A 21 30.088 25.142 13.803 1.00 18.43 N
+ATOM 160 CA ARG A 21 28.774 25.553 14.319 1.00 15.68 C
+ATOM 161 C ARG A 21 27.964 24.312 14.623 1.00 15.17 C
+ATOM 162 O ARG A 21 26.733 24.333 14.606 1.00 18.36 O
+ATOM 163 CB ARG A 21 28.014 26.565 13.453 1.00 19.21 C
+ATOM 164 CG ARG A 21 28.507 27.995 13.535 1.00 21.50 C
+ATOM 165 CD ARG A 21 28.110 28.755 14.765 1.00 25.00 C
+ATOM 166 NE ARG A 21 29.319 29.321 15.324 1.00 30.37 N
+ATOM 167 CZ ARG A 21 30.215 30.234 14.978 1.00 29.02 C
+ATOM 168 NH1 ARG A 21 31.501 29.856 14.846 1.00 29.04 N
+ATOM 169 NH2 ARG A 21 29.938 31.437 14.495 1.00 31.89 N
+ATOM 170 N GLY A 22 28.689 23.250 14.998 1.00 17.81 N
+ATOM 171 CA GLY A 22 28.103 22.021 15.519 1.00 17.72 C
+ATOM 172 C GLY A 22 27.748 21.018 14.436 1.00 18.89 C
+ATOM 173 O GLY A 22 27.085 20.022 14.784 1.00 23.26 O
+ATOM 174 N TYR A 23 28.209 21.230 13.216 1.00 18.20 N
+ATOM 175 CA TYR A 23 27.887 20.318 12.111 1.00 15.42 C
+ATOM 176 C TYR A 23 29.124 19.533 11.628 1.00 16.30 C
+ATOM 177 O TYR A 23 30.045 20.191 11.139 1.00 16.66 O
+ATOM 178 CB TYR A 23 27.351 21.107 10.913 1.00 15.82 C
+ATOM 179 CG TYR A 23 26.001 21.745 11.127 1.00 15.96 C
+ATOM 180 CD1 TYR A 23 24.846 20.962 11.139 1.00 14.81 C
+ATOM 181 CD2 TYR A 23 25.897 23.096 11.458 1.00 16.60 C
+ATOM 182 CE1 TYR A 23 23.600 21.518 11.422 1.00 17.08 C
+ATOM 183 CE2 TYR A 23 24.647 23.673 11.726 1.00 19.34 C
+ATOM 184 CZ TYR A 23 23.518 22.881 11.701 1.00 19.21 C
+ATOM 185 OH TYR A 23 22.289 23.438 11.912 1.00 25.61 O
+ATOM 186 N SER A 24 29.029 18.223 11.810 1.00 15.35 N
+ATOM 187 CA SER A 24 30.143 17.347 11.414 1.00 16.89 C
+ATOM 188 C SER A 24 30.359 17.379 9.895 1.00 15.61 C
+ATOM 189 O SER A 24 29.442 17.687 9.139 1.00 13.88 O
+ATOM 190 CB SER A 24 29.922 15.934 11.907 1.00 17.54 C
+ATOM 191 OG SER A 24 28.799 15.336 11.308 1.00 19.85 O
+ATOM 192 N LEU A 25 31.593 17.028 9.540 1.00 16.08 N
+ATOM 193 CA LEU A 25 32.035 17.092 8.138 1.00 13.16 C
+ATOM 194 C LEU A 25 31.030 16.437 7.183 1.00 13.39 C
+ATOM 195 O LEU A 25 30.874 16.924 6.056 1.00 15.34 O
+ATOM 196 CB LEU A 25 33.410 16.409 8.084 1.00 13.47 C
+ATOM 197 CG LEU A 25 34.015 16.477 6.689 1.00 12.91 C
+ATOM 198 CD1 LEU A 25 34.174 17.929 6.289 1.00 13.04 C
+ATOM 199 CD2 LEU A 25 35.398 15.810 6.752 1.00 14.54 C
+ATOM 200 N GLY A 26 30.501 15.280 7.576 1.00 13.10 N
+ATOM 201 CA GLY A 26 29.539 14.561 6.756 1.00 13.88 C
+ATOM 202 C GLY A 26 28.338 15.378 6.277 1.00 12.12 C
+ATOM 203 O GLY A 26 27.886 15.250 5.120 1.00 13.13 O
+ATOM 204 N ASN A 27 27.905 16.281 7.161 1.00 12.16 N
+ATOM 205 CA ASN A 27 26.827 17.227 6.857 1.00 14.74 C
+ATOM 206 C ASN A 27 27.164 18.015 5.597 1.00 15.43 C
+ATOM 207 O ASN A 27 26.317 18.208 4.720 1.00 15.27 O
+ATOM 208 CB ASN A 27 26.484 18.126 8.054 1.00 12.34 C
+ATOM 209 CG ASN A 27 25.681 17.267 9.048 1.00 12.22 C
+ATOM 210 OD1 ASN A 27 24.511 16.933 8.820 1.00 17.40 O
+ATOM 211 ND2 ASN A 27 26.348 17.052 10.169 1.00 18.27 N
+ATOM 212 N TRP A 28 28.344 18.591 5.583 1.00 16.78 N
+ATOM 213 CA TRP A 28 28.831 19.475 4.513 1.00 16.49 C
+ATOM 214 C TRP A 28 28.940 18.741 3.183 1.00 12.99 C
+ATOM 215 O TRP A 28 28.742 19.321 2.090 1.00 13.97 O
+ATOM 216 CB TRP A 28 30.104 20.145 5.023 1.00 14.55 C
+ATOM 217 CG TRP A 28 29.941 20.978 6.251 1.00 11.93 C
+ATOM 218 CD1 TRP A 28 30.176 20.624 7.546 1.00 14.42 C
+ATOM 219 CD2 TRP A 28 29.319 22.284 6.287 1.00 13.11 C
+ATOM 220 NE1 TRP A 28 29.924 21.690 8.365 1.00 16.94 N
+ATOM 221 CE2 TRP A 28 29.337 22.679 7.641 1.00 14.07 C
+ATOM 222 CE3 TRP A 28 28.894 23.168 5.295 1.00 15.97 C
+ATOM 223 CZ2 TRP A 28 28.913 23.943 8.038 1.00 18.07 C
+ATOM 224 CZ3 TRP A 28 28.398 24.404 5.682 1.00 18.26 C
+ATOM 225 CH2 TRP A 28 28.431 24.766 7.025 1.00 17.18 C
+ATOM 226 N VAL A 29 29.572 17.543 3.261 1.00 13.00 N
+ATOM 227 CA VAL A 29 29.729 16.711 2.047 1.00 14.15 C
+ATOM 228 C VAL A 29 28.379 16.340 1.429 1.00 10.43 C
+ATOM 229 O VAL A 29 28.166 16.496 0.228 1.00 13.40 O
+ATOM 230 CB VAL A 29 30.649 15.492 2.359 1.00 12.76 C
+ATOM 231 CG1 VAL A 29 30.782 14.596 1.136 1.00 15.37 C
+ATOM 232 CG2 VAL A 29 32.010 16.050 2.772 1.00 14.18 C
+ATOM 233 N CYS A 30 27.501 15.906 2.299 1.00 15.32 N
+ATOM 234 CA CYS A 30 26.115 15.567 1.991 1.00 15.59 C
+ATOM 235 C CYS A 30 25.388 16.723 1.302 1.00 12.37 C
+ATOM 236 O CYS A 30 24.894 16.516 0.172 1.00 14.44 O
+ATOM 237 CB CYS A 30 25.343 15.046 3.172 1.00 14.99 C
+ATOM 238 SG CYS A 30 23.719 14.376 2.695 1.00 17.71 S
+ATOM 239 N ALA A 31 25.533 17.913 1.870 1.00 16.06 N
+ATOM 240 CA ALA A 31 24.949 19.130 1.305 1.00 15.82 C
+ATOM 241 C ALA A 31 25.487 19.354 -0.115 1.00 15.34 C
+ATOM 242 O ALA A 31 24.675 19.686 -0.998 1.00 16.00 O
+ATOM 243 CB ALA A 31 25.167 20.335 2.200 1.00 14.90 C
+ATOM 244 N ALA A 32 26.807 19.354 -0.286 1.00 11.93 N
+ATOM 245 CA ALA A 32 27.461 19.536 -1.579 1.00 13.08 C
+ATOM 246 C ALA A 32 26.943 18.538 -2.620 1.00 12.38 C
+ATOM 247 O ALA A 32 26.767 18.857 -3.789 1.00 13.89 O
+ATOM 248 CB ALA A 32 28.982 19.476 -1.398 1.00 14.17 C
+ATOM 249 N LYS A 33 26.731 17.303 -2.193 1.00 15.16 N
+ATOM 250 CA LYS A 33 26.261 16.216 -3.037 1.00 16.16 C
+ATOM 251 C LYS A 33 24.903 16.555 -3.658 1.00 15.04 C
+ATOM 252 O LYS A 33 24.806 16.511 -4.890 1.00 15.00 O
+ATOM 253 CB LYS A 33 26.221 14.860 -2.351 1.00 16.71 C
+ATOM 254 CG LYS A 33 25.697 13.696 -3.185 1.00 19.51 C
+ATOM 255 CD LYS A 33 26.498 13.400 -4.446 1.00 17.12 C
+ATOM 256 CE LYS A 33 25.686 12.464 -5.331 1.00 24.06 C
+ATOM 257 NZ LYS A 33 26.423 11.979 -6.525 1.00 26.78 N
+ATOM 258 N PHE A 34 23.972 16.946 -2.817 1.00 16.81 N
+ATOM 259 CA PHE A 34 22.569 17.125 -3.247 1.00 17.51 C
+ATOM 260 C PHE A 34 22.346 18.506 -3.836 1.00 18.19 C
+ATOM 261 O PHE A 34 21.504 18.692 -4.759 1.00 20.21 O
+ATOM 262 CB PHE A 34 21.626 16.673 -2.130 1.00 18.58 C
+ATOM 263 CG PHE A 34 21.644 15.172 -1.965 1.00 22.22 C
+ATOM 264 CD1 PHE A 34 21.209 14.353 -3.007 1.00 20.24 C
+ATOM 265 CD2 PHE A 34 22.272 14.627 -0.851 1.00 20.00 C
+ATOM 266 CE1 PHE A 34 21.372 12.961 -2.910 1.00 22.03 C
+ATOM 267 CE2 PHE A 34 22.443 13.245 -0.743 1.00 21.96 C
+ATOM 268 CZ PHE A 34 21.923 12.406 -1.737 1.00 20.77 C
+ATOM 269 N GLU A 35 23.251 19.415 -3.451 1.00 15.27 N
+ATOM 270 CA GLU A 35 23.178 20.789 -3.996 1.00 15.45 C
+ATOM 271 C GLU A 35 23.661 20.944 -5.423 1.00 17.45 C
+ATOM 272 O GLU A 35 23.014 21.514 -6.310 1.00 17.91 O
+ATOM 273 CB GLU A 35 23.698 21.892 -3.107 1.00 14.42 C
+ATOM 274 CG GLU A 35 22.994 22.212 -1.809 1.00 11.08 C
+ATOM 275 CD GLU A 35 21.631 22.846 -1.864 1.00 13.55 C
+ATOM 276 OE1 GLU A 35 21.408 23.360 -2.981 1.00 20.77 O
+ATOM 277 OE2 GLU A 35 20.947 23.032 -0.874 1.00 22.72 O
+ATOM 278 N SER A 36 24.867 20.483 -5.674 1.00 15.66 N
+ATOM 279 CA SER A 36 25.626 20.615 -6.903 1.00 17.79 C
+ATOM 280 C SER A 36 26.139 19.341 -7.569 1.00 16.97 C
+ATOM 281 O SER A 36 26.750 19.464 -8.642 1.00 21.78 O
+ATOM 282 CB SER A 36 26.830 21.528 -6.654 1.00 18.12 C
+ATOM 283 OG SER A 36 27.747 20.951 -5.748 1.00 15.16 O
+ATOM 284 N ASN A 37 25.957 18.222 -6.927 1.00 20.15 N
+ATOM 285 CA ASN A 37 26.628 16.968 -7.297 1.00 20.85 C
+ATOM 286 C ASN A 37 28.149 17.091 -7.302 1.00 19.72 C
+ATOM 287 O ASN A 37 28.813 16.627 -8.254 1.00 20.79 O
+ATOM 288 CB ASN A 37 26.028 16.490 -8.617 1.00 20.82 C
+ATOM 289 CG ASN A 37 26.156 14.980 -8.782 1.00 23.63 C
+ATOM 290 OD1 ASN A 37 26.640 14.266 -7.885 1.00 28.05 O
+ATOM 291 ND2 ASN A 37 25.867 14.506 -9.990 1.00 29.61 N
+ATOM 292 N PHE A 38 28.691 17.882 -6.383 1.00 16.12 N
+ATOM 293 CA PHE A 38 30.129 18.115 -6.279 1.00 14.75 C
+ATOM 294 C PHE A 38 30.717 18.903 -7.448 1.00 13.86 C
+ATOM 295 O PHE A 38 31.923 18.794 -7.702 1.00 16.66 O
+ATOM 296 CB PHE A 38 30.914 16.823 -6.047 1.00 17.09 C
+ATOM 297 CG PHE A 38 30.487 16.006 -4.863 1.00 15.96 C
+ATOM 298 CD1 PHE A 38 30.100 16.572 -3.655 1.00 15.43 C
+ATOM 299 CD2 PHE A 38 30.507 14.603 -4.993 1.00 17.66 C
+ATOM 300 CE1 PHE A 38 29.766 15.808 -2.558 1.00 16.83 C
+ATOM 301 CE2 PHE A 38 30.136 13.814 -3.891 1.00 15.86 C
+ATOM 302 CZ PHE A 38 29.835 14.410 -2.646 1.00 18.90 C
+ATOM 303 N ASN A 39 29.936 19.792 -8.033 1.00 17.63 N
+ATOM 304 CA ASN A 39 30.341 20.573 -9.199 1.00 16.77 C
+ATOM 305 C ASN A 39 30.543 22.034 -8.823 1.00 17.13 C
+ATOM 306 O ASN A 39 29.544 22.649 -8.423 1.00 17.24 O
+ATOM 307 CB ASN A 39 29.406 20.300 -10.366 1.00 17.40 C
+ATOM 308 CG ASN A 39 29.876 20.771 -11.716 1.00 16.96 C
+ATOM 309 OD1 ASN A 39 30.579 21.750 -11.956 1.00 23.22 O
+ATOM 310 ND2 ASN A 39 29.578 19.864 -12.653 1.00 26.35 N
+ATOM 311 N THR A 40 31.766 22.492 -8.928 1.00 14.88 N
+ATOM 312 CA THR A 40 32.139 23.869 -8.657 1.00 16.08 C
+ATOM 313 C THR A 40 31.504 24.890 -9.589 1.00 16.31 C
+ATOM 314 O THR A 40 31.316 26.054 -9.213 1.00 17.50 O
+ATOM 315 CB THR A 40 33.684 24.103 -8.422 1.00 17.07 C
+ATOM 316 OG1 THR A 40 34.270 24.156 -9.775 1.00 23.76 O
+ATOM 317 CG2 THR A 40 34.414 23.119 -7.491 1.00 16.46 C
+ATOM 318 N GLN A 41 31.001 24.430 -10.706 1.00 16.39 N
+ATOM 319 CA GLN A 41 30.524 25.291 -11.812 1.00 16.67 C
+ATOM 320 C GLN A 41 28.993 25.381 -11.874 1.00 15.44 C
+ATOM 321 O GLN A 41 28.504 26.019 -12.837 1.00 18.55 O
+ATOM 322 CB GLN A 41 31.047 24.817 -13.168 1.00 19.65 C
+ATOM 323 CG GLN A 41 32.549 25.004 -13.279 1.00 21.26 C
+ATOM 324 CD GLN A 41 32.763 26.236 -14.129 1.00 26.23 C
+ATOM 325 OE1 GLN A 41 32.356 26.308 -15.291 1.00 24.68 O
+ATOM 326 NE2 GLN A 41 33.276 27.231 -13.420 1.00 25.96 N
+ATOM 327 N ALA A 42 28.329 24.640 -11.012 1.00 15.95 N
+ATOM 328 CA ALA A 42 26.859 24.579 -11.061 1.00 17.42 C
+ATOM 329 C ALA A 42 26.257 25.969 -10.807 1.00 18.93 C
+ATOM 330 O ALA A 42 26.645 26.686 -9.884 1.00 17.00 O
+ATOM 331 CB ALA A 42 26.355 23.604 -9.998 1.00 22.79 C
+ATOM 332 N THR A 43 25.276 26.293 -11.643 1.00 18.30 N
+ATOM 333 CA THR A 43 24.441 27.490 -11.476 1.00 17.73 C
+ATOM 334 C THR A 43 22.976 27.112 -11.714 1.00 19.61 C
+ATOM 335 O THR A 43 22.715 26.271 -12.594 1.00 22.06 O
+ATOM 336 CB THR A 43 24.814 28.728 -12.375 1.00 17.58 C
+ATOM 337 OG1 THR A 43 24.555 28.321 -13.756 1.00 20.94 O
+ATOM 338 CG2 THR A 43 26.247 29.213 -12.184 1.00 18.26 C
+ATOM 339 N ASN A 44 22.088 27.742 -10.971 1.00 19.77 N
+ATOM 340 CA ASN A 44 20.640 27.497 -11.108 1.00 19.51 C
+ATOM 341 C ASN A 44 19.903 28.842 -10.963 1.00 14.85 C
+ATOM 342 O ASN A 44 20.169 29.600 -10.033 1.00 19.43 O
+ATOM 343 CB ASN A 44 20.155 26.480 -10.080 1.00 19.93 C
+ATOM 344 CG ASN A 44 18.646 26.315 -10.115 1.00 22.01 C
+ATOM 345 OD1 ASN A 44 18.128 25.720 -11.078 1.00 29.53 O
+ATOM 346 ND2 ASN A 44 17.906 26.927 -9.188 1.00 22.94 N
+ATOM 347 N ARG A 45 19.058 29.117 -11.924 1.00 16.90 N
+ATOM 348 CA ARG A 45 18.303 30.363 -12.015 1.00 18.37 C
+ATOM 349 C ARG A 45 16.955 30.163 -11.326 1.00 18.76 C
+ATOM 350 O ARG A 45 16.396 29.062 -11.425 1.00 20.87 O
+ATOM 351 CB ARG A 45 18.143 30.836 -13.462 1.00 19.30 C
+ATOM 352 CG ARG A 45 17.012 31.859 -13.557 1.00 23.98 C
+ATOM 353 CD ARG A 45 17.502 33.134 -12.930 1.00 23.36 C
+ATOM 354 NE ARG A 45 18.311 33.758 -13.981 1.00 29.56 N
+ATOM 355 CZ ARG A 45 17.620 34.271 -15.020 1.00 27.18 C
+ATOM 356 NH1 ARG A 45 16.287 34.331 -15.098 1.00 31.99 N
+ATOM 357 NH2 ARG A 45 18.374 34.698 -16.030 1.00 32.43 N
+ATOM 358 N ASN A 46 16.553 31.171 -10.554 1.00 18.13 N
+ATOM 359 CA ASN A 46 15.304 31.071 -9.782 1.00 20.10 C
+ATOM 360 C ASN A 46 14.261 32.063 -10.313 1.00 17.35 C
+ATOM 361 O ASN A 46 14.617 33.104 -10.880 1.00 19.15 O
+ATOM 362 CB ASN A 46 15.576 31.229 -8.295 1.00 20.05 C
+ATOM 363 CG ASN A 46 16.543 30.240 -7.679 1.00 20.12 C
+ATOM 364 OD1 ASN A 46 17.659 30.661 -7.346 1.00 21.21 O
+ATOM 365 ND2 ASN A 46 16.125 28.975 -7.600 1.00 19.44 N
+ATOM 366 N THR A 47 13.027 31.834 -9.887 1.00 19.96 N
+ATOM 367 CA THR A 47 11.871 32.654 -10.246 1.00 19.12 C
+ATOM 368 C THR A 47 12.001 34.107 -9.810 1.00 19.44 C
+ATOM 369 O THR A 47 11.600 34.969 -10.606 1.00 23.16 O
+ATOM 370 CB THR A 47 10.499 32.017 -9.789 1.00 17.70 C
+ATOM 371 OG1 THR A 47 10.507 32.195 -8.342 1.00 23.76 O
+ATOM 372 CG2 THR A 47 10.331 30.554 -10.188 1.00 22.66 C
+ATOM 373 N ASP A 48 12.625 34.377 -8.683 1.00 19.25 N
+ATOM 374 CA ASP A 48 12.885 35.716 -8.168 1.00 17.33 C
+ATOM 375 C ASP A 48 14.010 36.505 -8.823 1.00 17.71 C
+ATOM 376 O ASP A 48 14.246 37.621 -8.309 1.00 23.04 O
+ATOM 377 CB ASP A 48 13.023 35.735 -6.640 1.00 18.02 C
+ATOM 378 CG ASP A 48 14.367 35.174 -6.168 1.00 17.88 C
+ATOM 379 OD1 ASP A 48 15.104 34.602 -6.991 1.00 18.55 O
+ATOM 380 OD2 ASP A 48 14.750 35.442 -5.013 1.00 22.86 O
+ATOM 381 N GLY A 49 14.650 36.018 -9.862 1.00 17.62 N
+ATOM 382 CA GLY A 49 15.744 36.702 -10.546 1.00 17.27 C
+ATOM 383 C GLY A 49 17.147 36.315 -10.096 1.00 16.80 C
+ATOM 384 O GLY A 49 18.168 36.688 -10.694 1.00 20.27 O
+ATOM 385 N SER A 50 17.173 35.661 -8.930 1.00 19.61 N
+ATOM 386 CA SER A 50 18.435 35.225 -8.279 1.00 14.28 C
+ATOM 387 C SER A 50 18.977 33.963 -8.941 1.00 18.09 C
+ATOM 388 O SER A 50 18.273 33.255 -9.697 1.00 16.76 O
+ATOM 389 CB SER A 50 18.272 35.089 -6.781 1.00 17.64 C
+ATOM 390 OG SER A 50 17.530 33.930 -6.463 1.00 17.54 O
+ATOM 391 N THR A 51 20.271 33.766 -8.734 1.00 16.00 N
+ATOM 392 CA THR A 51 20.970 32.557 -9.202 1.00 13.82 C
+ATOM 393 C THR A 51 21.718 31.969 -8.000 1.00 14.58 C
+ATOM 394 O THR A 51 22.160 32.712 -7.119 1.00 13.28 O
+ATOM 395 CB THR A 51 21.904 32.908 -10.419 1.00 12.66 C
+ATOM 396 OG1 THR A 51 21.099 33.576 -11.407 1.00 17.65 O
+ATOM 397 CG2 THR A 51 22.686 31.699 -10.952 1.00 14.39 C
+ATOM 398 N ASP A 52 21.708 30.650 -7.927 1.00 14.66 N
+ATOM 399 CA ASP A 52 22.528 29.900 -6.959 1.00 13.43 C
+ATOM 400 C ASP A 52 23.843 29.488 -7.635 1.00 12.35 C
+ATOM 401 O ASP A 52 23.847 29.066 -8.805 1.00 15.18 O
+ATOM 402 CB ASP A 52 21.765 28.649 -6.554 1.00 14.12 C
+ATOM 403 CG ASP A 52 20.396 28.991 -6.002 1.00 20.03 C
+ATOM 404 OD1 ASP A 52 20.220 29.928 -5.237 1.00 21.30 O
+ATOM 405 OD2 ASP A 52 19.517 28.144 -6.222 1.00 20.92 O
+ATOM 406 N TYR A 53 24.924 29.734 -6.905 1.00 14.56 N
+ATOM 407 CA TYR A 53 26.278 29.604 -7.450 1.00 13.61 C
+ATOM 408 C TYR A 53 27.161 28.595 -6.708 1.00 12.70 C
+ATOM 409 O TYR A 53 27.289 28.606 -5.486 1.00 13.36 O
+ATOM 410 CB TYR A 53 26.993 30.972 -7.489 1.00 12.10 C
+ATOM 411 CG TYR A 53 26.437 31.959 -8.487 1.00 11.48 C
+ATOM 412 CD1 TYR A 53 26.843 32.003 -9.821 1.00 17.21 C
+ATOM 413 CD2 TYR A 53 25.510 32.907 -8.050 1.00 14.42 C
+ATOM 414 CE1 TYR A 53 26.291 32.922 -10.717 1.00 17.40 C
+ATOM 415 CE2 TYR A 53 24.907 33.803 -8.932 1.00 12.97 C
+ATOM 416 CZ TYR A 53 25.357 33.847 -10.252 1.00 15.91 C
+ATOM 417 OH TYR A 53 24.864 34.804 -11.094 1.00 19.31 O
+ATOM 418 N GLY A 54 27.751 27.721 -7.493 1.00 16.54 N
+ATOM 419 CA GLY A 54 28.845 26.832 -7.121 1.00 15.67 C
+ATOM 420 C GLY A 54 28.499 25.601 -6.290 1.00 10.78 C
+ATOM 421 O GLY A 54 27.339 25.155 -6.255 1.00 13.16 O
+ATOM 422 N ILE A 55 29.560 25.088 -5.684 1.00 15.43 N
+ATOM 423 CA ILE A 55 29.452 23.795 -4.994 1.00 14.01 C
+ATOM 424 C ILE A 55 28.424 23.748 -3.872 1.00 12.26 C
+ATOM 425 O ILE A 55 27.770 22.697 -3.693 1.00 16.92 O
+ATOM 426 CB ILE A 55 30.891 23.340 -4.563 1.00 16.64 C
+ATOM 427 CG1 ILE A 55 30.785 21.812 -4.319 1.00 17.00 C
+ATOM 428 CG2 ILE A 55 31.396 24.210 -3.390 1.00 18.87 C
+ATOM 429 CD ILE A 55 32.101 21.018 -4.339 1.00 20.60 C
+ATOM 430 N LEU A 56 28.216 24.881 -3.236 1.00 12.85 N
+ATOM 431 CA LEU A 56 27.173 24.998 -2.203 1.00 14.96 C
+ATOM 432 C LEU A 56 25.981 25.838 -2.659 1.00 11.08 C
+ATOM 433 O LEU A 56 25.161 26.111 -1.774 1.00 16.40 O
+ATOM 434 CB LEU A 56 27.816 25.424 -0.877 1.00 14.44 C
+ATOM 435 CG LEU A 56 28.692 24.348 -0.204 1.00 14.92 C
+ATOM 436 CD1 LEU A 56 29.331 24.997 1.008 1.00 18.78 C
+ATOM 437 CD2 LEU A 56 27.808 23.177 0.192 1.00 19.47 C
+ATOM 438 N GLN A 57 25.865 26.104 -3.946 1.00 14.17 N
+ATOM 439 CA GLN A 57 24.668 26.785 -4.465 1.00 11.55 C
+ATOM 440 C GLN A 57 24.277 27.940 -3.558 1.00 15.09 C
+ATOM 441 O GLN A 57 23.116 28.031 -3.094 1.00 15.28 O
+ATOM 442 CB GLN A 57 23.521 25.765 -4.549 1.00 13.56 C
+ATOM 443 CG GLN A 57 23.733 24.790 -5.699 1.00 12.45 C
+ATOM 444 CD GLN A 57 23.684 25.440 -7.069 1.00 14.21 C
+ATOM 445 OE1 GLN A 57 22.574 25.602 -7.591 1.00 18.18 O
+ATOM 446 NE2 GLN A 57 24.813 25.805 -7.651 1.00 14.86 N
+ATOM 447 N ILE A 58 25.164 28.910 -3.428 1.00 14.04 N
+ATOM 448 CA ILE A 58 24.930 30.118 -2.649 1.00 16.09 C
+ATOM 449 C ILE A 58 24.204 31.163 -3.504 1.00 11.19 C
+ATOM 450 O ILE A 58 24.555 31.405 -4.667 1.00 14.34 O
+ATOM 451 CB ILE A 58 26.301 30.665 -2.134 1.00 14.90 C
+ATOM 452 CG1 ILE A 58 26.751 29.724 -0.985 1.00 13.85 C
+ATOM 453 CG2 ILE A 58 26.178 32.135 -1.693 1.00 15.47 C
+ATOM 454 CD ILE A 58 28.246 29.954 -0.641 1.00 16.12 C
+ATOM 455 N ASN A 59 23.145 31.671 -2.905 1.00 14.23 N
+ATOM 456 CA ASN A 59 22.146 32.510 -3.590 1.00 10.60 C
+ATOM 457 C ASN A 59 22.550 33.974 -3.730 1.00 13.03 C
+ATOM 458 O ASN A 59 22.917 34.607 -2.740 1.00 18.49 O
+ATOM 459 CB ASN A 59 20.805 32.306 -2.884 1.00 15.76 C
+ATOM 460 CG ASN A 59 19.650 32.986 -3.588 1.00 15.71 C
+ATOM 461 OD1 ASN A 59 19.464 34.171 -3.244 1.00 18.79 O
+ATOM 462 ND2 ASN A 59 19.155 32.320 -4.612 1.00 16.44 N
+ATOM 463 N SER A 60 22.268 34.485 -4.941 1.00 11.71 N
+ATOM 464 CA SER A 60 22.570 35.910 -5.255 1.00 13.81 C
+ATOM 465 C SER A 60 21.687 36.993 -4.642 1.00 15.28 C
+ATOM 466 O SER A 60 22.054 38.177 -4.774 1.00 17.67 O
+ATOM 467 CB SER A 60 22.643 36.139 -6.750 1.00 14.62 C
+ATOM 468 OG SER A 60 21.432 36.007 -7.444 1.00 14.30 O
+ATOM 469 N ARG A 61 20.526 36.660 -4.138 1.00 15.88 N
+ATOM 470 CA ARG A 61 19.691 37.653 -3.434 1.00 18.54 C
+ATOM 471 C ARG A 61 20.277 38.108 -2.106 1.00 19.97 C
+ATOM 472 O ARG A 61 20.282 39.333 -1.876 1.00 26.30 O
+ATOM 473 CB ARG A 61 18.267 37.195 -3.250 1.00 18.00 C
+ATOM 474 CG ARG A 61 17.315 38.350 -2.959 1.00 20.10 C
+ATOM 475 CD ARG A 61 16.063 37.657 -2.503 1.00 26.00 C
+ATOM 476 NE ARG A 61 15.101 38.653 -2.063 1.00 29.28 N
+ATOM 477 CZ ARG A 61 13.794 38.351 -2.111 1.00 29.36 C
+ATOM 478 NH1 ARG A 61 13.439 37.257 -2.784 1.00 26.50 N
+ATOM 479 NH2 ARG A 61 12.925 39.249 -1.646 1.00 32.93 N
+ATOM 480 N TRP A 62 20.773 37.202 -1.273 1.00 16.51 N
+ATOM 481 CA TRP A 62 21.321 37.563 0.032 1.00 16.06 C
+ATOM 482 C TRP A 62 22.848 37.643 0.101 1.00 15.55 C
+ATOM 483 O TRP A 62 23.323 38.396 0.968 1.00 18.96 O
+ATOM 484 CB TRP A 62 20.833 36.611 1.134 1.00 17.91 C
+ATOM 485 CG TRP A 62 19.360 36.361 1.096 1.00 18.99 C
+ATOM 486 CD1 TRP A 62 18.719 35.247 0.643 1.00 20.47 C
+ATOM 487 CD2 TRP A 62 18.326 37.305 1.427 1.00 20.79 C
+ATOM 488 NE1 TRP A 62 17.360 35.457 0.609 1.00 21.70 N
+ATOM 489 CE2 TRP A 62 17.090 36.696 1.096 1.00 21.11 C
+ATOM 490 CE3 TRP A 62 18.333 38.584 1.965 1.00 19.84 C
+ATOM 491 CZ2 TRP A 62 15.875 37.327 1.307 1.00 22.57 C
+ATOM 492 CZ3 TRP A 62 17.115 39.208 2.186 1.00 23.93 C
+ATOM 493 CH2 TRP A 62 15.906 38.611 1.814 1.00 19.55 C
+ATOM 494 N TRP A 63 23.537 36.731 -0.584 1.00 16.01 N
+ATOM 495 CA TRP A 63 24.906 36.398 -0.276 1.00 15.21 C
+ATOM 496 C TRP A 63 26.089 36.924 -1.052 1.00 15.84 C
+ATOM 497 O TRP A 63 27.142 37.177 -0.432 1.00 19.13 O
+ATOM 498 CB TRP A 63 25.068 34.919 0.112 1.00 15.47 C
+ATOM 499 CG TRP A 63 24.036 34.428 1.068 1.00 12.46 C
+ATOM 500 CD1 TRP A 63 22.959 33.620 0.777 1.00 16.95 C
+ATOM 501 CD2 TRP A 63 23.919 34.728 2.450 1.00 13.27 C
+ATOM 502 NE1 TRP A 63 22.243 33.344 1.899 1.00 17.64 N
+ATOM 503 CE2 TRP A 63 22.761 34.067 2.931 1.00 17.28 C
+ATOM 504 CE3 TRP A 63 24.694 35.480 3.323 1.00 15.25 C
+ATOM 505 CZ2 TRP A 63 22.393 34.133 4.278 1.00 18.56 C
+ATOM 506 CZ3 TRP A 63 24.302 35.586 4.648 1.00 18.76 C
+ATOM 507 CH2 TRP A 63 23.179 34.910 5.117 1.00 19.36 C
+ATOM 508 N CYS A 64 25.962 36.914 -2.353 1.00 17.00 N
+ATOM 509 CA CYS A 64 26.985 37.433 -3.271 1.00 15.76 C
+ATOM 510 C CYS A 64 26.324 38.355 -4.286 1.00 15.97 C
+ATOM 511 O CYS A 64 25.102 38.314 -4.475 1.00 13.75 O
+ATOM 512 CB CYS A 64 27.638 36.265 -3.988 1.00 16.64 C
+ATOM 513 SG CYS A 64 26.562 35.233 -5.007 1.00 17.83 S
+ATOM 514 N ASN A 65 27.157 39.165 -4.908 1.00 17.73 N
+ATOM 515 CA ASN A 65 26.700 40.134 -5.920 1.00 16.46 C
+ATOM 516 C ASN A 65 26.985 39.646 -7.342 1.00 13.16 C
+ATOM 517 O ASN A 65 28.130 39.316 -7.647 1.00 15.95 O
+ATOM 518 CB ASN A 65 27.381 41.492 -5.712 1.00 19.19 C
+ATOM 519 CG ASN A 65 26.910 42.423 -6.824 1.00 19.59 C
+ATOM 520 OD1 ASN A 65 25.736 42.559 -7.141 1.00 23.26 O
+ATOM 521 ND2 ASN A 65 27.914 42.938 -7.527 1.00 25.56 N
+ATOM 522 N ASP A 66 25.920 39.484 -8.116 1.00 15.60 N
+ATOM 523 CA ASP A 66 26.102 39.180 -9.545 1.00 15.28 C
+ATOM 524 C ASP A 66 25.664 40.317 -10.460 1.00 15.23 C
+ATOM 525 O ASP A 66 25.719 40.143 -11.673 1.00 17.91 O
+ATOM 526 CB ASP A 66 25.462 37.858 -9.894 1.00 14.84 C
+ATOM 527 CG ASP A 66 23.951 37.903 -9.833 1.00 12.12 C
+ATOM 528 OD1 ASP A 66 23.288 38.898 -9.542 1.00 16.56 O
+ATOM 529 OD2 ASP A 66 23.455 36.769 -10.048 1.00 16.91 O
+ATOM 530 N GLY A 67 25.234 41.408 -9.860 1.00 18.13 N
+ATOM 531 CA GLY A 67 24.817 42.607 -10.577 1.00 19.40 C
+ATOM 532 C GLY A 67 23.544 42.553 -11.401 1.00 20.37 C
+ATOM 533 O GLY A 67 23.191 43.542 -12.055 1.00 18.23 O
+ATOM 534 N ARG A 68 22.822 41.441 -11.348 1.00 18.79 N
+ATOM 535 CA ARG A 68 21.560 41.308 -12.092 1.00 19.77 C
+ATOM 536 C ARG A 68 20.424 40.765 -11.243 1.00 18.48 C
+ATOM 537 O ARG A 68 19.385 40.383 -11.795 1.00 21.54 O
+ATOM 538 CB ARG A 68 21.746 40.454 -13.339 1.00 18.97 C
+ATOM 539 CG ARG A 68 22.197 39.048 -12.946 1.00 18.77 C
+ATOM 540 CD ARG A 68 22.477 38.187 -14.122 1.00 23.25 C
+ATOM 541 NE ARG A 68 21.439 37.201 -14.281 1.00 29.75 N
+ATOM 542 CZ ARG A 68 20.242 37.255 -14.855 1.00 28.71 C
+ATOM 543 NH1 ARG A 68 19.503 38.311 -15.145 1.00 32.34 N
+ATOM 544 NH2 ARG A 68 19.897 36.127 -15.497 1.00 33.10 N
+ATOM 545 N THR A 69 20.590 40.896 -9.952 1.00 18.68 N
+ATOM 546 CA THR A 69 19.607 40.408 -8.973 1.00 20.02 C
+ATOM 547 C THR A 69 18.994 41.597 -8.224 1.00 16.46 C
+ATOM 548 O THR A 69 19.683 42.241 -7.425 1.00 23.13 O
+ATOM 549 CB THR A 69 20.208 39.384 -7.910 1.00 19.66 C
+ATOM 550 OG1 THR A 69 20.851 38.334 -8.715 1.00 19.19 O
+ATOM 551 CG2 THR A 69 19.123 38.863 -6.955 1.00 18.58 C
+ATOM 552 N PRO A 70 17.687 41.741 -8.418 1.00 20.50 N
+ATOM 553 CA PRO A 70 16.953 42.824 -7.733 1.00 21.73 C
+ATOM 554 C PRO A 70 16.955 42.520 -6.242 1.00 22.11 C
+ATOM 555 O PRO A 70 16.739 41.356 -5.886 1.00 27.13 O
+ATOM 556 CB PRO A 70 15.557 42.749 -8.333 1.00 23.50 C
+ATOM 557 CG PRO A 70 15.759 42.092 -9.671 1.00 24.66 C
+ATOM 558 CD PRO A 70 16.887 41.095 -9.463 1.00 21.80 C
+ATOM 559 N GLY A 71 17.163 43.493 -5.401 1.00 21.67 N
+ATOM 560 CA GLY A 71 17.135 43.383 -3.947 1.00 24.03 C
+ATOM 561 C GLY A 71 18.328 42.710 -3.287 1.00 26.98 C
+ATOM 562 O GLY A 71 18.257 42.257 -2.126 1.00 32.77 O
+ATOM 563 N SER A 72 19.418 42.627 -4.018 1.00 26.40 N
+ATOM 564 CA SER A 72 20.665 41.976 -3.588 1.00 26.94 C
+ATOM 565 C SER A 72 21.139 42.582 -2.276 1.00 24.66 C
+ATOM 566 O SER A 72 21.055 43.819 -2.125 1.00 29.91 O
+ATOM 567 CB SER A 72 21.659 42.002 -4.737 1.00 25.16 C
+ATOM 568 OG SER A 72 23.015 41.835 -4.343 1.00 32.21 O
+ATOM 569 N ARG A 73 21.646 41.775 -1.369 1.00 22.51 N
+ATOM 570 CA ARG A 73 22.254 42.196 -0.113 1.00 22.60 C
+ATOM 571 C ARG A 73 23.774 42.058 0.029 1.00 22.33 C
+ATOM 572 O ARG A 73 24.425 42.749 0.849 1.00 27.92 O
+ATOM 573 CB ARG A 73 21.615 41.555 1.127 1.00 20.14 C
+ATOM 574 CG ARG A 73 20.187 41.983 1.439 1.00 22.29 C
+ATOM 575 CD ARG A 73 20.209 43.299 2.123 1.00 26.95 C
+ATOM 576 NE ARG A 73 18.928 43.771 2.617 1.00 33.74 N
+ATOM 577 CZ ARG A 73 17.980 44.302 1.823 1.00 33.76 C
+ATOM 578 NH1 ARG A 73 17.841 43.934 0.544 1.00 35.78 N
+ATOM 579 NH2 ARG A 73 17.571 45.545 2.146 1.00 33.83 N
+ATOM 580 N ASN A 74 24.346 41.143 -0.705 1.00 17.74 N
+ATOM 581 CA ASN A 74 25.780 40.833 -0.695 1.00 18.87 C
+ATOM 582 C ASN A 74 26.315 40.718 0.731 1.00 16.22 C
+ATOM 583 O ASN A 74 27.255 41.471 1.060 1.00 20.87 O
+ATOM 584 CB ASN A 74 26.565 41.786 -1.589 1.00 19.51 C
+ATOM 585 CG ASN A 74 27.982 41.328 -1.909 1.00 16.31 C
+ATOM 586 OD1 ASN A 74 28.318 40.169 -1.652 1.00 18.61 O
+ATOM 587 ND2 ASN A 74 28.838 42.192 -2.436 1.00 19.22 N
+ATOM 588 N LEU A 75 25.723 39.860 1.544 1.00 15.25 N
+ATOM 589 CA LEU A 75 26.153 39.690 2.930 1.00 14.82 C
+ATOM 590 C LEU A 75 27.518 39.011 3.085 1.00 16.78 C
+ATOM 591 O LEU A 75 28.167 39.197 4.141 1.00 22.00 O
+ATOM 592 CB LEU A 75 25.009 39.055 3.733 1.00 16.64 C
+ATOM 593 CG LEU A 75 23.815 39.998 3.979 1.00 17.08 C
+ATOM 594 CD1 LEU A 75 22.574 39.193 4.336 1.00 25.82 C
+ATOM 595 CD2 LEU A 75 24.156 40.969 5.110 1.00 20.95 C
+ATOM 596 N CYS A 76 27.973 38.312 2.061 1.00 17.66 N
+ATOM 597 CA CYS A 76 29.299 37.680 2.111 1.00 16.46 C
+ATOM 598 C CYS A 76 30.390 38.598 1.589 1.00 15.66 C
+ATOM 599 O CYS A 76 31.573 38.229 1.568 1.00 17.59 O
+ATOM 600 CB CYS A 76 29.396 36.303 1.477 1.00 17.61 C
+ATOM 601 SG CYS A 76 28.595 34.961 2.361 1.00 18.07 S
+ATOM 602 N ASN A 77 29.964 39.681 0.971 1.00 18.55 N
+ATOM 603 CA ASN A 77 30.827 40.725 0.395 1.00 19.18 C
+ATOM 604 C ASN A 77 31.711 40.163 -0.702 1.00 16.58 C
+ATOM 605 O ASN A 77 32.947 40.331 -0.689 1.00 21.61 O
+ATOM 606 CB ASN A 77 31.589 41.488 1.483 1.00 17.72 C
+ATOM 607 CG ASN A 77 32.126 42.812 0.957 1.00 20.20 C
+ATOM 608 OD1 ASN A 77 31.351 43.589 0.396 1.00 28.77 O
+ATOM 609 ND2 ASN A 77 33.430 43.012 1.047 1.00 27.05 N
+ATOM 610 N ILE A 78 31.149 39.408 -1.616 1.00 18.88 N
+ATOM 611 CA ILE A 78 31.904 38.780 -2.713 1.00 20.14 C
+ATOM 612 C ILE A 78 31.099 38.850 -4.013 1.00 17.08 C
+ATOM 613 O ILE A 78 29.864 38.688 -3.972 1.00 16.28 O
+ATOM 614 CB ILE A 78 32.183 37.255 -2.384 1.00 19.93 C
+ATOM 615 CG1 ILE A 78 30.882 36.639 -1.851 1.00 21.17 C
+ATOM 616 CG2 ILE A 78 33.437 37.003 -1.524 1.00 24.25 C
+ATOM 617 CD ILE A 78 30.936 35.120 -1.546 1.00 25.54 C
+ATOM 618 N PRO A 79 31.828 38.795 -5.108 1.00 16.64 N
+ATOM 619 CA PRO A 79 31.195 38.634 -6.421 1.00 19.12 C
+ATOM 620 C PRO A 79 30.792 37.146 -6.446 1.00 14.71 C
+ATOM 621 O PRO A 79 31.576 36.273 -6.005 1.00 17.48 O
+ATOM 622 CB PRO A 79 32.261 38.967 -7.445 1.00 18.74 C
+ATOM 623 CG PRO A 79 33.555 39.029 -6.710 1.00 18.97 C
+ATOM 624 CD PRO A 79 33.276 39.023 -5.215 1.00 16.79 C
+ATOM 625 N CYS A 80 29.629 36.908 -7.033 1.00 13.55 N
+ATOM 626 CA CYS A 80 29.167 35.522 -7.236 1.00 14.33 C
+ATOM 627 C CYS A 80 30.150 34.716 -8.073 1.00 13.92 C
+ATOM 628 O CYS A 80 30.214 33.484 -7.880 1.00 16.74 O
+ATOM 629 CB CYS A 80 27.749 35.338 -7.747 1.00 16.10 C
+ATOM 630 SG CYS A 80 26.471 36.160 -6.762 1.00 16.97 S
+ATOM 631 N SER A 81 30.769 35.294 -9.083 1.00 15.04 N
+ATOM 632 CA SER A 81 31.775 34.671 -9.933 1.00 15.64 C
+ATOM 633 C SER A 81 32.907 34.027 -9.109 1.00 14.90 C
+ATOM 634 O SER A 81 33.338 32.939 -9.561 1.00 21.08 O
+ATOM 635 CB SER A 81 32.381 35.643 -10.953 1.00 18.65 C
+ATOM 636 OG SER A 81 33.035 36.681 -10.235 1.00 20.86 O
+ATOM 637 N ALA A 82 33.226 34.572 -7.950 1.00 15.59 N
+ATOM 638 CA ALA A 82 34.272 33.963 -7.107 1.00 18.01 C
+ATOM 639 C ALA A 82 33.869 32.604 -6.540 1.00 18.75 C
+ATOM 640 O ALA A 82 34.703 31.798 -6.081 1.00 19.60 O
+ATOM 641 CB ALA A 82 34.722 34.930 -6.020 1.00 20.54 C
+ATOM 642 N LEU A 83 32.571 32.338 -6.519 1.00 15.36 N
+ATOM 643 CA LEU A 83 31.973 31.093 -6.042 1.00 18.66 C
+ATOM 644 C LEU A 83 32.060 29.962 -7.049 1.00 17.84 C
+ATOM 645 O LEU A 83 31.671 28.815 -6.739 1.00 21.50 O
+ATOM 646 CB LEU A 83 30.618 31.424 -5.431 1.00 17.11 C
+ATOM 647 CG LEU A 83 30.511 32.364 -4.244 1.00 16.65 C
+ATOM 648 CD1 LEU A 83 29.040 32.573 -3.857 1.00 18.78 C
+ATOM 649 CD2 LEU A 83 31.277 31.872 -3.020 1.00 20.62 C
+ATOM 650 N LEU A 84 32.473 30.271 -8.267 1.00 17.31 N
+ATOM 651 CA LEU A 84 32.610 29.295 -9.347 1.00 16.38 C
+ATOM 652 C LEU A 84 34.047 28.841 -9.570 1.00 19.37 C
+ATOM 653 O LEU A 84 34.334 28.243 -10.622 1.00 23.48 O
+ATOM 654 CB LEU A 84 31.914 29.793 -10.614 1.00 20.87 C
+ATOM 655 CG LEU A 84 30.446 30.183 -10.573 1.00 14.26 C
+ATOM 656 CD1 LEU A 84 30.014 30.771 -11.916 1.00 21.15 C
+ATOM 657 CD2 LEU A 84 29.597 28.942 -10.329 1.00 18.96 C
+ATOM 658 N SER A 85 34.942 29.197 -8.676 1.00 21.00 N
+ATOM 659 CA SER A 85 36.340 28.754 -8.727 1.00 20.86 C
+ATOM 660 C SER A 85 36.474 27.245 -8.497 1.00 19.65 C
+ATOM 661 O SER A 85 35.765 26.640 -7.681 1.00 20.62 O
+ATOM 662 CB SER A 85 37.109 29.482 -7.633 1.00 20.91 C
+ATOM 663 OG SER A 85 38.484 29.212 -7.834 1.00 26.88 O
+ATOM 664 N SER A 86 37.619 26.742 -8.943 1.00 22.57 N
+ATOM 665 CA SER A 86 38.008 25.343 -8.700 1.00 20.44 C
+ATOM 666 C SER A 86 38.388 25.153 -7.233 1.00 19.98 C
+ATOM 667 O SER A 86 38.314 24.055 -6.671 1.00 23.62 O
+ATOM 668 CB SER A 86 39.107 24.868 -9.650 1.00 23.76 C
+ATOM 669 OG SER A 86 38.401 24.215 -10.691 1.00 30.29 O
+ATOM 670 N ASP A 87 38.846 26.244 -6.668 1.00 19.74 N
+ATOM 671 CA ASP A 87 39.282 26.393 -5.271 1.00 18.72 C
+ATOM 672 C ASP A 87 37.999 26.657 -4.471 1.00 17.93 C
+ATOM 673 O ASP A 87 37.490 27.762 -4.712 1.00 20.06 O
+ATOM 674 CB ASP A 87 40.221 27.607 -5.212 1.00 21.65 C
+ATOM 675 CG ASP A 87 40.762 28.041 -3.869 1.00 23.98 C
+ATOM 676 OD1 ASP A 87 40.335 27.702 -2.742 1.00 26.26 O
+ATOM 677 OD2 ASP A 87 41.785 28.802 -3.933 1.00 32.04 O
+ATOM 678 N ILE A 88 37.732 25.850 -3.461 1.00 15.96 N
+ATOM 679 CA ILE A 88 36.515 26.089 -2.658 1.00 16.22 C
+ATOM 680 C ILE A 88 36.582 27.142 -1.563 1.00 14.43 C
+ATOM 681 O ILE A 88 35.600 27.315 -0.801 1.00 16.28 O
+ATOM 682 CB ILE A 88 35.993 24.736 -2.046 1.00 16.45 C
+ATOM 683 CG1 ILE A 88 36.920 24.200 -0.934 1.00 15.71 C
+ATOM 684 CG2 ILE A 88 35.587 23.743 -3.163 1.00 19.87 C
+ATOM 685 CD ILE A 88 36.363 23.226 0.137 1.00 17.47 C
+ATOM 686 N THR A 89 37.742 27.786 -1.369 1.00 14.21 N
+ATOM 687 CA THR A 89 37.913 28.772 -0.306 1.00 16.87 C
+ATOM 688 C THR A 89 36.736 29.761 -0.161 1.00 11.06 C
+ATOM 689 O THR A 89 36.341 29.983 1.000 1.00 13.83 O
+ATOM 690 CB THR A 89 39.267 29.591 -0.423 1.00 18.61 C
+ATOM 691 OG1 THR A 89 40.339 28.592 -0.514 1.00 20.24 O
+ATOM 692 CG2 THR A 89 39.419 30.553 0.766 1.00 17.79 C
+ATOM 693 N ALA A 90 36.507 30.482 -1.242 1.00 17.37 N
+ATOM 694 CA ALA A 90 35.479 31.555 -1.244 1.00 16.63 C
+ATOM 695 C ALA A 90 34.125 31.066 -0.735 1.00 14.09 C
+ATOM 696 O ALA A 90 33.366 31.671 0.065 1.00 15.68 O
+ATOM 697 CB ALA A 90 35.366 32.212 -2.617 1.00 17.13 C
+ATOM 698 N SER A 91 33.746 29.919 -1.296 1.00 13.62 N
+ATOM 699 CA SER A 91 32.494 29.220 -1.024 1.00 11.35 C
+ATOM 700 C SER A 91 32.429 28.817 0.467 1.00 11.70 C
+ATOM 701 O SER A 91 31.407 29.057 1.110 1.00 14.31 O
+ATOM 702 CB SER A 91 32.282 28.035 -1.917 1.00 13.48 C
+ATOM 703 OG SER A 91 32.020 28.335 -3.260 1.00 14.66 O
+ATOM 704 N VAL A 92 33.502 28.211 0.953 1.00 13.17 N
+ATOM 705 CA VAL A 92 33.595 27.846 2.381 1.00 13.44 C
+ATOM 706 C VAL A 92 33.477 29.105 3.261 1.00 12.00 C
+ATOM 707 O VAL A 92 32.716 29.020 4.244 1.00 13.83 O
+ATOM 708 CB VAL A 92 34.890 27.038 2.650 1.00 11.69 C
+ATOM 709 CG1 VAL A 92 35.125 26.987 4.151 1.00 16.05 C
+ATOM 710 CG2 VAL A 92 34.776 25.672 2.013 1.00 15.64 C
+ATOM 711 N ASN A 93 34.199 30.163 2.912 1.00 15.12 N
+ATOM 712 CA ASN A 93 34.160 31.413 3.685 1.00 15.10 C
+ATOM 713 C ASN A 93 32.747 32.034 3.803 1.00 9.80 C
+ATOM 714 O ASN A 93 32.361 32.393 4.908 1.00 16.51 O
+ATOM 715 CB ASN A 93 35.168 32.472 3.247 1.00 16.33 C
+ATOM 716 CG ASN A 93 36.582 32.083 3.642 1.00 19.02 C
+ATOM 717 OD1 ASN A 93 37.546 32.671 3.120 1.00 29.57 O
+ATOM 718 ND2 ASN A 93 36.710 31.188 4.631 1.00 24.29 N
+ATOM 719 N CYS A 94 32.096 31.996 2.670 1.00 15.72 N
+ATOM 720 CA CYS A 94 30.695 32.449 2.633 1.00 13.58 C
+ATOM 721 C CYS A 94 29.778 31.527 3.424 1.00 13.05 C
+ATOM 722 O CYS A 94 28.973 32.025 4.236 1.00 16.42 O
+ATOM 723 CB CYS A 94 30.291 32.704 1.185 1.00 12.05 C
+ATOM 724 SG CYS A 94 28.644 33.431 1.046 1.00 15.81 S
+ATOM 725 N ALA A 95 29.945 30.225 3.263 1.00 13.56 N
+ATOM 726 CA ALA A 95 29.134 29.227 3.969 1.00 15.63 C
+ATOM 727 C ALA A 95 29.236 29.330 5.491 1.00 10.80 C
+ATOM 728 O ALA A 95 28.222 29.180 6.179 1.00 12.93 O
+ATOM 729 CB ALA A 95 29.495 27.794 3.612 1.00 14.09 C
+ATOM 730 N LYS A 96 30.424 29.628 5.987 1.00 11.19 N
+ATOM 731 CA LYS A 96 30.627 29.912 7.419 1.00 13.27 C
+ATOM 732 C LYS A 96 29.802 31.115 7.906 1.00 13.38 C
+ATOM 733 O LYS A 96 29.296 31.011 9.027 1.00 15.75 O
+ATOM 734 CB LYS A 96 32.100 30.112 7.775 1.00 12.67 C
+ATOM 735 CG LYS A 96 32.874 28.792 7.697 1.00 11.93 C
+ATOM 736 CD LYS A 96 34.358 29.071 7.879 1.00 15.55 C
+ATOM 737 CE LYS A 96 35.205 27.816 7.938 1.00 18.03 C
+ATOM 738 NZ LYS A 96 36.610 28.242 8.169 1.00 20.72 N
+ATOM 739 N LYS A 97 29.660 32.101 7.049 1.00 12.90 N
+ATOM 740 CA LYS A 97 28.811 33.263 7.379 1.00 16.43 C
+ATOM 741 C LYS A 97 27.333 32.905 7.386 1.00 18.88 C
+ATOM 742 O LYS A 97 26.570 33.318 8.272 1.00 19.20 O
+ATOM 743 CB LYS A 97 29.087 34.456 6.470 1.00 18.97 C
+ATOM 744 CG LYS A 97 30.537 34.927 6.563 1.00 19.81 C
+ATOM 745 CD LYS A 97 30.841 36.073 5.610 1.00 22.00 C
+ATOM 746 CE LYS A 97 32.340 36.293 5.510 1.00 23.71 C
+ATOM 747 NZ LYS A 97 32.569 37.524 4.708 1.00 29.75 N
+ATOM 748 N ILE A 98 26.897 32.127 6.416 1.00 15.72 N
+ATOM 749 CA ILE A 98 25.520 31.693 6.266 1.00 16.36 C
+ATOM 750 C ILE A 98 25.030 30.871 7.453 1.00 16.70 C
+ATOM 751 O ILE A 98 24.059 31.254 8.126 1.00 18.80 O
+ATOM 752 CB ILE A 98 25.307 30.997 4.896 1.00 15.14 C
+ATOM 753 CG1 ILE A 98 25.643 31.910 3.702 1.00 13.63 C
+ATOM 754 CG2 ILE A 98 23.887 30.386 4.817 1.00 15.62 C
+ATOM 755 CD ILE A 98 25.620 31.204 2.321 1.00 17.82 C
+ATOM 756 N VAL A 99 25.875 29.966 7.915 1.00 16.73 N
+ATOM 757 CA VAL A 99 25.488 29.009 8.955 1.00 18.71 C
+ATOM 758 C VAL A 99 25.431 29.697 10.316 1.00 20.36 C
+ATOM 759 O VAL A 99 24.737 29.212 11.233 1.00 25.30 O
+ATOM 760 CB VAL A 99 26.398 27.774 8.859 1.00 16.94 C
+ATOM 761 CG1 VAL A 99 27.811 28.138 9.279 1.00 19.19 C
+ATOM 762 CG2 VAL A 99 25.834 26.594 9.632 1.00 18.97 C
+ATOM 763 N SER A 100 26.205 30.752 10.409 1.00 17.04 N
+ATOM 764 CA SER A 100 26.297 31.529 11.650 1.00 23.81 C
+ATOM 765 C SER A 100 25.124 32.495 11.765 1.00 24.03 C
+ATOM 766 O SER A 100 24.995 33.131 12.820 1.00 28.66 O
+ATOM 767 CB SER A 100 27.647 32.194 11.723 1.00 19.71 C
+ATOM 768 OG SER A 100 28.714 31.264 11.818 1.00 25.04 O
+ATOM 769 N ASP A 101 24.307 32.599 10.750 1.00 25.78 N
+ATOM 770 CA ASP A 101 23.162 33.495 10.650 1.00 26.98 C
+ATOM 771 C ASP A 101 21.924 33.183 11.481 1.00 28.34 C
+ATOM 772 O ASP A 101 21.132 34.143 11.678 1.00 31.88 O
+ATOM 773 CB ASP A 101 22.806 33.854 9.207 1.00 27.75 C
+ATOM 774 CG ASP A 101 22.426 35.320 9.009 1.00 30.86 C
+ATOM 775 OD1 ASP A 101 23.248 36.223 9.266 1.00 34.67 O
+ATOM 776 OD2 ASP A 101 21.276 35.519 8.551 1.00 32.70 O
+ATOM 777 N GLY A 102 21.723 31.942 11.887 1.00 28.87 N
+ATOM 778 CA GLY A 102 20.622 31.656 12.823 1.00 30.67 C
+ATOM 779 C GLY A 102 19.812 30.413 12.505 1.00 27.92 C
+ATOM 780 O GLY A 102 19.195 29.898 13.458 1.00 30.42 O
+ATOM 781 N ASN A 103 19.805 30.005 11.244 1.00 29.26 N
+ATOM 782 CA ASN A 103 19.076 28.799 10.848 1.00 25.22 C
+ATOM 783 C ASN A 103 19.990 27.600 10.597 1.00 22.06 C
+ATOM 784 O ASN A 103 19.472 26.579 10.117 1.00 24.23 O
+ATOM 785 CB ASN A 103 17.976 29.046 9.824 1.00 24.87 C
+ATOM 786 CG ASN A 103 16.708 28.245 10.063 1.00 27.08 C
+ATOM 787 OD1 ASN A 103 16.513 27.577 11.098 1.00 30.30 O
+ATOM 788 ND2 ASN A 103 15.672 28.428 9.240 1.00 30.15 N
+ATOM 789 N GLY A 104 21.240 27.711 10.997 1.00 23.20 N
+ATOM 790 CA GLY A 104 22.177 26.567 10.860 1.00 19.51 C
+ATOM 791 C GLY A 104 22.173 26.142 9.388 1.00 15.58 C
+ATOM 792 O GLY A 104 22.151 27.040 8.541 1.00 22.50 O
+ATOM 793 N MET A 105 22.185 24.847 9.115 1.00 17.51 N
+ATOM 794 CA MET A 105 22.278 24.370 7.724 1.00 16.07 C
+ATOM 795 C MET A 105 20.915 24.309 7.063 1.00 13.35 C
+ATOM 796 O MET A 105 20.902 23.921 5.871 1.00 15.50 O
+ATOM 797 CB MET A 105 23.036 23.048 7.632 1.00 19.32 C
+ATOM 798 CG MET A 105 24.519 23.221 7.871 1.00 17.10 C
+ATOM 799 SD MET A 105 25.379 21.660 7.491 1.00 20.27 S
+ATOM 800 CE MET A 105 25.369 21.706 5.703 1.00 20.03 C
+ATOM 801 N ASN A 106 19.896 24.839 7.735 1.00 14.64 N
+ATOM 802 CA ASN A 106 18.557 24.898 7.103 1.00 18.58 C
+ATOM 803 C ASN A 106 18.566 25.831 5.892 1.00 18.20 C
+ATOM 804 O ASN A 106 17.678 25.748 5.021 1.00 22.14 O
+ATOM 805 CB ASN A 106 17.420 25.150 8.084 1.00 19.18 C
+ATOM 806 CG ASN A 106 17.207 23.938 8.967 1.00 19.21 C
+ATOM 807 OD1 ASN A 106 16.836 22.867 8.443 1.00 24.65 O
+ATOM 808 ND2 ASN A 106 17.542 24.047 10.255 1.00 25.28 N
+ATOM 809 N ALA A 107 19.617 26.647 5.800 1.00 18.54 N
+ATOM 810 CA ALA A 107 19.824 27.514 4.634 1.00 18.74 C
+ATOM 811 C ALA A 107 20.007 26.744 3.329 1.00 16.80 C
+ATOM 812 O ALA A 107 19.734 27.292 2.260 1.00 20.63 O
+ATOM 813 CB ALA A 107 21.060 28.374 4.877 1.00 19.47 C
+ATOM 814 N TRP A 108 20.371 25.465 3.434 1.00 16.46 N
+ATOM 815 CA TRP A 108 20.532 24.624 2.241 1.00 14.68 C
+ATOM 816 C TRP A 108 19.317 23.688 2.110 1.00 17.55 C
+ATOM 817 O TRP A 108 19.240 22.816 2.993 1.00 20.05 O
+ATOM 818 CB TRP A 108 21.840 23.826 2.338 1.00 16.18 C
+ATOM 819 CG TRP A 108 23.000 24.736 2.026 1.00 15.50 C
+ATOM 820 CD1 TRP A 108 23.360 25.234 0.803 1.00 15.45 C
+ATOM 821 CD2 TRP A 108 23.798 25.437 2.991 1.00 15.57 C
+ATOM 822 NE1 TRP A 108 24.414 26.102 0.952 1.00 17.40 N
+ATOM 823 CE2 TRP A 108 24.711 26.237 2.272 1.00 15.78 C
+ATOM 824 CE3 TRP A 108 23.833 25.426 4.379 1.00 12.79 C
+ATOM 825 CZ2 TRP A 108 25.682 26.985 2.917 1.00 15.77 C
+ATOM 826 CZ3 TRP A 108 24.773 26.200 5.033 1.00 16.28 C
+ATOM 827 CH2 TRP A 108 25.691 26.960 4.298 1.00 16.65 C
+ATOM 828 N VAL A 109 18.487 23.925 1.101 1.00 15.35 N
+ATOM 829 CA VAL A 109 17.265 23.096 1.025 1.00 19.96 C
+ATOM 830 C VAL A 109 17.573 21.611 0.884 1.00 17.16 C
+ATOM 831 O VAL A 109 16.923 20.811 1.587 1.00 20.77 O
+ATOM 832 CB VAL A 109 16.146 23.660 0.145 1.00 21.94 C
+ATOM 833 CG1 VAL A 109 16.607 23.905 -1.285 1.00 27.84 C
+ATOM 834 CG2 VAL A 109 14.901 22.783 0.136 1.00 21.22 C
+ATOM 835 N ALA A 110 18.562 21.308 0.075 1.00 20.97 N
+ATOM 836 CA ALA A 110 18.972 19.935 -0.237 1.00 18.78 C
+ATOM 837 C ALA A 110 19.502 19.244 1.006 1.00 18.30 C
+ATOM 838 O ALA A 110 19.197 18.046 1.174 1.00 18.47 O
+ATOM 839 CB ALA A 110 19.857 19.777 -1.455 1.00 20.83 C
+ATOM 840 N TRP A 111 20.121 19.983 1.892 1.00 16.62 N
+ATOM 841 CA TRP A 111 20.551 19.500 3.202 1.00 15.74 C
+ATOM 842 C TRP A 111 19.343 19.085 4.046 1.00 19.12 C
+ATOM 843 O TRP A 111 19.284 17.986 4.643 1.00 16.20 O
+ATOM 844 CB TRP A 111 21.486 20.451 3.925 1.00 14.63 C
+ATOM 845 CG TRP A 111 21.858 19.904 5.252 1.00 14.87 C
+ATOM 846 CD1 TRP A 111 22.856 18.975 5.486 1.00 18.11 C
+ATOM 847 CD2 TRP A 111 21.199 20.093 6.504 1.00 16.63 C
+ATOM 848 NE1 TRP A 111 22.848 18.592 6.808 1.00 17.16 N
+ATOM 849 CE2 TRP A 111 21.798 19.221 7.435 1.00 16.77 C
+ATOM 850 CE3 TRP A 111 20.182 20.959 6.908 1.00 15.16 C
+ATOM 851 CZ2 TRP A 111 21.492 19.284 8.784 1.00 17.69 C
+ATOM 852 CZ3 TRP A 111 19.818 20.954 8.240 1.00 16.88 C
+ATOM 853 CH2 TRP A 111 20.443 20.110 9.162 1.00 19.73 C
+ATOM 854 N ARG A 112 18.438 20.038 4.228 1.00 17.47 N
+ATOM 855 CA ARG A 112 17.185 19.830 4.955 1.00 19.60 C
+ATOM 856 C ARG A 112 16.472 18.593 4.391 1.00 17.68 C
+ATOM 857 O ARG A 112 16.000 17.792 5.220 1.00 22.77 O
+ATOM 858 CB ARG A 112 16.214 20.990 4.944 1.00 17.57 C
+ATOM 859 CG ARG A 112 16.592 22.438 5.091 1.00 25.27 C
+ATOM 860 CD ARG A 112 15.368 23.296 5.135 1.00 21.23 C
+ATOM 861 NE ARG A 112 14.776 23.555 3.836 1.00 28.06 N
+ATOM 862 CZ ARG A 112 14.785 24.695 3.143 1.00 27.89 C
+ATOM 863 NH1 ARG A 112 15.596 25.721 3.383 1.00 30.12 N
+ATOM 864 NH2 ARG A 112 13.717 25.008 2.398 1.00 30.39 N
+ATOM 865 N ASN A 113 16.307 18.521 3.074 1.00 19.43 N
+ATOM 866 CA ASN A 113 15.464 17.463 2.491 1.00 20.16 C
+ATOM 867 C ASN A 113 16.111 16.083 2.586 1.00 21.26 C
+ATOM 868 O ASN A 113 15.454 15.054 2.808 1.00 24.90 O
+ATOM 869 CB ASN A 113 14.966 17.779 1.085 1.00 20.43 C
+ATOM 870 CG ASN A 113 14.003 18.961 1.018 1.00 16.63 C
+ATOM 871 OD1 ASN A 113 13.454 19.344 2.059 1.00 25.68 O
+ATOM 872 ND2 ASN A 113 13.840 19.555 -0.159 1.00 22.00 N
+ATOM 873 N ARG A 114 17.401 16.041 2.355 1.00 19.72 N
+ATOM 874 CA ARG A 114 18.156 14.836 2.042 1.00 21.43 C
+ATOM 875 C ARG A 114 19.258 14.440 2.991 1.00 22.71 C
+ATOM 876 O ARG A 114 19.505 13.217 3.097 1.00 24.85 O
+ATOM 877 CB ARG A 114 18.622 14.910 0.576 1.00 21.05 C
+ATOM 878 CG ARG A 114 17.395 14.614 -0.300 1.00 26.59 C
+ATOM 879 CD ARG A 114 17.729 14.399 -1.731 1.00 26.92 C
+ATOM 880 NE ARG A 114 18.153 15.677 -2.301 1.00 33.46 N
+ATOM 881 CZ ARG A 114 17.826 16.080 -3.535 1.00 32.00 C
+ATOM 882 NH1 ARG A 114 17.378 15.225 -4.456 1.00 36.02 N
+ATOM 883 NH2 ARG A 114 17.735 17.388 -3.796 1.00 36.05 N
+ATOM 884 N CYS A 115 19.743 15.372 3.773 1.00 17.56 N
+ATOM 885 CA CYS A 115 20.843 15.041 4.708 1.00 15.08 C
+ATOM 886 C CYS A 115 20.448 14.933 6.159 1.00 16.64 C
+ATOM 887 O CYS A 115 20.972 14.116 6.940 1.00 21.71 O
+ATOM 888 CB CYS A 115 21.991 16.018 4.426 1.00 15.21 C
+ATOM 889 SG CYS A 115 22.563 16.009 2.739 1.00 19.35 S
+ATOM 890 N LYS A 116 19.714 15.918 6.619 1.00 18.76 N
+ATOM 891 CA LYS A 116 19.332 16.085 8.025 1.00 19.14 C
+ATOM 892 C LYS A 116 18.634 14.821 8.518 1.00 21.91 C
+ATOM 893 O LYS A 116 17.819 14.234 7.785 1.00 24.78 O
+ATOM 894 CB LYS A 116 18.492 17.363 8.126 1.00 21.01 C
+ATOM 895 CG LYS A 116 17.930 17.512 9.547 1.00 21.28 C
+ATOM 896 CD LYS A 116 16.745 18.481 9.554 1.00 25.86 C
+ATOM 897 CE LYS A 116 16.658 19.147 10.918 1.00 25.58 C
+ATOM 898 NZ LYS A 116 15.454 20.010 11.047 1.00 34.69 N
+ATOM 899 N GLY A 117 19.152 14.318 9.635 1.00 26.39 N
+ATOM 900 CA GLY A 117 18.558 13.126 10.267 1.00 29.06 C
+ATOM 901 C GLY A 117 19.018 11.781 9.733 1.00 28.29 C
+ATOM 902 O GLY A 117 18.499 10.733 10.164 1.00 31.90 O
+ATOM 903 N THR A 118 19.892 11.802 8.740 1.00 26.88 N
+ATOM 904 CA THR A 118 20.473 10.578 8.171 1.00 22.31 C
+ATOM 905 C THR A 118 21.868 10.375 8.761 1.00 21.43 C
+ATOM 906 O THR A 118 22.321 11.119 9.650 1.00 22.31 O
+ATOM 907 CB THR A 118 20.440 10.571 6.598 1.00 18.59 C
+ATOM 908 OG1 THR A 118 21.560 11.404 6.161 1.00 22.71 O
+ATOM 909 CG2 THR A 118 19.095 11.104 6.074 1.00 21.13 C
+ATOM 910 N ASP A 119 22.392 9.213 8.431 1.00 21.20 N
+ATOM 911 CA ASP A 119 23.768 8.830 8.756 1.00 22.61 C
+ATOM 912 C ASP A 119 24.713 9.543 7.779 1.00 20.13 C
+ATOM 913 O ASP A 119 25.178 8.950 6.780 1.00 20.57 O
+ATOM 914 CB ASP A 119 23.934 7.313 8.738 1.00 21.00 C
+ATOM 915 CG ASP A 119 25.347 6.900 9.121 1.00 25.32 C
+ATOM 916 OD1 ASP A 119 26.051 7.633 9.830 1.00 27.93 O
+ATOM 917 OD2 ASP A 119 25.715 5.746 8.804 1.00 27.31 O
+ATOM 918 N VAL A 120 24.988 10.793 8.094 1.00 23.41 N
+ATOM 919 CA VAL A 120 25.886 11.637 7.306 1.00 20.10 C
+ATOM 920 C VAL A 120 27.342 11.199 7.304 1.00 18.51 C
+ATOM 921 O VAL A 120 28.099 11.604 6.406 1.00 19.95 O
+ATOM 922 CB VAL A 120 25.721 13.134 7.630 1.00 19.91 C
+ATOM 923 CG1 VAL A 120 24.356 13.655 7.183 1.00 23.59 C
+ATOM 924 CG2 VAL A 120 26.088 13.478 9.055 1.00 20.79 C
+ATOM 925 N GLN A 121 27.701 10.430 8.306 1.00 21.83 N
+ATOM 926 CA GLN A 121 29.021 9.783 8.389 1.00 21.12 C
+ATOM 927 C GLN A 121 29.317 8.861 7.207 1.00 20.78 C
+ATOM 928 O GLN A 121 30.480 8.669 6.820 1.00 19.66 O
+ATOM 929 CB GLN A 121 29.088 9.048 9.728 1.00 24.21 C
+ATOM 930 CG GLN A 121 30.530 8.965 10.167 1.00 26.13 C
+ATOM 931 CD GLN A 121 30.615 8.877 11.674 1.00 26.94 C
+ATOM 932 OE1 GLN A 121 31.368 9.632 12.283 1.00 31.43 O
+ATOM 933 NE2 GLN A 121 29.884 7.871 12.151 1.00 28.26 N
+ATOM 934 N ALA A 122 28.300 8.271 6.576 1.00 17.62 N
+ATOM 935 CA ALA A 122 28.390 7.548 5.311 1.00 19.46 C
+ATOM 936 C ALA A 122 29.186 8.290 4.227 1.00 17.98 C
+ATOM 937 O ALA A 122 30.031 7.710 3.523 1.00 21.35 O
+ATOM 938 CB ALA A 122 26.999 7.244 4.783 1.00 18.29 C
+ATOM 939 N TRP A 123 29.021 9.616 4.240 1.00 18.07 N
+ATOM 940 CA TRP A 123 29.703 10.502 3.283 1.00 16.76 C
+ATOM 941 C TRP A 123 31.218 10.581 3.392 1.00 16.76 C
+ATOM 942 O TRP A 123 31.905 10.942 2.412 1.00 20.08 O
+ATOM 943 CB TRP A 123 29.027 11.872 3.347 1.00 19.49 C
+ATOM 944 CG TRP A 123 27.621 11.735 2.850 1.00 17.43 C
+ATOM 945 CD1 TRP A 123 26.485 11.608 3.588 1.00 19.42 C
+ATOM 946 CD2 TRP A 123 27.241 11.547 1.481 1.00 17.47 C
+ATOM 947 NE1 TRP A 123 25.405 11.458 2.774 1.00 18.86 N
+ATOM 948 CE2 TRP A 123 25.827 11.391 1.479 1.00 17.28 C
+ATOM 949 CE3 TRP A 123 27.947 11.468 0.283 1.00 20.03 C
+ATOM 950 CZ2 TRP A 123 25.111 11.184 0.311 1.00 18.33 C
+ATOM 951 CZ3 TRP A 123 27.222 11.329 -0.886 1.00 20.85 C
+ATOM 952 CH2 TRP A 123 25.835 11.127 -0.869 1.00 20.45 C
+ATOM 953 N ILE A 124 31.741 10.269 4.554 1.00 14.19 N
+ATOM 954 CA ILE A 124 33.186 10.292 4.801 1.00 16.82 C
+ATOM 955 C ILE A 124 33.863 8.955 5.024 1.00 18.45 C
+ATOM 956 O ILE A 124 35.100 8.892 5.134 1.00 21.02 O
+ATOM 957 CB ILE A 124 33.504 11.403 5.863 1.00 17.69 C
+ATOM 958 CG1 ILE A 124 32.956 10.984 7.234 1.00 18.86 C
+ATOM 959 CG2 ILE A 124 33.024 12.804 5.387 1.00 21.01 C
+ATOM 960 CD ILE A 124 33.729 11.437 8.488 1.00 22.81 C
+ATOM 961 N ARG A 125 33.080 7.898 5.131 1.00 21.05 N
+ATOM 962 CA ARG A 125 33.594 6.534 5.320 1.00 19.12 C
+ATOM 963 C ARG A 125 34.311 6.113 4.036 1.00 17.52 C
+ATOM 964 O ARG A 125 33.843 6.337 2.906 1.00 23.44 O
+ATOM 965 CB ARG A 125 32.476 5.551 5.650 1.00 19.54 C
+ATOM 966 CG ARG A 125 32.117 5.596 7.145 1.00 22.40 C
+ATOM 967 CD ARG A 125 31.277 4.392 7.482 1.00 24.05 C
+ATOM 968 NE ARG A 125 30.282 4.754 8.466 1.00 28.08 N
+ATOM 969 CZ ARG A 125 28.984 4.993 8.331 1.00 23.40 C
+ATOM 970 NH1 ARG A 125 28.334 4.690 7.207 1.00 23.69 N
+ATOM 971 NH2 ARG A 125 28.392 5.549 9.392 1.00 23.77 N
+ATOM 972 N GLY A 126 35.497 5.568 4.243 1.00 18.80 N
+ATOM 973 CA GLY A 126 36.291 5.058 3.102 1.00 21.28 C
+ATOM 974 C GLY A 126 37.334 6.066 2.658 1.00 22.50 C
+ATOM 975 O GLY A 126 38.220 5.729 1.855 1.00 23.59 O
+ATOM 976 N CYS A 127 37.335 7.221 3.297 1.00 19.05 N
+ATOM 977 CA CYS A 127 38.234 8.333 2.961 1.00 19.13 C
+ATOM 978 C CYS A 127 39.422 8.382 3.925 1.00 22.50 C
+ATOM 979 O CYS A 127 39.206 8.267 5.138 1.00 21.64 O
+ATOM 980 CB CYS A 127 37.453 9.628 2.990 1.00 18.75 C
+ATOM 981 SG CYS A 127 36.010 9.816 1.936 1.00 19.93 S
+ATOM 982 N ARG A 128 40.586 8.695 3.393 1.00 23.60 N
+ATOM 983 CA ARG A 128 41.774 8.960 4.217 1.00 28.29 C
+ATOM 984 C ARG A 128 41.820 10.438 4.578 1.00 25.64 C
+ATOM 985 O ARG A 128 41.976 11.291 3.694 1.00 30.98 O
+ATOM 986 CB ARG A 128 43.047 8.304 3.707 1.00 30.82 C
+ATOM 987 CG ARG A 128 43.231 6.886 4.280 1.00 34.25 C
+ATOM 988 CD ARG A 128 43.833 6.911 5.651 1.00 33.59 C
+ATOM 989 NE ARG A 128 45.246 7.263 5.636 1.00 37.63 N
+ATOM 990 CZ ARG A 128 45.862 8.258 6.281 1.00 38.37 C
+ATOM 991 NH1 ARG A 128 45.241 9.069 7.151 1.00 38.97 N
+ATOM 992 NH2 ARG A 128 47.134 8.554 5.973 1.00 40.22 N
+ATOM 993 N LEU A 129 41.289 10.715 5.771 1.00 26.05 N
+ATOM 994 CA LEU A 129 41.094 12.084 6.273 1.00 26.89 C
+ATOM 995 C LEU A 129 42.119 12.382 7.370 1.00 29.58 C
+ATOM 996 O LEU A 129 41.730 12.276 8.559 1.00 33.54 O
+ATOM 997 CB LEU A 129 39.635 12.335 6.646 1.00 26.31 C
+ATOM 998 CG LEU A 129 38.689 12.917 5.620 1.00 23.49 C
+ATOM 999 CD1 LEU A 129 39.112 12.657 4.191 1.00 26.43 C
+ATOM 1000 CD2 LEU A 129 37.310 12.325 5.886 1.00 25.15 C
+ATOM 1001 OXT LEU A 129 43.232 12.675 6.905 1.00 34.20 O
+TER 1002 LEU A 129
+CONECT 48 981
+CONECT 238 889
+CONECT 513 630
+CONECT 601 724
+CONECT 630 513
+CONECT 724 601
+CONECT 889 238
+CONECT 981 48
+MASTER 290 0 0 8 2 0 0 6 1079 1 8 10
+END
diff --git a/modules/mol/mm/examples/1AKI_original.pdb b/modules/mol/mm/examples/1AKI_original.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..5228267a3ffbba05f8205a1f504282a27a4265ba
--- /dev/null
+++ b/modules/mol/mm/examples/1AKI_original.pdb
@@ -0,0 +1,1436 @@
+HEADER HYDROLASE 19-MAY-97 1AKI
+TITLE THE STRUCTURE OF THE ORTHORHOMBIC FORM OF HEN EGG-WHITE
+TITLE 2 LYSOZYME AT 1.5 ANGSTROMS RESOLUTION
+COMPND MOL_ID: 1;
+COMPND 2 MOLECULE: LYSOZYME;
+COMPND 3 CHAIN: A;
+COMPND 4 EC: 3.2.1.17
+SOURCE MOL_ID: 1;
+SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
+SOURCE 3 ORGANISM_COMMON: CHICKEN;
+SOURCE 4 ORGANISM_TAXID: 9031;
+SOURCE 5 CELL: EGG
+KEYWDS HYDROLASE, GLYCOSIDASE
+EXPDTA X-RAY DIFFRACTION
+AUTHOR D.CARTER,J.HE,J.R.RUBLE,B.WRIGHT
+REVDAT 2 24-FEB-09 1AKI 1 VERSN
+REVDAT 1 19-NOV-97 1AKI 0
+JRNL AUTH P.J.ARTYMIUK,C.C.F.BLAKE,D.W.RICE,K.S.WILSON
+JRNL TITL THE STRUCTURES OF THE MONOCLINIC AND ORTHORHOMBIC
+JRNL TITL 2 FORMS OF HEN EGG-WHITE LYSOZYME AT 6 ANGSTROMS
+JRNL TITL 3 RESOLUTION
+JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 38 778 1982
+JRNL REFN ISSN 0108-7681
+REMARK 1
+REMARK 2
+REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
+REMARK 3
+REMARK 3 REFINEMENT.
+REMARK 3 PROGRAM : GPRLSA, X-PLOR
+REMARK 3 AUTHORS : FUREY
+REMARK 3
+REMARK 3 DATA USED IN REFINEMENT.
+REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
+REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
+REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
+REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1
+REMARK 3 NUMBER OF REFLECTIONS : 16327
+REMARK 3
+REMARK 3 FIT TO DATA USED IN REFINEMENT.
+REMARK 3 CROSS-VALIDATION METHOD : NULL
+REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
+REMARK 3 R VALUE (WORKING + TEST SET) : NULL
+REMARK 3 R VALUE (WORKING SET) : 0.212
+REMARK 3 FREE R VALUE : NULL
+REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
+REMARK 3 FREE R VALUE TEST SET COUNT : NULL
+REMARK 3
+REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
+REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
+REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
+REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
+REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
+REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
+REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
+REMARK 3
+REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
+REMARK 3 PROTEIN ATOMS : 1001
+REMARK 3 NUCLEIC ACID ATOMS : 0
+REMARK 3 HETEROGEN ATOMS : 0
+REMARK 3 SOLVENT ATOMS : 78
+REMARK 3
+REMARK 3 B VALUES.
+REMARK 3 FROM WILSON PLOT (A**2) : NULL
+REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
+REMARK 3 OVERALL ANISOTROPIC B VALUE.
+REMARK 3 B11 (A**2) : NULL
+REMARK 3 B22 (A**2) : NULL
+REMARK 3 B33 (A**2) : NULL
+REMARK 3 B12 (A**2) : NULL
+REMARK 3 B13 (A**2) : NULL
+REMARK 3 B23 (A**2) : NULL
+REMARK 3
+REMARK 3 ESTIMATED COORDINATE ERROR.
+REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
+REMARK 3 ESD FROM SIGMAA (A) : NULL
+REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.00
+REMARK 3
+REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
+REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
+REMARK 3 BOND LENGTH (A) : 0.009 ; 0.010
+REMARK 3 ANGLE DISTANCE (A) : 0.003 ; 0.025
+REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.024 ; 0.020
+REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
+REMARK 3
+REMARK 3 PLANE RESTRAINT (A) : 0.033 ; 0.030
+REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.212 ; 0.200
+REMARK 3
+REMARK 3 NON-BONDED CONTACT RESTRAINTS.
+REMARK 3 SINGLE TORSION (A) : 0.183 ; 0.300
+REMARK 3 MULTIPLE TORSION (A) : 0.159 ; 0.300
+REMARK 3 H-BOND (X...Y) (A) : 0.299 ; 0.300
+REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
+REMARK 3
+REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
+REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
+REMARK 3 PLANAR (DEGREES) : 7.900 ; 5.000
+REMARK 3 STAGGERED (DEGREES) : 17.800; 15.000
+REMARK 3 TRANSVERSE (DEGREES) : 18.900; 15.000
+REMARK 3
+REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
+REMARK 3 MAIN-CHAIN BOND (A**2) : 2.500 ; 3.000
+REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.900 ; 4.000
+REMARK 3 SIDE-CHAIN BOND (A**2) : 3.200 ; 4.000
+REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 3.000
+REMARK 3
+REMARK 3 OTHER REFINEMENT REMARKS: NULL
+REMARK 4
+REMARK 4 1AKI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
+REMARK 100
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
+REMARK 200
+REMARK 200 EXPERIMENTAL DETAILS
+REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
+REMARK 200 DATE OF DATA COLLECTION : NOV-95
+REMARK 200 TEMPERATURE (KELVIN) : 298
+REMARK 200 PH : 4.48
+REMARK 200 NUMBER OF CRYSTALS USED : 1
+REMARK 200
+REMARK 200 SYNCHROTRON (Y/N) : N
+REMARK 200 RADIATION SOURCE : ROTATING ANODE
+REMARK 200 BEAMLINE : NULL
+REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R
+REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
+REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
+REMARK 200 MONOCHROMATOR : GRAPHITE(002)
+REMARK 200 OPTICS : NULL
+REMARK 200
+REMARK 200 DETECTOR TYPE : IMAGE PLATE
+REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC
+REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU
+REMARK 200 DATA SCALING SOFTWARE : BIOTEX
+REMARK 200
+REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20571
+REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
+REMARK 200 RESOLUTION RANGE LOW (A) : 15.000
+REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
+REMARK 200
+REMARK 200 OVERALL.
+REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1
+REMARK 200 DATA REDUNDANCY : 3.100
+REMARK 200 R MERGE (I) : 0.04400
+REMARK 200 R SYM (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000
+REMARK 200
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
+REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
+REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
+REMARK 200 DATA REDUNDANCY IN SHELL : NULL
+REMARK 200 R MERGE FOR SHELL (I) : NULL
+REMARK 200 R SYM FOR SHELL (I) : NULL
+REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
+REMARK 200
+REMARK 200 DIFFRACTION PROTOCOL: NULL
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
+REMARK 200 SOFTWARE USED: X-PLOR
+REMARK 200 STARTING MODEL: PDB ENTRY 2LZH
+REMARK 200
+REMARK 200 REMARK: NULL
+REMARK 280
+REMARK 280 CRYSTAL
+REMARK 280 SOLVENT CONTENT, VS (%): 42.84
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
+REMARK 280
+REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.48
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
+REMARK 290
+REMARK 290 SYMOP SYMMETRY
+REMARK 290 NNNMMM OPERATOR
+REMARK 290 1555 X,Y,Z
+REMARK 290 2555 -X+1/2,-Y,Z+1/2
+REMARK 290 3555 -X,Y+1/2,-Z+1/2
+REMARK 290 4555 X+1/2,-Y+1/2,-Z
+REMARK 290
+REMARK 290 WHERE NNN -> OPERATOR NUMBER
+REMARK 290 MMM -> TRANSLATION VECTOR
+REMARK 290
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
+REMARK 290 RELATED MOLECULES.
+REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.53100
+REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
+REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.25850
+REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
+REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.22550
+REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.25850
+REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.53100
+REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.22550
+REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
+REMARK 290
+REMARK 290 REMARK: NULL
+REMARK 300
+REMARK 300 BIOMOLECULE: 1
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
+REMARK 300 BURIED SURFACE AREA.
+REMARK 350
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
+REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
+REMARK 350
+REMARK 350 BIOMOLECULE: 1
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
+REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
+REMARK 500 NH2 ARG A 45 NH2 ARG A 68 2.16
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: CLOSE CONTACTS
+REMARK 500
+REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
+REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
+REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
+REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
+REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
+REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
+REMARK 500
+REMARK 500 DISTANCE CUTOFF:
+REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
+REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
+REMARK 500
+REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
+REMARK 500 OD1 ASN A 19 ND2 ASN A 39 1556 2.09
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
+REMARK 500
+REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
+REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
+REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
+REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 STANDARD TABLE:
+REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
+REMARK 500
+REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
+REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
+REMARK 500
+REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
+REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES
+REMARK 500 ASP A 18 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
+REMARK 500 ARG A 21 CD - NE - CZ ANGL. DEV. = 13.6 DEGREES
+REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES
+REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES
+REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES
+REMARK 500 ASP A 66 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES
+REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES
+REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES
+REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES
+REMARK 500 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES
+REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 8.6 DEGREES
+REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES
+REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES
+REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: PLANAR GROUPS
+REMARK 500
+REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
+REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
+REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
+REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
+REMARK 500 AN RMSD GREATER THAN THIS VALUE
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI RMS TYPE
+REMARK 500 ARG A 14 0.12 SIDE_CHAIN
+REMARK 500 ARG A 21 0.21 SIDE_CHAIN
+REMARK 500 ARG A 68 0.15 SIDE_CHAIN
+REMARK 500 ARG A 73 0.25 SIDE_CHAIN
+REMARK 500 ARG A 112 0.15 SIDE_CHAIN
+REMARK 500 ARG A 114 0.13 SIDE_CHAIN
+REMARK 500
+REMARK 500 REMARK: NULL
+REMARK 500
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY
+REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
+REMARK 500
+REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
+REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER
+REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
+REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
+REMARK 500 I=INSERTION CODE).
+REMARK 500
+REMARK 500 M RES CSSEQI ANGLE
+REMARK 500 ARG A 128 10.17
+REMARK 500
+REMARK 500 REMARK: NULL
+DBREF 1AKI A 1 129 UNP P00698 LYSC_CHICK 19 147
+SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
+SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
+SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
+SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
+SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
+SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
+SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
+SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
+SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
+SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
+FORMUL 2 HOH *78(H2 O)
+HELIX 1 1 ARG A 5 ARG A 14 1 10
+HELIX 2 2 TYR A 20 GLY A 22 5 3
+HELIX 3 3 LEU A 25 SER A 36 1 12
+HELIX 4 4 CYS A 80 LEU A 84 5 5
+HELIX 5 5 THR A 89 ASP A 101 1 13
+HELIX 6 6 GLY A 104 ALA A 107 5 4
+HELIX 7 7 VAL A 109 ARG A 114 1 6
+HELIX 8 8 VAL A 120 TRP A 123 5 4
+SHEET 1 A 2 THR A 43 ARG A 45 0
+SHEET 2 A 2 THR A 51 TYR A 53 -1 N ASP A 52 O ASN A 44
+SSBOND 1 CYS A 6 CYS A 127 1555 1555 1.97
+SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.00
+SSBOND 3 CYS A 64 CYS A 80 1555 1555 1.99
+SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02
+CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 21 21 21 4
+ORIGX1 1.000000 0.000000 0.000000 0.00000
+ORIGX2 0.000000 1.000000 0.000000 0.00000
+ORIGX3 0.000000 0.000000 1.000000 0.00000
+SCALE1 0.016931 0.000000 0.000000 0.00000
+SCALE2 0.000000 0.014609 0.000000 0.00000
+SCALE3 0.000000 0.000000 0.032769 0.00000
+ATOM 1 N LYS A 1 35.365 22.342 -11.980 1.00 22.28 N
+ATOM 2 CA LYS A 1 35.892 21.073 -11.427 1.00 21.12 C
+ATOM 3 C LYS A 1 34.741 20.264 -10.844 1.00 16.85 C
+ATOM 4 O LYS A 1 33.945 20.813 -10.081 1.00 18.94 O
+ATOM 5 CB LYS A 1 36.872 21.435 -10.306 1.00 20.78 C
+ATOM 6 CG LYS A 1 37.453 20.248 -9.565 1.00 18.47 C
+ATOM 7 CD LYS A 1 38.688 20.649 -8.775 1.00 20.32 C
+ATOM 8 CE LYS A 1 39.057 19.508 -7.837 1.00 24.76 C
+ATOM 9 NZ LYS A 1 40.423 19.771 -7.299 1.00 28.27 N
+ATOM 10 N VAL A 2 34.739 18.961 -11.042 1.00 19.96 N
+ATOM 11 CA VAL A 2 33.903 17.998 -10.333 1.00 18.10 C
+ATOM 12 C VAL A 2 34.800 17.312 -9.294 1.00 19.39 C
+ATOM 13 O VAL A 2 35.759 16.605 -9.665 1.00 22.14 O
+ATOM 14 CB VAL A 2 33.140 17.034 -11.232 1.00 16.81 C
+ATOM 15 CG1 VAL A 2 32.251 16.084 -10.434 1.00 21.92 C
+ATOM 16 CG2 VAL A 2 32.294 17.714 -12.290 1.00 19.46 C
+ATOM 17 N PHE A 3 34.491 17.546 -8.038 1.00 19.89 N
+ATOM 18 CA PHE A 3 35.185 16.903 -6.918 1.00 17.43 C
+ATOM 19 C PHE A 3 34.742 15.441 -6.771 1.00 15.70 C
+ATOM 20 O PHE A 3 33.525 15.162 -6.862 1.00 18.52 O
+ATOM 21 CB PHE A 3 34.967 17.632 -5.594 1.00 17.94 C
+ATOM 22 CG PHE A 3 35.944 18.737 -5.375 1.00 16.78 C
+ATOM 23 CD1 PHE A 3 35.666 20.050 -5.798 1.00 15.97 C
+ATOM 24 CD2 PHE A 3 37.000 18.557 -4.473 1.00 19.95 C
+ATOM 25 CE1 PHE A 3 36.577 21.076 -5.568 1.00 17.32 C
+ATOM 26 CE2 PHE A 3 37.869 19.589 -4.157 1.00 17.65 C
+ATOM 27 CZ PHE A 3 37.636 20.873 -4.666 1.00 17.91 C
+ATOM 28 N GLY A 4 35.724 14.639 -6.331 1.00 16.79 N
+ATOM 29 CA GLY A 4 35.366 13.280 -5.870 1.00 16.34 C
+ATOM 30 C GLY A 4 34.924 13.420 -4.415 1.00 11.91 C
+ATOM 31 O GLY A 4 35.303 14.403 -3.781 1.00 16.23 O
+ATOM 32 N ARG A 5 34.053 12.538 -3.973 1.00 14.65 N
+ATOM 33 CA ARG A 5 33.565 12.538 -2.588 1.00 15.91 C
+ATOM 34 C ARG A 5 34.665 12.734 -1.556 1.00 15.38 C
+ATOM 35 O ARG A 5 34.669 13.651 -0.704 1.00 13.15 O
+ATOM 36 CB ARG A 5 32.765 11.262 -2.331 1.00 17.38 C
+ATOM 37 CG ARG A 5 32.213 11.203 -0.920 1.00 13.79 C
+ATOM 38 CD ARG A 5 31.375 10.001 -0.722 1.00 15.84 C
+ATOM 39 NE ARG A 5 32.059 8.749 -0.958 1.00 18.74 N
+ATOM 40 CZ ARG A 5 32.733 8.011 -0.097 1.00 15.19 C
+ATOM 41 NH1 ARG A 5 32.836 8.332 1.187 1.00 17.50 N
+ATOM 42 NH2 ARG A 5 33.245 6.836 -0.526 1.00 23.44 N
+ATOM 43 N CYS A 6 35.674 11.853 -1.612 1.00 14.07 N
+ATOM 44 CA CYS A 6 36.781 11.870 -0.654 1.00 14.62 C
+ATOM 45 C CYS A 6 37.747 13.050 -0.777 1.00 10.99 C
+ATOM 46 O CYS A 6 38.148 13.609 0.264 1.00 16.34 O
+ATOM 47 CB CYS A 6 37.491 10.532 -0.621 1.00 16.90 C
+ATOM 48 SG CYS A 6 36.540 9.205 0.140 1.00 18.61 S
+ATOM 49 N GLU A 7 37.861 13.481 -2.019 1.00 14.24 N
+ATOM 50 CA GLU A 7 38.685 14.686 -2.311 1.00 13.83 C
+ATOM 51 C GLU A 7 38.049 15.926 -1.658 1.00 14.86 C
+ATOM 52 O GLU A 7 38.744 16.729 -1.011 1.00 15.01 O
+ATOM 53 CB GLU A 7 38.784 14.846 -3.818 1.00 14.85 C
+ATOM 54 CG GLU A 7 39.540 16.051 -4.379 1.00 18.50 C
+ATOM 55 CD GLU A 7 39.576 16.242 -5.870 1.00 20.16 C
+ATOM 56 OE1 GLU A 7 38.672 15.644 -6.491 1.00 26.20 O
+ATOM 57 OE2 GLU A 7 40.415 16.953 -6.381 1.00 25.49 O
+ATOM 58 N LEU A 8 36.743 16.049 -1.819 1.00 15.18 N
+ATOM 59 CA LEU A 8 35.964 17.158 -1.255 1.00 12.72 C
+ATOM 60 C LEU A 8 36.051 17.132 0.266 1.00 9.45 C
+ATOM 61 O LEU A 8 36.159 18.166 0.920 1.00 13.45 O
+ATOM 62 CB LEU A 8 34.528 17.172 -1.811 1.00 14.31 C
+ATOM 63 CG LEU A 8 33.718 18.354 -1.305 1.00 15.95 C
+ATOM 64 CD1 LEU A 8 34.297 19.656 -1.841 1.00 16.56 C
+ATOM 65 CD2 LEU A 8 32.246 18.143 -1.596 1.00 15.88 C
+ATOM 66 N ALA A 9 35.754 15.980 0.828 1.00 14.24 N
+ATOM 67 CA ALA A 9 35.838 15.757 2.284 1.00 13.25 C
+ATOM 68 C ALA A 9 37.144 16.314 2.840 1.00 12.89 C
+ATOM 69 O ALA A 9 37.151 16.978 3.897 1.00 14.78 O
+ATOM 70 CB ALA A 9 35.656 14.287 2.623 1.00 13.89 C
+ATOM 71 N ALA A 10 38.272 15.983 2.204 1.00 12.54 N
+ATOM 72 CA ALA A 10 39.610 16.431 2.616 1.00 16.58 C
+ATOM 73 C ALA A 10 39.736 17.944 2.459 1.00 15.35 C
+ATOM 74 O ALA A 10 40.193 18.499 3.469 1.00 17.40 O
+ATOM 75 CB ALA A 10 40.708 15.706 1.842 1.00 15.49 C
+ATOM 76 N ALA A 11 39.227 18.519 1.385 1.00 13.54 N
+ATOM 77 CA ALA A 11 39.264 19.982 1.223 1.00 15.23 C
+ATOM 78 C ALA A 11 38.491 20.702 2.321 1.00 15.68 C
+ATOM 79 O ALA A 11 38.946 21.658 2.953 1.00 16.87 O
+ATOM 80 CB ALA A 11 38.869 20.421 -0.175 1.00 14.12 C
+ATOM 81 N MET A 12 37.288 20.214 2.590 1.00 15.47 N
+ATOM 82 CA MET A 12 36.398 20.781 3.612 1.00 13.69 C
+ATOM 83 C MET A 12 36.990 20.715 5.007 1.00 12.55 C
+ATOM 84 O MET A 12 36.906 21.637 5.840 1.00 17.69 O
+ATOM 85 CB MET A 12 34.993 20.213 3.515 1.00 11.18 C
+ATOM 86 CG MET A 12 34.320 20.724 2.265 1.00 15.06 C
+ATOM 87 SD MET A 12 32.634 19.986 2.235 1.00 17.81 S
+ATOM 88 CE MET A 12 31.788 21.135 1.138 1.00 18.08 C
+ATOM 89 N LYS A 13 37.688 19.628 5.314 1.00 12.42 N
+ATOM 90 CA LYS A 13 38.387 19.385 6.579 1.00 14.58 C
+ATOM 91 C LYS A 13 39.460 20.467 6.731 1.00 14.55 C
+ATOM 92 O LYS A 13 39.507 21.137 7.776 1.00 16.49 O
+ATOM 93 CB LYS A 13 38.934 17.952 6.572 1.00 15.36 C
+ATOM 94 CG LYS A 13 39.742 17.555 7.798 1.00 20.46 C
+ATOM 95 CD LYS A 13 38.973 16.777 8.834 1.00 23.53 C
+ATOM 96 CE LYS A 13 39.293 15.305 8.751 1.00 26.37 C
+ATOM 97 NZ LYS A 13 38.077 14.461 8.946 1.00 30.88 N
+ATOM 98 N ARG A 14 40.267 20.629 5.688 1.00 18.91 N
+ATOM 99 CA ARG A 14 41.387 21.577 5.713 1.00 17.66 C
+ATOM 100 C ARG A 14 40.927 23.017 5.881 1.00 16.78 C
+ATOM 101 O ARG A 14 41.557 23.834 6.584 1.00 20.06 O
+ATOM 102 CB ARG A 14 42.388 21.351 4.601 1.00 20.89 C
+ATOM 103 CG ARG A 14 42.173 22.079 3.289 1.00 25.07 C
+ATOM 104 CD ARG A 14 43.444 22.075 2.490 1.00 23.98 C
+ATOM 105 NE ARG A 14 43.687 20.710 2.012 1.00 31.92 N
+ATOM 106 CZ ARG A 14 43.098 20.255 0.892 1.00 26.04 C
+ATOM 107 NH1 ARG A 14 42.695 21.186 0.018 1.00 33.46 N
+ATOM 108 NH2 ARG A 14 42.949 18.957 0.689 1.00 25.91 N
+ATOM 109 N HIS A 15 39.681 23.247 5.463 1.00 17.84 N
+ATOM 110 CA HIS A 15 39.075 24.591 5.526 1.00 15.99 C
+ATOM 111 C HIS A 15 38.310 24.861 6.814 1.00 17.70 C
+ATOM 112 O HIS A 15 37.608 25.875 6.952 1.00 22.68 O
+ATOM 113 CB HIS A 15 38.223 24.918 4.285 1.00 19.19 C
+ATOM 114 CG HIS A 15 39.085 25.388 3.171 1.00 20.14 C
+ATOM 115 ND1 HIS A 15 39.457 24.635 2.091 1.00 24.53 N
+ATOM 116 CD2 HIS A 15 39.739 26.570 2.993 1.00 24.44 C
+ATOM 117 CE1 HIS A 15 40.211 25.312 1.258 1.00 20.68 C
+ATOM 118 NE2 HIS A 15 40.524 26.419 1.889 1.00 27.34 N
+ATOM 119 N GLY A 16 38.296 23.927 7.720 1.00 17.50 N
+ATOM 120 CA GLY A 16 37.765 24.025 9.072 1.00 18.71 C
+ATOM 121 C GLY A 16 36.264 23.799 9.210 1.00 18.40 C
+ATOM 122 O GLY A 16 35.646 24.400 10.127 1.00 21.57 O
+ATOM 123 N LEU A 17 35.665 23.073 8.274 1.00 17.56 N
+ATOM 124 CA LEU A 17 34.238 22.795 8.298 1.00 15.38 C
+ATOM 125 C LEU A 17 33.845 21.682 9.266 1.00 18.28 C
+ATOM 126 O LEU A 17 32.643 21.594 9.552 1.00 18.24 O
+ATOM 127 CB LEU A 17 33.648 22.647 6.901 1.00 15.02 C
+ATOM 128 CG LEU A 17 33.451 23.889 6.060 1.00 16.08 C
+ATOM 129 CD1 LEU A 17 32.933 23.420 4.705 1.00 13.83 C
+ATOM 130 CD2 LEU A 17 32.556 24.946 6.679 1.00 18.60 C
+ATOM 131 N ASP A 18 34.785 20.814 9.605 1.00 16.36 N
+ATOM 132 CA ASP A 18 34.492 19.722 10.526 1.00 16.25 C
+ATOM 133 C ASP A 18 34.015 20.222 11.901 1.00 17.32 C
+ATOM 134 O ASP A 18 34.826 20.778 12.658 1.00 20.27 O
+ATOM 135 CB ASP A 18 35.557 18.633 10.598 1.00 19.37 C
+ATOM 136 CG ASP A 18 35.017 17.408 11.311 1.00 20.25 C
+ATOM 137 OD1 ASP A 18 33.805 17.154 11.455 1.00 21.00 O
+ATOM 138 OD2 ASP A 18 35.925 16.603 11.662 1.00 27.06 O
+ATOM 139 N ASN A 19 32.746 19.990 12.205 1.00 18.55 N
+ATOM 140 CA ASN A 19 32.123 20.431 13.448 1.00 17.19 C
+ATOM 141 C ASN A 19 31.854 21.941 13.497 1.00 16.61 C
+ATOM 142 O ASN A 19 31.426 22.398 14.573 1.00 18.56 O
+ATOM 143 CB ASN A 19 32.767 20.004 14.770 1.00 18.92 C
+ATOM 144 CG ASN A 19 32.162 20.512 16.064 1.00 24.64 C
+ATOM 145 OD1 ASN A 19 30.967 20.273 16.355 1.00 32.53 O
+ATOM 146 ND2 ASN A 19 32.847 21.361 16.852 1.00 24.14 N
+ATOM 147 N TYR A 20 31.969 22.650 12.406 1.00 16.84 N
+ATOM 148 CA TYR A 20 31.707 24.099 12.411 1.00 15.54 C
+ATOM 149 C TYR A 20 30.231 24.343 12.759 1.00 15.81 C
+ATOM 150 O TYR A 20 29.288 23.874 12.118 1.00 16.89 O
+ATOM 151 CB TYR A 20 32.070 24.736 11.066 1.00 18.16 C
+ATOM 152 CG TYR A 20 32.061 26.250 11.144 1.00 20.28 C
+ATOM 153 CD1 TYR A 20 33.141 26.886 11.760 1.00 21.42 C
+ATOM 154 CD2 TYR A 20 30.979 27.004 10.691 1.00 20.44 C
+ATOM 155 CE1 TYR A 20 33.206 28.277 11.794 1.00 22.24 C
+ATOM 156 CE2 TYR A 20 31.018 28.399 10.779 1.00 21.36 C
+ATOM 157 CZ TYR A 20 32.102 29.017 11.383 1.00 19.38 C
+ATOM 158 OH TYR A 20 32.136 30.371 11.525 1.00 26.77 O
+ATOM 159 N ARG A 21 30.088 25.142 13.803 1.00 18.43 N
+ATOM 160 CA ARG A 21 28.774 25.553 14.319 1.00 15.68 C
+ATOM 161 C ARG A 21 27.964 24.312 14.623 1.00 15.17 C
+ATOM 162 O ARG A 21 26.733 24.333 14.606 1.00 18.36 O
+ATOM 163 CB ARG A 21 28.014 26.565 13.453 1.00 19.21 C
+ATOM 164 CG ARG A 21 28.507 27.995 13.535 1.00 21.50 C
+ATOM 165 CD ARG A 21 28.110 28.755 14.765 1.00 25.00 C
+ATOM 166 NE ARG A 21 29.319 29.321 15.324 1.00 30.37 N
+ATOM 167 CZ ARG A 21 30.215 30.234 14.978 1.00 29.02 C
+ATOM 168 NH1 ARG A 21 31.501 29.856 14.846 1.00 29.04 N
+ATOM 169 NH2 ARG A 21 29.938 31.437 14.495 1.00 31.89 N
+ATOM 170 N GLY A 22 28.689 23.250 14.998 1.00 17.81 N
+ATOM 171 CA GLY A 22 28.103 22.021 15.519 1.00 17.72 C
+ATOM 172 C GLY A 22 27.748 21.018 14.436 1.00 18.89 C
+ATOM 173 O GLY A 22 27.085 20.022 14.784 1.00 23.26 O
+ATOM 174 N TYR A 23 28.209 21.230 13.216 1.00 18.20 N
+ATOM 175 CA TYR A 23 27.887 20.318 12.111 1.00 15.42 C
+ATOM 176 C TYR A 23 29.124 19.533 11.628 1.00 16.30 C
+ATOM 177 O TYR A 23 30.045 20.191 11.139 1.00 16.66 O
+ATOM 178 CB TYR A 23 27.351 21.107 10.913 1.00 15.82 C
+ATOM 179 CG TYR A 23 26.001 21.745 11.127 1.00 15.96 C
+ATOM 180 CD1 TYR A 23 24.846 20.962 11.139 1.00 14.81 C
+ATOM 181 CD2 TYR A 23 25.897 23.096 11.458 1.00 16.60 C
+ATOM 182 CE1 TYR A 23 23.600 21.518 11.422 1.00 17.08 C
+ATOM 183 CE2 TYR A 23 24.647 23.673 11.726 1.00 19.34 C
+ATOM 184 CZ TYR A 23 23.518 22.881 11.701 1.00 19.21 C
+ATOM 185 OH TYR A 23 22.289 23.438 11.912 1.00 25.61 O
+ATOM 186 N SER A 24 29.029 18.223 11.810 1.00 15.35 N
+ATOM 187 CA SER A 24 30.143 17.347 11.414 1.00 16.89 C
+ATOM 188 C SER A 24 30.359 17.379 9.895 1.00 15.61 C
+ATOM 189 O SER A 24 29.442 17.687 9.139 1.00 13.88 O
+ATOM 190 CB SER A 24 29.922 15.934 11.907 1.00 17.54 C
+ATOM 191 OG SER A 24 28.799 15.336 11.308 1.00 19.85 O
+ATOM 192 N LEU A 25 31.593 17.028 9.540 1.00 16.08 N
+ATOM 193 CA LEU A 25 32.035 17.092 8.138 1.00 13.16 C
+ATOM 194 C LEU A 25 31.030 16.437 7.183 1.00 13.39 C
+ATOM 195 O LEU A 25 30.874 16.924 6.056 1.00 15.34 O
+ATOM 196 CB LEU A 25 33.410 16.409 8.084 1.00 13.47 C
+ATOM 197 CG LEU A 25 34.015 16.477 6.689 1.00 12.91 C
+ATOM 198 CD1 LEU A 25 34.174 17.929 6.289 1.00 13.04 C
+ATOM 199 CD2 LEU A 25 35.398 15.810 6.752 1.00 14.54 C
+ATOM 200 N GLY A 26 30.501 15.280 7.576 1.00 13.10 N
+ATOM 201 CA GLY A 26 29.539 14.561 6.756 1.00 13.88 C
+ATOM 202 C GLY A 26 28.338 15.378 6.277 1.00 12.12 C
+ATOM 203 O GLY A 26 27.886 15.250 5.120 1.00 13.13 O
+ATOM 204 N ASN A 27 27.905 16.281 7.161 1.00 12.16 N
+ATOM 205 CA ASN A 27 26.827 17.227 6.857 1.00 14.74 C
+ATOM 206 C ASN A 27 27.164 18.015 5.597 1.00 15.43 C
+ATOM 207 O ASN A 27 26.317 18.208 4.720 1.00 15.27 O
+ATOM 208 CB ASN A 27 26.484 18.126 8.054 1.00 12.34 C
+ATOM 209 CG ASN A 27 25.681 17.267 9.048 1.00 12.22 C
+ATOM 210 OD1 ASN A 27 24.511 16.933 8.820 1.00 17.40 O
+ATOM 211 ND2 ASN A 27 26.348 17.052 10.169 1.00 18.27 N
+ATOM 212 N TRP A 28 28.344 18.591 5.583 1.00 16.78 N
+ATOM 213 CA TRP A 28 28.831 19.475 4.513 1.00 16.49 C
+ATOM 214 C TRP A 28 28.940 18.741 3.183 1.00 12.99 C
+ATOM 215 O TRP A 28 28.742 19.321 2.090 1.00 13.97 O
+ATOM 216 CB TRP A 28 30.104 20.145 5.023 1.00 14.55 C
+ATOM 217 CG TRP A 28 29.941 20.978 6.251 1.00 11.93 C
+ATOM 218 CD1 TRP A 28 30.176 20.624 7.546 1.00 14.42 C
+ATOM 219 CD2 TRP A 28 29.319 22.284 6.287 1.00 13.11 C
+ATOM 220 NE1 TRP A 28 29.924 21.690 8.365 1.00 16.94 N
+ATOM 221 CE2 TRP A 28 29.337 22.679 7.641 1.00 14.07 C
+ATOM 222 CE3 TRP A 28 28.894 23.168 5.295 1.00 15.97 C
+ATOM 223 CZ2 TRP A 28 28.913 23.943 8.038 1.00 18.07 C
+ATOM 224 CZ3 TRP A 28 28.398 24.404 5.682 1.00 18.26 C
+ATOM 225 CH2 TRP A 28 28.431 24.766 7.025 1.00 17.18 C
+ATOM 226 N VAL A 29 29.572 17.543 3.261 1.00 13.00 N
+ATOM 227 CA VAL A 29 29.729 16.711 2.047 1.00 14.15 C
+ATOM 228 C VAL A 29 28.379 16.340 1.429 1.00 10.43 C
+ATOM 229 O VAL A 29 28.166 16.496 0.228 1.00 13.40 O
+ATOM 230 CB VAL A 29 30.649 15.492 2.359 1.00 12.76 C
+ATOM 231 CG1 VAL A 29 30.782 14.596 1.136 1.00 15.37 C
+ATOM 232 CG2 VAL A 29 32.010 16.050 2.772 1.00 14.18 C
+ATOM 233 N CYS A 30 27.501 15.906 2.299 1.00 15.32 N
+ATOM 234 CA CYS A 30 26.115 15.567 1.991 1.00 15.59 C
+ATOM 235 C CYS A 30 25.388 16.723 1.302 1.00 12.37 C
+ATOM 236 O CYS A 30 24.894 16.516 0.172 1.00 14.44 O
+ATOM 237 CB CYS A 30 25.343 15.046 3.172 1.00 14.99 C
+ATOM 238 SG CYS A 30 23.719 14.376 2.695 1.00 17.71 S
+ATOM 239 N ALA A 31 25.533 17.913 1.870 1.00 16.06 N
+ATOM 240 CA ALA A 31 24.949 19.130 1.305 1.00 15.82 C
+ATOM 241 C ALA A 31 25.487 19.354 -0.115 1.00 15.34 C
+ATOM 242 O ALA A 31 24.675 19.686 -0.998 1.00 16.00 O
+ATOM 243 CB ALA A 31 25.167 20.335 2.200 1.00 14.90 C
+ATOM 244 N ALA A 32 26.807 19.354 -0.286 1.00 11.93 N
+ATOM 245 CA ALA A 32 27.461 19.536 -1.579 1.00 13.08 C
+ATOM 246 C ALA A 32 26.943 18.538 -2.620 1.00 12.38 C
+ATOM 247 O ALA A 32 26.767 18.857 -3.789 1.00 13.89 O
+ATOM 248 CB ALA A 32 28.982 19.476 -1.398 1.00 14.17 C
+ATOM 249 N LYS A 33 26.731 17.303 -2.193 1.00 15.16 N
+ATOM 250 CA LYS A 33 26.261 16.216 -3.037 1.00 16.16 C
+ATOM 251 C LYS A 33 24.903 16.555 -3.658 1.00 15.04 C
+ATOM 252 O LYS A 33 24.806 16.511 -4.890 1.00 15.00 O
+ATOM 253 CB LYS A 33 26.221 14.860 -2.351 1.00 16.71 C
+ATOM 254 CG LYS A 33 25.697 13.696 -3.185 1.00 19.51 C
+ATOM 255 CD LYS A 33 26.498 13.400 -4.446 1.00 17.12 C
+ATOM 256 CE LYS A 33 25.686 12.464 -5.331 1.00 24.06 C
+ATOM 257 NZ LYS A 33 26.423 11.979 -6.525 1.00 26.78 N
+ATOM 258 N PHE A 34 23.972 16.946 -2.817 1.00 16.81 N
+ATOM 259 CA PHE A 34 22.569 17.125 -3.247 1.00 17.51 C
+ATOM 260 C PHE A 34 22.346 18.506 -3.836 1.00 18.19 C
+ATOM 261 O PHE A 34 21.504 18.692 -4.759 1.00 20.21 O
+ATOM 262 CB PHE A 34 21.626 16.673 -2.130 1.00 18.58 C
+ATOM 263 CG PHE A 34 21.644 15.172 -1.965 1.00 22.22 C
+ATOM 264 CD1 PHE A 34 21.209 14.353 -3.007 1.00 20.24 C
+ATOM 265 CD2 PHE A 34 22.272 14.627 -0.851 1.00 20.00 C
+ATOM 266 CE1 PHE A 34 21.372 12.961 -2.910 1.00 22.03 C
+ATOM 267 CE2 PHE A 34 22.443 13.245 -0.743 1.00 21.96 C
+ATOM 268 CZ PHE A 34 21.923 12.406 -1.737 1.00 20.77 C
+ATOM 269 N GLU A 35 23.251 19.415 -3.451 1.00 15.27 N
+ATOM 270 CA GLU A 35 23.178 20.789 -3.996 1.00 15.45 C
+ATOM 271 C GLU A 35 23.661 20.944 -5.423 1.00 17.45 C
+ATOM 272 O GLU A 35 23.014 21.514 -6.310 1.00 17.91 O
+ATOM 273 CB GLU A 35 23.698 21.892 -3.107 1.00 14.42 C
+ATOM 274 CG GLU A 35 22.994 22.212 -1.809 1.00 11.08 C
+ATOM 275 CD GLU A 35 21.631 22.846 -1.864 1.00 13.55 C
+ATOM 276 OE1 GLU A 35 21.408 23.360 -2.981 1.00 20.77 O
+ATOM 277 OE2 GLU A 35 20.947 23.032 -0.874 1.00 22.72 O
+ATOM 278 N SER A 36 24.867 20.483 -5.674 1.00 15.66 N
+ATOM 279 CA SER A 36 25.626 20.615 -6.903 1.00 17.79 C
+ATOM 280 C SER A 36 26.139 19.341 -7.569 1.00 16.97 C
+ATOM 281 O SER A 36 26.750 19.464 -8.642 1.00 21.78 O
+ATOM 282 CB SER A 36 26.830 21.528 -6.654 1.00 18.12 C
+ATOM 283 OG SER A 36 27.747 20.951 -5.748 1.00 15.16 O
+ATOM 284 N ASN A 37 25.957 18.222 -6.927 1.00 20.15 N
+ATOM 285 CA ASN A 37 26.628 16.968 -7.297 1.00 20.85 C
+ATOM 286 C ASN A 37 28.149 17.091 -7.302 1.00 19.72 C
+ATOM 287 O ASN A 37 28.813 16.627 -8.254 1.00 20.79 O
+ATOM 288 CB ASN A 37 26.028 16.490 -8.617 1.00 20.82 C
+ATOM 289 CG ASN A 37 26.156 14.980 -8.782 1.00 23.63 C
+ATOM 290 OD1 ASN A 37 26.640 14.266 -7.885 1.00 28.05 O
+ATOM 291 ND2 ASN A 37 25.867 14.506 -9.990 1.00 29.61 N
+ATOM 292 N PHE A 38 28.691 17.882 -6.383 1.00 16.12 N
+ATOM 293 CA PHE A 38 30.129 18.115 -6.279 1.00 14.75 C
+ATOM 294 C PHE A 38 30.717 18.903 -7.448 1.00 13.86 C
+ATOM 295 O PHE A 38 31.923 18.794 -7.702 1.00 16.66 O
+ATOM 296 CB PHE A 38 30.914 16.823 -6.047 1.00 17.09 C
+ATOM 297 CG PHE A 38 30.487 16.006 -4.863 1.00 15.96 C
+ATOM 298 CD1 PHE A 38 30.100 16.572 -3.655 1.00 15.43 C
+ATOM 299 CD2 PHE A 38 30.507 14.603 -4.993 1.00 17.66 C
+ATOM 300 CE1 PHE A 38 29.766 15.808 -2.558 1.00 16.83 C
+ATOM 301 CE2 PHE A 38 30.136 13.814 -3.891 1.00 15.86 C
+ATOM 302 CZ PHE A 38 29.835 14.410 -2.646 1.00 18.90 C
+ATOM 303 N ASN A 39 29.936 19.792 -8.033 1.00 17.63 N
+ATOM 304 CA ASN A 39 30.341 20.573 -9.199 1.00 16.77 C
+ATOM 305 C ASN A 39 30.543 22.034 -8.823 1.00 17.13 C
+ATOM 306 O ASN A 39 29.544 22.649 -8.423 1.00 17.24 O
+ATOM 307 CB ASN A 39 29.406 20.300 -10.366 1.00 17.40 C
+ATOM 308 CG ASN A 39 29.876 20.771 -11.716 1.00 16.96 C
+ATOM 309 OD1 ASN A 39 30.579 21.750 -11.956 1.00 23.22 O
+ATOM 310 ND2 ASN A 39 29.578 19.864 -12.653 1.00 26.35 N
+ATOM 311 N THR A 40 31.766 22.492 -8.928 1.00 14.88 N
+ATOM 312 CA THR A 40 32.139 23.869 -8.657 1.00 16.08 C
+ATOM 313 C THR A 40 31.504 24.890 -9.589 1.00 16.31 C
+ATOM 314 O THR A 40 31.316 26.054 -9.213 1.00 17.50 O
+ATOM 315 CB THR A 40 33.684 24.103 -8.422 1.00 17.07 C
+ATOM 316 OG1 THR A 40 34.270 24.156 -9.775 1.00 23.76 O
+ATOM 317 CG2 THR A 40 34.414 23.119 -7.491 1.00 16.46 C
+ATOM 318 N GLN A 41 31.001 24.430 -10.706 1.00 16.39 N
+ATOM 319 CA GLN A 41 30.524 25.291 -11.812 1.00 16.67 C
+ATOM 320 C GLN A 41 28.993 25.381 -11.874 1.00 15.44 C
+ATOM 321 O GLN A 41 28.504 26.019 -12.837 1.00 18.55 O
+ATOM 322 CB GLN A 41 31.047 24.817 -13.168 1.00 19.65 C
+ATOM 323 CG GLN A 41 32.549 25.004 -13.279 1.00 21.26 C
+ATOM 324 CD GLN A 41 32.763 26.236 -14.129 1.00 26.23 C
+ATOM 325 OE1 GLN A 41 32.356 26.308 -15.291 1.00 24.68 O
+ATOM 326 NE2 GLN A 41 33.276 27.231 -13.420 1.00 25.96 N
+ATOM 327 N ALA A 42 28.329 24.640 -11.012 1.00 15.95 N
+ATOM 328 CA ALA A 42 26.859 24.579 -11.061 1.00 17.42 C
+ATOM 329 C ALA A 42 26.257 25.969 -10.807 1.00 18.93 C
+ATOM 330 O ALA A 42 26.645 26.686 -9.884 1.00 17.00 O
+ATOM 331 CB ALA A 42 26.355 23.604 -9.998 1.00 22.79 C
+ATOM 332 N THR A 43 25.276 26.293 -11.643 1.00 18.30 N
+ATOM 333 CA THR A 43 24.441 27.490 -11.476 1.00 17.73 C
+ATOM 334 C THR A 43 22.976 27.112 -11.714 1.00 19.61 C
+ATOM 335 O THR A 43 22.715 26.271 -12.594 1.00 22.06 O
+ATOM 336 CB THR A 43 24.814 28.728 -12.375 1.00 17.58 C
+ATOM 337 OG1 THR A 43 24.555 28.321 -13.756 1.00 20.94 O
+ATOM 338 CG2 THR A 43 26.247 29.213 -12.184 1.00 18.26 C
+ATOM 339 N ASN A 44 22.088 27.742 -10.971 1.00 19.77 N
+ATOM 340 CA ASN A 44 20.640 27.497 -11.108 1.00 19.51 C
+ATOM 341 C ASN A 44 19.903 28.842 -10.963 1.00 14.85 C
+ATOM 342 O ASN A 44 20.169 29.600 -10.033 1.00 19.43 O
+ATOM 343 CB ASN A 44 20.155 26.480 -10.080 1.00 19.93 C
+ATOM 344 CG ASN A 44 18.646 26.315 -10.115 1.00 22.01 C
+ATOM 345 OD1 ASN A 44 18.128 25.720 -11.078 1.00 29.53 O
+ATOM 346 ND2 ASN A 44 17.906 26.927 -9.188 1.00 22.94 N
+ATOM 347 N ARG A 45 19.058 29.117 -11.924 1.00 16.90 N
+ATOM 348 CA ARG A 45 18.303 30.363 -12.015 1.00 18.37 C
+ATOM 349 C ARG A 45 16.955 30.163 -11.326 1.00 18.76 C
+ATOM 350 O ARG A 45 16.396 29.062 -11.425 1.00 20.87 O
+ATOM 351 CB ARG A 45 18.143 30.836 -13.462 1.00 19.30 C
+ATOM 352 CG ARG A 45 17.012 31.859 -13.557 1.00 23.98 C
+ATOM 353 CD ARG A 45 17.502 33.134 -12.930 1.00 23.36 C
+ATOM 354 NE ARG A 45 18.311 33.758 -13.981 1.00 29.56 N
+ATOM 355 CZ ARG A 45 17.620 34.271 -15.020 1.00 27.18 C
+ATOM 356 NH1 ARG A 45 16.287 34.331 -15.098 1.00 31.99 N
+ATOM 357 NH2 ARG A 45 18.374 34.698 -16.030 1.00 32.43 N
+ATOM 358 N ASN A 46 16.553 31.171 -10.554 1.00 18.13 N
+ATOM 359 CA ASN A 46 15.304 31.071 -9.782 1.00 20.10 C
+ATOM 360 C ASN A 46 14.261 32.063 -10.313 1.00 17.35 C
+ATOM 361 O ASN A 46 14.617 33.104 -10.880 1.00 19.15 O
+ATOM 362 CB ASN A 46 15.576 31.229 -8.295 1.00 20.05 C
+ATOM 363 CG ASN A 46 16.543 30.240 -7.679 1.00 20.12 C
+ATOM 364 OD1 ASN A 46 17.659 30.661 -7.346 1.00 21.21 O
+ATOM 365 ND2 ASN A 46 16.125 28.975 -7.600 1.00 19.44 N
+ATOM 366 N THR A 47 13.027 31.834 -9.887 1.00 19.96 N
+ATOM 367 CA THR A 47 11.871 32.654 -10.246 1.00 19.12 C
+ATOM 368 C THR A 47 12.001 34.107 -9.810 1.00 19.44 C
+ATOM 369 O THR A 47 11.600 34.969 -10.606 1.00 23.16 O
+ATOM 370 CB THR A 47 10.499 32.017 -9.789 1.00 17.70 C
+ATOM 371 OG1 THR A 47 10.507 32.195 -8.342 1.00 23.76 O
+ATOM 372 CG2 THR A 47 10.331 30.554 -10.188 1.00 22.66 C
+ATOM 373 N ASP A 48 12.625 34.377 -8.683 1.00 19.25 N
+ATOM 374 CA ASP A 48 12.885 35.716 -8.168 1.00 17.33 C
+ATOM 375 C ASP A 48 14.010 36.505 -8.823 1.00 17.71 C
+ATOM 376 O ASP A 48 14.246 37.621 -8.309 1.00 23.04 O
+ATOM 377 CB ASP A 48 13.023 35.735 -6.640 1.00 18.02 C
+ATOM 378 CG ASP A 48 14.367 35.174 -6.168 1.00 17.88 C
+ATOM 379 OD1 ASP A 48 15.104 34.602 -6.991 1.00 18.55 O
+ATOM 380 OD2 ASP A 48 14.750 35.442 -5.013 1.00 22.86 O
+ATOM 381 N GLY A 49 14.650 36.018 -9.862 1.00 17.62 N
+ATOM 382 CA GLY A 49 15.744 36.702 -10.546 1.00 17.27 C
+ATOM 383 C GLY A 49 17.147 36.315 -10.096 1.00 16.80 C
+ATOM 384 O GLY A 49 18.168 36.688 -10.694 1.00 20.27 O
+ATOM 385 N SER A 50 17.173 35.661 -8.930 1.00 19.61 N
+ATOM 386 CA SER A 50 18.435 35.225 -8.279 1.00 14.28 C
+ATOM 387 C SER A 50 18.977 33.963 -8.941 1.00 18.09 C
+ATOM 388 O SER A 50 18.273 33.255 -9.697 1.00 16.76 O
+ATOM 389 CB SER A 50 18.272 35.089 -6.781 1.00 17.64 C
+ATOM 390 OG SER A 50 17.530 33.930 -6.463 1.00 17.54 O
+ATOM 391 N THR A 51 20.271 33.766 -8.734 1.00 16.00 N
+ATOM 392 CA THR A 51 20.970 32.557 -9.202 1.00 13.82 C
+ATOM 393 C THR A 51 21.718 31.969 -8.000 1.00 14.58 C
+ATOM 394 O THR A 51 22.160 32.712 -7.119 1.00 13.28 O
+ATOM 395 CB THR A 51 21.904 32.908 -10.419 1.00 12.66 C
+ATOM 396 OG1 THR A 51 21.099 33.576 -11.407 1.00 17.65 O
+ATOM 397 CG2 THR A 51 22.686 31.699 -10.952 1.00 14.39 C
+ATOM 398 N ASP A 52 21.708 30.650 -7.927 1.00 14.66 N
+ATOM 399 CA ASP A 52 22.528 29.900 -6.959 1.00 13.43 C
+ATOM 400 C ASP A 52 23.843 29.488 -7.635 1.00 12.35 C
+ATOM 401 O ASP A 52 23.847 29.066 -8.805 1.00 15.18 O
+ATOM 402 CB ASP A 52 21.765 28.649 -6.554 1.00 14.12 C
+ATOM 403 CG ASP A 52 20.396 28.991 -6.002 1.00 20.03 C
+ATOM 404 OD1 ASP A 52 20.220 29.928 -5.237 1.00 21.30 O
+ATOM 405 OD2 ASP A 52 19.517 28.144 -6.222 1.00 20.92 O
+ATOM 406 N TYR A 53 24.924 29.734 -6.905 1.00 14.56 N
+ATOM 407 CA TYR A 53 26.278 29.604 -7.450 1.00 13.61 C
+ATOM 408 C TYR A 53 27.161 28.595 -6.708 1.00 12.70 C
+ATOM 409 O TYR A 53 27.289 28.606 -5.486 1.00 13.36 O
+ATOM 410 CB TYR A 53 26.993 30.972 -7.489 1.00 12.10 C
+ATOM 411 CG TYR A 53 26.437 31.959 -8.487 1.00 11.48 C
+ATOM 412 CD1 TYR A 53 26.843 32.003 -9.821 1.00 17.21 C
+ATOM 413 CD2 TYR A 53 25.510 32.907 -8.050 1.00 14.42 C
+ATOM 414 CE1 TYR A 53 26.291 32.922 -10.717 1.00 17.40 C
+ATOM 415 CE2 TYR A 53 24.907 33.803 -8.932 1.00 12.97 C
+ATOM 416 CZ TYR A 53 25.357 33.847 -10.252 1.00 15.91 C
+ATOM 417 OH TYR A 53 24.864 34.804 -11.094 1.00 19.31 O
+ATOM 418 N GLY A 54 27.751 27.721 -7.493 1.00 16.54 N
+ATOM 419 CA GLY A 54 28.845 26.832 -7.121 1.00 15.67 C
+ATOM 420 C GLY A 54 28.499 25.601 -6.290 1.00 10.78 C
+ATOM 421 O GLY A 54 27.339 25.155 -6.255 1.00 13.16 O
+ATOM 422 N ILE A 55 29.560 25.088 -5.684 1.00 15.43 N
+ATOM 423 CA ILE A 55 29.452 23.795 -4.994 1.00 14.01 C
+ATOM 424 C ILE A 55 28.424 23.748 -3.872 1.00 12.26 C
+ATOM 425 O ILE A 55 27.770 22.697 -3.693 1.00 16.92 O
+ATOM 426 CB ILE A 55 30.891 23.340 -4.563 1.00 16.64 C
+ATOM 427 CG1 ILE A 55 30.785 21.812 -4.319 1.00 17.00 C
+ATOM 428 CG2 ILE A 55 31.396 24.210 -3.390 1.00 18.87 C
+ATOM 429 CD1 ILE A 55 32.101 21.018 -4.339 1.00 20.60 C
+ATOM 430 N LEU A 56 28.216 24.881 -3.236 1.00 12.85 N
+ATOM 431 CA LEU A 56 27.173 24.998 -2.203 1.00 14.96 C
+ATOM 432 C LEU A 56 25.981 25.838 -2.659 1.00 11.08 C
+ATOM 433 O LEU A 56 25.161 26.111 -1.774 1.00 16.40 O
+ATOM 434 CB LEU A 56 27.816 25.424 -0.877 1.00 14.44 C
+ATOM 435 CG LEU A 56 28.692 24.348 -0.204 1.00 14.92 C
+ATOM 436 CD1 LEU A 56 29.331 24.997 1.008 1.00 18.78 C
+ATOM 437 CD2 LEU A 56 27.808 23.177 0.192 1.00 19.47 C
+ATOM 438 N GLN A 57 25.865 26.104 -3.946 1.00 14.17 N
+ATOM 439 CA GLN A 57 24.668 26.785 -4.465 1.00 11.55 C
+ATOM 440 C GLN A 57 24.277 27.940 -3.558 1.00 15.09 C
+ATOM 441 O GLN A 57 23.116 28.031 -3.094 1.00 15.28 O
+ATOM 442 CB GLN A 57 23.521 25.765 -4.549 1.00 13.56 C
+ATOM 443 CG GLN A 57 23.733 24.790 -5.699 1.00 12.45 C
+ATOM 444 CD GLN A 57 23.684 25.440 -7.069 1.00 14.21 C
+ATOM 445 OE1 GLN A 57 22.574 25.602 -7.591 1.00 18.18 O
+ATOM 446 NE2 GLN A 57 24.813 25.805 -7.651 1.00 14.86 N
+ATOM 447 N ILE A 58 25.164 28.910 -3.428 1.00 14.04 N
+ATOM 448 CA ILE A 58 24.930 30.118 -2.649 1.00 16.09 C
+ATOM 449 C ILE A 58 24.204 31.163 -3.504 1.00 11.19 C
+ATOM 450 O ILE A 58 24.555 31.405 -4.667 1.00 14.34 O
+ATOM 451 CB ILE A 58 26.301 30.665 -2.134 1.00 14.90 C
+ATOM 452 CG1 ILE A 58 26.751 29.724 -0.985 1.00 13.85 C
+ATOM 453 CG2 ILE A 58 26.178 32.135 -1.693 1.00 15.47 C
+ATOM 454 CD1 ILE A 58 28.246 29.954 -0.641 1.00 16.12 C
+ATOM 455 N ASN A 59 23.145 31.671 -2.905 1.00 14.23 N
+ATOM 456 CA ASN A 59 22.146 32.510 -3.590 1.00 10.60 C
+ATOM 457 C ASN A 59 22.550 33.974 -3.730 1.00 13.03 C
+ATOM 458 O ASN A 59 22.917 34.607 -2.740 1.00 18.49 O
+ATOM 459 CB ASN A 59 20.805 32.306 -2.884 1.00 15.76 C
+ATOM 460 CG ASN A 59 19.650 32.986 -3.588 1.00 15.71 C
+ATOM 461 OD1 ASN A 59 19.464 34.171 -3.244 1.00 18.79 O
+ATOM 462 ND2 ASN A 59 19.155 32.320 -4.612 1.00 16.44 N
+ATOM 463 N SER A 60 22.268 34.485 -4.941 1.00 11.71 N
+ATOM 464 CA SER A 60 22.570 35.910 -5.255 1.00 13.81 C
+ATOM 465 C SER A 60 21.687 36.993 -4.642 1.00 15.28 C
+ATOM 466 O SER A 60 22.054 38.177 -4.774 1.00 17.67 O
+ATOM 467 CB SER A 60 22.643 36.139 -6.750 1.00 14.62 C
+ATOM 468 OG SER A 60 21.432 36.007 -7.444 1.00 14.30 O
+ATOM 469 N ARG A 61 20.526 36.660 -4.138 1.00 15.88 N
+ATOM 470 CA ARG A 61 19.691 37.653 -3.434 1.00 18.54 C
+ATOM 471 C ARG A 61 20.277 38.108 -2.106 1.00 19.97 C
+ATOM 472 O ARG A 61 20.282 39.333 -1.876 1.00 26.30 O
+ATOM 473 CB ARG A 61 18.267 37.195 -3.250 1.00 18.00 C
+ATOM 474 CG ARG A 61 17.315 38.350 -2.959 1.00 20.10 C
+ATOM 475 CD ARG A 61 16.063 37.657 -2.503 1.00 26.00 C
+ATOM 476 NE ARG A 61 15.101 38.653 -2.063 1.00 29.28 N
+ATOM 477 CZ ARG A 61 13.794 38.351 -2.111 1.00 29.36 C
+ATOM 478 NH1 ARG A 61 13.439 37.257 -2.784 1.00 26.50 N
+ATOM 479 NH2 ARG A 61 12.925 39.249 -1.646 1.00 32.93 N
+ATOM 480 N TRP A 62 20.773 37.202 -1.273 1.00 16.51 N
+ATOM 481 CA TRP A 62 21.321 37.563 0.032 1.00 16.06 C
+ATOM 482 C TRP A 62 22.848 37.643 0.101 1.00 15.55 C
+ATOM 483 O TRP A 62 23.323 38.396 0.968 1.00 18.96 O
+ATOM 484 CB TRP A 62 20.833 36.611 1.134 1.00 17.91 C
+ATOM 485 CG TRP A 62 19.360 36.361 1.096 1.00 18.99 C
+ATOM 486 CD1 TRP A 62 18.719 35.247 0.643 1.00 20.47 C
+ATOM 487 CD2 TRP A 62 18.326 37.305 1.427 1.00 20.79 C
+ATOM 488 NE1 TRP A 62 17.360 35.457 0.609 1.00 21.70 N
+ATOM 489 CE2 TRP A 62 17.090 36.696 1.096 1.00 21.11 C
+ATOM 490 CE3 TRP A 62 18.333 38.584 1.965 1.00 19.84 C
+ATOM 491 CZ2 TRP A 62 15.875 37.327 1.307 1.00 22.57 C
+ATOM 492 CZ3 TRP A 62 17.115 39.208 2.186 1.00 23.93 C
+ATOM 493 CH2 TRP A 62 15.906 38.611 1.814 1.00 19.55 C
+ATOM 494 N TRP A 63 23.537 36.731 -0.584 1.00 16.01 N
+ATOM 495 CA TRP A 63 24.906 36.398 -0.276 1.00 15.21 C
+ATOM 496 C TRP A 63 26.089 36.924 -1.052 1.00 15.84 C
+ATOM 497 O TRP A 63 27.142 37.177 -0.432 1.00 19.13 O
+ATOM 498 CB TRP A 63 25.068 34.919 0.112 1.00 15.47 C
+ATOM 499 CG TRP A 63 24.036 34.428 1.068 1.00 12.46 C
+ATOM 500 CD1 TRP A 63 22.959 33.620 0.777 1.00 16.95 C
+ATOM 501 CD2 TRP A 63 23.919 34.728 2.450 1.00 13.27 C
+ATOM 502 NE1 TRP A 63 22.243 33.344 1.899 1.00 17.64 N
+ATOM 503 CE2 TRP A 63 22.761 34.067 2.931 1.00 17.28 C
+ATOM 504 CE3 TRP A 63 24.694 35.480 3.323 1.00 15.25 C
+ATOM 505 CZ2 TRP A 63 22.393 34.133 4.278 1.00 18.56 C
+ATOM 506 CZ3 TRP A 63 24.302 35.586 4.648 1.00 18.76 C
+ATOM 507 CH2 TRP A 63 23.179 34.910 5.117 1.00 19.36 C
+ATOM 508 N CYS A 64 25.962 36.914 -2.353 1.00 17.00 N
+ATOM 509 CA CYS A 64 26.985 37.433 -3.271 1.00 15.76 C
+ATOM 510 C CYS A 64 26.324 38.355 -4.286 1.00 15.97 C
+ATOM 511 O CYS A 64 25.102 38.314 -4.475 1.00 13.75 O
+ATOM 512 CB CYS A 64 27.638 36.265 -3.988 1.00 16.64 C
+ATOM 513 SG CYS A 64 26.562 35.233 -5.007 1.00 17.83 S
+ATOM 514 N ASN A 65 27.157 39.165 -4.908 1.00 17.73 N
+ATOM 515 CA ASN A 65 26.700 40.134 -5.920 1.00 16.46 C
+ATOM 516 C ASN A 65 26.985 39.646 -7.342 1.00 13.16 C
+ATOM 517 O ASN A 65 28.130 39.316 -7.647 1.00 15.95 O
+ATOM 518 CB ASN A 65 27.381 41.492 -5.712 1.00 19.19 C
+ATOM 519 CG ASN A 65 26.910 42.423 -6.824 1.00 19.59 C
+ATOM 520 OD1 ASN A 65 25.736 42.559 -7.141 1.00 23.26 O
+ATOM 521 ND2 ASN A 65 27.914 42.938 -7.527 1.00 25.56 N
+ATOM 522 N ASP A 66 25.920 39.484 -8.116 1.00 15.60 N
+ATOM 523 CA ASP A 66 26.102 39.180 -9.545 1.00 15.28 C
+ATOM 524 C ASP A 66 25.664 40.317 -10.460 1.00 15.23 C
+ATOM 525 O ASP A 66 25.719 40.143 -11.673 1.00 17.91 O
+ATOM 526 CB ASP A 66 25.462 37.858 -9.894 1.00 14.84 C
+ATOM 527 CG ASP A 66 23.951 37.903 -9.833 1.00 12.12 C
+ATOM 528 OD1 ASP A 66 23.288 38.898 -9.542 1.00 16.56 O
+ATOM 529 OD2 ASP A 66 23.455 36.769 -10.048 1.00 16.91 O
+ATOM 530 N GLY A 67 25.234 41.408 -9.860 1.00 18.13 N
+ATOM 531 CA GLY A 67 24.817 42.607 -10.577 1.00 19.40 C
+ATOM 532 C GLY A 67 23.544 42.553 -11.401 1.00 20.37 C
+ATOM 533 O GLY A 67 23.191 43.542 -12.055 1.00 18.23 O
+ATOM 534 N ARG A 68 22.822 41.441 -11.348 1.00 18.79 N
+ATOM 535 CA ARG A 68 21.560 41.308 -12.092 1.00 19.77 C
+ATOM 536 C ARG A 68 20.424 40.765 -11.243 1.00 18.48 C
+ATOM 537 O ARG A 68 19.385 40.383 -11.795 1.00 21.54 O
+ATOM 538 CB ARG A 68 21.746 40.454 -13.339 1.00 18.97 C
+ATOM 539 CG ARG A 68 22.197 39.048 -12.946 1.00 18.77 C
+ATOM 540 CD ARG A 68 22.477 38.187 -14.122 1.00 23.25 C
+ATOM 541 NE ARG A 68 21.439 37.201 -14.281 1.00 29.75 N
+ATOM 542 CZ ARG A 68 20.242 37.255 -14.855 1.00 28.71 C
+ATOM 543 NH1 ARG A 68 19.503 38.311 -15.145 1.00 32.34 N
+ATOM 544 NH2 ARG A 68 19.897 36.127 -15.497 1.00 33.10 N
+ATOM 545 N THR A 69 20.590 40.896 -9.952 1.00 18.68 N
+ATOM 546 CA THR A 69 19.607 40.408 -8.973 1.00 20.02 C
+ATOM 547 C THR A 69 18.994 41.597 -8.224 1.00 16.46 C
+ATOM 548 O THR A 69 19.683 42.241 -7.425 1.00 23.13 O
+ATOM 549 CB THR A 69 20.208 39.384 -7.910 1.00 19.66 C
+ATOM 550 OG1 THR A 69 20.851 38.334 -8.715 1.00 19.19 O
+ATOM 551 CG2 THR A 69 19.123 38.863 -6.955 1.00 18.58 C
+ATOM 552 N PRO A 70 17.687 41.741 -8.418 1.00 20.50 N
+ATOM 553 CA PRO A 70 16.953 42.824 -7.733 1.00 21.73 C
+ATOM 554 C PRO A 70 16.955 42.520 -6.242 1.00 22.11 C
+ATOM 555 O PRO A 70 16.739 41.356 -5.886 1.00 27.13 O
+ATOM 556 CB PRO A 70 15.557 42.749 -8.333 1.00 23.50 C
+ATOM 557 CG PRO A 70 15.759 42.092 -9.671 1.00 24.66 C
+ATOM 558 CD PRO A 70 16.887 41.095 -9.463 1.00 21.80 C
+ATOM 559 N GLY A 71 17.163 43.493 -5.401 1.00 21.67 N
+ATOM 560 CA GLY A 71 17.135 43.383 -3.947 1.00 24.03 C
+ATOM 561 C GLY A 71 18.328 42.710 -3.287 1.00 26.98 C
+ATOM 562 O GLY A 71 18.257 42.257 -2.126 1.00 32.77 O
+ATOM 563 N SER A 72 19.418 42.627 -4.018 1.00 26.40 N
+ATOM 564 CA SER A 72 20.665 41.976 -3.588 1.00 26.94 C
+ATOM 565 C SER A 72 21.139 42.582 -2.276 1.00 24.66 C
+ATOM 566 O SER A 72 21.055 43.819 -2.125 1.00 29.91 O
+ATOM 567 CB SER A 72 21.659 42.002 -4.737 1.00 25.16 C
+ATOM 568 OG SER A 72 23.015 41.835 -4.343 1.00 32.21 O
+ATOM 569 N ARG A 73 21.646 41.775 -1.369 1.00 22.51 N
+ATOM 570 CA ARG A 73 22.254 42.196 -0.113 1.00 22.60 C
+ATOM 571 C ARG A 73 23.774 42.058 0.029 1.00 22.33 C
+ATOM 572 O ARG A 73 24.425 42.749 0.849 1.00 27.92 O
+ATOM 573 CB ARG A 73 21.615 41.555 1.127 1.00 20.14 C
+ATOM 574 CG ARG A 73 20.187 41.983 1.439 1.00 22.29 C
+ATOM 575 CD ARG A 73 20.209 43.299 2.123 1.00 26.95 C
+ATOM 576 NE ARG A 73 18.928 43.771 2.617 1.00 33.74 N
+ATOM 577 CZ ARG A 73 17.980 44.302 1.823 1.00 33.76 C
+ATOM 578 NH1 ARG A 73 17.841 43.934 0.544 1.00 35.78 N
+ATOM 579 NH2 ARG A 73 17.571 45.545 2.146 1.00 33.83 N
+ATOM 580 N ASN A 74 24.346 41.143 -0.705 1.00 17.74 N
+ATOM 581 CA ASN A 74 25.780 40.833 -0.695 1.00 18.87 C
+ATOM 582 C ASN A 74 26.315 40.718 0.731 1.00 16.22 C
+ATOM 583 O ASN A 74 27.255 41.471 1.060 1.00 20.87 O
+ATOM 584 CB ASN A 74 26.565 41.786 -1.589 1.00 19.51 C
+ATOM 585 CG ASN A 74 27.982 41.328 -1.909 1.00 16.31 C
+ATOM 586 OD1 ASN A 74 28.318 40.169 -1.652 1.00 18.61 O
+ATOM 587 ND2 ASN A 74 28.838 42.192 -2.436 1.00 19.22 N
+ATOM 588 N LEU A 75 25.723 39.860 1.544 1.00 15.25 N
+ATOM 589 CA LEU A 75 26.153 39.690 2.930 1.00 14.82 C
+ATOM 590 C LEU A 75 27.518 39.011 3.085 1.00 16.78 C
+ATOM 591 O LEU A 75 28.167 39.197 4.141 1.00 22.00 O
+ATOM 592 CB LEU A 75 25.009 39.055 3.733 1.00 16.64 C
+ATOM 593 CG LEU A 75 23.815 39.998 3.979 1.00 17.08 C
+ATOM 594 CD1 LEU A 75 22.574 39.193 4.336 1.00 25.82 C
+ATOM 595 CD2 LEU A 75 24.156 40.969 5.110 1.00 20.95 C
+ATOM 596 N CYS A 76 27.973 38.312 2.061 1.00 17.66 N
+ATOM 597 CA CYS A 76 29.299 37.680 2.111 1.00 16.46 C
+ATOM 598 C CYS A 76 30.390 38.598 1.589 1.00 15.66 C
+ATOM 599 O CYS A 76 31.573 38.229 1.568 1.00 17.59 O
+ATOM 600 CB CYS A 76 29.396 36.303 1.477 1.00 17.61 C
+ATOM 601 SG CYS A 76 28.595 34.961 2.361 1.00 18.07 S
+ATOM 602 N ASN A 77 29.964 39.681 0.971 1.00 18.55 N
+ATOM 603 CA ASN A 77 30.827 40.725 0.395 1.00 19.18 C
+ATOM 604 C ASN A 77 31.711 40.163 -0.702 1.00 16.58 C
+ATOM 605 O ASN A 77 32.947 40.331 -0.689 1.00 21.61 O
+ATOM 606 CB ASN A 77 31.589 41.488 1.483 1.00 17.72 C
+ATOM 607 CG ASN A 77 32.126 42.812 0.957 1.00 20.20 C
+ATOM 608 OD1 ASN A 77 31.351 43.589 0.396 1.00 28.77 O
+ATOM 609 ND2 ASN A 77 33.430 43.012 1.047 1.00 27.05 N
+ATOM 610 N ILE A 78 31.149 39.408 -1.616 1.00 18.88 N
+ATOM 611 CA ILE A 78 31.904 38.780 -2.713 1.00 20.14 C
+ATOM 612 C ILE A 78 31.099 38.850 -4.013 1.00 17.08 C
+ATOM 613 O ILE A 78 29.864 38.688 -3.972 1.00 16.28 O
+ATOM 614 CB ILE A 78 32.183 37.255 -2.384 1.00 19.93 C
+ATOM 615 CG1 ILE A 78 30.882 36.639 -1.851 1.00 21.17 C
+ATOM 616 CG2 ILE A 78 33.437 37.003 -1.524 1.00 24.25 C
+ATOM 617 CD1 ILE A 78 30.936 35.120 -1.546 1.00 25.54 C
+ATOM 618 N PRO A 79 31.828 38.795 -5.108 1.00 16.64 N
+ATOM 619 CA PRO A 79 31.195 38.634 -6.421 1.00 19.12 C
+ATOM 620 C PRO A 79 30.792 37.146 -6.446 1.00 14.71 C
+ATOM 621 O PRO A 79 31.576 36.273 -6.005 1.00 17.48 O
+ATOM 622 CB PRO A 79 32.261 38.967 -7.445 1.00 18.74 C
+ATOM 623 CG PRO A 79 33.555 39.029 -6.710 1.00 18.97 C
+ATOM 624 CD PRO A 79 33.276 39.023 -5.215 1.00 16.79 C
+ATOM 625 N CYS A 80 29.629 36.908 -7.033 1.00 13.55 N
+ATOM 626 CA CYS A 80 29.167 35.522 -7.236 1.00 14.33 C
+ATOM 627 C CYS A 80 30.150 34.716 -8.073 1.00 13.92 C
+ATOM 628 O CYS A 80 30.214 33.484 -7.880 1.00 16.74 O
+ATOM 629 CB CYS A 80 27.749 35.338 -7.747 1.00 16.10 C
+ATOM 630 SG CYS A 80 26.471 36.160 -6.762 1.00 16.97 S
+ATOM 631 N SER A 81 30.769 35.294 -9.083 1.00 15.04 N
+ATOM 632 CA SER A 81 31.775 34.671 -9.933 1.00 15.64 C
+ATOM 633 C SER A 81 32.907 34.027 -9.109 1.00 14.90 C
+ATOM 634 O SER A 81 33.338 32.939 -9.561 1.00 21.08 O
+ATOM 635 CB SER A 81 32.381 35.643 -10.953 1.00 18.65 C
+ATOM 636 OG SER A 81 33.035 36.681 -10.235 1.00 20.86 O
+ATOM 637 N ALA A 82 33.226 34.572 -7.950 1.00 15.59 N
+ATOM 638 CA ALA A 82 34.272 33.963 -7.107 1.00 18.01 C
+ATOM 639 C ALA A 82 33.869 32.604 -6.540 1.00 18.75 C
+ATOM 640 O ALA A 82 34.703 31.798 -6.081 1.00 19.60 O
+ATOM 641 CB ALA A 82 34.722 34.930 -6.020 1.00 20.54 C
+ATOM 642 N LEU A 83 32.571 32.338 -6.519 1.00 15.36 N
+ATOM 643 CA LEU A 83 31.973 31.093 -6.042 1.00 18.66 C
+ATOM 644 C LEU A 83 32.060 29.962 -7.049 1.00 17.84 C
+ATOM 645 O LEU A 83 31.671 28.815 -6.739 1.00 21.50 O
+ATOM 646 CB LEU A 83 30.618 31.424 -5.431 1.00 17.11 C
+ATOM 647 CG LEU A 83 30.511 32.364 -4.244 1.00 16.65 C
+ATOM 648 CD1 LEU A 83 29.040 32.573 -3.857 1.00 18.78 C
+ATOM 649 CD2 LEU A 83 31.277 31.872 -3.020 1.00 20.62 C
+ATOM 650 N LEU A 84 32.473 30.271 -8.267 1.00 17.31 N
+ATOM 651 CA LEU A 84 32.610 29.295 -9.347 1.00 16.38 C
+ATOM 652 C LEU A 84 34.047 28.841 -9.570 1.00 19.37 C
+ATOM 653 O LEU A 84 34.334 28.243 -10.622 1.00 23.48 O
+ATOM 654 CB LEU A 84 31.914 29.793 -10.614 1.00 20.87 C
+ATOM 655 CG LEU A 84 30.446 30.183 -10.573 1.00 14.26 C
+ATOM 656 CD1 LEU A 84 30.014 30.771 -11.916 1.00 21.15 C
+ATOM 657 CD2 LEU A 84 29.597 28.942 -10.329 1.00 18.96 C
+ATOM 658 N SER A 85 34.942 29.197 -8.676 1.00 21.00 N
+ATOM 659 CA SER A 85 36.340 28.754 -8.727 1.00 20.86 C
+ATOM 660 C SER A 85 36.474 27.245 -8.497 1.00 19.65 C
+ATOM 661 O SER A 85 35.765 26.640 -7.681 1.00 20.62 O
+ATOM 662 CB SER A 85 37.109 29.482 -7.633 1.00 20.91 C
+ATOM 663 OG SER A 85 38.484 29.212 -7.834 1.00 26.88 O
+ATOM 664 N SER A 86 37.619 26.742 -8.943 1.00 22.57 N
+ATOM 665 CA SER A 86 38.008 25.343 -8.700 1.00 20.44 C
+ATOM 666 C SER A 86 38.388 25.153 -7.233 1.00 19.98 C
+ATOM 667 O SER A 86 38.314 24.055 -6.671 1.00 23.62 O
+ATOM 668 CB SER A 86 39.107 24.868 -9.650 1.00 23.76 C
+ATOM 669 OG SER A 86 38.401 24.215 -10.691 1.00 30.29 O
+ATOM 670 N ASP A 87 38.846 26.244 -6.668 1.00 19.74 N
+ATOM 671 CA ASP A 87 39.282 26.393 -5.271 1.00 18.72 C
+ATOM 672 C ASP A 87 37.999 26.657 -4.471 1.00 17.93 C
+ATOM 673 O ASP A 87 37.490 27.762 -4.712 1.00 20.06 O
+ATOM 674 CB ASP A 87 40.221 27.607 -5.212 1.00 21.65 C
+ATOM 675 CG ASP A 87 40.762 28.041 -3.869 1.00 23.98 C
+ATOM 676 OD1 ASP A 87 40.335 27.702 -2.742 1.00 26.26 O
+ATOM 677 OD2 ASP A 87 41.785 28.802 -3.933 1.00 32.04 O
+ATOM 678 N ILE A 88 37.732 25.850 -3.461 1.00 15.96 N
+ATOM 679 CA ILE A 88 36.515 26.089 -2.658 1.00 16.22 C
+ATOM 680 C ILE A 88 36.582 27.142 -1.563 1.00 14.43 C
+ATOM 681 O ILE A 88 35.600 27.315 -0.801 1.00 16.28 O
+ATOM 682 CB ILE A 88 35.993 24.736 -2.046 1.00 16.45 C
+ATOM 683 CG1 ILE A 88 36.920 24.200 -0.934 1.00 15.71 C
+ATOM 684 CG2 ILE A 88 35.587 23.743 -3.163 1.00 19.87 C
+ATOM 685 CD1 ILE A 88 36.363 23.226 0.137 1.00 17.47 C
+ATOM 686 N THR A 89 37.742 27.786 -1.369 1.00 14.21 N
+ATOM 687 CA THR A 89 37.913 28.772 -0.306 1.00 16.87 C
+ATOM 688 C THR A 89 36.736 29.761 -0.161 1.00 11.06 C
+ATOM 689 O THR A 89 36.341 29.983 1.000 1.00 13.83 O
+ATOM 690 CB THR A 89 39.267 29.591 -0.423 1.00 18.61 C
+ATOM 691 OG1 THR A 89 40.339 28.592 -0.514 1.00 20.24 O
+ATOM 692 CG2 THR A 89 39.419 30.553 0.766 1.00 17.79 C
+ATOM 693 N ALA A 90 36.507 30.482 -1.242 1.00 17.37 N
+ATOM 694 CA ALA A 90 35.479 31.555 -1.244 1.00 16.63 C
+ATOM 695 C ALA A 90 34.125 31.066 -0.735 1.00 14.09 C
+ATOM 696 O ALA A 90 33.366 31.671 0.065 1.00 15.68 O
+ATOM 697 CB ALA A 90 35.366 32.212 -2.617 1.00 17.13 C
+ATOM 698 N SER A 91 33.746 29.919 -1.296 1.00 13.62 N
+ATOM 699 CA SER A 91 32.494 29.220 -1.024 1.00 11.35 C
+ATOM 700 C SER A 91 32.429 28.817 0.467 1.00 11.70 C
+ATOM 701 O SER A 91 31.407 29.057 1.110 1.00 14.31 O
+ATOM 702 CB SER A 91 32.282 28.035 -1.917 1.00 13.48 C
+ATOM 703 OG SER A 91 32.020 28.335 -3.260 1.00 14.66 O
+ATOM 704 N VAL A 92 33.502 28.211 0.953 1.00 13.17 N
+ATOM 705 CA VAL A 92 33.595 27.846 2.381 1.00 13.44 C
+ATOM 706 C VAL A 92 33.477 29.105 3.261 1.00 12.00 C
+ATOM 707 O VAL A 92 32.716 29.020 4.244 1.00 13.83 O
+ATOM 708 CB VAL A 92 34.890 27.038 2.650 1.00 11.69 C
+ATOM 709 CG1 VAL A 92 35.125 26.987 4.151 1.00 16.05 C
+ATOM 710 CG2 VAL A 92 34.776 25.672 2.013 1.00 15.64 C
+ATOM 711 N ASN A 93 34.199 30.163 2.912 1.00 15.12 N
+ATOM 712 CA ASN A 93 34.160 31.413 3.685 1.00 15.10 C
+ATOM 713 C ASN A 93 32.747 32.034 3.803 1.00 9.80 C
+ATOM 714 O ASN A 93 32.361 32.393 4.908 1.00 16.51 O
+ATOM 715 CB ASN A 93 35.168 32.472 3.247 1.00 16.33 C
+ATOM 716 CG ASN A 93 36.582 32.083 3.642 1.00 19.02 C
+ATOM 717 OD1 ASN A 93 37.546 32.671 3.120 1.00 29.57 O
+ATOM 718 ND2 ASN A 93 36.710 31.188 4.631 1.00 24.29 N
+ATOM 719 N CYS A 94 32.096 31.996 2.670 1.00 15.72 N
+ATOM 720 CA CYS A 94 30.695 32.449 2.633 1.00 13.58 C
+ATOM 721 C CYS A 94 29.778 31.527 3.424 1.00 13.05 C
+ATOM 722 O CYS A 94 28.973 32.025 4.236 1.00 16.42 O
+ATOM 723 CB CYS A 94 30.291 32.704 1.185 1.00 12.05 C
+ATOM 724 SG CYS A 94 28.644 33.431 1.046 1.00 15.81 S
+ATOM 725 N ALA A 95 29.945 30.225 3.263 1.00 13.56 N
+ATOM 726 CA ALA A 95 29.134 29.227 3.969 1.00 15.63 C
+ATOM 727 C ALA A 95 29.236 29.330 5.491 1.00 10.80 C
+ATOM 728 O ALA A 95 28.222 29.180 6.179 1.00 12.93 O
+ATOM 729 CB ALA A 95 29.495 27.794 3.612 1.00 14.09 C
+ATOM 730 N LYS A 96 30.424 29.628 5.987 1.00 11.19 N
+ATOM 731 CA LYS A 96 30.627 29.912 7.419 1.00 13.27 C
+ATOM 732 C LYS A 96 29.802 31.115 7.906 1.00 13.38 C
+ATOM 733 O LYS A 96 29.296 31.011 9.027 1.00 15.75 O
+ATOM 734 CB LYS A 96 32.100 30.112 7.775 1.00 12.67 C
+ATOM 735 CG LYS A 96 32.874 28.792 7.697 1.00 11.93 C
+ATOM 736 CD LYS A 96 34.358 29.071 7.879 1.00 15.55 C
+ATOM 737 CE LYS A 96 35.205 27.816 7.938 1.00 18.03 C
+ATOM 738 NZ LYS A 96 36.610 28.242 8.169 1.00 20.72 N
+ATOM 739 N LYS A 97 29.660 32.101 7.049 1.00 12.90 N
+ATOM 740 CA LYS A 97 28.811 33.263 7.379 1.00 16.43 C
+ATOM 741 C LYS A 97 27.333 32.905 7.386 1.00 18.88 C
+ATOM 742 O LYS A 97 26.570 33.318 8.272 1.00 19.20 O
+ATOM 743 CB LYS A 97 29.087 34.456 6.470 1.00 18.97 C
+ATOM 744 CG LYS A 97 30.537 34.927 6.563 1.00 19.81 C
+ATOM 745 CD LYS A 97 30.841 36.073 5.610 1.00 22.00 C
+ATOM 746 CE LYS A 97 32.340 36.293 5.510 1.00 23.71 C
+ATOM 747 NZ LYS A 97 32.569 37.524 4.708 1.00 29.75 N
+ATOM 748 N ILE A 98 26.897 32.127 6.416 1.00 15.72 N
+ATOM 749 CA ILE A 98 25.520 31.693 6.266 1.00 16.36 C
+ATOM 750 C ILE A 98 25.030 30.871 7.453 1.00 16.70 C
+ATOM 751 O ILE A 98 24.059 31.254 8.126 1.00 18.80 O
+ATOM 752 CB ILE A 98 25.307 30.997 4.896 1.00 15.14 C
+ATOM 753 CG1 ILE A 98 25.643 31.910 3.702 1.00 13.63 C
+ATOM 754 CG2 ILE A 98 23.887 30.386 4.817 1.00 15.62 C
+ATOM 755 CD1 ILE A 98 25.620 31.204 2.321 1.00 17.82 C
+ATOM 756 N VAL A 99 25.875 29.966 7.915 1.00 16.73 N
+ATOM 757 CA VAL A 99 25.488 29.009 8.955 1.00 18.71 C
+ATOM 758 C VAL A 99 25.431 29.697 10.316 1.00 20.36 C
+ATOM 759 O VAL A 99 24.737 29.212 11.233 1.00 25.30 O
+ATOM 760 CB VAL A 99 26.398 27.774 8.859 1.00 16.94 C
+ATOM 761 CG1 VAL A 99 27.811 28.138 9.279 1.00 19.19 C
+ATOM 762 CG2 VAL A 99 25.834 26.594 9.632 1.00 18.97 C
+ATOM 763 N SER A 100 26.205 30.752 10.409 1.00 17.04 N
+ATOM 764 CA SER A 100 26.297 31.529 11.650 1.00 23.81 C
+ATOM 765 C SER A 100 25.124 32.495 11.765 1.00 24.03 C
+ATOM 766 O SER A 100 24.995 33.131 12.820 1.00 28.66 O
+ATOM 767 CB SER A 100 27.647 32.194 11.723 1.00 19.71 C
+ATOM 768 OG SER A 100 28.714 31.264 11.818 1.00 25.04 O
+ATOM 769 N ASP A 101 24.307 32.599 10.750 1.00 25.78 N
+ATOM 770 CA ASP A 101 23.162 33.495 10.650 1.00 26.98 C
+ATOM 771 C ASP A 101 21.924 33.183 11.481 1.00 28.34 C
+ATOM 772 O ASP A 101 21.132 34.143 11.678 1.00 31.88 O
+ATOM 773 CB ASP A 101 22.806 33.854 9.207 1.00 27.75 C
+ATOM 774 CG ASP A 101 22.426 35.320 9.009 1.00 30.86 C
+ATOM 775 OD1 ASP A 101 23.248 36.223 9.266 1.00 34.67 O
+ATOM 776 OD2 ASP A 101 21.276 35.519 8.551 1.00 32.70 O
+ATOM 777 N GLY A 102 21.723 31.942 11.887 1.00 28.87 N
+ATOM 778 CA GLY A 102 20.622 31.656 12.823 1.00 30.67 C
+ATOM 779 C GLY A 102 19.812 30.413 12.505 1.00 27.92 C
+ATOM 780 O GLY A 102 19.195 29.898 13.458 1.00 30.42 O
+ATOM 781 N ASN A 103 19.805 30.005 11.244 1.00 29.26 N
+ATOM 782 CA ASN A 103 19.076 28.799 10.848 1.00 25.22 C
+ATOM 783 C ASN A 103 19.990 27.600 10.597 1.00 22.06 C
+ATOM 784 O ASN A 103 19.472 26.579 10.117 1.00 24.23 O
+ATOM 785 CB ASN A 103 17.976 29.046 9.824 1.00 24.87 C
+ATOM 786 CG ASN A 103 16.708 28.245 10.063 1.00 27.08 C
+ATOM 787 OD1 ASN A 103 16.513 27.577 11.098 1.00 30.30 O
+ATOM 788 ND2 ASN A 103 15.672 28.428 9.240 1.00 30.15 N
+ATOM 789 N GLY A 104 21.240 27.711 10.997 1.00 23.20 N
+ATOM 790 CA GLY A 104 22.177 26.567 10.860 1.00 19.51 C
+ATOM 791 C GLY A 104 22.173 26.142 9.388 1.00 15.58 C
+ATOM 792 O GLY A 104 22.151 27.040 8.541 1.00 22.50 O
+ATOM 793 N MET A 105 22.185 24.847 9.115 1.00 17.51 N
+ATOM 794 CA MET A 105 22.278 24.370 7.724 1.00 16.07 C
+ATOM 795 C MET A 105 20.915 24.309 7.063 1.00 13.35 C
+ATOM 796 O MET A 105 20.902 23.921 5.871 1.00 15.50 O
+ATOM 797 CB MET A 105 23.036 23.048 7.632 1.00 19.32 C
+ATOM 798 CG MET A 105 24.519 23.221 7.871 1.00 17.10 C
+ATOM 799 SD MET A 105 25.379 21.660 7.491 1.00 20.27 S
+ATOM 800 CE MET A 105 25.369 21.706 5.703 1.00 20.03 C
+ATOM 801 N ASN A 106 19.896 24.839 7.735 1.00 14.64 N
+ATOM 802 CA ASN A 106 18.557 24.898 7.103 1.00 18.58 C
+ATOM 803 C ASN A 106 18.566 25.831 5.892 1.00 18.20 C
+ATOM 804 O ASN A 106 17.678 25.748 5.021 1.00 22.14 O
+ATOM 805 CB ASN A 106 17.420 25.150 8.084 1.00 19.18 C
+ATOM 806 CG ASN A 106 17.207 23.938 8.967 1.00 19.21 C
+ATOM 807 OD1 ASN A 106 16.836 22.867 8.443 1.00 24.65 O
+ATOM 808 ND2 ASN A 106 17.542 24.047 10.255 1.00 25.28 N
+ATOM 809 N ALA A 107 19.617 26.647 5.800 1.00 18.54 N
+ATOM 810 CA ALA A 107 19.824 27.514 4.634 1.00 18.74 C
+ATOM 811 C ALA A 107 20.007 26.744 3.329 1.00 16.80 C
+ATOM 812 O ALA A 107 19.734 27.292 2.260 1.00 20.63 O
+ATOM 813 CB ALA A 107 21.060 28.374 4.877 1.00 19.47 C
+ATOM 814 N TRP A 108 20.371 25.465 3.434 1.00 16.46 N
+ATOM 815 CA TRP A 108 20.532 24.624 2.241 1.00 14.68 C
+ATOM 816 C TRP A 108 19.317 23.688 2.110 1.00 17.55 C
+ATOM 817 O TRP A 108 19.240 22.816 2.993 1.00 20.05 O
+ATOM 818 CB TRP A 108 21.840 23.826 2.338 1.00 16.18 C
+ATOM 819 CG TRP A 108 23.000 24.736 2.026 1.00 15.50 C
+ATOM 820 CD1 TRP A 108 23.360 25.234 0.803 1.00 15.45 C
+ATOM 821 CD2 TRP A 108 23.798 25.437 2.991 1.00 15.57 C
+ATOM 822 NE1 TRP A 108 24.414 26.102 0.952 1.00 17.40 N
+ATOM 823 CE2 TRP A 108 24.711 26.237 2.272 1.00 15.78 C
+ATOM 824 CE3 TRP A 108 23.833 25.426 4.379 1.00 12.79 C
+ATOM 825 CZ2 TRP A 108 25.682 26.985 2.917 1.00 15.77 C
+ATOM 826 CZ3 TRP A 108 24.773 26.200 5.033 1.00 16.28 C
+ATOM 827 CH2 TRP A 108 25.691 26.960 4.298 1.00 16.65 C
+ATOM 828 N VAL A 109 18.487 23.925 1.101 1.00 15.35 N
+ATOM 829 CA VAL A 109 17.265 23.096 1.025 1.00 19.96 C
+ATOM 830 C VAL A 109 17.573 21.611 0.884 1.00 17.16 C
+ATOM 831 O VAL A 109 16.923 20.811 1.587 1.00 20.77 O
+ATOM 832 CB VAL A 109 16.146 23.660 0.145 1.00 21.94 C
+ATOM 833 CG1 VAL A 109 16.607 23.905 -1.285 1.00 27.84 C
+ATOM 834 CG2 VAL A 109 14.901 22.783 0.136 1.00 21.22 C
+ATOM 835 N ALA A 110 18.562 21.308 0.075 1.00 20.97 N
+ATOM 836 CA ALA A 110 18.972 19.935 -0.237 1.00 18.78 C
+ATOM 837 C ALA A 110 19.502 19.244 1.006 1.00 18.30 C
+ATOM 838 O ALA A 110 19.197 18.046 1.174 1.00 18.47 O
+ATOM 839 CB ALA A 110 19.857 19.777 -1.455 1.00 20.83 C
+ATOM 840 N TRP A 111 20.121 19.983 1.892 1.00 16.62 N
+ATOM 841 CA TRP A 111 20.551 19.500 3.202 1.00 15.74 C
+ATOM 842 C TRP A 111 19.343 19.085 4.046 1.00 19.12 C
+ATOM 843 O TRP A 111 19.284 17.986 4.643 1.00 16.20 O
+ATOM 844 CB TRP A 111 21.486 20.451 3.925 1.00 14.63 C
+ATOM 845 CG TRP A 111 21.858 19.904 5.252 1.00 14.87 C
+ATOM 846 CD1 TRP A 111 22.856 18.975 5.486 1.00 18.11 C
+ATOM 847 CD2 TRP A 111 21.199 20.093 6.504 1.00 16.63 C
+ATOM 848 NE1 TRP A 111 22.848 18.592 6.808 1.00 17.16 N
+ATOM 849 CE2 TRP A 111 21.798 19.221 7.435 1.00 16.77 C
+ATOM 850 CE3 TRP A 111 20.182 20.959 6.908 1.00 15.16 C
+ATOM 851 CZ2 TRP A 111 21.492 19.284 8.784 1.00 17.69 C
+ATOM 852 CZ3 TRP A 111 19.818 20.954 8.240 1.00 16.88 C
+ATOM 853 CH2 TRP A 111 20.443 20.110 9.162 1.00 19.73 C
+ATOM 854 N ARG A 112 18.438 20.038 4.228 1.00 17.47 N
+ATOM 855 CA ARG A 112 17.185 19.830 4.955 1.00 19.60 C
+ATOM 856 C ARG A 112 16.472 18.593 4.391 1.00 17.68 C
+ATOM 857 O ARG A 112 16.000 17.792 5.220 1.00 22.77 O
+ATOM 858 CB ARG A 112 16.214 20.990 4.944 1.00 17.57 C
+ATOM 859 CG ARG A 112 16.592 22.438 5.091 1.00 25.27 C
+ATOM 860 CD ARG A 112 15.368 23.296 5.135 1.00 21.23 C
+ATOM 861 NE ARG A 112 14.776 23.555 3.836 1.00 28.06 N
+ATOM 862 CZ ARG A 112 14.785 24.695 3.143 1.00 27.89 C
+ATOM 863 NH1 ARG A 112 15.596 25.721 3.383 1.00 30.12 N
+ATOM 864 NH2 ARG A 112 13.717 25.008 2.398 1.00 30.39 N
+ATOM 865 N ASN A 113 16.307 18.521 3.074 1.00 19.43 N
+ATOM 866 CA ASN A 113 15.464 17.463 2.491 1.00 20.16 C
+ATOM 867 C ASN A 113 16.111 16.083 2.586 1.00 21.26 C
+ATOM 868 O ASN A 113 15.454 15.054 2.808 1.00 24.90 O
+ATOM 869 CB ASN A 113 14.966 17.779 1.085 1.00 20.43 C
+ATOM 870 CG ASN A 113 14.003 18.961 1.018 1.00 16.63 C
+ATOM 871 OD1 ASN A 113 13.454 19.344 2.059 1.00 25.68 O
+ATOM 872 ND2 ASN A 113 13.840 19.555 -0.159 1.00 22.00 N
+ATOM 873 N ARG A 114 17.401 16.041 2.355 1.00 19.72 N
+ATOM 874 CA ARG A 114 18.156 14.836 2.042 1.00 21.43 C
+ATOM 875 C ARG A 114 19.258 14.440 2.991 1.00 22.71 C
+ATOM 876 O ARG A 114 19.505 13.217 3.097 1.00 24.85 O
+ATOM 877 CB ARG A 114 18.622 14.910 0.576 1.00 21.05 C
+ATOM 878 CG ARG A 114 17.395 14.614 -0.300 1.00 26.59 C
+ATOM 879 CD ARG A 114 17.729 14.399 -1.731 1.00 26.92 C
+ATOM 880 NE ARG A 114 18.153 15.677 -2.301 1.00 33.46 N
+ATOM 881 CZ ARG A 114 17.826 16.080 -3.535 1.00 32.00 C
+ATOM 882 NH1 ARG A 114 17.378 15.225 -4.456 1.00 36.02 N
+ATOM 883 NH2 ARG A 114 17.735 17.388 -3.796 1.00 36.05 N
+ATOM 884 N CYS A 115 19.743 15.372 3.773 1.00 17.56 N
+ATOM 885 CA CYS A 115 20.843 15.041 4.708 1.00 15.08 C
+ATOM 886 C CYS A 115 20.448 14.933 6.159 1.00 16.64 C
+ATOM 887 O CYS A 115 20.972 14.116 6.940 1.00 21.71 O
+ATOM 888 CB CYS A 115 21.991 16.018 4.426 1.00 15.21 C
+ATOM 889 SG CYS A 115 22.563 16.009 2.739 1.00 19.35 S
+ATOM 890 N LYS A 116 19.714 15.918 6.619 1.00 18.76 N
+ATOM 891 CA LYS A 116 19.332 16.085 8.025 1.00 19.14 C
+ATOM 892 C LYS A 116 18.634 14.821 8.518 1.00 21.91 C
+ATOM 893 O LYS A 116 17.819 14.234 7.785 1.00 24.78 O
+ATOM 894 CB LYS A 116 18.492 17.363 8.126 1.00 21.01 C
+ATOM 895 CG LYS A 116 17.930 17.512 9.547 1.00 21.28 C
+ATOM 896 CD LYS A 116 16.745 18.481 9.554 1.00 25.86 C
+ATOM 897 CE LYS A 116 16.658 19.147 10.918 1.00 25.58 C
+ATOM 898 NZ LYS A 116 15.454 20.010 11.047 1.00 34.69 N
+ATOM 899 N GLY A 117 19.152 14.318 9.635 1.00 26.39 N
+ATOM 900 CA GLY A 117 18.558 13.126 10.267 1.00 29.06 C
+ATOM 901 C GLY A 117 19.018 11.781 9.733 1.00 28.29 C
+ATOM 902 O GLY A 117 18.499 10.733 10.164 1.00 31.90 O
+ATOM 903 N THR A 118 19.892 11.802 8.740 1.00 26.88 N
+ATOM 904 CA THR A 118 20.473 10.578 8.171 1.00 22.31 C
+ATOM 905 C THR A 118 21.868 10.375 8.761 1.00 21.43 C
+ATOM 906 O THR A 118 22.321 11.119 9.650 1.00 22.31 O
+ATOM 907 CB THR A 118 20.440 10.571 6.598 1.00 18.59 C
+ATOM 908 OG1 THR A 118 21.560 11.404 6.161 1.00 22.71 O
+ATOM 909 CG2 THR A 118 19.095 11.104 6.074 1.00 21.13 C
+ATOM 910 N ASP A 119 22.392 9.213 8.431 1.00 21.20 N
+ATOM 911 CA ASP A 119 23.768 8.830 8.756 1.00 22.61 C
+ATOM 912 C ASP A 119 24.713 9.543 7.779 1.00 20.13 C
+ATOM 913 O ASP A 119 25.178 8.950 6.780 1.00 20.57 O
+ATOM 914 CB ASP A 119 23.934 7.313 8.738 1.00 21.00 C
+ATOM 915 CG ASP A 119 25.347 6.900 9.121 1.00 25.32 C
+ATOM 916 OD1 ASP A 119 26.051 7.633 9.830 1.00 27.93 O
+ATOM 917 OD2 ASP A 119 25.715 5.746 8.804 1.00 27.31 O
+ATOM 918 N VAL A 120 24.988 10.793 8.094 1.00 23.41 N
+ATOM 919 CA VAL A 120 25.886 11.637 7.306 1.00 20.10 C
+ATOM 920 C VAL A 120 27.342 11.199 7.304 1.00 18.51 C
+ATOM 921 O VAL A 120 28.099 11.604 6.406 1.00 19.95 O
+ATOM 922 CB VAL A 120 25.721 13.134 7.630 1.00 19.91 C
+ATOM 923 CG1 VAL A 120 24.356 13.655 7.183 1.00 23.59 C
+ATOM 924 CG2 VAL A 120 26.088 13.478 9.055 1.00 20.79 C
+ATOM 925 N GLN A 121 27.701 10.430 8.306 1.00 21.83 N
+ATOM 926 CA GLN A 121 29.021 9.783 8.389 1.00 21.12 C
+ATOM 927 C GLN A 121 29.317 8.861 7.207 1.00 20.78 C
+ATOM 928 O GLN A 121 30.480 8.669 6.820 1.00 19.66 O
+ATOM 929 CB GLN A 121 29.088 9.048 9.728 1.00 24.21 C
+ATOM 930 CG GLN A 121 30.530 8.965 10.167 1.00 26.13 C
+ATOM 931 CD GLN A 121 30.615 8.877 11.674 1.00 26.94 C
+ATOM 932 OE1 GLN A 121 31.368 9.632 12.283 1.00 31.43 O
+ATOM 933 NE2 GLN A 121 29.884 7.871 12.151 1.00 28.26 N
+ATOM 934 N ALA A 122 28.300 8.271 6.576 1.00 17.62 N
+ATOM 935 CA ALA A 122 28.390 7.548 5.311 1.00 19.46 C
+ATOM 936 C ALA A 122 29.186 8.290 4.227 1.00 17.98 C
+ATOM 937 O ALA A 122 30.031 7.710 3.523 1.00 21.35 O
+ATOM 938 CB ALA A 122 26.999 7.244 4.783 1.00 18.29 C
+ATOM 939 N TRP A 123 29.021 9.616 4.240 1.00 18.07 N
+ATOM 940 CA TRP A 123 29.703 10.502 3.283 1.00 16.76 C
+ATOM 941 C TRP A 123 31.218 10.581 3.392 1.00 16.76 C
+ATOM 942 O TRP A 123 31.905 10.942 2.412 1.00 20.08 O
+ATOM 943 CB TRP A 123 29.027 11.872 3.347 1.00 19.49 C
+ATOM 944 CG TRP A 123 27.621 11.735 2.850 1.00 17.43 C
+ATOM 945 CD1 TRP A 123 26.485 11.608 3.588 1.00 19.42 C
+ATOM 946 CD2 TRP A 123 27.241 11.547 1.481 1.00 17.47 C
+ATOM 947 NE1 TRP A 123 25.405 11.458 2.774 1.00 18.86 N
+ATOM 948 CE2 TRP A 123 25.827 11.391 1.479 1.00 17.28 C
+ATOM 949 CE3 TRP A 123 27.947 11.468 0.283 1.00 20.03 C
+ATOM 950 CZ2 TRP A 123 25.111 11.184 0.311 1.00 18.33 C
+ATOM 951 CZ3 TRP A 123 27.222 11.329 -0.886 1.00 20.85 C
+ATOM 952 CH2 TRP A 123 25.835 11.127 -0.869 1.00 20.45 C
+ATOM 953 N ILE A 124 31.741 10.269 4.554 1.00 14.19 N
+ATOM 954 CA ILE A 124 33.186 10.292 4.801 1.00 16.82 C
+ATOM 955 C ILE A 124 33.863 8.955 5.024 1.00 18.45 C
+ATOM 956 O ILE A 124 35.100 8.892 5.134 1.00 21.02 O
+ATOM 957 CB ILE A 124 33.504 11.403 5.863 1.00 17.69 C
+ATOM 958 CG1 ILE A 124 32.956 10.984 7.234 1.00 18.86 C
+ATOM 959 CG2 ILE A 124 33.024 12.804 5.387 1.00 21.01 C
+ATOM 960 CD1 ILE A 124 33.729 11.437 8.488 1.00 22.81 C
+ATOM 961 N ARG A 125 33.080 7.898 5.131 1.00 21.05 N
+ATOM 962 CA ARG A 125 33.594 6.534 5.320 1.00 19.12 C
+ATOM 963 C ARG A 125 34.311 6.113 4.036 1.00 17.52 C
+ATOM 964 O ARG A 125 33.843 6.337 2.906 1.00 23.44 O
+ATOM 965 CB ARG A 125 32.476 5.551 5.650 1.00 19.54 C
+ATOM 966 CG ARG A 125 32.117 5.596 7.145 1.00 22.40 C
+ATOM 967 CD ARG A 125 31.277 4.392 7.482 1.00 24.05 C
+ATOM 968 NE ARG A 125 30.282 4.754 8.466 1.00 28.08 N
+ATOM 969 CZ ARG A 125 28.984 4.993 8.331 1.00 23.40 C
+ATOM 970 NH1 ARG A 125 28.334 4.690 7.207 1.00 23.69 N
+ATOM 971 NH2 ARG A 125 28.392 5.549 9.392 1.00 23.77 N
+ATOM 972 N GLY A 126 35.497 5.568 4.243 1.00 18.80 N
+ATOM 973 CA GLY A 126 36.291 5.058 3.102 1.00 21.28 C
+ATOM 974 C GLY A 126 37.334 6.066 2.658 1.00 22.50 C
+ATOM 975 O GLY A 126 38.220 5.729 1.855 1.00 23.59 O
+ATOM 976 N CYS A 127 37.335 7.221 3.297 1.00 19.05 N
+ATOM 977 CA CYS A 127 38.234 8.333 2.961 1.00 19.13 C
+ATOM 978 C CYS A 127 39.422 8.382 3.925 1.00 22.50 C
+ATOM 979 O CYS A 127 39.206 8.267 5.138 1.00 21.64 O
+ATOM 980 CB CYS A 127 37.453 9.628 2.990 1.00 18.75 C
+ATOM 981 SG CYS A 127 36.010 9.816 1.936 1.00 19.93 S
+ATOM 982 N ARG A 128 40.586 8.695 3.393 1.00 23.60 N
+ATOM 983 CA ARG A 128 41.774 8.960 4.217 1.00 28.29 C
+ATOM 984 C ARG A 128 41.820 10.438 4.578 1.00 25.64 C
+ATOM 985 O ARG A 128 41.976 11.291 3.694 1.00 30.98 O
+ATOM 986 CB ARG A 128 43.047 8.304 3.707 1.00 30.82 C
+ATOM 987 CG ARG A 128 43.231 6.886 4.280 1.00 34.25 C
+ATOM 988 CD ARG A 128 43.833 6.911 5.651 1.00 33.59 C
+ATOM 989 NE ARG A 128 45.246 7.263 5.636 1.00 37.63 N
+ATOM 990 CZ ARG A 128 45.862 8.258 6.281 1.00 38.37 C
+ATOM 991 NH1 ARG A 128 45.241 9.069 7.151 1.00 38.97 N
+ATOM 992 NH2 ARG A 128 47.134 8.554 5.973 1.00 40.22 N
+ATOM 993 N LEU A 129 41.289 10.715 5.771 1.00 26.05 N
+ATOM 994 CA LEU A 129 41.094 12.084 6.273 1.00 26.89 C
+ATOM 995 C LEU A 129 42.119 12.382 7.370 1.00 29.58 C
+ATOM 996 O LEU A 129 41.730 12.276 8.559 1.00 33.54 O
+ATOM 997 CB LEU A 129 39.635 12.335 6.646 1.00 26.31 C
+ATOM 998 CG LEU A 129 38.689 12.917 5.620 1.00 23.49 C
+ATOM 999 CD1 LEU A 129 39.112 12.657 4.191 1.00 26.43 C
+ATOM 1000 CD2 LEU A 129 37.310 12.325 5.886 1.00 25.15 C
+ATOM 1001 OXT LEU A 129 43.232 12.675 6.905 1.00 34.20 O
+TER 1002 LEU A 129
+HETATM 1003 O HOH A 130 23.434 40.063 -6.661 1.00 19.48 O
+HETATM 1004 O HOH A 131 31.994 26.416 -6.047 0.90 22.43 O
+HETATM 1005 O HOH A 132 30.250 13.337 9.787 0.98 20.93 O
+HETATM 1006 O HOH A 133 22.384 42.331 -8.165 0.90 21.85 O
+HETATM 1007 O HOH A 134 29.239 27.621 -3.670 1.00 17.47 O
+HETATM 1008 O HOH A 135 29.464 37.761 -10.492 0.98 20.05 O
+HETATM 1009 O HOH A 136 20.807 36.305 -11.082 1.00 18.47 O
+HETATM 1010 O HOH A 137 41.318 17.849 -1.378 0.98 20.99 O
+HETATM 1011 O HOH A 138 34.697 29.056 -4.039 0.89 22.31 O
+HETATM 1012 O HOH A 139 26.871 17.298 13.496 1.00 20.31 O
+HETATM 1013 O HOH A 140 32.131 11.050 -5.817 0.97 21.39 O
+HETATM 1014 O HOH A 141 23.468 40.040 -2.372 0.91 23.40 O
+HETATM 1015 O HOH A 142 21.390 45.524 -11.035 0.96 20.63 O
+HETATM 1016 O HOH A 143 34.490 26.578 -5.741 0.75 22.11 O
+HETATM 1017 O HOH A 144 16.422 34.139 -3.527 0.91 20.71 O
+HETATM 1018 O HOH A 145 21.374 29.926 8.946 0.83 24.21 O
+HETATM 1019 O HOH A 146 41.048 12.539 -0.011 0.70 22.71 O
+HETATM 1020 O HOH A 147 32.794 35.686 2.558 0.78 20.71 O
+HETATM 1021 O HOH A 148 49.648 8.964 6.343 0.83 21.93 O
+HETATM 1022 O HOH A 149 14.452 34.901 -13.339 0.69 23.89 O
+HETATM 1023 O HOH A 150 22.930 10.839 4.044 0.92 22.02 O
+HETATM 1024 O HOH A 151 16.012 18.490 -2.200 0.85 24.37 O
+HETATM 1025 O HOH A 152 12.130 21.587 3.044 0.78 24.35 O
+HETATM 1026 O HOH A 153 15.684 38.922 -5.813 0.76 24.50 O
+HETATM 1027 O HOH A 154 10.652 24.228 3.428 0.80 21.12 O
+HETATM 1028 O HOH A 155 44.070 17.975 2.852 0.80 21.64 O
+HETATM 1029 O HOH A 156 32.029 13.080 -8.110 0.85 20.63 O
+HETATM 1030 O HOH A 157 36.425 19.613 15.174 0.56 23.44 O
+HETATM 1031 O HOH A 158 37.941 30.505 -3.686 0.79 21.54 O
+HETATM 1032 O HOH A 159 30.710 42.741 -6.289 0.72 22.79 O
+HETATM 1033 O HOH A 160 23.922 44.367 -7.653 0.62 22.78 O
+HETATM 1034 O HOH A 161 33.829 34.252 0.626 0.73 20.81 O
+HETATM 1035 O HOH A 162 29.613 40.730 -9.602 0.78 22.12 O
+HETATM 1036 O HOH A 163 23.563 7.995 4.406 0.58 22.93 O
+HETATM 1037 O HOH A 164 31.511 42.362 -4.183 0.73 22.01 O
+HETATM 1038 O HOH A 165 21.882 29.536 -15.013 0.81 22.04 O
+HETATM 1039 O HOH A 166 37.763 20.913 9.782 0.86 21.57 O
+HETATM 1040 O HOH A 167 42.338 17.481 5.165 0.65 22.17 O
+HETATM 1041 O HOH A 168 23.344 39.739 -4.358 0.72 21.56 O
+HETATM 1042 O HOH A 169 22.984 29.224 13.124 0.75 22.56 O
+HETATM 1043 O HOH A 170 30.778 7.794 -3.514 0.65 21.58 O
+HETATM 1044 O HOH A 171 42.965 14.657 4.991 0.63 23.91 O
+HETATM 1045 O HOH A 172 36.927 17.948 -13.093 0.62 23.36 O
+HETATM 1046 O HOH A 173 35.412 25.852 -11.575 0.58 23.42 O
+HETATM 1047 O HOH A 174 37.428 32.540 -5.787 0.62 21.98 O
+HETATM 1048 O HOH A 175 37.317 8.592 7.456 0.64 22.92 O
+HETATM 1049 O HOH A 176 9.314 36.705 -11.546 0.69 23.77 O
+HETATM 1050 O HOH A 177 39.972 23.760 -2.655 0.86 18.96 O
+HETATM 1051 O HOH A 178 22.128 30.274 -0.543 0.76 18.78 O
+HETATM 1052 O HOH A 179 22.244 15.813 10.000 0.68 19.66 O
+HETATM 1053 O HOH A 180 40.729 9.223 0.292 0.64 20.15 O
+HETATM 1054 O HOH A 181 12.500 15.267 4.097 0.56 20.12 O
+HETATM 1055 O HOH A 182 20.372 28.618 -2.353 0.64 20.17 O
+HETATM 1056 O HOH A 183 22.793 15.462 -6.673 0.63 20.60 O
+HETATM 1057 O HOH A 184 23.138 31.809 15.121 0.55 20.90 O
+HETATM 1058 O HOH A 185 22.671 38.691 8.245 0.48 21.16 O
+HETATM 1059 O HOH A 186 33.966 33.112 6.837 0.59 19.45 O
+HETATM 1060 O HOH A 187 19.572 25.423 -1.420 0.53 19.94 O
+HETATM 1061 O HOH A 188 14.790 15.672 7.259 0.52 21.22 O
+HETATM 1062 O HOH A 189 19.112 28.022 -14.647 0.49 19.83 O
+HETATM 1063 O HOH A 190 17.302 39.059 -12.453 0.52 20.14 O
+HETATM 1064 O HOH A 191 16.198 14.502 5.577 0.46 20.78 O
+HETATM 1065 O HOH A 192 17.345 46.346 -7.080 0.50 18.13 O
+HETATM 1066 O HOH A 193 14.992 31.300 -4.242 0.46 17.90 O
+HETATM 1067 O HOH A 194 28.196 44.775 -3.148 0.44 18.15 O
+HETATM 1068 O HOH A 195 29.479 13.863 -9.107 0.44 18.30 O
+HETATM 1069 O HOH A 196 23.613 44.811 2.608 0.45 17.66 O
+HETATM 1070 O HOH A 197 40.572 22.184 -6.358 0.42 18.06 O
+HETATM 1071 O HOH A 198 12.475 31.860 -6.226 0.47 17.85 O
+HETATM 1072 O HOH A 199 16.684 13.594 -5.832 0.31 18.51 O
+HETATM 1073 O HOH A 200 27.534 38.059 -12.862 0.48 18.19 O
+HETATM 1074 O HOH A 201 25.892 35.973 11.563 0.46 18.15 O
+HETATM 1075 O HOH A 202 24.790 25.182 16.063 0.46 17.64 O
+HETATM 1076 O HOH A 203 12.580 21.214 5.006 0.51 17.97 O
+HETATM 1077 O HOH A 204 19.687 23.750 -4.851 0.37 18.08 O
+HETATM 1078 O HOH A 205 27.098 35.956 -12.358 0.39 18.71 O
+HETATM 1079 O HOH A 206 37.255 9.634 10.002 0.46 18.39 O
+HETATM 1080 O HOH A 207 43.755 23.843 8.038 0.38 17.96 O
+CONECT 48 981
+CONECT 238 889
+CONECT 513 630
+CONECT 601 724
+CONECT 630 513
+CONECT 724 601
+CONECT 889 238
+CONECT 981 48
+MASTER 290 0 0 8 2 0 0 6 1079 1 8 10
+END
diff --git a/modules/mol/mm/examples/1CRN.pdb b/modules/mol/mm/examples/1CRN.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..13ca618d438ae60a55a8ce1c532cd23bf545e200
--- /dev/null
+++ b/modules/mol/mm/examples/1CRN.pdb
@@ -0,0 +1,329 @@
+ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
+ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
+ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
+ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
+ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C
+ATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N
+ATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C
+ATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C
+ATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O
+ATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C
+ATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C
+ATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C
+ATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S
+ATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C
+ATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C
+ATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S
+ATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C
+ATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C
+ATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C
+ATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N
+ATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C
+ATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C
+ATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O
+ATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C
+ATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O
+ATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C
+ATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C
+ATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C
+ATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C
+ATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C
+ATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C
+ATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C
+ATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C
+ATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C
+ATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C
+ATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C
+ATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N
+ATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N
+ATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C
+ATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C
+ATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O
+ATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C
+ATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O
+ATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C
+ATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C
+ATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N
+ATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N
+ATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C
+ATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C
+ATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C
+ATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C
+ATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C
+ATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C
+ATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N
+ATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C
+ATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C
+ATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C
+ATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C
+ATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C
+ATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O
+ATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S
+ATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C
+ATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C
+ATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N
+ATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C
+ATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C
+ATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C
+ATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C
+ATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C
+ATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C
+ATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C
+ATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C
+ATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O
+ATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N
+ATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C
+ATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C
+ATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O
+ATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C
+ATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C
+ATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C
+ATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C
+ATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C
+ATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C
+ATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C
+ATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
+ATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C
+ATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C
+ATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C
+ATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N
+ATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C
+ATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C
+ATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O
+ATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C
+ATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C
+ATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C
+ATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C
+ATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N
+ATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C
+ATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C
+ATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O
+ATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C
+ATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S
+ATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N
+ATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C
+ATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C
+ATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O
+ATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C
+ATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N
+ATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C
+ATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C
+ATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O
+ATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C
+ATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O
+ATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C
+ATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N
+ATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C
+ATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C
+ATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O
+ATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C
+ATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C
+ATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C
+ATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C
+ATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C
+ATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C
+ATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C
+ATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O
+ATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N
+ATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C
+ATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C
+ATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O
+ATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C
+ATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O
+ATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C
+ATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N
+ATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C
+ATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C
+ATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O
+ATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C
+ATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C
+ATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S
+ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
+ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
+ATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C
+ATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C
+ATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C
+ATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O
+ATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C
+ATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C
+ATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C
+ATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C
+ATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C
+ATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C
+ATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C
+ATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N
+ATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C
+ATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C
+ATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O
+ATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C
+ATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C
+ATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C
+ATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N
+ATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C
+ATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C
+ATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O
+ATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C
+ATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C
+ATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C
+ATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S
+ATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C
+ATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C
+ATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C
+ATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C
+ATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C
+ATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O
+ATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C
+ATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C
+ATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O
+ATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C
+ATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C
+ATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O
+ATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C
+ATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C
+ATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C
+ATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C
+ATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C
+ATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O
+TER 328 ASN A 46
+END
diff --git a/modules/mol/mm/examples/ethanol.pdb b/modules/mol/mm/examples/ethanol.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..4d16716e8bd096575463cc1c3bb0a13d435873d2
--- /dev/null
+++ b/modules/mol/mm/examples/ethanol.pdb
@@ -0,0 +1,10 @@
+ATOM 1 C1 ETH A 1 -0.246 0.000 1.285 1.00 0.00 C
+ATOM 2 C2 ETH A 1 0.566 0.000 -0.011 1.00 0.00 C
+ATOM 3 O ETH A 1 -0.322 0.000 -1.130 1.00 0.00 O
+ATOM 4 H11 ETH A 1 0.376 0.000 2.068 1.00 0.00 H
+ATOM 5 H12 ETH A 1 -0.847 0.866 1.302 1.00 0.00 H
+ATOM 6 H13 ETH A 1 -0.847 -0.866 1.302 1.00 0.00 H
+ATOM 7 H21 ETH A 1 1.142 0.816 -0.043 1.00 0.00 H
+ATOM 8 H22 ETH A 1 1.142 -0.816 -0.043 1.00 0.00 H
+ATOM 9 OH ETH A 1 0.209 0.000 -1.977 1.00 0.00 H
+END
diff --git a/modules/mol/mm/examples/ethanol_example.py b/modules/mol/mm/examples/ethanol_example.py
new file mode 100644
index 0000000000000000000000000000000000000000..f76253adcc377cbfd9102c2e0a44a057da2069ae
--- /dev/null
+++ b/modules/mol/mm/examples/ethanol_example.py
@@ -0,0 +1,198 @@
+from ost.mol.mm import *
+from PyQt4 import QtCore
+
+class Anim(QtCore.QTimer):
+ def __init__(self,sim,go):
+ QtCore.QTimer.__init__(self)
+ self.ent=sim.GetEntity()
+ self.sim=sim
+ self.go = go
+ self.ed = ent.EditXCS()
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+
+ def OnTimer(self):
+ self.sim.Steps(1)
+ positions = sim.GetPositions()
+ for a, pos in zip(self.ent.atoms,positions):
+ self.ed.SetAtomPos(a,pos)
+ self.go.UpdatePositions()
+
+
+#Let's create an ethanol without its hydrogens
+ent = ost.mol.CreateEntity()
+ed = ent.EditXCS()
+chain = ed.InsertChain('A')
+res = ed.AppendResidue(chain,"ETH")
+c1 = ed.InsertAtom(res,"C1",geom.Vec3(-0.246,0.0,1.285),"C")
+c2 = ed.InsertAtom(res,"C2",geom.Vec3(0.566,0.0,-0.011),"C")
+o = ed.InsertAtom(res,"O",geom.Vec3(-0.322,0.0,-1.130),"O")
+ed.Connect(c1,c2)
+ed.Connect(c2,o)
+
+
+ff = Forcefield()
+
+#generate hydrogen constructor and add it to the forcefield
+h_constructor = GromacsHydrogenConstructor()
+h_constructor.AddHydrogenRule(3,4,["H11","H12","H13"],["C1","C2","O"])
+h_constructor.AddHydrogenRule(2,6,["H21","H22"],["C2","O","C1"])
+h_constructor.AddHydrogenRule(1,2,["OH"],["O","C2","C1"])
+ff.AddHydrogenConstructor("ETH",h_constructor)
+
+#generate buildingblock and add it to the forcefield
+building_block = BuildingBlock()
+building_block.AddAtom("C1","C",-0.18)
+building_block.AddAtom("C2","C",0.145)
+building_block.AddAtom("O","O",-0.683)
+building_block.AddAtom("H11","H",0.06)
+building_block.AddAtom("H12","H",0.06)
+building_block.AddAtom("H13","H",0.06)
+building_block.AddAtom("H21","H",0.06)
+building_block.AddAtom("H22","H",0.06)
+building_block.AddAtom("OH","OH",0.418)
+
+bonds = list()
+for i in range(8):
+ bonds.append(MMInteraction(FuncType.HarmonicBond))
+
+bonds[0].SetNames(["H11","C1"])
+bonds[1].SetNames(["H12","C1"])
+bonds[2].SetNames(["H13","C1"])
+bonds[3].SetNames(["C1","C2"])
+bonds[4].SetNames(["C2","H21"])
+bonds[5].SetNames(["C2","H22"])
+bonds[6].SetNames(["O","C2"])
+bonds[7].SetNames(["O","OH"])
+
+for b in bonds:
+ building_block.AddBond(b)
+
+ff.AddBuildingBlock("ETH",building_block)
+
+#add masses to the forcefield
+ff.AddMass("C",12.011)
+ff.AddMass("O",15.999)
+ff.AddMass("H",1.008)
+ff.AddMass("OH",1.008)
+
+#generate bonds and add them to the forcefield
+h_c_bond = MMInteraction(FuncType.HarmonicBond)
+c_c_bond = MMInteraction(FuncType.HarmonicBond)
+c_o_bond = MMInteraction(FuncType.HarmonicBond)
+o_h_bond = MMInteraction(FuncType.HarmonicBond)
+
+h_c_bond.SetTypes(["H","C"])
+c_c_bond.SetTypes(["C","C"])
+c_o_bond.SetTypes(["C","O"])
+o_h_bond.SetTypes(["O","OH"])
+
+h_c_bond.SetParam([0.1111,269449.6])
+c_c_bond.SetParam([0.153,186188.0])
+c_o_bond.SetParam([0.142,358150.4])
+o_h_bond.SetParam([0.096,456056.0])
+
+ff.AddBond(h_c_bond)
+ff.AddBond(c_c_bond)
+ff.AddBond(c_o_bond)
+ff.AddBond(o_h_bond)
+
+#generate angles and add them to the forcefield
+h_c_h_angle = MMInteraction(FuncType.UreyBradleyAngle)
+h_c_c_angle = MMInteraction(FuncType.UreyBradleyAngle)
+h_c_o_angle = MMInteraction(FuncType.UreyBradleyAngle)
+c_c_o_angle = MMInteraction(FuncType.UreyBradleyAngle)
+c_o_h_angle = MMInteraction(FuncType.UreyBradleyAngle)
+
+h_c_h_angle.SetTypes(["H","C","H"])
+h_c_c_angle.SetTypes(["H","C","C"])
+h_c_o_angle.SetTypes(["H","C","O"])
+c_c_o_angle.SetTypes(["C","C","O"])
+c_o_h_angle.SetTypes(["C","O","OH"])
+
+h_c_h_angle.SetParam([1.892,297.064,0.1802,4518.72])
+h_c_c_angle.SetParam([1.922,289.5328,0.2179,18853.104])
+h_c_o_angle.SetParam([1.900,384.0912,0.0,0.0])
+c_c_o_angle.SetParam([1.920,633.4576,0.0,0.0])
+c_o_h_angle.SetParam([1.850,481.16,0.0,0.0])
+
+ff.AddAngle(h_c_h_angle)
+ff.AddAngle(h_c_c_angle)
+ff.AddAngle(h_c_o_angle)
+ff.AddAngle(c_c_o_angle)
+ff.AddAngle(c_o_h_angle)
+
+#generate dihedrals and add them to the forcefield
+x_c_c_x_dihedral = MMInteraction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_one = MMInteraction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_two = MMInteraction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_three = MMInteraction(FuncType.PeriodicDihedral)
+x_c_o_x_dihedral = MMInteraction(FuncType.PeriodicDihedral)
+
+x_c_c_x_dihedral.SetTypes(["X","C","C","X"])
+c_c_o_h_dihedral_one.SetTypes(["C","C","O","OH"])
+c_c_o_h_dihedral_two.SetTypes(["C","C","O","OH"])
+c_c_o_h_dihedral_three.SetTypes(["C","C","O","OH"])
+x_c_o_x_dihedral.SetTypes(["X","C","O","X"])
+
+x_c_c_x_dihedral.SetParam([3,0.0,0.66944])
+c_c_o_h_dihedral_one.SetParam([1,0.0,5.4392])
+c_c_o_h_dihedral_two.SetParam([2,0.0,1.2552])
+c_c_o_h_dihedral_three.SetParam([3,0.0,1.75728])
+x_c_o_x_dihedral.SetParam([3,0.0,0.58576])
+
+ff.AddDihedral(x_c_c_x_dihedral)
+ff.AddDihedral(c_c_o_h_dihedral_one)
+ff.AddDihedral(c_c_o_h_dihedral_two)
+ff.AddDihedral(c_c_o_h_dihedral_three)
+ff.AddDihedral(x_c_o_x_dihedral)
+
+#add lj parameters
+c_lj = MMInteraction(FuncType.LJ)
+o_lj = MMInteraction(FuncType.LJ)
+h_lj = MMInteraction(FuncType.LJ)
+oh_lj = MMInteraction(FuncType.LJ)
+
+c_lj.SetTypes(["C"])
+o_lj.SetTypes(["O"])
+h_lj.SetTypes(["H"])
+oh_lj.SetTypes(["OH"])
+
+c_lj.SetParam([0.37,0.28])
+o_lj.SetParam([0.32,0.64])
+h_lj.SetParam([0.24,0.09])
+oh_lj.SetParam([0.04,0.2])
+
+ff.AddLJ(c_lj)
+ff.AddLJ(o_lj)
+ff.AddLJ(h_lj)
+ff.AddLJ(oh_lj)
+
+#we do not explicitely set the 1,4 interactions,
+#we rather decrease it by a certain factor
+ff.SetFudgeLJ(0.5)
+ff.SetFudgeQQ(0.5)
+
+#construct settings
+settings = MMSettings()
+settings.init_temperature = 310
+settings.forcefield = ff
+
+#construct integrator with tiny timesteps
+settings.integrator = VerletIntegrator(0.0001)
+
+
+#create the simulation
+sim = Simulation(ent,settings)
+
+io.SavePDB(sim.GetEntity(),'ethanol.pdb')
+
+
+go = gfx.Entity("ethanol",sim.GetEntity())
+go.SetRenderMode(gfx.CUSTOM)
+scene.Add(go)
+
+anim = Anim(sim,go)
+anim.start(2)
+
+
diff --git a/modules/mol/mm/examples/ethanol_example_using_topology.py b/modules/mol/mm/examples/ethanol_example_using_topology.py
new file mode 100644
index 0000000000000000000000000000000000000000..8cca033a9eba699b4558c013f20822d97aef721a
--- /dev/null
+++ b/modules/mol/mm/examples/ethanol_example_using_topology.py
@@ -0,0 +1,155 @@
+from ost.mol.mm import *
+from PyQt4 import QtCore
+from math import sqrt
+from math import sin
+
+class Anim(QtCore.QTimer):
+ def __init__(self,sim,go,cc_bond_index):
+ QtCore.QTimer.__init__(self)
+ self.ent=sim.GetEntity()
+ self.sim=sim
+ self.go = go
+ self.ed = ent.EditXCS()
+ self.bond_index = cc_bond_index
+ top = sim.GetTopology()
+ param = top.GetHarmonicBondParameters(cc_bond_index)
+ self.bond_length = param[2]
+ self.force_constant = param[3]
+ self.steps = 0
+ self.counter = 0
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+ def OnTimer(self):
+ if self.steps % 20 == 0:
+ sim.ResetHarmonicBond(self.bond_index,sin(self.counter*3.1416/100)*self.bond_length*0.75 + self.bond_length,self.force_constant)
+ self.counter += 1
+
+ self.sim.Steps(1)
+ positions = sim.GetPositions()
+ for a, pos in zip(self.ent.atoms,positions):
+ self.ed.SetAtomPos(a,pos)
+ self.go.UpdatePositions()
+ self.steps+=1
+
+
+#create topology by only defining masses
+
+prof = io.IOProfile(dialect='PDB', fault_tolerant=False,
+ quack_mode=False, processor=conop.HeuristicProcessor())
+
+ent = io.LoadPDB('ethanol.pdb', profile=prof)
+masses = [12.011,12.011,15.999,1.008,1.008,1.008,1.008,1.008,1.008]
+top = Topology(ent,masses)
+
+#all per atom parameters have to be set at once...
+charges = [-0.18,0.145,-0.683,0.06,0.06,0.06,0.06,0.06,0.418]
+sigmas = [0.37,0.37,0.32,0.24,0.24,0.24,0.24,0.24,0.04]
+epsilons = [0.28,0.28,0.64,0.09,0.09,0.09,0.09,0.09,0.2]
+
+top.SetCharges(charges)
+top.SetSigmas(sigmas)
+top.SetEpsilons(epsilons)
+
+#we can set the fudge parameters for 1,4 interactions also in the topology
+top.SetFudgeQQ(0.5)
+top.SetFudgeLJ(0.5)
+
+#add the bonds
+top.AddHarmonicBond(0,1,0.153,186188.0) #C-C
+top.AddHarmonicBond(0,3,0.1111,269449.6) #C-H
+top.AddHarmonicBond(0,4,0.1111,269449.6) #C-H
+top.AddHarmonicBond(0,5,0.1111,269449.6) #C-H
+top.AddHarmonicBond(1,6,0.1111,269449.6) #C-H
+top.AddHarmonicBond(1,7,0.1111,269449.6) #C-H
+top.AddHarmonicBond(1,2,0.142,358150.4) #C-O
+top.AddHarmonicBond(2,8,0.096,456056.0) #O-H
+
+#add the angles
+top.AddUreyBradleyAngle(3,0,4,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(3,0,5,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(4,0,5,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(3,0,1,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(4,0,1,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(5,0,1,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(0,1,6,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(0,1,7,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(0,1,2,1.920,633.4576,0.0,0.0) #C-C-O
+top.AddUreyBradleyAngle(6,1,2,1.900,384.0912,0.0,0.0) #H-C-O
+top.AddUreyBradleyAngle(7,1,2,1.900,384.0912,0.0,0.0) #H-C-O
+top.AddUreyBradleyAngle(6,1,7,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(1,2,8,1.850,481.16,0.0,0.0) #C-O-H
+
+
+#add the dihedrals
+top.AddPeriodicDihedral(3,0,1,6,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(3,0,1,7,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(3,0,1,2,3,0.0,0.66944) #H-C-C-O
+top.AddPeriodicDihedral(4,0,1,6,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(4,0,1,7,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(4,0,1,2,3,0.0,0.66944) #H-C-C-O
+top.AddPeriodicDihedral(5,0,1,6,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(5,0,1,7,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(5,0,1,2,3,0.0,0.66944) #H-C-C-O
+top.AddPeriodicDihedral(6,1,2,8,3,0.0,0.58576) #H-C-O-H
+top.AddPeriodicDihedral(7,1,2,8,3,0.0,0.58576) #H-C-O-H
+top.AddPeriodicDihedral(0,1,2,8,1,0.0,5.4392) #C-C-O-H
+top.AddPeriodicDihedral(0,1,2,8,2,0.0,1.2552) #C-C-O-H
+top.AddPeriodicDihedral(0,1,2,8,3,0.0,1.75728) #C-C-O-H
+
+#we have to manually set the exclusions for the nonbonded interaction...
+
+#1,2 interactions
+top.AddExclusion(3,0)
+top.AddExclusion(4,0)
+top.AddExclusion(5,0)
+top.AddExclusion(0,1)
+top.AddExclusion(1,6)
+top.AddExclusion(1,7)
+top.AddExclusion(1,2)
+top.AddExclusion(2,8)
+
+#1,3 interactions
+top.AddExclusion(3,4)
+top.AddExclusion(3,5)
+top.AddExclusion(4,5)
+top.AddExclusion(3,1)
+top.AddExclusion(4,1)
+top.AddExclusion(5,1)
+top.AddExclusion(0,6)
+top.AddExclusion(0,7)
+top.AddExclusion(0,2)
+top.AddExclusion(6,2)
+top.AddExclusion(7,2)
+top.AddExclusion(1,8)
+
+#add lj-pairs, note, that the fudge parameters still get applied during system setup
+top.AddLJPair(3,6,0.5*(sigmas[3]+sigmas[6]),sqrt(epsilons[3]*epsilons[6]))
+top.AddLJPair(3,7,0.5*(sigmas[3]+sigmas[7]),sqrt(epsilons[3]*epsilons[7]))
+top.AddLJPair(3,2,0.5*(sigmas[3]+sigmas[2]),sqrt(epsilons[3]*epsilons[2]))
+top.AddLJPair(4,6,0.5*(sigmas[4]+sigmas[6]),sqrt(epsilons[4]*epsilons[6]))
+top.AddLJPair(4,7,0.5*(sigmas[4]+sigmas[7]),sqrt(epsilons[4]*epsilons[7]))
+top.AddLJPair(4,2,0.5*(sigmas[4]+sigmas[2]),sqrt(epsilons[4]*epsilons[2]))
+top.AddLJPair(5,6,0.5*(sigmas[5]+sigmas[6]),sqrt(epsilons[5]*epsilons[6]))
+top.AddLJPair(5,7,0.5*(sigmas[5]+sigmas[7]),sqrt(epsilons[5]*epsilons[7]))
+top.AddLJPair(5,2,0.5*(sigmas[5]+sigmas[2]),sqrt(epsilons[5]*epsilons[2]))
+top.AddLJPair(6,8,0.5*(sigmas[6]+sigmas[8]),sqrt(epsilons[6]*epsilons[8]))
+top.AddLJPair(7,8,0.5*(sigmas[7]+sigmas[8]),sqrt(epsilons[7]*epsilons[8]))
+top.AddLJPair(0,8,0.5*(sigmas[0]+sigmas[8]),sqrt(epsilons[0]*epsilons[8]))
+
+settings = MMSettings()
+settings.init_temperature = 310
+settings.integrator = VerletIntegrator(0.0001)
+
+#let's extract the cc_bond_index to have some fun with it
+cc_bond_index = top.GetHarmonicBondIndices(0,1)[0]
+
+#create the simulation
+sim = Simulation(top,settings)
+go = gfx.Entity("ethanol",sim.GetEntity())
+go.SetRenderMode(gfx.CUSTOM)
+scene.Add(go)
+
+anim = Anim(sim,go,cc_bond_index)
+anim.start(2)
+
+
diff --git a/modules/mol/mm/examples/gb_example.py b/modules/mol/mm/examples/gb_example.py
new file mode 100644
index 0000000000000000000000000000000000000000..61a563e2e8d7621d147832e94c11a38943266cef
--- /dev/null
+++ b/modules/mol/mm/examples/gb_example.py
@@ -0,0 +1,51 @@
+from ost.mol import mm
+from PyQt4 import QtCore
+
+class Anim(QtCore.QTimer):
+ def __init__(self,sim,ent,go):
+ QtCore.QTimer.__init__(self)
+ self.ent=ent
+ self.sim=sim
+ self.go = go
+ self.ed = ent.EditXCS(ost.mol.BUFFERED_EDIT)
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+
+ def OnTimer(self):
+ self.sim.Steps(5)
+ positions = sim.GetPositions()
+ for a, pos in zip(self.ent.atoms,positions):
+ self.ed.SetAtomPos(a,pos)
+ self.ed.UpdateICS()
+ self.go.UpdatePositions()
+
+
+prot=ost.mol.CreateEntityFromView(io.LoadPDB('1CRN.pdb').Select('peptide=true'),True)
+
+settings = mm.MMSettings()
+
+settings.integrator = mm.LangevinIntegrator(310,1,0.002)
+settings.constrain_bonds = True
+settings.constrain_hbonds = True
+settings.constrain_hangles = True
+#settings.add_gbsa = True
+#settings.add_thermostat = True
+#settings.thermostat_temperature = 310.0
+#settings.thermostat_collision_frequency = 1
+settings.init_temperature = 0
+settings.forcefield = mm.LoadCHARMMForcefield()
+settings.platform = mm.Platform.CPU
+#settings.nonbonded_cutoff = 10.0
+settings.nonbonded_method = mm.NonbondedMethod.CutoffNonPeriodic
+
+sim = mm.Simulation(prot,settings)
+sim.MinimizeEnergy(type = "lbfgs",tolerance = 1.0, max_iterations = 200)
+sim.UpdateTopologyPositions()
+
+ent = sim.GetEntity()
+go = gfx.Entity("crambin",ent)
+scene.Add(go)
+
+anim = Anim(sim,ent,go)
+anim.start(1)
+
diff --git a/modules/mol/mm/examples/gb_example_traj.dcd b/modules/mol/mm/examples/gb_example_traj.dcd
new file mode 100644
index 0000000000000000000000000000000000000000..913d8d33f5f4f0a55f44002966ec332007c7dffe
Binary files /dev/null and b/modules/mol/mm/examples/gb_example_traj.dcd differ
diff --git a/modules/mol/mm/examples/gb_example_traj.pdb b/modules/mol/mm/examples/gb_example_traj.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..afb415a36cb19b045dff9136144b7355face8c46
--- /dev/null
+++ b/modules/mol/mm/examples/gb_example_traj.pdb
@@ -0,0 +1,643 @@
+ATOM 1 N THR 1 17.047 14.099 3.625 1.00 13.79 A N
+ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 A C
+ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19 A C
+ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85 A O
+ATOM 5 CB THR 1 18.170 12.703 5.337 1.00 13.02 A C
+ATOM 6 OG1 THR 1 19.334 12.829 4.463 1.00 15.06 A O
+ATOM 7 CG2 THR 1 18.150 11.546 6.304 1.00 14.23 A C
+ATOM 8 HA THR 1 16.993 12.024 3.689 1.00 0.00 A H
+ATOM 9 HB THR 1 18.153 13.430 6.024 1.00 0.00 A H
+ATOM 10 HG1 THR 1 20.169 12.789 5.012 1.00 0.00 A H
+ATOM 11 HG21 THR 1 18.958 11.589 6.892 1.00 0.00 A H
+ATOM 12 HG22 THR 1 17.275 11.615 6.888 1.00 0.00 A H
+ATOM 13 HG23 THR 1 18.155 10.649 5.751 1.00 0.00 A H
+ATOM 14 H1 THR 1 17.892 14.138 3.091 1.00 0.00 A H
+ATOM 15 H2 THR 1 16.213 14.183 2.986 1.00 0.00 A H
+ATOM 16 H3 THR 1 17.040 14.869 4.345 1.00 0.00 A H
+ATOM 17 N THR 2 15.115 11.555 5.265 1.00 7.81 A N
+ATOM 18 CA THR 2 13.856 11.469 6.066 1.00 8.31 A C
+ATOM 19 C THR 2 14.164 10.785 7.379 1.00 5.80 A C
+ATOM 20 O THR 2 14.993 9.862 7.443 1.00 6.94 A O
+ATOM 21 CB THR 2 12.732 10.711 5.261 1.00 10.32 A C
+ATOM 22 OG1 THR 2 13.308 9.439 4.926 1.00 12.81 A O
+ATOM 23 CG2 THR 2 12.484 11.442 3.895 1.00 11.90 A C
+ATOM 24 HN THR 2 15.516 10.742 4.843 1.00 0.00 A H
+ATOM 25 HA THR 2 13.507 12.387 6.253 1.00 0.00 A H
+ATOM 26 HB THR 2 11.884 10.657 5.788 1.00 0.00 A H
+ATOM 27 HG1 THR 2 12.645 8.898 4.409 1.00 0.00 A H
+ATOM 28 HG21 THR 2 11.771 10.961 3.384 1.00 0.00 A H
+ATOM 29 HG22 THR 2 12.179 12.430 4.097 1.00 0.00 A H
+ATOM 30 HG23 THR 2 13.384 11.439 3.347 1.00 0.00 A H
+ATOM 31 N CYS2 3 13.488 11.241 8.417 1.00 5.24 A N
+ATOM 32 CA CYS2 3 13.660 10.707 9.787 1.00 5.39 A C
+ATOM 33 C CYS2 3 12.269 10.431 10.323 1.00 4.45 A C
+ATOM 34 O CYS2 3 11.393 11.308 10.185 1.00 6.54 A O
+ATOM 35 CB CYS2 3 14.368 11.748 10.691 1.00 5.99 A C
+ATOM 36 SG CYS2 3 15.885 12.426 10.016 1.00 7.01 A S
+ATOM 37 HN CYS2 3 12.830 11.980 8.271 1.00 0.00 A H
+ATOM 38 HA CYS2 3 14.221 9.880 9.776 1.00 0.00 A H
+ATOM 39 HB1 CYS2 3 13.733 12.504 10.850 1.00 0.00 A H
+ATOM 40 HB2 CYS2 3 14.585 11.307 11.562 1.00 0.00 A H
+ATOM 41 N CYS2 4 12.019 9.272 10.928 1.00 3.90 A N
+ATOM 42 CA CYS2 4 10.646 8.991 11.408 1.00 4.24 A C
+ATOM 43 C CYS2 4 10.654 8.793 12.919 1.00 3.72 A C
+ATOM 44 O CYS2 4 11.659 8.296 13.491 1.00 5.30 A O
+ATOM 45 CB CYS2 4 10.057 7.752 10.682 1.00 4.41 A C
+ATOM 46 SG CYS2 4 9.837 8.018 8.904 1.00 4.72 A S
+ATOM 47 HN CYS2 4 12.748 8.600 11.057 1.00 0.00 A H
+ATOM 48 HA CYS2 4 10.060 9.774 11.196 1.00 0.00 A H
+ATOM 49 HB1 CYS2 4 10.677 6.979 10.815 1.00 0.00 A H
+ATOM 50 HB2 CYS2 4 9.167 7.538 11.085 1.00 0.00 A H
+ATOM 51 N PRO 5 9.561 9.108 13.563 1.00 3.96 A N
+ATOM 52 CA PRO 5 9.448 9.034 15.012 1.00 4.25 A C
+ATOM 53 C PRO 5 9.288 7.670 15.606 1.00 4.96 A C
+ATOM 54 O PRO 5 9.490 7.519 16.819 1.00 7.44 A O
+ATOM 55 CB PRO 5 8.230 9.957 15.345 1.00 5.11 A C
+ATOM 56 CG PRO 5 7.338 9.786 14.114 1.00 5.24 A C
+ATOM 57 CD PRO 5 8.366 9.804 12.958 1.00 5.20 A C
+ATOM 58 HA PRO 5 10.312 9.323 15.424 1.00 0.00 A H
+ATOM 59 HB1 PRO 5 7.762 9.653 16.175 1.00 0.00 A H
+ATOM 60 HB2 PRO 5 8.517 10.909 15.454 1.00 0.00 A H
+ATOM 61 HG1 PRO 5 6.842 8.918 14.144 1.00 0.00 A H
+ATOM 62 HG2 PRO 5 6.686 10.540 14.031 1.00 0.00 A H
+ATOM 63 HD1 PRO 5 8.023 9.304 12.163 1.00 0.00 A H
+ATOM 64 HD2 PRO 5 8.592 10.741 12.691 1.00 0.00 A H
+ATOM 65 N SER 6 8.875 6.686 14.796 1.00 4.83 A N
+ATOM 66 CA SER 6 8.673 5.314 15.279 1.00 4.45 A C
+ATOM 67 C SER 6 8.753 4.376 14.083 1.00 4.99 A C
+ATOM 68 O SER 6 8.726 4.858 12.923 1.00 4.61 A O
+ATOM 69 CB SER 6 7.340 5.121 15.996 1.00 5.05 A C
+ATOM 70 OG SER 6 6.274 5.220 15.031 1.00 6.39 A O
+ATOM 71 HN SER 6 8.699 6.892 13.833 1.00 0.00 A H
+ATOM 72 HA SER 6 9.386 5.114 15.951 1.00 0.00 A H
+ATOM 73 HB1 SER 6 7.319 4.220 16.429 1.00 0.00 A H
+ATOM 74 HB2 SER 6 7.228 5.829 16.694 1.00 0.00 A H
+ATOM 75 HG1 SER 6 5.395 5.095 15.491 1.00 0.00 A H
+ATOM 76 N ILE 7 8.881 3.075 14.358 1.00 4.94 A N
+ATOM 77 CA ILE 7 8.912 2.083 13.258 1.00 6.33 A C
+ATOM 78 C ILE 7 7.581 2.090 12.506 1.00 5.32 A C
+ATOM 79 O ILE 7 7.670 2.031 11.245 1.00 6.85 A O
+ATOM 80 CB ILE 7 9.207 0.677 13.924 1.00 8.43 A C
+ATOM 81 CG1 ILE 7 10.714 0.702 14.312 1.00 9.78 A C
+ATOM 82 CG2 ILE 7 8.811 -0.477 12.969 1.00 11.70 A C
+ATOM 83 CD ILE 7 11.185 -0.516 15.142 1.00 9.92 A C
+ATOM 84 HN ILE 7 8.956 2.770 15.307 1.00 0.00 A H
+ATOM 85 HA ILE 7 9.620 2.297 12.585 1.00 0.00 A H
+ATOM 86 HB ILE 7 8.659 0.511 14.744 1.00 0.00 A H
+ATOM 87 HG11 ILE 7 11.253 0.733 13.470 1.00 0.00 A H
+ATOM 88 HG12 ILE 7 10.885 1.529 14.847 1.00 0.00 A H
+ATOM 89 HG21 ILE 7 9.005 -1.354 13.408 1.00 0.00 A H
+ATOM 90 HG22 ILE 7 7.781 -0.398 12.761 1.00 0.00 A H
+ATOM 91 HG23 ILE 7 9.375 -0.385 12.083 1.00 0.00 A H
+ATOM 92 HD1 ILE 7 12.159 -0.422 15.348 1.00 0.00 A H
+ATOM 93 HD2 ILE 7 10.629 -0.545 16.037 1.00 0.00 A H
+ATOM 94 HD3 ILE 7 11.019 -1.389 14.576 1.00 0.00 A H
+ATOM 95 N VAL 8 6.458 2.162 13.159 1.00 5.02 A N
+ATOM 96 CA VAL 8 5.145 2.209 12.453 1.00 6.93 A C
+ATOM 97 C VAL 8 5.115 3.379 11.461 1.00 5.39 A C
+ATOM 98 O VAL 8 4.664 3.268 10.343 1.00 6.30 A O
+ATOM 99 CB VAL 8 3.995 2.354 13.478 1.00 9.64 A C
+ATOM 100 CG1 VAL 8 2.716 2.891 12.869 1.00 13.85 A C
+ATOM 101 CG2 VAL 8 3.758 1.032 14.208 1.00 11.97 A C
+ATOM 102 HN VAL 8 6.476 2.186 14.159 1.00 0.00 A H
+ATOM 103 HA VAL 8 5.023 1.355 11.947 1.00 0.00 A H
+ATOM 104 HB VAL 8 4.286 3.040 14.145 1.00 0.00 A H
+ATOM 105 HG11 VAL 8 2.014 2.962 13.577 1.00 0.00 A H
+ATOM 106 HG12 VAL 8 2.915 3.843 12.462 1.00 0.00 A H
+ATOM 107 HG13 VAL 8 2.401 2.226 12.115 1.00 0.00 A H
+ATOM 108 HG21 VAL 8 3.013 1.143 14.866 1.00 0.00 A H
+ATOM 109 HG22 VAL 8 3.503 0.299 13.495 1.00 0.00 A H
+ATOM 110 HG23 VAL 8 4.645 0.765 14.711 1.00 0.00 A H
+ATOM 111 N ALA 9 5.606 4.546 11.941 1.00 3.73 A N
+ATOM 112 CA ALA 9 5.598 5.767 11.082 1.00 3.56 A C
+ATOM 113 C ALA 9 6.441 5.527 9.850 1.00 4.13 A C
+ATOM 114 O ALA 9 6.052 5.933 8.744 1.00 4.36 A O
+ATOM 115 CB ALA 9 6.022 6.977 11.891 1.00 4.80 A C
+ATOM 116 HN ALA 9 5.974 4.590 12.870 1.00 0.00 A H
+ATOM 117 HA ALA 9 4.672 5.963 10.759 1.00 0.00 A H
+ATOM 118 HB1 ALA 9 6.013 7.788 11.307 1.00 0.00 A H
+ATOM 119 HB2 ALA 9 5.343 7.100 12.688 1.00 0.00 A H
+ATOM 120 HB3 ALA 9 6.996 6.808 12.258 1.00 0.00 A H
+ATOM 121 N ARG 10 7.647 4.909 10.005 1.00 3.73 A N
+ATOM 122 CA ARG 10 8.496 4.609 8.837 1.00 3.38 A C
+ATOM 123 C ARG 10 7.798 3.609 7.876 1.00 3.47 A C
+ATOM 124 O ARG 10 7.878 3.778 6.651 1.00 4.67 A O
+ATOM 125 CB ARG 10 9.847 4.020 9.305 1.00 3.95 A C
+ATOM 126 CG ARG 10 10.752 3.607 8.149 1.00 4.55 A C
+ATOM 127 CD ARG 10 11.226 4.699 7.244 1.00 5.89 A C
+ATOM 128 NE ARG 10 12.143 5.571 8.035 1.00 6.20 A N
+ATOM 129 CZ ARG 10 12.758 6.609 7.443 1.00 7.52 A C
+ATOM 130 NH1 ARG 10 12.539 6.932 6.158 1.00 10.68 A N
+ATOM 131 NH2 ARG 10 13.601 7.322 8.202 1.00 9.48 A N
+ATOM 132 HN ARG 10 7.959 4.656 10.921 1.00 0.00 A H
+ATOM 133 HA ARG 10 8.654 5.464 8.342 1.00 0.00 A H
+ATOM 134 HB1 ARG 10 10.323 4.710 9.851 1.00 0.00 A H
+ATOM 135 HB2 ARG 10 9.665 3.215 9.870 1.00 0.00 A H
+ATOM 136 HG1 ARG 10 11.560 3.165 8.539 1.00 0.00 A H
+ATOM 137 HG2 ARG 10 10.248 2.948 7.591 1.00 0.00 A H
+ATOM 138 HD1 ARG 10 11.715 4.308 6.464 1.00 0.00 A H
+ATOM 139 HD2 ARG 10 10.447 5.232 6.915 1.00 0.00 A H
+ATOM 140 HE ARG 10 12.300 5.383 9.005 1.00 0.00 A H
+ATOM 141 HH11 ARG 10 11.900 6.393 5.609 1.00 0.00 A H
+ATOM 142 HH12 ARG 10 13.015 7.711 5.750 1.00 0.00 A H
+ATOM 143 HH21 ARG 10 13.746 7.071 9.159 1.00 0.00 A H
+ATOM 144 HH22 ARG 10 14.085 8.105 7.811 1.00 0.00 A H
+ATOM 145 N SER 11 7.186 2.582 8.445 1.00 5.19 A N
+ATOM 146 CA SER 11 6.500 1.584 7.565 1.00 4.60 A C
+ATOM 147 C SER 11 5.382 2.313 6.773 1.00 4.84 A C
+ATOM 148 O SER 11 5.213 2.016 5.557 1.00 5.84 A O
+ATOM 149 CB SER 11 5.908 0.462 8.400 1.00 5.91 A C
+ATOM 150 OG SER 11 6.990 -0.272 9.012 1.00 8.38 A O
+ATOM 151 HN SER 11 7.182 2.475 9.439 1.00 0.00 A H
+ATOM 152 HA SER 11 7.160 1.182 6.930 1.00 0.00 A H
+ATOM 153 HB1 SER 11 5.316 0.845 9.109 1.00 0.00 A H
+ATOM 154 HB2 SER 11 5.374 -0.149 7.815 1.00 0.00 A H
+ATOM 155 HG1 SER 11 6.617 -1.016 9.567 1.00 0.00 A H
+ATOM 156 N ASN 12 4.648 3.182 7.446 1.00 3.54 A N
+ATOM 157 CA ASN 12 3.545 3.935 6.751 1.00 4.57 A C
+ATOM 158 C ASN 12 4.107 4.851 5.691 1.00 4.14 A C
+ATOM 159 O ASN 12 3.536 5.001 4.617 1.00 5.52 A O
+ATOM 160 CB ASN 12 2.663 4.677 7.748 1.00 6.42 A C
+ATOM 161 CG ASN 12 1.802 3.735 8.610 1.00 8.25 A C
+ATOM 162 OD1 ASN 12 1.567 2.613 8.165 1.00 12.72 A O
+ATOM 163 ND2 ASN 12 1.394 4.252 9.767 1.00 9.92 A N
+ATOM 164 HN ASN 12 4.825 3.339 8.417 1.00 0.00 A H
+ATOM 165 HA ASN 12 2.957 3.271 6.289 1.00 0.00 A H
+ATOM 166 HB1 ASN 12 3.250 5.215 8.353 1.00 0.00 A H
+ATOM 167 HB2 ASN 12 2.056 5.289 7.242 1.00 0.00 A H
+ATOM 168 HD21 ASN 12 1.651 5.186 10.016 1.00 0.00 A H
+ATOM 169 HD22 ASN 12 0.830 3.707 10.387 1.00 0.00 A H
+ATOM 170 N PHE 13 5.259 5.498 6.005 1.00 3.43 A N
+ATOM 171 CA PHE 13 5.929 6.358 5.055 1.00 3.49 A C
+ATOM 172 C PHE 13 6.304 5.578 3.799 1.00 3.40 A C
+ATOM 173 O PHE 13 6.136 6.072 2.653 1.00 4.07 A O
+ATOM 174 CB PHE 13 7.183 6.994 5.754 1.00 5.48 A C
+ATOM 175 CG PHE 13 7.884 8.006 4.883 1.00 5.57 A C
+ATOM 176 CD1 PHE 13 8.906 7.586 4.027 1.00 6.99 A C
+ATOM 177 CD2 PHE 13 7.532 9.373 4.983 1.00 6.52 A C
+ATOM 178 CE1 PHE 13 9.560 8.539 3.194 1.00 8.20 A C
+ATOM 179 CE2 PHE 13 8.176 10.281 4.145 1.00 6.34 A C
+ATOM 180 CZ PHE 13 9.141 9.845 3.292 1.00 6.84 A C
+ATOM 181 HN PHE 13 5.654 5.377 6.916 1.00 0.00 A H
+ATOM 182 HA PHE 13 5.319 7.094 4.762 1.00 0.00 A H
+ATOM 183 HB1 PHE 13 6.885 7.447 6.595 1.00 0.00 A H
+ATOM 184 HB2 PHE 13 7.828 6.264 5.979 1.00 0.00 A H
+ATOM 185 HD1 PHE 13 9.176 6.624 3.999 1.00 0.00 A H
+ATOM 186 HD2 PHE 13 6.840 9.679 5.637 1.00 0.00 A H
+ATOM 187 HE1 PHE 13 10.291 8.270 2.566 1.00 0.00 A H
+ATOM 188 HE2 PHE 13 7.929 11.250 4.171 1.00 0.00 A H
+ATOM 189 HZ PHE 13 9.575 10.520 2.696 1.00 0.00 A H
+ATOM 190 N ASN 14 6.900 4.390 3.989 1.00 3.64 A N
+ATOM 191 CA ASN 14 7.331 3.607 2.791 1.00 4.31 A C
+ATOM 192 C ASN 14 6.116 3.210 1.915 1.00 3.98 A C
+ATOM 193 O ASN 14 6.240 3.144 0.684 1.00 6.22 A O
+ATOM 194 CB ASN 14 8.145 2.404 3.240 1.00 5.81 A C
+ATOM 195 CG ASN 14 9.555 2.856 3.730 1.00 6.82 A C
+ATOM 196 OD1 ASN 14 10.013 3.895 3.323 1.00 9.43 A O
+ATOM 197 ND2 ASN 14 10.120 1.956 4.539 1.00 8.21 A N
+ATOM 198 HN ASN 14 7.052 4.037 4.912 1.00 0.00 A H
+ATOM 199 HA ASN 14 7.915 4.177 2.213 1.00 0.00 A H
+ATOM 200 HB1 ASN 14 7.668 1.944 3.988 1.00 0.00 A H
+ATOM 201 HB2 ASN 14 8.250 1.772 2.472 1.00 0.00 A H
+ATOM 202 HD21 ASN 14 9.635 1.110 4.762 1.00 0.00 A H
+ATOM 203 HD22 ASN 14 11.028 2.128 4.922 1.00 0.00 A H
+ATOM 204 N VAL 15 4.993 2.927 2.571 1.00 3.76 A N
+ATOM 205 CA VAL 15 3.782 2.599 1.742 1.00 3.98 A C
+ATOM 206 C VAL 15 3.296 3.871 1.004 1.00 3.80 A C
+ATOM 207 O VAL 15 2.947 3.817 -0.189 1.00 4.85 A O
+ATOM 208 CB VAL 15 2.698 1.953 2.608 1.00 4.71 A C
+ATOM 209 CG1 VAL 15 1.384 1.826 1.806 1.00 6.67 A C
+ATOM 210 CG2 VAL 15 3.174 0.533 3.005 1.00 6.26 A C
+ATOM 211 HN VAL 15 4.956 2.932 3.570 1.00 0.00 A H
+ATOM 212 HA VAL 15 4.019 1.925 1.042 1.00 0.00 A H
+ATOM 213 HB VAL 15 2.537 2.517 3.418 1.00 0.00 A H
+ATOM 214 HG11 VAL 15 0.683 1.403 2.380 1.00 0.00 A H
+ATOM 215 HG12 VAL 15 1.077 2.791 1.514 1.00 0.00 A H
+ATOM 216 HG13 VAL 15 1.567 1.225 0.959 1.00 0.00 A H
+ATOM 217 HG21 VAL 15 2.477 0.094 3.572 1.00 0.00 A H
+ATOM 218 HG22 VAL 15 3.326 -0.026 2.124 1.00 0.00 A H
+ATOM 219 HG23 VAL 15 4.075 0.622 3.545 1.00 0.00 A H
+ATOM 220 N CYS2 16 3.321 4.987 1.720 1.00 3.79 A N
+ATOM 221 CA CYS2 16 2.890 6.285 1.126 1.00 3.54 A C
+ATOM 222 C CYS2 16 3.687 6.597 -0.111 1.00 3.48 A C
+ATOM 223 O CYS2 16 3.200 7.147 -1.103 1.00 4.63 A O
+ATOM 224 CB CYS2 16 3.039 7.369 2.240 1.00 4.58 A C
+ATOM 225 SG CYS2 16 2.559 9.014 1.649 1.00 5.66 A S
+ATOM 226 HN CYS2 16 3.633 4.958 2.670 1.00 0.00 A H
+ATOM 227 HA CYS2 16 1.937 6.253 0.824 1.00 0.00 A H
+ATOM 228 HB1 CYS2 16 2.456 7.120 3.013 1.00 0.00 A H
+ATOM 229 HB2 CYS2 16 3.993 7.398 2.538 1.00 0.00 A H
+ATOM 230 N ARG 17 4.997 6.227 -0.100 1.00 3.99 A N
+ATOM 231 CA ARG 17 5.895 6.489 -1.213 1.00 3.83 A C
+ATOM 232 C ARG 17 5.738 5.560 -2.409 1.00 3.79 A C
+ATOM 233 O ARG 17 6.228 5.901 -3.507 1.00 5.39 A O
+ATOM 234 CB ARG 17 7.370 6.507 -0.731 1.00 4.11 A C
+ATOM 235 CG ARG 17 7.717 7.687 0.206 1.00 4.69 A C
+ATOM 236 CD ARG 17 7.949 8.947 -0.615 1.00 5.10 A C
+ATOM 237 NE ARG 17 9.212 8.856 -1.337 1.00 4.71 A N
+ATOM 238 CZ ARG 17 9.537 9.533 -2.431 1.00 5.28 A C
+ATOM 239 NH1 ARG 17 8.659 10.350 -3.032 1.00 6.67 A N
+ATOM 240 NH2 ARG 17 10.793 9.491 -2.899 1.00 6.41 A N
+ATOM 241 HN ARG 17 5.356 5.756 0.706 1.00 0.00 A H
+ATOM 242 HA ARG 17 5.629 7.392 -1.550 1.00 0.00 A H
+ATOM 243 HB1 ARG 17 7.550 5.654 -0.241 1.00 0.00 A H
+ATOM 244 HB2 ARG 17 7.962 6.561 -1.535 1.00 0.00 A H
+ATOM 245 HG1 ARG 17 6.960 7.840 0.842 1.00 0.00 A H
+ATOM 246 HG2 ARG 17 8.546 7.469 0.721 1.00 0.00 A H
+ATOM 247 HD1 ARG 17 7.202 9.056 -1.270 1.00 0.00 A H
+ATOM 248 HD2 ARG 17 7.975 9.738 -0.004 1.00 0.00 A H
+ATOM 249 HE ARG 17 9.897 8.225 -0.974 1.00 0.00 A H
+ATOM 250 HH11 ARG 17 7.739 10.458 -2.656 1.00 0.00 A H
+ATOM 251 HH12 ARG 17 8.925 10.851 -3.856 1.00 0.00 A H
+ATOM 252 HH21 ARG 17 11.486 8.949 -2.423 1.00 0.00 A H
+ATOM 253 HH22 ARG 17 11.037 10.002 -3.724 1.00 0.00 A H
+ATOM 254 N LEU 18 5.051 4.411 -2.204 1.00 4.70 A N
+ATOM 255 CA LEU 18 4.933 3.431 -3.326 1.00 5.46 A C
+ATOM 256 C LEU 18 4.397 4.014 -4.620 1.00 5.13 A C
+ATOM 257 O LEU 18 4.988 3.755 -5.687 1.00 5.55 A O
+ATOM 258 CB LEU 18 4.196 2.184 -2.863 1.00 6.47 A C
+ATOM 259 CG LEU 18 4.960 1.178 -1.991 1.00 7.43 A C
+ATOM 260 CD1 LEU 18 3.907 0.097 -1.634 1.00 8.70 A C
+ATOM 261 CD2 LEU 18 6.129 0.606 -2.768 1.00 9.39 A C
+ATOM 262 HN LEU 18 4.630 4.222 -1.317 1.00 0.00 A H
+ATOM 263 HA LEU 18 5.863 3.161 -3.574 1.00 0.00 A H
+ATOM 264 HB1 LEU 18 3.399 2.486 -2.340 1.00 0.00 A H
+ATOM 265 HB2 LEU 18 3.892 1.697 -3.682 1.00 0.00 A H
+ATOM 266 HG LEU 18 5.353 1.584 -1.166 1.00 0.00 A H
+ATOM 267 HD11 LEU 18 4.330 -0.604 -1.060 1.00 0.00 A H
+ATOM 268 HD12 LEU 18 3.117 0.561 -1.113 1.00 0.00 A H
+ATOM 269 HD13 LEU 18 3.555 -0.334 -2.529 1.00 0.00 A H
+ATOM 270 HD21 LEU 18 6.622 -0.048 -2.195 1.00 0.00 A H
+ATOM 271 HD22 LEU 18 5.754 0.122 -3.626 1.00 0.00 A H
+ATOM 272 HD23 LEU 18 6.768 1.399 -3.041 1.00 0.00 A H
+ATOM 273 N PRO 19 3.329 4.795 -4.543 1.00 4.28 A N
+ATOM 274 CA PRO 19 2.792 5.376 -5.797 1.00 5.38 A C
+ATOM 275 C PRO 19 3.573 6.540 -6.322 1.00 6.30 A C
+ATOM 276 O PRO 19 3.260 7.045 -7.422 1.00 9.62 A O
+ATOM 277 CB PRO 19 1.358 5.766 -5.472 1.00 5.87 A C
+ATOM 278 CG PRO 19 1.223 5.694 -3.993 1.00 6.47 A C
+ATOM 279 CD PRO 19 2.421 4.941 -3.408 1.00 6.45 A C
+ATOM 280 HA PRO 19 2.853 4.706 -6.537 1.00 0.00 A H
+ATOM 281 HB1 PRO 19 1.173 6.696 -5.791 1.00 0.00 A H
+ATOM 282 HB2 PRO 19 0.720 5.131 -5.908 1.00 0.00 A H
+ATOM 283 HG1 PRO 19 1.194 6.619 -3.615 1.00 0.00 A H
+ATOM 284 HG2 PRO 19 0.379 5.212 -3.758 1.00 0.00 A H
+ATOM 285 HD1 PRO 19 2.850 5.468 -2.674 1.00 0.00 A H
+ATOM 286 HD2 PRO 19 2.143 4.047 -3.057 1.00 0.00 A H
+ATOM 287 N GLY 20 4.565 7.047 -5.559 1.00 4.94 A N
+ATOM 288 CA GLY 20 5.366 8.191 -6.018 1.00 5.39 A C
+ATOM 289 C GLY 20 5.007 9.481 -5.280 1.00 5.03 A C
+ATOM 290 O GLY 20 5.535 10.510 -5.730 1.00 7.34 A O
+ATOM 291 HN GLY 20 4.758 6.638 -4.667 1.00 0.00 A H
+ATOM 292 HA1 GLY 20 6.333 7.990 -5.863 1.00 0.00 A H
+ATOM 293 HA2 GLY 20 5.206 8.324 -6.996 1.00 0.00 A H
+ATOM 294 N THR 21 4.181 9.438 -4.262 1.00 4.10 A N
+ATOM 295 CA THR 21 3.767 10.609 -3.513 1.00 3.94 A C
+ATOM 296 C THR 21 5.017 11.397 -3.042 1.00 3.96 A C
+ATOM 297 O THR 21 5.947 10.757 -2.523 1.00 5.82 A O
+ATOM 298 CB THR 21 2.992 10.188 -2.225 1.00 4.13 A C
+ATOM 299 OG1 THR 21 2.051 9.144 -2.623 1.00 5.45 A O
+ATOM 300 CG2 THR 21 2.260 11.349 -1.551 1.00 5.41 A C
+ATOM 301 HN THR 21 3.816 8.548 -3.987 1.00 0.00 A H
+ATOM 302 HA THR 21 3.187 11.164 -4.110 1.00 0.00 A H
+ATOM 303 HB THR 21 3.644 9.861 -1.541 1.00 0.00 A H
+ATOM 304 HG1 THR 21 1.530 8.842 -1.825 1.00 0.00 A H
+ATOM 305 HG21 THR 21 1.786 11.016 -0.736 1.00 0.00 A H
+ATOM 306 HG22 THR 21 2.971 12.079 -1.281 1.00 0.00 A H
+ATOM 307 HG23 THR 21 1.564 11.747 -2.236 1.00 0.00 A H
+ATOM 308 N PRO 22 4.971 12.703 -3.176 1.00 5.04 A N
+ATOM 309 CA PRO 22 6.143 13.513 -2.696 1.00 4.69 A C
+ATOM 310 C PRO 22 6.400 13.233 -1.225 1.00 4.19 A C
+ATOM 311 O PRO 22 5.485 13.061 -0.382 1.00 4.47 A O
+ATOM 312 CB PRO 22 5.703 14.969 -2.920 1.00 7.12 A C
+ATOM 313 CG PRO 22 4.676 14.893 -3.996 1.00 7.03 A C
+ATOM 314 CD PRO 22 3.964 13.567 -3.811 1.00 4.90 A C
+ATOM 315 HA PRO 22 6.995 13.300 -3.174 1.00 0.00 A H
+ATOM 316 HB1 PRO 22 5.310 15.351 -2.084 1.00 0.00 A H
+ATOM 317 HB2 PRO 22 6.478 15.531 -3.211 1.00 0.00 A H
+ATOM 318 HG1 PRO 22 4.027 15.649 -3.910 1.00 0.00 A H
+ATOM 319 HG2 PRO 22 5.113 14.929 -4.895 1.00 0.00 A H
+ATOM 320 HD1 PRO 22 3.164 13.673 -3.220 1.00 0.00 A H
+ATOM 321 HD2 PRO 22 3.679 13.191 -4.693 1.00 0.00 A H
+ATOM 322 N GLU 23 7.728 13.297 -0.921 1.00 5.16 A N
+ATOM 323 CA GLU 23 8.114 13.103 0.500 1.00 5.31 A C
+ATOM 324 C GLU 23 7.427 14.073 1.410 1.00 4.11 A C
+ATOM 325 O GLU 23 7.036 13.682 2.540 1.00 5.11 A O
+ATOM 326 CB GLU 23 9.648 13.285 0.660 1.00 6.16 A C
+ATOM 327 CG GLU 23 10.440 12.093 0.063 1.00 7.48 A C
+ATOM 328 CD GLU 23 11.941 12.170 0.391 1.00 9.40 A C
+ATOM 329 OE1 GLU 23 12.416 13.225 0.681 1.00 10.40 A O
+ATOM 330 OE2 GLU 23 12.539 11.070 0.292 1.00 13.32 A O
+ATOM 331 HN GLU 23 8.415 13.468 -1.627 1.00 0.00 A H
+ATOM 332 HA GLU 23 7.836 12.177 0.754 1.00 0.00 A H
+ATOM 333 HB1 GLU 23 9.924 14.124 0.191 1.00 0.00 A H
+ATOM 334 HB2 GLU 23 9.864 13.361 1.633 1.00 0.00 A H
+ATOM 335 HG1 GLU 23 10.072 11.242 0.437 1.00 0.00 A H
+ATOM 336 HG2 GLU 23 10.327 12.097 -0.931 1.00 0.00 A H
+ATOM 337 N ALA 24 7.212 15.334 0.966 1.00 4.56 A N
+ATOM 338 CA ALA 24 6.614 16.317 1.913 1.00 4.49 A C
+ATOM 339 C ALA 24 5.212 15.936 2.350 1.00 4.10 A C
+ATOM 340 O ALA 24 4.782 16.166 3.495 1.00 5.64 A O
+ATOM 341 CB ALA 24 6.605 17.695 1.246 1.00 5.80 A C
+ATOM 342 HN ALA 24 7.447 15.598 0.031 1.00 0.00 A H
+ATOM 343 HA ALA 24 7.174 16.328 2.742 1.00 0.00 A H
+ATOM 344 HB1 ALA 24 6.206 18.365 1.871 1.00 0.00 A H
+ATOM 345 HB2 ALA 24 7.599 17.962 1.019 1.00 0.00 A H
+ATOM 346 HB3 ALA 24 6.028 17.635 0.366 1.00 0.00 A H
+ATOM 347 N ILE 25 4.445 15.318 1.405 1.00 4.37 A N
+ATOM 348 CA ILE 25 3.074 14.894 1.756 1.00 5.44 A C
+ATOM 349 C ILE 25 3.085 13.643 2.645 1.00 4.32 A C
+ATOM 350 O ILE 25 2.315 13.523 3.578 1.00 4.72 A O
+ATOM 351 CB ILE 25 2.204 14.637 0.462 1.00 6.42 A C
+ATOM 352 CG1 ILE 25 1.815 16.048 -0.129 1.00 7.50 A C
+ATOM 353 CG2 ILE 25 0.903 13.864 0.811 1.00 7.65 A C
+ATOM 354 CD ILE 25 0.756 16.761 0.757 1.00 7.80 A C
+ATOM 355 HN ILE 25 4.806 15.154 0.487 1.00 0.00 A H
+ATOM 356 HA ILE 25 2.657 15.642 2.273 1.00 0.00 A H
+ATOM 357 HB ILE 25 2.726 14.090 -0.193 1.00 0.00 A H
+ATOM 358 HG11 ILE 25 2.635 16.618 -0.178 1.00 0.00 A H
+ATOM 359 HG12 ILE 25 1.440 15.924 -1.048 1.00 0.00 A H
+ATOM 360 HG21 ILE 25 0.371 13.714 -0.022 1.00 0.00 A H
+ATOM 361 HG22 ILE 25 1.170 12.939 1.240 1.00 0.00 A H
+ATOM 362 HG23 ILE 25 0.346 14.441 1.495 1.00 0.00 A H
+ATOM 363 HD1 ILE 25 0.531 17.650 0.357 1.00 0.00 A H
+ATOM 364 HD2 ILE 25 -0.106 16.156 0.798 1.00 0.00 A H
+ATOM 365 HD3 ILE 25 1.162 16.892 1.721 1.00 0.00 A H
+ATOM 366 N CYS2 26 4.032 12.764 2.313 1.00 3.92 A N
+ATOM 367 CA CYS2 26 4.180 11.549 3.187 1.00 4.37 A C
+ATOM 368 C CYS2 26 4.632 11.944 4.596 1.00 3.95 A C
+ATOM 369 O CYS2 26 4.227 11.252 5.547 1.00 4.74 A O
+ATOM 370 CB CYS2 26 5.038 10.518 2.539 1.00 4.63 A C
+ATOM 371 SG CYS2 26 4.349 9.794 1.022 1.00 5.61 A S
+ATOM 372 HN CYS2 26 4.619 12.907 1.516 1.00 0.00 A H
+ATOM 373 HA CYS2 26 3.285 11.116 3.298 1.00 0.00 A H
+ATOM 374 HB1 CYS2 26 5.914 10.942 2.311 1.00 0.00 A H
+ATOM 375 HB2 CYS2 26 5.186 9.779 3.196 1.00 0.00 A H
+ATOM 376 N ALA 27 5.408 13.012 4.694 1.00 3.89 A N
+ATOM 377 CA ALA 27 5.879 13.502 6.026 1.00 4.43 A C
+ATOM 378 C ALA 27 4.696 13.908 6.882 1.00 4.26 A C
+ATOM 379 O ALA 27 4.528 13.422 8.025 1.00 5.44 A O
+ATOM 380 CB ALA 27 6.880 14.615 5.830 1.00 5.36 A C
+ATOM 381 HN ALA 27 5.683 13.498 3.865 1.00 0.00 A H
+ATOM 382 HA ALA 27 6.347 12.769 6.519 1.00 0.00 A H
+ATOM 383 HB1 ALA 27 7.194 14.942 6.721 1.00 0.00 A H
+ATOM 384 HB2 ALA 27 7.694 14.237 5.277 1.00 0.00 A H
+ATOM 385 HB3 ALA 27 6.409 15.398 5.305 1.00 0.00 A H
+ATOM 386 N THR 28 3.827 14.802 6.358 1.00 4.53 A N
+ATOM 387 CA THR 28 2.691 15.221 7.194 1.00 5.08 A C
+ATOM 388 C THR 28 1.672 14.132 7.434 1.00 4.62 A C
+ATOM 389 O THR 28 0.947 14.112 8.468 1.00 7.80 A O
+ATOM 390 CB THR 28 1.986 16.520 6.614 1.00 6.03 A C
+ATOM 391 OG1 THR 28 1.664 16.221 5.230 1.00 7.19 A O
+ATOM 392 CG2 THR 28 2.914 17.739 6.700 1.00 7.34 A C
+ATOM 393 HN THR 28 3.952 15.165 5.435 1.00 0.00 A H
+ATOM 394 HA THR 28 3.090 15.437 8.085 1.00 0.00 A H
+ATOM 395 HB THR 28 1.167 16.747 7.141 1.00 0.00 A H
+ATOM 396 HG1 THR 28 1.215 17.011 4.814 1.00 0.00 A H
+ATOM 397 HG21 THR 28 2.446 18.541 6.329 1.00 0.00 A H
+ATOM 398 HG22 THR 28 3.159 17.901 7.712 1.00 0.00 A H
+ATOM 399 HG23 THR 28 3.783 17.537 6.138 1.00 0.00 A H
+ATOM 400 N TYR 29 1.621 13.190 6.511 1.00 5.01 A N
+ATOM 401 CA TYR 29 0.715 12.045 6.657 1.00 6.60 A C
+ATOM 402 C TYR 29 1.125 11.125 7.815 1.00 4.92 A C
+ATOM 403 O TYR 29 0.286 10.632 8.545 1.00 7.13 A O
+ATOM 404 CB TYR 29 0.755 11.229 5.322 1.00 9.66 A C
+ATOM 405 CG TYR 29 -0.203 10.044 5.354 1.00 11.56 A C
+ATOM 406 CD1 TYR 29 -1.547 10.337 5.645 1.00 12.85 A C
+ATOM 407 CD2 TYR 29 0.193 8.750 5.100 1.00 14.44 A C
+ATOM 408 CE1 TYR 29 -2.496 9.329 5.673 1.00 16.61 A C
+ATOM 409 CE2 TYR 29 -0.801 7.705 5.156 1.00 17.11 A C
+ATOM 410 CZ TYR 29 -2.079 8.031 5.430 1.00 19.99 A C
+ATOM 411 OH TYR 29 -3.097 7.057 5.458 1.00 28.98 A O
+ATOM 412 HN TYR 29 2.206 13.257 5.703 1.00 0.00 A H
+ATOM 413 HA TYR 29 -0.203 12.388 6.857 1.00 0.00 A H
+ATOM 414 HB1 TYR 29 0.499 11.832 4.566 1.00 0.00 A H
+ATOM 415 HB2 TYR 29 1.685 10.890 5.178 1.00 0.00 A H
+ATOM 416 HD1 TYR 29 -1.820 11.281 5.833 1.00 0.00 A H
+ATOM 417 HD2 TYR 29 1.146 8.539 4.882 1.00 0.00 A H
+ATOM 418 HE1 TYR 29 -3.456 9.533 5.864 1.00 0.00 A H
+ATOM 419 HE2 TYR 29 -0.545 6.752 4.994 1.00 0.00 A H
+ATOM 420 HH TYR 29 -2.703 6.157 5.273 1.00 0.00 A H
+ATOM 421 N THR 30 2.470 10.984 7.995 1.00 5.31 A N
+ATOM 422 CA THR 30 2.986 9.994 8.950 1.00 5.70 A C
+ATOM 423 C THR 30 3.609 10.505 10.230 1.00 6.28 A C
+ATOM 424 O THR 30 3.766 9.715 11.186 1.00 8.77 A O
+ATOM 425 CB THR 30 4.076 9.103 8.225 1.00 6.55 A C
+ATOM 426 OG1 THR 30 5.125 10.027 7.824 1.00 6.57 A O
+ATOM 427 CG2 THR 30 3.493 8.324 7.035 1.00 7.29 A C
+ATOM 428 HN THR 30 3.106 11.555 7.476 1.00 0.00 A H
+ATOM 429 HA THR 30 2.164 9.501 9.237 1.00 0.00 A H
+ATOM 430 HB THR 30 4.432 8.393 8.833 1.00 0.00 A H
+ATOM 431 HG1 THR 30 5.852 9.524 7.356 1.00 0.00 A H
+ATOM 432 HG21 THR 30 4.214 7.777 6.609 1.00 0.00 A H
+ATOM 433 HG22 THR 30 2.727 7.694 7.392 1.00 0.00 A H
+ATOM 434 HG23 THR 30 3.108 9.016 6.340 1.00 0.00 A H
+ATOM 435 N GLY 31 3.984 11.764 10.241 1.00 4.99 A N
+ATOM 436 CA GLY 31 4.769 12.336 11.360 1.00 5.50 A C
+ATOM 437 C GLY 31 6.255 12.243 11.106 1.00 4.19 A C
+ATOM 438 O GLY 31 7.037 12.750 11.954 1.00 6.12 A O
+ATOM 439 HN GLY 31 3.733 12.353 9.473 1.00 0.00 A H
+ATOM 440 HA1 GLY 31 4.519 13.298 11.473 1.00 0.00 A H
+ATOM 441 HA2 GLY 31 4.552 11.835 12.198 1.00 0.00 A H
+ATOM 442 N CYS2 32 6.710 11.631 9.992 1.00 4.30 A N
+ATOM 443 CA CYS2 32 8.140 11.694 9.635 1.00 4.89 A C
+ATOM 444 C CYS2 32 8.500 13.141 9.206 1.00 5.50 A C
+ATOM 445 O CYS2 32 7.581 13.949 8.944 1.00 5.82 A O
+ATOM 446 CB CYS2 32 8.504 10.686 8.530 1.00 4.66 A C
+ATOM 447 SG CYS2 32 8.048 8.987 8.881 1.00 5.33 A S
+ATOM 448 HN CYS2 32 6.073 11.131 9.405 1.00 0.00 A H
+ATOM 449 HA CYS2 32 8.676 11.442 10.441 1.00 0.00 A H
+ATOM 450 HB1 CYS2 32 8.040 10.965 7.689 1.00 0.00 A H
+ATOM 451 HB2 CYS2 32 9.494 10.720 8.392 1.00 0.00 A H
+ATOM 452 N ILE 33 9.793 13.410 9.173 1.00 6.02 A N
+ATOM 453 CA ILE 33 10.280 14.760 8.823 1.00 5.24 A C
+ATOM 454 C ILE 33 11.346 14.658 7.743 1.00 5.16 A C
+ATOM 455 O ILE 33 11.971 13.583 7.552 1.00 7.19 A O
+ATOM 456 CB ILE 33 10.790 15.535 10.085 1.00 5.49 A C
+ATOM 457 CG1 ILE 33 12.059 14.803 10.671 1.00 6.85 A C
+ATOM 458 CG2 ILE 33 9.684 15.686 11.138 1.00 6.45 A C
+ATOM 459 CD ILE 33 12.733 15.676 11.781 1.00 8.94 A C
+ATOM 460 HN ILE 33 10.452 12.689 9.388 1.00 0.00 A H
+ATOM 461 HA ILE 33 9.516 15.293 8.459 1.00 0.00 A H
+ATOM 462 HB ILE 33 11.051 16.462 9.814 1.00 0.00 A H
+ATOM 463 HG11 ILE 33 11.781 13.927 11.065 1.00 0.00 A H
+ATOM 464 HG12 ILE 33 12.716 14.643 9.934 1.00 0.00 A H
+ATOM 465 HG21 ILE 33 10.042 16.184 11.928 1.00 0.00 A H
+ATOM 466 HG22 ILE 33 8.884 16.221 10.707 1.00 0.00 A H
+ATOM 467 HG23 ILE 33 9.369 14.724 11.431 1.00 0.00 A H
+ATOM 468 HD1 ILE 33 13.534 15.198 12.141 1.00 0.00 A H
+ATOM 469 HD2 ILE 33 13.024 16.594 11.352 1.00 0.00 A H
+ATOM 470 HD3 ILE 33 12.032 15.835 12.552 1.00 0.00 A H
+ATOM 471 N ILE 34 11.490 15.773 7.038 1.00 5.52 A N
+ATOM 472 CA ILE 34 12.552 15.877 6.036 1.00 6.82 A C
+ATOM 473 C ILE 34 13.590 16.917 6.560 1.00 6.92 A C
+ATOM 474 O ILE 34 13.168 18.006 6.945 1.00 9.22 A O
+ATOM 475 CB ILE 34 11.987 16.360 4.681 1.00 8.11 A C
+ATOM 476 CG1 ILE 34 10.914 15.338 4.163 1.00 9.59 A C
+ATOM 477 CG2 ILE 34 13.131 16.517 3.629 1.00 9.73 A C
+ATOM 478 CD ILE 34 10.151 16.024 2.938 1.00 13.41 A C
+ATOM 479 HN ILE 34 10.872 16.544 7.192 1.00 0.00 A H
+ATOM 480 HA ILE 34 12.972 14.981 5.894 1.00 0.00 A H
+ATOM 481 HB ILE 34 11.558 17.254 4.812 1.00 0.00 A H
+ATOM 482 HG11 ILE 34 11.362 14.497 3.859 1.00 0.00 A H
+ATOM 483 HG12 ILE 34 10.265 15.125 4.893 1.00 0.00 A H
+ATOM 484 HG21 ILE 34 12.745 16.830 2.761 1.00 0.00 A H
+ATOM 485 HG22 ILE 34 13.823 17.225 3.992 1.00 0.00 A H
+ATOM 486 HG23 ILE 34 13.596 15.580 3.500 1.00 0.00 A H
+ATOM 487 HD1 ILE 34 9.458 15.396 2.584 1.00 0.00 A H
+ATOM 488 HD2 ILE 34 9.693 16.908 3.284 1.00 0.00 A H
+ATOM 489 HD3 ILE 34 10.857 16.243 2.186 1.00 0.00 A H
+ATOM 490 N ILE 35 14.856 16.493 6.536 1.00 7.06 A N
+ATOM 491 CA ILE 35 15.930 17.454 6.941 1.00 7.52 A C
+ATOM 492 C ILE 35 16.913 17.550 5.819 1.00 6.63 A C
+ATOM 493 O ILE 35 17.097 16.660 4.970 1.00 7.90 A O
+ATOM 494 CB ILE 35 16.622 16.995 8.285 1.00 8.07 A C
+ATOM 495 CG1 ILE 35 17.360 15.651 8.067 1.00 9.41 A C
+ATOM 496 CG2 ILE 35 15.592 16.974 9.434 1.00 9.46 A C
+ATOM 497 CD ILE 35 18.298 15.206 9.219 1.00 9.85 A C
+ATOM 498 HN ILE 35 15.080 15.560 6.255 1.00 0.00 A H
+ATOM 499 HA ILE 35 15.537 18.356 7.118 1.00 0.00 A H
+ATOM 500 HB ILE 35 17.323 17.653 8.560 1.00 0.00 A H
+ATOM 501 HG11 ILE 35 16.670 14.938 7.940 1.00 0.00 A H
+ATOM 502 HG12 ILE 35 17.911 15.734 7.237 1.00 0.00 A H
+ATOM 503 HG21 ILE 35 16.041 16.682 10.279 1.00 0.00 A H
+ATOM 504 HG22 ILE 35 15.202 17.947 9.550 1.00 0.00 A H
+ATOM 505 HG23 ILE 35 14.825 16.297 9.181 1.00 0.00 A H
+ATOM 506 HD1 ILE 35 18.724 14.333 8.983 1.00 0.00 A H
+ATOM 507 HD2 ILE 35 19.039 15.945 9.350 1.00 0.00 A H
+ATOM 508 HD3 ILE 35 17.722 15.101 10.096 1.00 0.00 A H
+ATOM 509 N PRO 36 17.664 18.669 5.806 1.00 8.07 A N
+ATOM 510 CA PRO 36 18.635 18.861 4.738 1.00 8.78 A C
+ATOM 511 C PRO 36 19.925 18.042 4.949 1.00 8.31 A C
+ATOM 512 O PRO 36 20.593 17.742 3.945 1.00 9.09 A O
+ATOM 513 CB PRO 36 18.945 20.364 4.783 1.00 9.67 A C
+ATOM 514 CG PRO 36 18.238 20.937 5.908 1.00 10.15 A C
+ATOM 515 CD PRO 36 17.371 19.900 6.596 1.00 9.53 A C
+ATOM 516 HA PRO 36 18.272 18.552 3.859 1.00 0.00 A H
+ATOM 517 HB1 PRO 36 19.929 20.504 4.895 1.00 0.00 A H
+ATOM 518 HB2 PRO 36 18.641 20.798 3.935 1.00 0.00 A H
+ATOM 519 HG1 PRO 36 18.903 21.293 6.564 1.00 0.00 A H
+ATOM 520 HG2 PRO 36 17.658 21.684 5.583 1.00 0.00 A H
+ATOM 521 HD1 PRO 36 17.633 19.787 7.554 1.00 0.00 A H
+ATOM 522 HD2 PRO 36 16.403 20.144 6.542 1.00 0.00 A H
+ATOM 523 N GLY 37 20.172 17.730 6.217 1.00 8.48 A N
+ATOM 524 CA GLY 37 21.452 16.969 6.513 1.00 9.20 A C
+ATOM 525 C GLY 37 21.143 15.478 6.427 1.00 10.41 A C
+ATOM 526 O GLY 37 20.138 15.023 5.878 1.00 12.06 A O
+ATOM 527 HN GLY 37 19.539 17.986 6.948 1.00 0.00 A H
+ATOM 528 HA1 GLY 37 22.153 17.210 5.842 1.00 0.00 A H
+ATOM 529 HA2 GLY 37 21.777 17.196 7.431 1.00 0.00 A H
+ATOM 530 N ALA 38 22.055 14.701 7.032 1.00 9.24 A N
+ATOM 531 CA ALA 38 22.019 13.242 7.020 1.00 9.24 A C
+ATOM 532 C ALA 38 21.944 12.628 8.396 1.00 9.60 A C
+ATOM 533 O ALA 38 21.869 11.387 8.435 1.00 13.65 A O
+ATOM 534 CB ALA 38 23.246 12.697 6.275 1.00 10.43 A C
+ATOM 535 HN ALA 38 22.804 15.149 7.520 1.00 0.00 A H
+ATOM 536 HA ALA 38 21.177 12.983 6.547 1.00 0.00 A H
+ATOM 537 HB1 ALA 38 23.216 11.697 6.270 1.00 0.00 A H
+ATOM 538 HB2 ALA 38 23.226 13.063 5.287 1.00 0.00 A H
+ATOM 539 HB3 ALA 38 24.113 13.029 6.774 1.00 0.00 A H
+ATOM 540 N THR 39 21.894 13.435 9.436 1.00 8.70 A N
+ATOM 541 CA THR 39 21.936 12.911 10.809 1.00 9.46 A C
+ATOM 542 C THR 39 20.615 13.191 11.521 1.00 8.32 A C
+ATOM 543 O THR 39 20.357 14.317 11.948 1.00 9.89 A O
+ATOM 544 CB THR 39 23.131 13.601 11.593 1.00 10.72 A C
+ATOM 545 OG1 THR 39 24.284 13.401 10.709 1.00 11.66 A O
+ATOM 546 CG2 THR 39 23.340 12.935 12.962 1.00 11.81 A C
+ATOM 547 HN THR 39 21.826 14.422 9.289 1.00 0.00 A H
+ATOM 548 HA THR 39 22.079 11.922 10.782 1.00 0.00 A H
+ATOM 549 HB THR 39 22.968 14.568 11.791 1.00 0.00 A H
+ATOM 550 HG1 THR 39 25.098 13.808 11.124 1.00 0.00 A H
+ATOM 551 HG21 THR 39 24.096 13.384 13.439 1.00 0.00 A H
+ATOM 552 HG22 THR 39 22.452 13.035 13.520 1.00 0.00 A H
+ATOM 553 HG23 THR 39 23.565 11.917 12.807 1.00 0.00 A H
+ATOM 554 N CYS2 40 19.827 12.110 11.642 1.00 7.64 A N
+ATOM 555 CA CYS2 40 18.504 12.312 12.298 1.00 8.05 A C
+ATOM 556 C CYS2 40 18.684 12.451 13.784 1.00 7.63 A C
+ATOM 557 O CYS2 40 19.533 11.718 14.362 1.00 9.64 A O
+ATOM 558 CB CYS2 40 17.582 11.117 11.996 1.00 7.80 A C
+ATOM 559 SG CYS2 40 17.199 10.929 10.237 1.00 7.30 A S
+ATOM 560 HN CYS2 40 20.114 11.212 11.308 1.00 0.00 A H
+ATOM 561 HA CYS2 40 18.088 13.147 11.939 1.00 0.00 A H
+ATOM 562 HB1 CYS2 40 18.032 10.282 12.313 1.00 0.00 A H
+ATOM 563 HB2 CYS2 40 16.725 11.244 12.495 1.00 0.00 A H
+ATOM 564 N PRO 41 17.880 13.266 14.426 1.00 8.00 A N
+ATOM 565 CA PRO 41 17.924 13.421 15.877 1.00 8.96 A C
+ATOM 566 C PRO 41 17.392 12.206 16.594 1.00 9.06 A C
+ATOM 567 O PRO 41 16.652 11.368 16.033 1.00 8.82 A O
+ATOM 568 CB PRO 41 17.076 14.658 16.145 1.00 10.39 A C
+ATOM 569 CG PRO 41 16.098 14.689 14.997 1.00 10.99 A C
+ATOM 570 CD PRO 41 16.859 14.150 13.779 1.00 10.49 A C
+ATOM 571 HA PRO 41 18.859 13.521 16.218 1.00 0.00 A H
+ATOM 572 HB1 PRO 41 16.596 14.577 17.018 1.00 0.00 A H
+ATOM 573 HB2 PRO 41 17.642 15.482 16.151 1.00 0.00 A H
+ATOM 574 HG1 PRO 41 15.308 14.109 15.198 1.00 0.00 A H
+ATOM 575 HG2 PRO 41 15.790 15.625 14.828 1.00 0.00 A H
+ATOM 576 HD1 PRO 41 16.257 13.629 13.174 1.00 0.00 A H
+ATOM 577 HD2 PRO 41 17.291 14.889 13.263 1.00 0.00 A H
+ATOM 578 N GLY 42 17.728 12.124 17.884 1.00 7.55 A N
+ATOM 579 CA GLY 42 17.334 10.956 18.691 1.00 8.00 A C
+ATOM 580 C GLY 42 15.875 10.688 18.871 1.00 7.22 A C
+ATOM 581 O GLY 42 15.434 9.550 19.166 1.00 8.41 A O
+ATOM 582 HN GLY 42 18.253 12.863 18.307 1.00 0.00 A H
+ATOM 583 HA1 GLY 42 17.734 10.148 18.259 1.00 0.00 A H
+ATOM 584 HA2 GLY 42 17.729 11.077 19.602 1.00 0.00 A H
+ATOM 585 N ASP 43 15.036 11.747 18.715 1.00 5.54 A N
+ATOM 586 CA ASP 43 13.564 11.573 18.836 1.00 5.85 A C
+ATOM 587 C ASP 43 12.936 11.227 17.470 1.00 5.87 A C
+ATOM 588 O ASP 43 11.720 11.040 17.428 1.00 7.29 A O
+ATOM 589 CB ASP 43 12.933 12.737 19.580 1.00 6.72 A C
+ATOM 590 CG ASP 43 13.140 14.094 18.958 1.00 8.59 A C
+ATOM 591 OD1 ASP 43 14.109 14.303 18.212 1.00 9.59 A O
+ATOM 592 OD2 ASP 43 12.267 14.963 19.265 1.00 11.45 A O
+ATOM 593 HN ASP 43 15.413 12.652 18.517 1.00 0.00 A H
+ATOM 594 HA ASP 43 13.363 10.779 19.410 1.00 0.00 A H
+ATOM 595 HB1 ASP 43 11.949 12.570 19.635 1.00 0.00 A H
+ATOM 596 HB2 ASP 43 13.319 12.759 20.502 1.00 0.00 A H
+ATOM 597 N TYR 44 13.725 11.174 16.425 1.00 5.22 A N
+ATOM 598 CA TYR 44 13.257 10.745 15.081 1.00 5.56 A C
+ATOM 599 C TYR 44 14.275 9.687 14.612 1.00 4.61 A C
+ATOM 600 O TYR 44 14.930 9.862 13.568 1.00 6.04 A O
+ATOM 601 CB TYR 44 13.200 11.914 14.071 1.00 5.41 A C
+ATOM 602 CG TYR 44 12.000 12.819 14.399 1.00 5.34 A C
+ATOM 603 CD1 TYR 44 12.119 13.853 15.332 1.00 6.59 A C
+ATOM 604 CD2 TYR 44 10.775 12.617 13.762 1.00 5.94 A C
+ATOM 605 CE1 TYR 44 11.045 14.675 15.610 1.00 5.97 A C
+ATOM 606 CE2 TYR 44 9.676 13.433 14.048 1.00 5.17 A C
+ATOM 607 CZ TYR 44 9.802 14.456 14.996 1.00 5.96 A C
+ATOM 608 OH TYR 44 8.740 15.265 15.269 1.00 8.60 A O
+ATOM 609 HN TYR 44 14.684 11.434 16.537 1.00 0.00 A H
+ATOM 610 HA TYR 44 12.324 10.389 15.134 1.00 0.00 A H
+ATOM 611 HB1 TYR 44 14.045 12.446 14.130 1.00 0.00 A H
+ATOM 612 HB2 TYR 44 13.099 11.550 13.145 1.00 0.00 A H
+ATOM 613 HD1 TYR 44 12.989 13.999 15.802 1.00 0.00 A H
+ATOM 614 HD2 TYR 44 10.682 11.880 13.093 1.00 0.00 A H
+ATOM 615 HE1 TYR 44 11.154 15.432 16.254 1.00 0.00 A H
+ATOM 616 HE2 TYR 44 8.805 13.287 13.578 1.00 0.00 A H
+ATOM 617 HH TYR 44 7.945 14.960 14.745 1.00 0.00 A H
+ATOM 618 N ALA 45 14.342 8.640 15.422 1.00 4.76 A N
+ATOM 619 CA ALA 45 15.445 7.667 15.246 1.00 5.89 A C
+ATOM 620 C ALA 45 15.171 6.533 14.280 1.00 6.67 A C
+ATOM 621 O ALA 45 16.093 5.705 14.039 1.00 7.56 A O
+ATOM 622 CB ALA 45 15.680 7.099 16.682 1.00 6.82 A C
+ATOM 623 HN ALA 45 13.659 8.509 16.140 1.00 0.00 A H
+ATOM 624 HA ALA 45 16.233 8.130 14.839 1.00 0.00 A H
+ATOM 625 HB1 ALA 45 16.418 6.425 16.657 1.00 0.00 A H
+ATOM 626 HB2 ALA 45 15.943 7.898 17.318 1.00 0.00 A H
+ATOM 627 HB3 ALA 45 14.788 6.644 17.011 1.00 0.00 A H
+ATOM 628 N ASN 46 13.966 6.502 13.739 1.00 5.80 A N
+ATOM 629 CA ASN 46 13.512 5.395 12.878 1.00 6.15 A C
+ATOM 630 C ASN 46 13.311 5.853 11.455 1.00 6.61 A C
+ATOM 631 OT1 ASN 46 13.733 6.929 11.026 1.00 7.18 A O
+ATOM 632 CB ASN 46 12.266 4.769 13.501 1.00 7.27 A C
+ATOM 633 CG ASN 46 12.538 4.304 14.922 1.00 7.98 A C
+ATOM 634 OD1 ASN 46 11.982 4.849 15.886 1.00 11.00 A O
+ATOM 635 ND2 ASN 46 13.407 3.298 15.015 1.00 10.32 A N
+ATOM 636 OT2 ASN 46 12.703 4.973 10.746 1.00 7.86 A O
+ATOM 637 HN ASN 46 13.338 7.259 13.921 1.00 0.00 A H
+ATOM 638 HA ASN 46 14.216 4.687 12.825 1.00 0.00 A H
+ATOM 639 HB1 ASN 46 11.532 5.448 13.515 1.00 0.00 A H
+ATOM 640 HB2 ASN 46 11.984 3.984 12.949 1.00 0.00 A H
+ATOM 641 HD21 ASN 46 13.819 2.915 14.188 1.00 0.00 A H
+ATOM 642 HD22 ASN 46 13.647 2.926 15.912 1.00 0.00 A H
+END
diff --git a/modules/mol/mm/examples/gb_example_view_trajectory.py b/modules/mol/mm/examples/gb_example_view_trajectory.py
new file mode 100644
index 0000000000000000000000000000000000000000..2075c4c4535593ae2d2c21f033a9a194eed0c36d
--- /dev/null
+++ b/modules/mol/mm/examples/gb_example_view_trajectory.py
@@ -0,0 +1,5 @@
+from ost.gui import traj
+
+t = io.LoadCHARMMTraj("gb_example_traj.pdb","gb_example_traj.dcd")
+w = traj.TrajWidget(t)
+w.show()
diff --git a/modules/mol/mm/examples/gb_example_writing_trajectory.py b/modules/mol/mm/examples/gb_example_writing_trajectory.py
new file mode 100644
index 0000000000000000000000000000000000000000..a6a18cd5e5836e38164d392e38dc3265b07c4f94
--- /dev/null
+++ b/modules/mol/mm/examples/gb_example_writing_trajectory.py
@@ -0,0 +1,31 @@
+from ost.mol.mm import *
+
+prot=io.LoadPDB('1CRN.pdb')
+
+#set up the simulation
+settings = MMSettings()
+settings.integrator = LangevinIntegrator(310,1,0.002)
+settings.add_gbsa = True
+settings.forcefield = LoadCHARMMForcefield()
+settings.nonbonded_cutoff = 8.0
+settings.nonbonded_method = NonbondedMethod.CutoffNonPeriodic
+settings.platform = Platform.CPU
+
+sim = Simulation(prot,settings)
+
+#minimize it
+sim.MinimizeEnergy(type = "steep",tolerance = 1.0, max_iterations = 200)
+
+#create a trajectory observer and register it to the simulation
+observer = TrajWriter(10,"gb_example_traj.pdb","gb_example_traj.dcd")
+sim.Register(observer)
+
+#run the simulation
+sim.Steps(10000)
+
+#Trajectory Observer needs to finalize, otherwise you might get a corrupt dcd file
+observer.Finalize()
+
+
+
+
diff --git a/modules/mol/mm/pymod/CMakeLists.txt b/modules/mol/mm/pymod/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..825dda3a463a4591d67f02558f65179dcddeddcb
--- /dev/null
+++ b/modules/mol/mm/pymod/CMakeLists.txt
@@ -0,0 +1,22 @@
+set(OST_MOL_MM_PYMOD_SOURCES
+ export_forcefield.cc
+ export_settings.cc
+ export_simulation.cc
+ export_openmm.cc
+ export_observers.cc
+ export_gromacs_reader.cc
+ export_interaction.cc
+ export_buildingblock.cc
+ export_block_modifiers.cc
+ export_topology.cc
+ wrap_mol_mm.cc
+)
+
+set(OST_MOL_MM_PYMOD_MODULES
+ "__init__.py"
+)
+
+if (NOT ENABLE_STATIC)
+ pymod(NAME mol_mm OUTPUT_DIR ost/mol/mm CPP ${OST_MOL_MM_PYMOD_SOURCES}
+ PY ${OST_MOL_MM_PYMOD_MODULES})
+endif()
diff --git a/modules/mol/mm/pymod/__init__.py b/modules/mol/mm/pymod/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5c1138cd0354113ea8d1744912a0cc0868202d2b
--- /dev/null
+++ b/modules/mol/mm/pymod/__init__.py
@@ -0,0 +1,9 @@
+import os.path
+from _ost_mol_mm import *
+import ost
+
+def LoadAMBERForcefield():
+ return Forcefield.Load(os.path.join(ost.GetSharedDataPath(),'forcefields','AMBER03.dat'))
+
+def LoadCHARMMForcefield():
+ return Forcefield.Load(os.path.join(ost.GetSharedDataPath(),'forcefields','CHARMM27.dat'))
diff --git a/modules/mol/mm/pymod/export_block_modifiers.cc b/modules/mol/mm/pymod/export_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..d26cf2f30e4def0958fa42fd4da25cae30aa606f
--- /dev/null
+++ b/modules/mol/mm/pymod/export_block_modifiers.cc
@@ -0,0 +1,63 @@
+#include <boost/python.hpp>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+std::vector<T> ListToVec(boost::python::list& l){
+ std::vector<T> vec;
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+}
+
+
+void WrapAddHydrogenRule(ost::mol::mm::GromacsHydrogenConstructorPtr p, int number, int method,
+ boost::python::list hydrogen_names, boost::python::list anchors){
+ std::vector<String> v_hydrogen_names = ListToVec<String>(hydrogen_names);
+ std::vector<String> v_anchors = ListToVec<String>(anchors);
+ p->AddHydrogenRule(number,method,v_hydrogen_names,v_anchors);
+}
+
+
+}
+
+
+void export_BlockModifiers()
+{
+
+ class_<ost::mol::mm::HydrogenConstructor, boost::noncopyable>("HydrogenConstructor",no_init);
+ boost::python::register_ptr_to_python<ost::mol::mm::HydrogenConstructorPtr>();
+
+ class_<ost::mol::mm::BlockModifier, boost::noncopyable>("BlockModifier",no_init);
+ boost::python::register_ptr_to_python<ost::mol::mm::BlockModifierPtr>();
+
+ class_<ost::mol::mm::GromacsHydrogenConstructor, bases<ost::mol::mm::HydrogenConstructor> >("GromacsHydrogenConstructor", init<>())
+ .def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnBuildingBlock)
+ .def("ApplyOnResidue",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnResidue)
+ .def("AddHydrogenRule",&WrapAddHydrogenRule)
+ ;
+
+ class_<ost::mol::mm::GromacsBlockModifier, bases<ost::mol::mm::BlockModifier> >("GromacsBlockModifier", init<>())
+ .def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsBlockModifier::ApplyOnBuildingBlock)
+ .def("ApplyOnResidue",&ost::mol::mm::GromacsBlockModifier::ApplyOnResidue)
+ .def("AddReplaceRule",&ost::mol::mm::GromacsBlockModifier::AddReplaceRule)
+ .def("AddAddRule",&ost::mol::mm::GromacsBlockModifier::AddAddRule)
+ .def("AddBond",&ost::mol::mm::GromacsBlockModifier::AddBond)
+ .def("AddAngle",&ost::mol::mm::GromacsBlockModifier::AddAngle)
+ .def("AddDihedral",&ost::mol::mm::GromacsBlockModifier::AddDihedral)
+ .def("AddImproper",&ost::mol::mm::GromacsBlockModifier::AddImproper)
+ .def("AddCMap",&ost::mol::mm::GromacsBlockModifier::AddDeleteAtom)
+ .def("AddDeleteAtom",&ost::mol::mm::GromacsBlockModifier::AddDeleteAtom)
+ ;
+
+
+ boost::python::register_ptr_to_python<ost::mol::mm::GromacsHydrogenConstructorPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::GromacsBlockModifierPtr>();
+
+}
+
diff --git a/modules/mol/mm/pymod/export_buildingblock.cc b/modules/mol/mm/pymod/export_buildingblock.cc
new file mode 100644
index 0000000000000000000000000000000000000000..b9388cb81bd76c4caec097ea8faee138d583d52c
--- /dev/null
+++ b/modules/mol/mm/pymod/export_buildingblock.cc
@@ -0,0 +1,89 @@
+#include <ost/log.hh>
+#include <boost/python.hpp>
+#include <ost/mol/mm/buildingblock.hh>
+#include <vector>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+boost::python::list VecToList(std::vector<T>& vec){
+ boost::python::list l;
+ for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
+ l.append(*it);
+ }
+ return l;
+}
+
+bool WrapMatch(ost::mol::mm::BuildingBlockPtr p, const ost::mol::ResidueHandle& res, bool match_connectivity){
+ String match_fail_info;
+ bool match = p->Match(res,match_connectivity,match_fail_info);
+ if(!match){
+ std::stringstream ss;
+ ss << "Residue "<< res.GetQualifiedName() << " does not match the building";
+ ss << "block. "<<match_fail_info;
+ LOG_INFO(ss.str());
+ }
+ return match;
+}
+
+boost::python::list WrapGetAtoms(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<String> atoms = p->GetAtoms();
+ return VecToList<String>(atoms);
+}
+
+boost::python::list WrapGetTypes(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<String> types = p->GetTypes();
+ return VecToList<String>(types);
+}
+
+boost::python::list WrapGetCharges(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<Real> charges = p->GetCharges();
+ return VecToList<Real>(charges);
+}
+
+boost::python::list WrapGetMasses(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<Real> masses = p->GetMasses();
+ return VecToList<Real>(masses);
+}
+
+
+}
+
+void export_Buildingblock()
+{
+ class_<ost::mol::mm::BuildingBlock>("BuildingBlock",init<>())
+ .def("Match",&WrapMatch,(arg("res"),arg("match_connectivity")=true))
+ .def("Connect",&ost::mol::mm::BuildingBlock::Connect)
+ .def("GetAtoms",&WrapGetAtoms)
+ .def("GetTypes",&WrapGetTypes)
+ .def("GetCharges",&WrapGetCharges)
+ .def("GetMasses",&WrapGetMasses)
+ .def("GetType",&ost::mol::mm::BuildingBlock::GetType)
+ .def("GetCharge",&ost::mol::mm::BuildingBlock::GetCharge)
+ .def("GetMass",&ost::mol::mm::BuildingBlock::GetMass)
+ .def("GetBonds",&ost::mol::mm::BuildingBlock::GetBonds)
+ .def("GetAngles",&ost::mol::mm::BuildingBlock::GetAngles)
+ .def("GetDihedrals",&ost::mol::mm::BuildingBlock::GetDihedrals)
+ .def("GetImpropers",&ost::mol::mm::BuildingBlock::GetImpropers)
+ .def("GetCMaps",&ost::mol::mm::BuildingBlock::GetCMaps)
+ .def("GetExclusions",&ost::mol::mm::BuildingBlock::GetExclusions)
+ .def("GetConstraints",&ost::mol::mm::BuildingBlock::GetConstraints)
+ .def("AddAtom",&ost::mol::mm::BuildingBlock::AddAtom,(arg("name"),arg("type"),arg("charge"),arg("mass")=std::numeric_limits<Real>::quiet_NaN()))
+ .def("AddBond",&ost::mol::mm::BuildingBlock::AddBond,(arg("bond"),arg("replace_existing")=false))
+ .def("AddAngle",&ost::mol::mm::BuildingBlock::AddAngle,(arg("angle"),arg("replace_existing")=false))
+ .def("AddDihedral",&ost::mol::mm::BuildingBlock::AddDihedral,(arg("dihedral"),arg("replace_existing")=false))
+ .def("AddImproper",&ost::mol::mm::BuildingBlock::AddImproper,(arg("improper"),arg("replace_existing")=false))
+ .def("AddExclusion",&ost::mol::mm::BuildingBlock::AddExclusion,(arg("exclusion"),arg("replace_existing")=false))
+ .def("AddCMap",&ost::mol::mm::BuildingBlock::AddBond,(arg("cmap"),arg("replace_existing")=false))
+ .def("AddConstraint",&ost::mol::mm::BuildingBlock::AddConstraint,(arg("constraint"),arg("replace_existing")=false))
+ .def("RemoveAtom",&ost::mol::mm::BuildingBlock::RemoveAtom)
+ .def("ReplaceAtom",&ost::mol::mm::BuildingBlock::ReplaceAtom)
+ .def("RemoveInteractionsToNext",&ost::mol::mm::BuildingBlock::RemoveInteractionsToNext)
+ .def("RemoveInteractionsToPrev",&ost::mol::mm::BuildingBlock::RemoveInteractionsToPrev)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::BuildingBlockPtr>();
+
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_forcefield.cc b/modules/mol/mm/pymod/export_forcefield.cc
new file mode 100644
index 0000000000000000000000000000000000000000..750159c6f4478575324a8a7bf7348f18c735fb9c
--- /dev/null
+++ b/modules/mol/mm/pymod/export_forcefield.cc
@@ -0,0 +1,86 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/mm/forcefield.hh>
+
+using namespace boost::python;
+
+namespace{
+
+
+ ost::mol::mm::MMInteractionPtr GetLJOneType(ost::mol::mm::ForcefieldPtr p, String type){
+ return p->GetLJ(type);
+ }
+
+ ost::mol::mm::MMInteractionPtr GetLJTwoTypes(ost::mol::mm::ForcefieldPtr p, String type1, String type2, bool pair){
+ return p->GetLJ(type1,type2,pair);
+ }
+
+}
+
+
+void export_Forcefield()
+{
+
+ class_<ost::mol::mm::Forcefield>("Forcefield", init<>())
+ .def("Load",&ost::mol::mm::Forcefield::Load).staticmethod("Load")
+ .def("Save",&ost::mol::mm::Forcefield::Save)
+ .def("GetBuildingBlock",&ost::mol::mm::Forcefield::GetBuildingBlock)
+ .def("GetAtomType",&ost::mol::mm::Forcefield::GetAtomType)
+ .def("GetHydrogenConstructor",&ost::mol::mm::Forcefield::GetHydrogenConstructor)
+ .def("GetNTerModifier",&ost::mol::mm::Forcefield::GetNTerModifier,(arg("residue_name"),arg("ter_name")=""))
+ .def("GetCTerModifier",&ost::mol::mm::Forcefield::GetCTerModifier,(arg("residue_name"),arg("ter_name")=""))
+ .def("GetBond",&ost::mol::mm::Forcefield::GetBond)
+ .def("GetAngle",&ost::mol::mm::Forcefield::GetAngle)
+ .def("GetDihedrals",&ost::mol::mm::Forcefield::GetDihedrals)
+ .def("GetImpropers",&ost::mol::mm::Forcefield::GetImpropers)
+ .def("GetCMap",&ost::mol::mm::Forcefield::GetCMap)
+ .def("GetImplicitGenborn",&ost::mol::mm::Forcefield::GetImplicitGenborn)
+ .def("GetLJ",&GetLJOneType)
+ .def("GetLJ",&GetLJTwoTypes)
+ .def("GetConstraint",&ost::mol::mm::Forcefield::GetConstraint)
+ .def("GetMass",&ost::mol::mm::Forcefield::GetMass)
+ .def("GetFudgeLJ",&ost::mol::mm::Forcefield::GetFudgeLJ)
+ .def("GetFudgeQQ",&ost::mol::mm::Forcefield::GetFudgeQQ)
+ .def("AddBuildingBlock",&ost::mol::mm::Forcefield::AddBuildingBlock)
+ .def("AddBond",&ost::mol::mm::Forcefield::AddBond)
+ .def("AddAngle",&ost::mol::mm::Forcefield::AddAngle)
+ .def("AddDihedral",&ost::mol::mm::Forcefield::AddDihedral)
+ .def("AddImproper",&ost::mol::mm::Forcefield::AddImproper)
+ .def("AddCMap",&ost::mol::mm::Forcefield::AddCMap)
+ .def("AddImplicitGenborn",&ost::mol::mm::Forcefield::AddImplicitGenborn)
+ .def("AddLJ",&ost::mol::mm::Forcefield::AddLJ)
+ .def("AddLJPair",&ost::mol::mm::Forcefield::AddLJPair)
+ .def("AddMass",&ost::mol::mm::Forcefield::AddMass)
+ .def("AddResidueRenamingRule",&ost::mol::mm::Forcefield::AddResidueRenamingRule)
+ .def("AddAtomRenamingRule",&ost::mol::mm::Forcefield::AddAtomRenamingRule)
+ .def("AddHydrogenConstructor",&ost::mol::mm::Forcefield::AddHydrogenConstructor)
+ .def("AddBlockModifier",&ost::mol::mm::Forcefield::AddBlockModifier)
+ .def("SetStandardCTer",&ost::mol::mm::Forcefield::SetStandardCTer)
+ .def("SetStandardNTer",&ost::mol::mm::Forcefield::SetStandardNTer)
+ .def("SetFudgeLJ",&ost::mol::mm::Forcefield::SetFudgeLJ)
+ .def("SetFudgeQQ",&ost::mol::mm::Forcefield::SetFudgeQQ)
+ .def("SetGenPairs",&ost::mol::mm::Forcefield::SetGenPairs)
+ .def("AssignFFSpecificNames",&ost::mol::mm::Forcefield::AssignFFSpecificNames,(arg("ent"),arg("reverse")=true))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::ForcefieldPtr>();
+
+}
diff --git a/modules/mol/mm/pymod/export_gromacs_reader.cc b/modules/mol/mm/pymod/export_gromacs_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..fe41bfccb8ae798815d09c676a967fb8a0a849b9
--- /dev/null
+++ b/modules/mol/mm/pymod/export_gromacs_reader.cc
@@ -0,0 +1,41 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <ost/mol/mm/gromacs_reader.hh>
+#include <ost/mol/residue_handle.hh>
+
+using namespace boost::python;
+using namespace ost::mol::mm;
+
+
+void export_GromacsReader()
+{
+ class_<ost::mol::mm::GromacsReader>("GromacsReader",init<String>())
+ .def("ReadGromacsForcefield",&ost::mol::mm::GromacsReader::ReadGromacsForcefield)
+ .def("SetPreprocessorDefinition",&ost::mol::mm::GromacsReader::SetPreprocessorDefinition)
+ .def("GetForcefield",&ost::mol::mm::GromacsReader::GetForcefield)
+ .def("SetForcefield",&ost::mol::mm::GromacsReader::SetForcefield)
+ .def("ReadResidueDatabase",&ost::mol::mm::GromacsReader::ReadResidueDatabase)
+ .def("ReadITP",&ost::mol::mm::GromacsReader::ReadITP)
+ .def("ReadCHARMMPRM",&ost::mol::mm::GromacsReader::ReadCHARMMPRM)
+ .def("ReadCHARMMRTF",&ost::mol::mm::GromacsReader::ReadCHARMMRTF)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::GromacsReaderPtr>();
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_index.cc b/modules/mol/mm/pymod/export_index.cc
new file mode 100644
index 0000000000000000000000000000000000000000..ace9ccbd2aaee6e4f97980adf72695be8796f535
--- /dev/null
+++ b/modules/mol/mm/pymod/export_index.cc
@@ -0,0 +1,55 @@
+#include <boost/python.hpp>
+#include <ost/mol/mm/index.hh>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+int Get(T index, uint i){
+ return index[i];
+}
+
+template<typename T>
+void Set(T& index, uint i, uint v){
+ index[i] = v;
+}
+}
+
+void export_Index()
+{
+ class_<ost::mol::mm::Index<1> >("Index1", init<uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<1> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<1> >)
+ ;
+
+ class_<ost::mol::mm::Index<2> >("Index2", init<uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<2> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<2> >)
+ ;
+
+ class_<ost::mol::mm::Index<3> >("Index3", init<uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<3> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<3> >)
+ ;
+
+ class_<ost::mol::mm::Index<4> >("Index4", init<uint, uint, uint,uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<4> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<4> >)
+ ;
+
+ class_<ost::mol::mm::Index<5> >("Index5", init<uint, uint, uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<5> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<5> >)
+ ;
+
+ class_<ost::mol::mm::Index<6> >("Index6", init<uint, uint, uint, uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<6> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<6> >)
+ ;
+
+ class_<ost::mol::mm::Index<7> >("Index7", init<uint, uint, uint, uint, uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<7> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<7> >)
+ ;
+}
diff --git a/modules/mol/mm/pymod/export_interaction.cc b/modules/mol/mm/pymod/export_interaction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..d95c80d740bbe7f860d4ec2b01338f8398112122
--- /dev/null
+++ b/modules/mol/mm/pymod/export_interaction.cc
@@ -0,0 +1,109 @@
+#include <vector>
+
+#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+
+#include <ost/mol/mm/mm_interaction.hh>
+
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+boost::python::list VecToList(std::vector<T>& vec){
+ boost::python::list l;
+ for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
+ l.append(*it);
+ }
+ return l;
+}
+
+template<typename T>
+std::vector<T> ListToVec(boost::python::list& l){
+ std::vector<T> vec;
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+}
+
+boost::python::list WrapGetNames(ost::mol::mm::MMInteractionPtr p){
+ std::vector<String> names = p->GetNames();
+ return VecToList<String>(names);
+}
+
+boost::python::list WrapGetTypes(ost::mol::mm::MMInteractionPtr p){
+ std::vector<String> types = p->GetTypes();
+ return VecToList<String>(types);
+}
+
+boost::python::list WrapGetParam(ost::mol::mm::MMInteractionPtr p){
+ std::vector<Real> param = p->GetParam();
+ return VecToList<Real>(param);
+}
+
+void WrapSetNames(ost::mol::mm::MMInteractionPtr p, boost::python::list l){
+ std::vector<String> names = ListToVec<String>(l);
+ p->SetNames(names);
+}
+
+void WrapSetTypes(ost::mol::mm::MMInteractionPtr p, boost::python::list l){
+ std::vector<String> types = ListToVec<String>(l);
+ p->SetTypes(types);
+}
+
+void WrapSetParam(ost::mol::mm::MMInteractionPtr p, boost::python::list l){
+ std::vector<Real> param = ListToVec<Real>(l);
+ p->SetParam(param);
+}
+
+}
+
+void export_MMInteraction()
+{
+
+ enum_<ost::mol::mm::FuncType>("FuncType")
+ .value("Invalid", ost::mol::mm::Invalid)
+ .value("HarmonicBond", ost::mol::mm::HarmonicBond)
+ .value("HarmonicAngle", ost::mol::mm::HarmonicAngle)
+ .value("UreyBradleyAngle", ost::mol::mm::UreyBradleyAngle)
+ .value("PeriodicDihedral", ost::mol::mm::PeriodicDihedral)
+ .value("PeriodicImproper", ost::mol::mm::PeriodicImproper)
+ .value("HarmonicImproper", ost::mol::mm::HarmonicImproper)
+ .value("CMap", ost::mol::mm::CMap)
+ .value("LJ", ost::mol::mm::LJ)
+ .value("LJPair", ost::mol::mm::LJPair)
+ .value("GBSA", ost::mol::mm::GBSA)
+ .value("DistanceConstraint", ost::mol::mm::DistanceConstraint)
+ .value("Exclusion", ost::mol::mm::Exclusion)
+ .value("HarmonicPositionRestraint", ost::mol::mm::HarmonicPositionRestraint)
+ .value("HarmonicDistanceRestraint", ost::mol::mm::HarmonicDistanceRestraint)
+ ;
+
+ class_<ost::mol::mm::MMInteraction>("MMInteraction",init<ost::mol::mm::FuncType>())
+ .def("SetTypes",&WrapSetTypes)
+ .def("SetNames",&WrapSetNames)
+ .def("SetParam",&WrapSetParam)
+ .def("GetTypes",&WrapGetTypes)
+ .def("GetNames",&WrapGetNames)
+ .def("GetParam",&WrapGetParam)
+ .def("GetAtoms",&ost::mol::mm::MMInteraction::GetAtoms)
+ .def("GetFuncType",&ost::mol::mm::MMInteraction::GetFuncType)
+ .def("ReplaceAtom",&ost::mol::mm::MMInteraction::ReplaceAtom)
+ .def("MatchTypes",&ost::mol::mm::MMInteraction::MatchTypes)
+ .def("MatchNames",&ost::mol::mm::MMInteraction::MatchNames)
+ .def("HasName",&ost::mol::mm::MMInteraction::HasName)
+ .def("HasType",&ost::mol::mm::MMInteraction::HasType)
+ .def("IsParametrized",&ost::mol::mm::MMInteraction::IsParametrized)
+ .def("HasTypeWildcard",&ost::mol::mm::MMInteraction::HasTypeWildcard)
+ .def("HasNameWildcard",&ost::mol::mm::MMInteraction::HasNameWildcard)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::MMInteractionPtr>();
+
+ class_<std::vector<ost::mol::mm::MMInteractionPtr> >("MMInteractionList", init<>())
+ .def(vector_indexing_suite<std::vector<ost::mol::mm::MMInteractionPtr>, true>())
+ ;
+
+}
diff --git a/modules/mol/mm/pymod/export_mm.cc b/modules/mol/mm/pymod/export_mm.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7a4e4ab5ce887f1b4dd3590a350c9562c9560202
--- /dev/null
+++ b/modules/mol/mm/pymod/export_mm.cc
@@ -0,0 +1,189 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <OpenMM.h>
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/mm/force_field.hh>
+#include <ost/mol/mm/simulation.hh>
+#include <ost/mol/mm/mm_algorithms.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/mm/mm_settings.hh>
+
+using namespace boost::python;
+using namespace ost::mol::mm;
+
+namespace{
+
+std::vector<std::pair<String, ost::mol::ResNum> > list_to_vec(boost::python::list& l){
+ std::vector<std::pair<String,ost::mol::ResNum> > return_vec;
+ boost::python::tuple t;
+ String s;
+ ost::mol::ResNum rn;
+ for(int i = 0; i < boost::python::len(l); ++i){
+ t = boost::python::extract<boost::python::tuple>(l[0]);
+ s = boost::python::extract<String>(t[0]);
+ rn = boost::python::extract<ost::mol::ResNum>(t[1]);
+ return_vec.push_back(std::make_pair(s,rn));
+ }
+ return return_vec;
+}
+
+ost::mol::mm::SimulationPtr WrapSimulationConstructor(ost::mol::EntityHandle& e, ost::mol::mm::ForcefieldPtr ff,
+ ost::mol::mm::IntegratorPtr integrator, ost::mol::mm::MMSettingsPtr settings,
+ list& d_protonated_his,
+ list& e_protonated_his,
+ list& positive_his,
+ list& neutral_glutamates,
+ list& neutral_aspartates){
+
+ std::vector<std::pair<String,ost::mol::ResNum> > v_d_protonated_his = list_to_vec(d_protonated_his);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_e_protonated_his = list_to_vec(e_protonated_his);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_positive_his = list_to_vec(positive_his);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_glutamates = list_to_vec(neutral_glutamates);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_aspartates = list_to_vec(neutral_aspartates);
+
+ ost::mol::mm::SimulationPtr p(new ost::mol::mm::Simulation(e,ff,integrator, settings,
+ v_d_protonated_his,
+ v_e_protonated_his,
+ v_positive_his,
+ v_neutral_glutamates,
+ v_neutral_aspartates));
+ return p;
+}
+
+ost::mol::mm::SimulationPtr WrapSimulationConstructorNoSettings(ost::mol::EntityHandle& e, ost::mol::mm::ForcefieldPtr ff,
+ ost::mol::mm::IntegratorPtr integrator,
+ list& d_protonated_his,
+ list& e_protonated_his,
+ list& positive_his,
+ list& neutral_glutamates,
+ list& neutral_aspartates){
+
+ ost::mol::mm::MMSettingsPtr p(new ost::mol::mm::MMSettings);
+ return WrapSimulationConstructor(e,ff,integrator,p,
+ d_protonated_his,
+ e_protonated_his,
+ positive_his,
+ neutral_glutamates,
+ neutral_aspartates);
+
+
+}
+
+void WrapAssignFFSpecificNames(ost::mol::mm::ForcefieldPtr p,
+ ost::mol::EntityHandle& e,
+ boost::python::list& d_protonated_his,
+ boost::python::list& e_protonated_his,
+ boost::python::list& positive_his,
+ boost::python::list& neutral_glutamates,
+ boost::python::list& neutral_aspartates){
+
+ std::vector<std::pair<String,ost::mol::ResNum> > v_d_protonated_his = list_to_vec(d_protonated_his);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_e_protonated_his = list_to_vec(e_protonated_his);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_positive_his = list_to_vec(positive_his);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_glutamates = list_to_vec(neutral_glutamates);
+ std::vector<std::pair<String,ost::mol::ResNum> > v_neutral_aspartates = list_to_vec(neutral_aspartates);
+
+ p->AssignFFSpecificNames(e,v_d_protonated_his,
+ v_e_protonated_his,
+ v_positive_his,
+ v_neutral_glutamates,
+ v_neutral_aspartates);
+
+}
+
+}
+
+
+
+void export_MM()
+{
+
+ //export the settings
+
+ class_<ost::mol::mm::MMSettings>("MMSettings",init<>())
+ .def_readwrite("add_bonds",&ost::mol::mm::MMSettings::add_bonds)
+ .def_readwrite("add_angles",&ost::mol::mm::MMSettings::add_angles)
+ .def_readwrite("add_dihedrals",&ost::mol::mm::MMSettings::add_dihedrals)
+ .def_readwrite("add_impropers",&ost::mol::mm::MMSettings::add_impropers)
+ .def_readwrite("add_cmaps",&ost::mol::mm::MMSettings::add_cmaps)
+ .def_readwrite("add_exclusions",&ost::mol::mm::MMSettings::add_exclusions)
+ .def_readwrite("add_nonbonded",&ost::mol::mm::MMSettings::add_nonbonded)
+ .def_readwrite("kill_electrostatics",&ost::mol::mm::MMSettings::kill_electrostatics)
+ .def_readwrite("nonbonded_method",&ost::mol::mm::MMSettings::nonbonded_method)
+ .def_readwrite("nonbonded_cutoff",&ost::mol::mm::MMSettings::nonbonded_cutoff)
+ .def_readwrite("rigid_water",&ost::mol::mm::MMSettings::rigid_water)
+ .def_readwrite("removeCMMMotion",&ost::mol::mm::MMSettings::removeCMMMotion)
+ .def_readwrite("constraints",&ost::mol::mm::MMSettings::constraints)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::MMSettingsPtr>();
+
+ //we have to tell boost, that the Integrator class is around...
+ class_<OpenMM::Integrator, boost::noncopyable>("Integrator",no_init);
+ //We do not export any further function for the Verlet integrator, since we want
+ //to perform the steps via the simulation...
+ class_<OpenMM::VerletIntegrator, bases<OpenMM::Integrator> >("VerletIntegrator", init<Real>());
+ boost::python::register_ptr_to_python<ost::mol::mm::IntegratorPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::VerletIntegratorPtr>();
+
+ class_<ost::mol::mm::Forcefield>("Forcefield", init<const String&>())
+ .def("AssignFFSpecificNames", &WrapAssignFFSpecificNames, (arg("entity"),
+ arg("d_protonated_his") = boost::python::list(),
+ arg("e_protonated_his") = boost::python::list(),
+ arg("positive_his") = boost::python::list(),
+ arg("neutral_glutamates") = boost::python::list(),
+ arg("neutral_aspartates") = boost::python::list()))
+ .def("AddHydrogens", &ost::mol::mm::Forcefield::AddHydrogens)
+ .def("ReadResidueDatabase", &ost::mol::mm::Forcefield::ReadResidueDatabase)
+ ;
+
+ class_<ost::mol::mm::Simulation>("Simulation",no_init)
+ .def("__init__",boost::python::make_constructor(&WrapSimulationConstructor,default_call_policies(),
+ (arg("entity"),arg("forcefield"),
+ arg("integrator"),arg("settings"),
+ arg("d_protonated_his") = boost::python::list(),
+ arg("e_protonated_his") = boost::python::list(),
+ arg("positive_his") = boost::python::list(),
+ arg("neutral_glutamates") = boost::python::list(),
+ arg("neutral_aspartates") = boost::python::list())))
+ .def("__init__",boost::python::make_constructor(&WrapSimulationConstructorNoSettings,default_call_policies(),
+ (arg("entity"),arg("forcefield"),
+ arg("integrator"),
+ arg("d_protonated_his") = boost::python::list(),
+ arg("e_protonated_his") = boost::python::list(),
+ arg("positive_his") = boost::python::list(),
+ arg("neutral_glutamates") = boost::python::list(),
+ arg("neutral_aspartates") = boost::python::list())))
+ .def("GetEntity",&ost::mol::mm::Simulation::GetEntity)
+ .def("GetMMEntity",&ost::mol::mm::Simulation::GetMMEntity)
+ .def("UpdatePositions",&ost::mol::mm::Simulation::UpdatePositions)
+ .def("MinimizeEnergy",&ost::mol::mm::Simulation::MinimizeEnergy, (arg("tolerance")=1.0,arg("max_iterations")=1000))
+ .def("GetTimeSteps",&ost::mol::mm::Simulation::GetTimeSteps)
+ .def("Steps",&ost::mol::mm::Simulation::Steps, (arg("steps")=1))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::SimulationPtr>();
+
+ //functions from mm_algorithms
+ def("Minimize",&ost::mol::mm::Minimize, (arg("ent"), arg("ff")));
+
+}
+
+
diff --git a/modules/mol/mm/pymod/export_observers.cc b/modules/mol/mm/pymod/export_observers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1fa316c6986279c9a0e907159ec458484b4376e3
--- /dev/null
+++ b/modules/mol/mm/pymod/export_observers.cc
@@ -0,0 +1,25 @@
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/mm/mm_observer.hh>
+
+using namespace boost::python;
+
+
+void export_Observers()
+{
+
+ class_<ost::mol::mm::MMObserver, boost::noncopyable>("MMObserver", no_init);
+
+ class_<ost::mol::mm::TrajObserver, bases<ost::mol::mm::MMObserver> >("TrajObserver", init<int>())
+ .def("GetTraj", &ost::mol::mm::TrajObserver::GetTraj)
+ ;
+
+ //noncopyable, because TrajWriter contains a unique ofstream
+ class_<ost::mol::mm::TrajWriter, boost::noncopyable, bases<ost::mol::mm::MMObserver> >("TrajWriter", init<int, String, String>())
+ .def("Finalize", &ost::mol::mm::TrajWriter::Finalize)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::MMObserverPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::TrajObserverPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::TrajWriterPtr>();
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_openmm.cc b/modules/mol/mm/pymod/export_openmm.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7c97b7964854d551106ff1d07f68da85915194f9
--- /dev/null
+++ b/modules/mol/mm/pymod/export_openmm.cc
@@ -0,0 +1,93 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <OpenMM.h>
+#include <boost/python.hpp>
+#include <ost/mol/mm/simulation.hh>
+
+using namespace boost::python;
+using namespace ost::mol::mm;
+
+
+void export_OpenMM()
+{
+
+ //we have to tell boost, that the Integrator class is around...
+ class_<OpenMM::Integrator, boost::noncopyable>("Integrator",no_init)
+ .def("GetConstraintTolerance",&OpenMM::Integrator::getConstraintTolerance)
+ .def("SetConstraintTolerance",&OpenMM::Integrator::setConstraintTolerance)
+
+ ;
+ boost::python::register_ptr_to_python<ost::mol::mm::IntegratorPtr>();
+
+
+ class_<OpenMM::VerletIntegrator, bases<OpenMM::Integrator> >("VerletIntegrator", init<Real>());
+ boost::python::register_ptr_to_python<ost::mol::mm::VerletIntegratorPtr>();
+
+
+ class_<OpenMM::BrownianIntegrator, bases<OpenMM::Integrator> >("BrownianIntegrator", init<Real,Real,Real>())
+ .def("GetTemperature",&OpenMM::BrownianIntegrator::getTemperature)
+ .def("SetTemperature",&OpenMM::BrownianIntegrator::setTemperature)
+ .def("GetFriction",&OpenMM::BrownianIntegrator::getFriction)
+ .def("SetFriction",&OpenMM::BrownianIntegrator::setFriction)
+ .def("GetRandomNumberSeed",&OpenMM::BrownianIntegrator::getRandomNumberSeed)
+ .def("SetRandomNumberSeed",&OpenMM::BrownianIntegrator::setRandomNumberSeed)
+ ;
+ boost::python::register_ptr_to_python<ost::mol::mm::BrownianIntegratorPtr>();
+
+
+ class_<OpenMM::LangevinIntegrator, bases<OpenMM::Integrator> >("LangevinIntegrator", init<Real,Real,Real>())
+ .def("GetTemperature",&OpenMM::LangevinIntegrator::getTemperature)
+ .def("SetTemperature",&OpenMM::LangevinIntegrator::setTemperature)
+ .def("GetFriction",&OpenMM::LangevinIntegrator::getFriction)
+ .def("SetFriction",&OpenMM::LangevinIntegrator::setFriction)
+ .def("GetRandomNumberSeed",&OpenMM::LangevinIntegrator::getRandomNumberSeed)
+ .def("SetRandomNumberSeed",&OpenMM::LangevinIntegrator::setRandomNumberSeed)
+ ;
+ boost::python::register_ptr_to_python<ost::mol::mm::LangevinIntegratorPtr>();
+
+
+ class_<OpenMM::VariableVerletIntegrator, bases<OpenMM::Integrator> >("VariableVerletIntegrator",init<Real>())
+ .def("GetErrorTolerance", &OpenMM::VariableVerletIntegrator::getErrorTolerance)
+ .def("SetErrorTolerance", &OpenMM::VariableVerletIntegrator::setErrorTolerance)
+ ;
+ boost::python::register_ptr_to_python<ost::mol::mm::VariableVerletIntegratorPtr>();
+
+
+ class_<OpenMM::VariableLangevinIntegrator, bases<OpenMM::Integrator> >("VaribaleLangevinIntegrator", init<Real,Real,Real>())
+ .def("GetTemperature",&OpenMM::VariableLangevinIntegrator::getTemperature)
+ .def("SetTemperature",&OpenMM::VariableLangevinIntegrator::setTemperature)
+ .def("GetFriction",&OpenMM::VariableLangevinIntegrator::getFriction)
+ .def("SetFriction",&OpenMM::VariableLangevinIntegrator::setFriction)
+ .def("GetRandomNumberSeed",&OpenMM::VariableLangevinIntegrator::getRandomNumberSeed)
+ .def("SetRandomNumberSeed",&OpenMM::VariableLangevinIntegrator::setRandomNumberSeed)
+ .def("GetErrorTolerance",&OpenMM::VariableLangevinIntegrator::getErrorTolerance)
+ .def("SetErrorTolerance",&OpenMM::VariableLangevinIntegrator::setErrorTolerance)
+ ;
+ boost::python::register_ptr_to_python<ost::mol::mm::VariableLangevinIntegratorPtr>();
+
+ enum_<OpenMM::NonbondedForce::NonbondedMethod>("NonbondedMethod")
+ .value("NoCutoff", OpenMM::NonbondedForce::NoCutoff)
+ .value("CutoffNonPeriodic", OpenMM::NonbondedForce::CutoffNonPeriodic)
+ .value("CutoffPeriodic", OpenMM::NonbondedForce::CutoffPeriodic)
+ .value("Ewald", OpenMM::NonbondedForce::Ewald)
+ .value("PME", OpenMM::NonbondedForce::PME)
+ ;
+
+
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_settings.cc b/modules/mol/mm/pymod/export_settings.cc
new file mode 100644
index 0000000000000000000000000000000000000000..9d65cacd869e955fa5bb9235853ae69cc5907ce3
--- /dev/null
+++ b/modules/mol/mm/pymod/export_settings.cc
@@ -0,0 +1,92 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <ost/mol/mm/mm_settings.hh>
+
+using namespace boost::python;
+
+
+void export_MMSettings()
+{
+
+ enum_<ost::mol::mm::Platform>("Platform")
+ .value("Reference", ost::mol::mm::Reference)
+ .value("OpenCL", ost::mol::mm::OpenCL)
+ .value("CUDA", ost::mol::mm::CUDA)
+ .value("CPU", ost::mol::mm::CPU)
+ ;
+
+ //export the termini exceptions object
+ class_<ost::mol::mm::TerminiExceptions>("TerminiExceptions",init<>())
+ .def("SetException", &ost::mol::mm::TerminiExceptions::SetException)
+ .def("HasException", &ost::mol::mm::TerminiExceptions::HasException)
+ .def("GetException", &ost::mol::mm::TerminiExceptions::GetException)
+ ;
+
+
+ //export the settings
+
+ class_<ost::mol::mm::MMSettings>("MMSettings",init<>())
+ .def_readwrite("add_bonds",&ost::mol::mm::MMSettings::add_bonds)
+ .def_readwrite("add_angles",&ost::mol::mm::MMSettings::add_angles)
+ .def_readwrite("add_dihedrals",&ost::mol::mm::MMSettings::add_dihedrals)
+ .def_readwrite("add_impropers",&ost::mol::mm::MMSettings::add_impropers)
+ .def_readwrite("add_cmaps",&ost::mol::mm::MMSettings::add_cmaps)
+ .def_readwrite("add_exclusions",&ost::mol::mm::MMSettings::add_exclusions)
+ .def_readwrite("add_nonbonded",&ost::mol::mm::MMSettings::add_nonbonded)
+ .def_readwrite("add_gbsa",&ost::mol::mm::MMSettings::add_gbsa)
+ .def_readwrite("constrain_hbonds",&ost::mol::mm::MMSettings::constrain_hbonds)
+ .def_readwrite("constrain_hangles",&ost::mol::mm::MMSettings::constrain_hangles)
+ .def_readwrite("constrain_bonds",&ost::mol::mm::MMSettings::constrain_bonds)
+ .def_readwrite("rigid_water",&ost::mol::mm::MMSettings::rigid_water)
+ .def_readwrite("strict_interactions",&ost::mol::mm::MMSettings::strict_interactions)
+ .def_readwrite("ideal_bond_length_constraints",&ost::mol::mm::MMSettings::ideal_bond_length_constraints)
+ .def_readwrite("fix_heavy_atoms",&ost::mol::mm::MMSettings::fix_heavy_atoms)
+ .def_readwrite("kill_electrostatics",&ost::mol::mm::MMSettings::kill_electrostatics)
+ .def_readwrite("generate_disulfid_bonds",&ost::mol::mm::MMSettings::generate_disulfid_bonds)
+ .def_readwrite("nonbonded_method",&ost::mol::mm::MMSettings::nonbonded_method)
+ .def_readwrite("nonbonded_cutoff",&ost::mol::mm::MMSettings::nonbonded_cutoff)
+ .def_readwrite("remove_cmm_motion",&ost::mol::mm::MMSettings::remove_cmm_motion)
+ .def_readwrite("periodic_box_extents",&ost::mol::mm::MMSettings::periodic_box_extents)
+ .def_readwrite("init_temperature",&ost::mol::mm::MMSettings::init_temperature)
+ .def_readwrite("forcefield",&ost::mol::mm::MMSettings::forcefield)
+ .def_readwrite("termini_exceptions",&ost::mol::mm::MMSettings::termini_exceptions)
+ .def_readwrite("platform",&ost::mol::mm::MMSettings::platform)
+ .def_readwrite("add_thermostat",&ost::mol::mm::MMSettings::add_thermostat)
+ .def_readwrite("thermostat_temperature",&ost::mol::mm::MMSettings::thermostat_temperature)
+ .def_readwrite("thermostat_collision_frequency",&ost::mol::mm::MMSettings::thermostat_collision_frequency)
+ .def_readwrite("add_barostat",&ost::mol::mm::MMSettings::add_barostat)
+ .def_readwrite("barostat_temperature",&ost::mol::mm::MMSettings::barostat_temperature)
+ .def_readwrite("barostat_pressure",&ost::mol::mm::MMSettings::barostat_pressure)
+ .def_readwrite("barostat_frequency",&ost::mol::mm::MMSettings::barostat_frequency)
+ .def_readwrite("integrator",&ost::mol::mm::MMSettings::integrator)
+ .def_readwrite("solvent_dielectric",&ost::mol::mm::MMSettings::solvent_dielectric)
+ .def_readwrite("solute_dielectric",&ost::mol::mm::MMSettings::solute_dielectric)
+ .def_readwrite("reaction_field_dielectric",&ost::mol::mm::MMSettings::reaction_field_dielectric)
+ .def_readwrite("use_dispersion_correction",&ost::mol::mm::MMSettings::use_dispersion_correction)
+ .def_readwrite("openmm_plugin_directory",&ost::mol::mm::MMSettings::openmm_plugin_directory)
+ .def_readwrite("custom_plugin_directory",&ost::mol::mm::MMSettings::custom_plugin_directory)
+
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::MMSettingsPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::TerminiExceptionsPtr>();
+
+}
+
diff --git a/modules/mol/mm/pymod/export_simulation.cc b/modules/mol/mm/pymod/export_simulation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..92b96b0839eb245830f2db1e636d697ffa498b63
--- /dev/null
+++ b/modules/mol/mm/pymod/export_simulation.cc
@@ -0,0 +1,90 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <ost/mol/mm/simulation.hh>
+
+using namespace boost::python;
+
+
+
+namespace{
+
+
+template<typename T>
+std::vector<T> ListToVec(const boost::python::list& l){
+ std::vector<T> vec;
+
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+}
+
+void WrapAddPositionConstraints(ost::mol::mm::SimulationPtr p, const boost::python::list& l){
+ std::vector<uint> vec = ListToVec<uint>(l);
+ p->AddPositionConstraints(vec);
+}
+
+}
+
+
+void export_Simulation()
+{
+
+ class_<ost::mol::mm::Simulation>("Simulation",no_init)
+ .def(init<ost::mol::EntityHandle, ost::mol::mm::MMSettingsPtr>())
+ .def(init<ost::mol::mm::TopologyPtr,ost::mol::mm::MMSettingsPtr>())
+ .def("Steps",&ost::mol::mm::Simulation::Steps)
+ .def("GetPositions",&ost::mol::mm::Simulation::GetPositions,(arg("enforce_periodic_box")=false, arg("in_angstrom")=true))
+ .def("GetVelocities",&ost::mol::mm::Simulation::GetVelocities)
+ .def("GetForces",&ost::mol::mm::Simulation::GetForces)
+ .def("SetPositions",&ost::mol::mm::Simulation::SetPositions,(arg("positions"),arg("in_angstrom")=true))
+ .def("SetVelocities",&ost::mol::mm::Simulation::SetVelocities)
+ .def("GetEntity",&ost::mol::mm::Simulation::GetEntity)
+ .def("GetEntityStandardNaming",&ost::mol::mm::Simulation::GetEntityStandardNaming)
+ .def("MinimizeEnergy",&ost::mol::mm::Simulation::MinimizeEnergy, (arg("type")="steep",arg("tolerance")=1.0,arg("max_iterations")=1000))
+ .def("GetEnergy",&ost::mol::mm::Simulation::GetEnergy)
+ .def("GetPotentialEnergy",&ost::mol::mm::Simulation::GetPotentialEnergy)
+ .def("GetKineticEnergy",&ost::mol::mm::Simulation::GetKineticEnergy)
+ .def("Register",&ost::mol::mm::Simulation::Register)
+ .def("UpdateTopologyPositions",&ost::mol::mm::Simulation::UpdateTopologyPositions, (arg("enforce_periodic_box")=false))
+ .def("GetTopology",&ost::mol::mm::Simulation::GetTopology)
+ .def("ResetHarmonicBond",&ost::mol::mm::Simulation::ResetHarmonicBond)
+ .def("ResetHarmonicAngle",&ost::mol::mm::Simulation::ResetHarmonicAngle)
+ .def("ResetUreyBradleyAngle",&ost::mol::mm::Simulation::ResetUreyBradleyAngle)
+ .def("ResetPeriodicDihedral",&ost::mol::mm::Simulation::ResetPeriodicDihedral)
+ .def("ResetPeriodicImproper",&ost::mol::mm::Simulation::ResetPeriodicImproper)
+ .def("ResetHarmonicImproper",&ost::mol::mm::Simulation::ResetHarmonicImproper)
+ .def("ResetLJPair",&ost::mol::mm::Simulation::ResetLJPair)
+ .def("ResetDistanceConstraint",&ost::mol::mm::Simulation::ResetDistanceConstraint)
+ .def("ResetHarmonicPositionRestraint",&ost::mol::mm::Simulation::ResetHarmonicPositionRestraint,(arg("index"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
+ .def("ResetHarmonicDistanceRestraint",&ost::mol::mm::Simulation::ResetHarmonicDistanceRestraint)
+ .def("ResetLJ",&ost::mol::mm::Simulation::ResetLJ)
+ .def("ResetGBSA",&ost::mol::mm::Simulation::ResetGBSA)
+ .def("ResetCharge",&ost::mol::mm::Simulation::ResetCharge)
+ .def("ResetMass",&ost::mol::mm::Simulation::ResetMass)
+ .def("AddPositionConstraint",&ost::mol::mm::Simulation::AddPositionConstraint)
+ .def("AddPositionConstraints",&WrapAddPositionConstraints)
+ .def("ResetPositionConstraints",&ost::mol::mm::Simulation::ResetPositionConstraints)
+ .def("GetPeriodicBoxExtents",&ost::mol::mm::Simulation::GetPeriodicBoxExtents)
+ .def("SetPeriodicBoxExtents",&ost::mol::mm::Simulation::SetPeriodicBoxExtents,(arg("extents")))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::SimulationPtr>();
+}
diff --git a/modules/mol/mm/pymod/export_topology.cc b/modules/mol/mm/pymod/export_topology.cc
new file mode 100644
index 0000000000000000000000000000000000000000..bd0defb9a72d7c6bf60259a231db03eb12fa3a85
--- /dev/null
+++ b/modules/mol/mm/pymod/export_topology.cc
@@ -0,0 +1,432 @@
+#include <boost/python.hpp>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/entity_handle.hh>
+#include <vector>
+
+using namespace boost::python;
+namespace{
+
+ template<typename T>
+ int Get(T index, int i){
+ return index[i];
+ }
+
+ template<typename T>
+ void Set(T& index, int i, int v){
+ index[i] = v;
+ }
+
+ template<typename T>
+ std::vector<T> ListToVec(const boost::python::list& l){
+
+ std::vector<T> vec;
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+ }
+
+ template<typename T>
+ boost::python::list VecToList(std::vector<T>& vec){
+ boost::python::list l;
+ for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
+ l.append(*it);
+ }
+ return l;
+ }
+
+ ost::mol::mm::TopologyPtr WrapTopologyConstructor(ost::mol::EntityHandle& handle,
+ const boost::python::list& masses_list){
+ std::vector<Real> masses_vector = ListToVec<Real>(masses_list);
+ ost::mol::mm::TopologyPtr p(new ost::mol::mm::Topology(handle,masses_vector));
+ return p;
+ }
+
+ void WrapAddCMap(ost::mol::mm::TopologyPtr p, int index_one, int index_two, int index_three,
+ int index_four, int index_five, uint dimension, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->AddCMap(index_one,index_two,index_three,index_four,index_five,dimension,v);
+ }
+
+ void WrapSetSigmas(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetSigmas(v);
+ }
+
+ void WrapSetEpsilons(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetEpsilons(v);
+ }
+
+ void WrapSetGBSARadii(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetGBSARadii(v);
+ }
+
+ void WrapSetOBCScalings(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetOBCScalings(v);
+ }
+
+ void WrapSetCharges(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetCharges(v);
+ }
+
+ void WrapSetMasses(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetMasses(v);
+ }
+
+
+ boost::python::list WrapGetSigmas(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetSigmas();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetEpsilons(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetEpsilons();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetGBSARadii(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetGBSARadii();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetOBCScalings(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetOBCScalings();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetCharges(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetCharges();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetMasses(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetMasses();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+
+ boost::python::tuple WrapGetHarmonicBondParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2;
+ Real b,k;
+ p->GetHarmonicBondParameters(index,i1,i2,b,k);
+ return boost::python::make_tuple(i1,i2,b,k);
+ }
+
+ boost::python::tuple WrapGetHarmonicAngleParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3;
+ Real a,k;
+ p->GetHarmonicAngleParameters(index,i1,i2,i3,a,k);
+ return boost::python::make_tuple(i1,i2,i3,a,k);
+ }
+
+ boost::python::tuple WrapGetUreyBradleyAngleParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3;
+ Real a,a_k,b,b_k;
+ p->GetUreyBradleyAngleParameters(index,i1,i2,i3,a,a_k,b,b_k);
+ return boost::python::make_tuple(i1,i2,i3,a,a_k,b,b_k);
+ }
+
+ boost::python::tuple WrapGetPeriodicDihedralParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3,i4;
+ int m;
+ Real ph,k;
+ p->GetPeriodicDihedralParameters(index,i1,i2,i3,i4,m,ph,k);
+ return boost::python::make_tuple(i1,i2,i3,i4,m,ph,k);
+ }
+
+ boost::python::tuple WrapGetPeriodicImproperParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3,i4;
+ int m;
+ Real ph,k;
+ p->GetPeriodicImproperParameters(index,i1,i2,i3,i4,m,ph,k);
+ return boost::python::make_tuple(i1,i2,i3,i4,m,ph,k);
+ }
+
+ boost::python::tuple WrapGetHarmonicImproperParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3,i4;
+ Real a,k;
+ p->GetHarmonicImproperParameters(index,i1,i2,i3,i4,a,k);
+ return boost::python::make_tuple(i1,i2,i3,i4,a,k);
+ }
+
+ boost::python::tuple WrapGetCMapParam(ost::mol::mm::TopologyPtr p, uint index){
+ std::vector<Real> map;
+ int dimension;
+ uint i1,i2,i3,i4,i5;
+ p->GetCMapParameters(index,i1,i2,i3,i4,i5,dimension,map);
+ boost::python::list l = VecToList<Real>(map);
+ return boost::python::make_tuple(i1,i2,i3,i4,i5,dimension,l);
+ }
+
+ boost::python::tuple WrapGetLJPairParam(ost::mol::mm::TopologyPtr p, uint index){
+ uint i1,i2;
+ Real s,e;
+ p->GetLJPairParameters(index,i1,i2,s,e);
+ return boost::python::make_tuple(i1,i2,s,e);
+ }
+
+ boost::python::tuple WrapGetDistanceConstraintParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2;
+ Real d;
+ p->GetDistanceConstraintParameters(index,i1,i2,d);
+ return boost::python::make_tuple(i1,i2,d);
+ }
+
+ boost::python::tuple WrapGetHarmonicPositionRestraintParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint atom_index;
+ geom::Vec3 ref_pos;
+ Real k;
+ Real x_scale, y_scale, z_scale;
+ p->GetHarmonicPositionRestraintParameters(index,atom_index,ref_pos,k,x_scale,y_scale,z_scale);
+ return boost::python::make_tuple(atom_index,ref_pos,k,x_scale,y_scale,z_scale);
+ }
+
+ boost::python::tuple WrapGetHarmonicDistanceRestraintParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2;
+ Real l,k;
+ p->GetHarmonicDistanceRestraintParameters(index,i1,i2,l,k);
+ return boost::python::make_tuple(i1,i2,l,k);
+ }
+
+ void WrapSetCMapParameters(ost::mol::mm::TopologyPtr p, uint index, int dimension, boost::python::list l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetCMapParameters(index,dimension,v);
+ }
+
+ boost::python::list GetHarmonicBondIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2){
+ std::vector<uint> return_vec = p->GetHarmonicBondIndices(i1,i2);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicBondIndicesSingleIndex(ost::mol::mm::TopologyPtr p, int i){
+ std::vector<uint> return_vec = p->GetHarmonicBondIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicAngleIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3){
+ std::vector<uint> return_vec = p->GetHarmonicAngleIndices(i1,i2,i3);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicAngleIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicAngleIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetUreyBradleyAngleIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3){
+ std::vector<uint> return_vec = p->GetUreyBradleyAngleIndices(i1,i2,i3);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetUreyBradleyAngleIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetUreyBradleyAngleIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicDihedralIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, int i4){
+ std::vector<uint> return_vec = p->GetPeriodicDihedralIndices(i1,i2,i3,i4);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicDihedralIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetPeriodicDihedralIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicImproperIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, uint i4){
+ std::vector<uint> return_vec = p->GetPeriodicImproperIndices(i1,i2,i3,i4);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicImproperIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetPeriodicImproperIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicImproperIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, uint i4){
+ std::vector<uint> return_vec = p->GetHarmonicImproperIndices(i1,i2,i3,i4);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicImproperIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicImproperIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetCMapIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, uint i4, uint i5){
+ std::vector<uint> return_vec = p->GetCMapIndices(i1,i2,i3,i4,i5);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetCMapIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetCMapIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetLJPairIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetLJPairIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetDistanceConstraintIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetDistanceConstraintIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicDistanceRestraintIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2){
+ std::vector<uint> return_vec = p->GetHarmonicDistanceRestraintIndices(i1,i2);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicDistanceRestraintIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicDistanceRestraintIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicPositionRestraintIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicPositionRestraintIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+}
+
+long GetIndexA(ost::mol::mm::TopologyPtr top,ost::mol::AtomHandle& at) { return top->GetAtomIndex(at); }
+long GetIndexB(ost::mol::mm::TopologyPtr top,int r_idx,const String& aname) { return top->GetAtomIndex(r_idx,aname); }
+
+
+void export_Topology()
+{
+
+ class_<ost::mol::mm::TopologyCreator>("TopologyCreator",no_init)
+ .def("Create",&ost::mol::mm::TopologyCreator::Create).staticmethod("Create")
+ ;
+
+ class_<ost::mol::mm::Topology>("Topology",no_init)
+// .def(init<ost::mol::EntityHandle&,ost::mol::mm::MMSettingsPtr>())
+// .def(init<ost::mol::EntityHandle&, std::vector<Real>&>())
+
+ .def("__init__",make_constructor(&WrapTopologyConstructor))
+ .def("GetEntity",&ost::mol::mm::Topology::GetEntity)
+ //interaction adding functions
+ .def("AddHarmonicBond",&ost::mol::mm::Topology::AddHarmonicBond)
+ .def("AddHarmonicAngle",&ost::mol::mm::Topology::AddHarmonicAngle)
+ .def("AddUreyBradleyAngle",&ost::mol::mm::Topology::AddUreyBradleyAngle)
+ .def("AddPeriodicDihedral",&ost::mol::mm::Topology::AddPeriodicDihedral)
+ .def("AddPeriodicImproper",&ost::mol::mm::Topology::AddPeriodicImproper)
+ .def("AddHarmonicImproper",&ost::mol::mm::Topology::AddHarmonicImproper)
+ .def("AddCMap",&WrapAddCMap)
+ .def("AddLJPair",&ost::mol::mm::Topology::AddLJPair)
+ .def("AddDistanceConstraint",&ost::mol::mm::Topology::AddDistanceConstraint)
+ .def("AddExclusion",&ost::mol::mm::Topology::AddExclusion)
+ .def("AddPositionConstraint",&ost::mol::mm::Topology::AddPositionConstraint)
+ .def("ResetPositionConstraints",&ost::mol::mm::Topology::ResetPositionConstraints)
+ .def("ResetExclusions",&ost::mol::mm::Topology::ResetExclusions)
+ .def("AddHarmonicPositionRestraint",&ost::mol::mm::Topology::AddHarmonicPositionRestraint,(arg("index"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
+ .def("AddHarmonicDistanceRestraint",&ost::mol::mm::Topology::AddHarmonicDistanceRestraint)
+ //single atom parameter getter and setter functions
+ .def("SetSigmas",&WrapSetSigmas)
+ .def("SetSigma",&ost::mol::mm::Topology::SetSigma)
+ .def("SetEpsilons",&WrapSetEpsilons)
+ .def("SetEpsilon",&ost::mol::mm::Topology::SetEpsilon)
+ .def("SetGBSARadii",&WrapSetGBSARadii)
+ .def("SetGBSARadius",&ost::mol::mm::Topology::SetGBSARadius)
+ .def("SetOBCScalings",&WrapSetOBCScalings)
+ .def("SetOBCScaling",&ost::mol::mm::Topology::SetOBCScaling)
+ .def("SetCharges",&WrapSetCharges)
+ .def("SetCharge",&ost::mol::mm::Topology::SetCharge)
+ .def("SetMasses",&WrapSetMasses)
+ .def("SetMass",&ost::mol::mm::Topology::SetMass)
+ .def("GetSigmas",&WrapGetSigmas)
+ .def("GetEpsilons",&WrapGetEpsilons)
+ .def("GetGBSARadii",&WrapGetGBSARadii)
+ .def("GetOBCScalings",&WrapGetOBCScalings)
+ .def("GetCharges",&WrapGetCharges)
+ .def("GetMasses",&WrapGetMasses)
+ .def("GetCharge",&ost::mol::mm::Topology::GetCharge)
+ .def("GetMass",&ost::mol::mm::Topology::GetMass)
+ .def("GetOBCScaling",&ost::mol::mm::Topology::GetOBCScaling)
+ .def("GetGBSARadius",&ost::mol::mm::Topology::GetGBSARadius)
+ //getter and setter functions for nonbonded fudge parameters
+ .def("SetFudgeLJ",&ost::mol::mm::Topology::SetFudgeLJ)
+ .def("SetFudgeQQ",&ost::mol::mm::Topology::SetFudgeQQ)
+ .def("GetFudgeLJ",&ost::mol::mm::Topology::GetFudgeLJ)
+ .def("GetFudgeQQ",&ost::mol::mm::Topology::GetFudgeQQ)
+ //getter functions for interaction parameters
+ .def("GetHarmonicBondParameters",&WrapGetHarmonicBondParam)
+ .def("GetHarmonicAngleParameters",&WrapGetHarmonicAngleParam)
+ .def("GetUreyBradleyAngleParameters",&WrapGetUreyBradleyAngleParam)
+ .def("GetPeriodicDihedralParameters",&WrapGetPeriodicDihedralParam)
+ .def("GetPeriodicImproperParameters",&WrapGetPeriodicImproperParam)
+ .def("GetHarmonicImproperParameters",&WrapGetHarmonicImproperParam)
+ .def("GetCMapParameters",&WrapGetCMapParam)
+ .def("GetLJPairParameters",&WrapGetLJPairParam)
+ .def("GetDistanceConstraintParameters",&WrapGetDistanceConstraintParam)
+ .def("GetHarmonicPositionRestraintParameters",&WrapGetHarmonicPositionRestraintParam)
+ .def("GetHarmonicDistanceRestraintParameters",&WrapGetHarmonicDistanceRestraintParam)
+ //setter functions for interaction parameters
+ .def("SetHarmonicBondParameters",&ost::mol::mm::Topology::SetHarmonicBondParameters)
+ .def("SetHarmonicAngleParameters",&ost::mol::mm::Topology::SetHarmonicAngleParameters)
+ .def("SetUreyBradleyAngleParameters",&ost::mol::mm::Topology::SetUreyBradleyAngleParameters)
+ .def("SetPeriodicDihedralParameters",&ost::mol::mm::Topology::SetPeriodicDihedralParameters)
+ .def("SetPeriodicImproperParameters",&ost::mol::mm::Topology::SetPeriodicImproperParameters)
+ .def("SetHarmonicImproperParameters",&ost::mol::mm::Topology::SetHarmonicImproperParameters)
+ .def("SetCMapParameters",&WrapSetCMapParameters)
+ .def("SetLJPairParameters",&ost::mol::mm::Topology::SetLJPairParameters)
+ .def("SetDistanceConstraintParameters",&ost::mol::mm::Topology::SetDistanceConstraintParameters)
+ .def("SetHarmonicPositionRestraintParameters",&ost::mol::mm::Topology::SetHarmonicPositionRestraintParameters)
+ .def("SetHarmonicDistanceRestraintParameters",&ost::mol::mm::Topology::SetHarmonicDistanceRestraintParameters)
+ //functions to find interactions certain atoms are involved in
+ .def("GetHarmonicBondIndices",&GetHarmonicBondIndices)
+ .def("GetHarmonicBondIndices",&GetHarmonicBondIndicesSingleIndex)
+ .def("GetHarmonicAngleIndices",&GetHarmonicAngleIndices)
+ .def("GetHarmonicAngleIndices",&GetHarmonicAngleIndicesSingleIndex)
+ .def("GetUreyBradleyAngleIndices",&GetUreyBradleyAngleIndices)
+ .def("GetUreyBradleyAngleIndices",&GetUreyBradleyAngleIndicesSingleIndex)
+ .def("GetPeriodicDihedralIndices",&GetPeriodicDihedralIndices)
+ .def("GetPeriodicDihedralIndices",&GetPeriodicDihedralIndicesSingleIndex)
+ .def("GetPeriodicImproperIndices",&GetPeriodicImproperIndices)
+ .def("GetPeriodicImproperIndices",&GetPeriodicImproperIndicesSingleIndex)
+ .def("GetHarmonicImproperIndices",&GetHarmonicImproperIndices)
+ .def("GetHarmonicImproperIndices",&GetHarmonicImproperIndicesSingleIndex)
+ .def("GetDistanceConstraintIndex",&ost::mol::mm::Topology::GetDistanceConstraintIndex)
+ .def("GetDistanceConstraintIndices",&GetDistanceConstraintIndicesSingleIndex)
+ .def("GetCMapIndices",&GetCMapIndices)
+ .def("GetCMapIndices",&GetCMapIndicesSingleIndex)
+ .def("GetLJPairIndex",&ost::mol::mm::Topology::GetLJPairIndex)
+ .def("GetLJPairIndices",&GetLJPairIndicesSingleIndex)
+ .def("GetHarmonicDistanceRestraintIndices",&GetHarmonicDistanceRestraintIndices)
+ .def("GetHarmonicDistanceRestraintIndices",&GetHarmonicDistanceRestraintIndicesSingleIndex)
+ .def("GetHarmonicPositionRestraintIndices",&GetHarmonicPositionRestraintIndicesSingleIndex)
+
+ //functions to get amount of data in topology
+ .def("GetNumAtoms",&ost::mol::mm::Topology::GetNumAtoms)
+ .def("GetNumHarmonicBonds",&ost::mol::mm::Topology::GetNumHarmonicBonds)
+ .def("GetNumHarmonicAngles",&ost::mol::mm::Topology::GetNumHarmonicAngles)
+ .def("GetNumPeriodicDihedrals",&ost::mol::mm::Topology::GetNumPeriodicDihedrals)
+ .def("GetNumPeriodicImpropers",&ost::mol::mm::Topology::GetNumPeriodicImpropers)
+ .def("GetNumHarmonicImpropers",&ost::mol::mm::Topology::GetNumHarmonicImpropers)
+ .def("GetNumCMaps",&ost::mol::mm::Topology::GetNumCMaps)
+ .def("GetNumLJPairs",&ost::mol::mm::Topology::GetNumLJPairs)
+ .def("GetNumDistanceConstraints",&ost::mol::mm::Topology::GetNumDistanceConstraints)
+ .def("GetNumExclusions",&ost::mol::mm::Topology::GetNumExclusions)
+ .def("GetNumHarmonicPositionRestraints",&ost::mol::mm::Topology::GetNumHarmonicPositionRestraints)
+ .def("GetNumHarmonicDistanceRestraints",&ost::mol::mm::Topology::GetNumHarmonicDistanceRestraints)
+ //get internal indices
+ .def("GetAtomIndex",&GetIndexA)
+ .def("GetAtomIndex",&GetIndexB)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::TopologyPtr>();
+}
diff --git a/modules/mol/mm/pymod/wrap_mol_mm.cc b/modules/mol/mm/pymod/wrap_mol_mm.cc
new file mode 100644
index 0000000000000000000000000000000000000000..a0d16cdc5be6ce53a35f9a3fbb8d1d65a73f418c
--- /dev/null
+++ b/modules/mol/mm/pymod/wrap_mol_mm.cc
@@ -0,0 +1,31 @@
+#include <boost/python.hpp>
+
+
+using namespace boost::python;
+
+
+void export_MMSettings();
+void export_Simulation();
+void export_OpenMM();
+void export_Observers();
+void export_GromacsReader();
+void export_MMInteraction();
+void export_Buildingblock();
+void export_Forcefield();
+void export_BlockModifiers();
+void export_Topology();
+
+
+BOOST_PYTHON_MODULE(_ost_mol_mm)
+{
+ export_Forcefield();
+ export_MMSettings();
+ export_Simulation();
+ export_OpenMM();
+ export_Observers();
+ export_GromacsReader();
+ export_MMInteraction();
+ export_Buildingblock();
+ export_BlockModifiers();
+ export_Topology();
+}
diff --git a/modules/mol/mm/src/AMBER03.dat b/modules/mol/mm/src/AMBER03.dat
new file mode 100644
index 0000000000000000000000000000000000000000..69e7d22171f447229ce354d731773876fcba7bd4
Binary files /dev/null and b/modules/mol/mm/src/AMBER03.dat differ
diff --git a/modules/mol/mm/src/CHARMM27.dat b/modules/mol/mm/src/CHARMM27.dat
new file mode 100644
index 0000000000000000000000000000000000000000..9a9459fb0c9882ff4db05a70560389124a73f2e6
Binary files /dev/null and b/modules/mol/mm/src/CHARMM27.dat differ
diff --git a/modules/mol/mm/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94c9b323d36d5e54c8679c76b5cf96950bce3460
--- /dev/null
+++ b/modules/mol/mm/src/CMakeLists.txt
@@ -0,0 +1,56 @@
+set(OST_MOL_MM_HEADERS
+ forcefield.hh
+ gromacs_reader.hh
+ buildingblock.hh
+ block_modifiers.hh
+ gromacs_block_modifiers.hh
+ mm_interaction.hh
+ mm_settings.hh
+ simulation.hh
+ mm_modeller.hh
+ mm_observer.hh
+ state_extractor.hh
+ system_creator.hh
+ topology_creator.hh
+ index.hh
+ topology.hh
+ steep.hh
+
+)
+
+set(OST_MOL_MM_SOURCES
+ forcefield.cc
+ gromacs_reader.cc
+ buildingblock.cc
+ gromacs_block_modifiers.cc
+ mm_interaction.cc
+ simulation.cc
+ mm_modeller.cc
+ state_extractor.cc
+ mm_observer.cc
+ system_creator.cc
+ topology_creator.cc
+ topology.cc
+ steep.cc
+)
+
+set(MOL_MM_DEPS ost_mol ost_io)
+
+
+module(NAME mol_mm SOURCES ${OST_MOL_MM_SOURCES}
+ HEADERS ${OST_MOL_MM_HEADERS}
+ HEADER_OUTPUT_DIR ost/mol/mm
+ DEPENDS_ON ${MOL_MM_DEPS}
+ LINK ${BOOST_PROGRAM_OPTIONS})
+
+target_link_libraries(ost_mol_mm ${OPEN_MM_LIBRARIES})
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/forcefields"
+ "AMBER03.dat" "AMBER_03_FORCEFIELD"
+ "ost_mol_mm")
+install(FILES "AMBER03.dat" DESTINATION "share/openstructure/forcefields/")
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/forcefields"
+ "CHARMM27.dat" "CHARMM_27_FORCEFIELD"
+ "ost_mol_mm")
+install(FILES "CHARMM27.dat" DESTINATION "share/openstructure/forcefields/")
diff --git a/modules/mol/mm/src/block_modifiers.hh b/modules/mol/mm/src/block_modifiers.hh
new file mode 100644
index 0000000000000000000000000000000000000000..9174c514a570eb87eea853358f9ecb92dc12ed72
--- /dev/null
+++ b/modules/mol/mm/src/block_modifiers.hh
@@ -0,0 +1,55 @@
+#ifndef BLOCK_MODIFIERS
+#define BLOCK_MODIFIERS
+
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/io/binary_data_source.hh>
+#include <ost/io/binary_data_sink.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+class HydrogenConstructor;
+class TerminiConstructor;
+class BlockModifier;
+
+typedef boost::shared_ptr<HydrogenConstructor> HydrogenConstructorPtr;
+typedef boost::shared_ptr<TerminiConstructor> TerminiConstructorPtr;
+typedef boost::shared_ptr<BlockModifier> BlockModifierPtr;
+
+typedef enum {
+ GromacsBlockModifiers
+} BlockModifierType;
+
+class HydrogenConstructor{
+public:
+ HydrogenConstructor() { }
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p) = 0;
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed) = 0;
+ virtual void OnSave(ost::io::BinaryDataSink& ds) = 0;
+ virtual BlockModifierType GetBlockModifierType() = 0;
+};
+
+class TerminiConstructor{
+public:
+ TerminiConstructor() { }
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p) = 0;
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed) = 0;
+ virtual void OnSave(ost::io::BinaryDataSink& ds) = 0;
+ virtual BlockModifierType GetBlockModifierType() = 0;
+};
+
+class BlockModifier{
+public:
+ BlockModifier() { }
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p) = 0;
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed) = 0;
+ virtual void OnSave(ost::io::BinaryDataSink& ds) = 0;
+ virtual BlockModifierType GetBlockModifierType() = 0;
+};
+
+
+}}} //ns
+
+#endif
\ No newline at end of file
diff --git a/modules/mol/mm/src/buildingblock.cc b/modules/mol/mm/src/buildingblock.cc
new file mode 100644
index 0000000000000000000000000000000000000000..3d6a8b2b1b2cecc5d08784fd48dfd989928a1685
--- /dev/null
+++ b/modules/mol/mm/src/buildingblock.cc
@@ -0,0 +1,687 @@
+#include <ost/mol/mm/buildingblock.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+BuildingBlock::BuildingBlock(const BuildingBlock& block){
+
+ atoms_ = block.GetAtoms();
+ types_ = block.GetTypes();
+ charges_ = block.GetCharges();
+ masses_ = block.GetMasses();
+
+ //We have to force to create new interactions with new!!!
+ //There would be to danger to mess around with an interaction,
+ //that is associated with another building block.
+
+ std::vector<MMInteractionPtr> bonds = block.GetBonds();
+ std::vector<MMInteractionPtr> angles = block.GetAngles();
+ std::vector<MMInteractionPtr> dihedrals = block.GetDihedrals();
+ std::vector<MMInteractionPtr> impropers = block.GetImpropers();
+ std::vector<MMInteractionPtr> exclusions = block.GetExclusions();
+ std::vector<MMInteractionPtr> cmaps = block.GetCMaps();
+ std::vector<MMInteractionPtr> constraints = block.GetConstraints();
+
+ for(std::vector<MMInteractionPtr>::iterator i = bonds.begin();
+ i != bonds.end(); ++i){
+ bonds_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+ for(std::vector<MMInteractionPtr>::iterator i = angles.begin();
+ i != angles.end(); ++i){
+ angles_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+ for(std::vector<MMInteractionPtr>::iterator i = dihedrals.begin();
+ i != dihedrals.end(); ++i){
+ dihedrals_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+ for(std::vector<MMInteractionPtr>::iterator i = impropers.begin();
+ i != impropers.end(); ++i){
+ impropers_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+ for(std::vector<MMInteractionPtr>::iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ exclusions_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+ for(std::vector<MMInteractionPtr>::iterator i = cmaps.begin();
+ i != cmaps.end(); ++i){
+ cmaps_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+ for(std::vector<MMInteractionPtr>::iterator i = constraints.begin();
+ i != constraints.end(); ++i){
+ constraints_.push_back(MMInteractionPtr(new MMInteraction(**i)));
+ }
+}
+
+int BuildingBlock::GetAtomIndex(const String& atom_name) const{
+
+ uint ind = std::find(atoms_.begin(),atoms_.end(),atom_name) - atoms_.begin();
+
+ if(ind<atoms_.size()){
+ return ind;
+ }
+ return -1;
+}
+
+bool BuildingBlock::Match(const ost::mol::ResidueHandle& handle, bool match_connectivity, String& info) const{
+
+ //check for size
+ if(uint(handle.GetAtomCount()) != atoms_.size()){
+ std::stringstream ss;
+ ss << "Expected "<<atoms_.size()<<" atoms, got "<<handle.GetAtomCount();
+ info = ss.str();
+ return false;
+ }
+
+ //check for presence of particular atoms
+ for(std::vector<String>::const_iterator i = atoms_.begin(); i!=atoms_.end(); ++i){
+ if(!handle.FindAtom(*i).IsValid()){
+ std::stringstream ss;
+ ss << "Buildingblock has atom of name " << *i;
+ ss << ", which is not present in residue";
+ info = ss.str();
+ return false;
+ }
+ }
+
+ if(!match_connectivity) return true;
+
+ //check connectivity by extracting all unique bonds from handle,
+ //also bonds to other residues.
+ std::set<std::pair<String,String> > raw_bonds_handle;
+ std::vector<MMInteractionPtr> bonds_handle;
+ ost::mol::AtomHandleList atom_list = handle.GetAtomList();
+ ost::mol::ResidueHandle prev = handle.GetPrev();
+ ost::mol::ResidueHandle next = handle.GetNext();
+ ost::mol::AtomHandle atom_one;
+ ost::mol::AtomHandle atom_two;
+ String name_one;
+ String name_two;
+ std::vector<String> names;
+ names.push_back("");
+ names.push_back("");
+ ost::mol::BondHandleList bond_list;
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i != atom_list.end(); ++i){
+ bond_list = i->GetBondList();
+ for(ost::mol::BondHandleList::iterator j = bond_list.begin();
+ j != bond_list.end(); ++j){
+ atom_one = j->GetFirst();
+ atom_two = j->GetSecond();
+ name_one = atom_one.GetName();
+ name_two = atom_two.GetName();
+
+ if(atom_one.GetResidue() == prev) name_one = "-"+name_one;
+ else if(atom_one.GetResidue() == next) name_one = "+"+name_one;
+ else if(atom_one.GetResidue() != handle) continue; //in the building block
+ //there can only be atoms
+ //to previous or subsequent
+ //residues. So we don't check
+ //cases as they occur for example
+ //in disulfid bridges
+ if(atom_two.GetResidue() == prev) name_two = "-"+name_two;
+ else if(atom_two.GetResidue() == next) name_two = "+"+name_two;
+ else if(atom_two.GetResidue() != handle) continue; //dito
+
+ if(atom_one.GetIndex()<atom_two.GetIndex()) raw_bonds_handle.insert(std::make_pair(name_one,name_two));
+ else raw_bonds_handle.insert(std::make_pair(name_two,name_one));
+
+ }
+ }
+
+ for(std::set<std::pair<String,String> >::iterator i = raw_bonds_handle.begin();
+ i != raw_bonds_handle.end(); ++i){
+ MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ names[0] = i->first;
+ names[1] = i->second;
+ p->SetNames(names);
+ bonds_handle.push_back(p);
+ }
+
+ bool found;
+ //let's first check for bonds
+ for(std::vector<MMInteractionPtr>::const_iterator i = bonds_.begin();
+ i!=bonds_.end(); ++i){
+ found = false;
+ for(std::vector<MMInteractionPtr>::iterator j = bonds_handle.begin();
+ j != bonds_handle.end(); ++j){
+ if((*j)->MatchNames((*i)->GetNames())){
+ found = true;
+ std::vector<String> names = (*j)->GetNames();
+ raw_bonds_handle.erase(std::make_pair(names[0],names[1]));
+ break;
+ }
+ }
+ if(!found){
+ std::stringstream ss;
+ std::vector<String> names_for_info = (*i)->GetNames();
+ ss << "Buildingblock defines bond between \"" <<names_for_info[0];
+ ss << "\" and \"" << names_for_info[1] << "\". Those atoms are not connected in your residue";
+ info = ss.str();
+ return false;
+ }
+ }
+ //If there is a distance constraint matching a remaining raw bond, we also
+ //remove it from raw bonds
+ for(std::vector<MMInteractionPtr>::const_iterator i = constraints_.begin();
+ i != constraints_.end(); ++i){
+ for(std::vector<MMInteractionPtr>::iterator j = bonds_handle.begin();
+ j != bonds_handle.end(); ++j){
+ if((*j)->MatchNames((*i)->GetNames())){
+ std::vector<String> names = (*j)->GetNames();
+ raw_bonds_handle.erase(std::make_pair(names[0],names[1]));
+ break;
+ }
+ }
+ }
+ //we finally check whether there is an additional internal bond in the
+ //residue. Note, that a remaining bond to another residue (starting with +/-)
+ //is not a criterium for failing the match procedure
+ for(std::set<std::pair<String,String> >::iterator i = raw_bonds_handle.begin();
+ i != raw_bonds_handle.end(); ++i){
+ if( i->first.at(0) == '+' || i->first.at(0) == '-') continue;
+ if( i->second.at(0) == '+' || i->second.at(0) == '-') continue;
+ std::stringstream ss;
+ ss << "Your residue has a bond between atoms of name \"" << i->first << "\" and \"";
+ ss << i->second << "\", which is not defined in the buildingblock";
+ info = ss.str();
+ return false;
+ }
+ return true;
+}
+
+void BuildingBlock::Connect(ost::mol::ResidueHandle& handle, ost::mol::XCSEditor& ed){
+
+ if(!handle.IsValid()) throw ost::Error("Invalid Residue encountered in connecting procedure!");
+
+ ost::mol::ResidueHandle prev = handle.GetPrev();
+ ost::mol::ResidueHandle next = handle.GetNext();
+
+ //Let's build the connectivity
+ ost::mol::AtomHandle atom1,atom2;
+ std::vector<String> names;
+ String name1, name2;
+
+
+ for(std::vector<MMInteractionPtr>::iterator i = bonds_.begin();
+ i != bonds_.end(); ++i){
+
+ names = (*i)->GetNames();
+ name1 = names[0];
+ name2 = names[1];
+
+ if(name1[0] == '-'){
+ if(!prev.IsValid()) throw ost::Error("Cannot access previous residue in connecting procedure!");
+ atom1 = prev.FindAtom(name1.substr(1));
+ }
+ else if(name1[0] == '+'){
+ if(!next.IsValid()) throw ost::Error("Cannot access next residue in connecting procedure!");
+ atom1 = next.FindAtom(name1.substr(1));
+ }
+ else{
+ atom1 = handle.FindAtom(name1);
+ }
+
+ if(name2[0] == '-'){
+ if(!prev.IsValid()) throw ost::Error("Cannot access previous residue in connecting procedure!");
+ atom2 = prev.FindAtom(name2.substr(1));
+ }
+ else if(name2[0] == '+'){
+ if(!next.IsValid()) throw ost::Error("Cannot access next residue in connecting procedure!");
+ atom2 = next.FindAtom(name2.substr(1));
+ }
+ else{
+ atom2 = handle.FindAtom(name2);
+ }
+
+ if(!atom1.IsValid() || !atom2.IsValid()) throw ost::Error("Could not find required atom in connecting procedure!");
+
+ ed.Connect(atom1,atom2);
+ }
+}
+
+String BuildingBlock::GetType(const String& name) const{
+ int index = this->GetAtomIndex(name);
+ if(index!=-1) return types_[index];
+ std::stringstream ss;
+ ss << "Could not find requested atom of name \""<<name;
+ ss << "\" in buildingblock!";
+ throw ost::Error(ss.str());
+}
+
+Real BuildingBlock::GetCharge(const String& name) const{
+ int index = this->GetAtomIndex(name);
+ if(index!=-1) return charges_[index];
+ std::stringstream ss;
+ ss << "Could not find requested atom of name \""<<name;
+ ss << "\" in buildingblock!";
+ throw ost::Error(ss.str());
+}
+
+Real BuildingBlock::GetMass(const String& name) const{
+ int index = this->GetAtomIndex(name);
+ if(index!=-1) return masses_[index];
+ std::stringstream ss;
+ ss << "Could not find requested atom of name \""<<name;
+ ss << "\" in buildingblock!";
+ throw ost::Error(ss.str());
+}
+
+
+void BuildingBlock::AddBond(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < bonds_.size(); ++i){
+ if(bonds_[i]->MatchNames(names)){
+ bonds_.erase(bonds_.begin() + i);
+ --i;
+ }
+ }
+ }
+ bonds_.push_back(p);
+}
+
+void BuildingBlock::AddAngle(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < angles_.size(); ++i){
+ if(angles_[i]->MatchNames(names)){
+ angles_.erase(angles_.begin() + i);
+ --i;
+ }
+ }
+ }
+ angles_.push_back(p);
+}
+
+void BuildingBlock::AddDihedral(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ if(dihedrals_[i]->MatchNames(names)){
+ dihedrals_.erase(dihedrals_.begin() + i);
+ --i;
+ }
+ }
+ }
+ dihedrals_.push_back(p);
+}
+
+void BuildingBlock::AddImproper(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < impropers_.size(); ++i){
+ if(impropers_[i]->MatchNames(names)){
+ impropers_.erase(impropers_.begin() + i);
+ --i;
+ }
+ }
+ }
+ impropers_.push_back(p);
+}
+
+void BuildingBlock::AddExclusion(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ if(exclusions_[i]->MatchNames(names)){
+ exclusions_.erase(exclusions_.begin() + i);
+ --i;
+ }
+ }
+ }
+ exclusions_.push_back(p);
+}
+
+void BuildingBlock::AddCMap(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(cmaps_[i]->MatchNames(names)){
+ cmaps_.erase(cmaps_.begin() + i);
+ --i;
+ }
+ }
+ }
+ cmaps_.push_back(p);
+}
+
+void BuildingBlock::AddConstraint(MMInteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < constraints_.size(); ++i){
+ if(constraints_[i]->MatchNames(names)){
+ constraints_.erase(constraints_.begin() + i);
+ --i;
+ }
+ }
+ }
+ constraints_.push_back(p);
+}
+
+void BuildingBlock::RemoveAtom(const String& name){
+ int index = this->GetAtomIndex(name);
+ if(index != -1){
+ atoms_.erase(atoms_.begin()+index);
+ types_.erase(types_.begin()+index);
+ charges_.erase(charges_.begin()+index);
+ masses_.erase(masses_.begin()+index);
+ }
+
+ //All interactions, that contain this atom get deleted as well
+ //note, that we're looking at all interactions independently whether tere
+ //really is such an atom in the building block
+ for(uint i = 0; i < bonds_.size(); ++i){
+ if(bonds_[i]->HasName(name)){
+ bonds_.erase(bonds_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < angles_.size(); ++i){
+ if(angles_[i]->HasName(name)){
+ angles_.erase(angles_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ if(dihedrals_[i]->HasName(name)){
+ dihedrals_.erase(dihedrals_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < impropers_.size(); ++i){
+ if(impropers_[i]->HasName(name)){
+ impropers_.erase(impropers_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ if(exclusions_[i]->HasName(name)){
+ exclusions_.erase(exclusions_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(cmaps_[i]->HasName(name)){
+ cmaps_.erase(cmaps_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < constraints_.size(); ++i){
+ if(constraints_[i]->HasName(name)){
+ constraints_.erase(constraints_.begin()+i);
+ --i;
+ }
+ }
+}
+
+void BuildingBlock::ReplaceAtom(const String& name,const String& new_name,
+ const String& new_type, Real new_charge, Real new_mass){
+
+ int index = this->GetAtomIndex(name);
+ if(index != -1){
+ atoms_[index] = new_name;
+ types_[index] = new_type;
+ charges_[index] = new_charge;
+ masses_[index] = new_mass;
+
+ //we don't want to search every interaction associated with this
+ //atom, so we call the ReplaceAtom method for every interaction
+ //nothing will happen, if the atom of interest is not part of
+ //that interaction.
+
+ for(std::vector<MMInteractionPtr>::iterator i = bonds_.begin();
+ i!=bonds_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = angles_.begin();
+ i!=angles_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = dihedrals_.begin();
+ i!=dihedrals_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = impropers_.begin();
+ i!=impropers_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = exclusions_.begin();
+ i!=exclusions_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = cmaps_.begin();
+ i!=cmaps_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+ }
+}
+
+void BuildingBlock::AddAtom(const String& name, const String& type, Real charge, Real mass){
+ if (std::find(atoms_.begin(),atoms_.end(),name) != atoms_.end()) return;
+ atoms_.push_back(name);
+ types_.push_back(type);
+ charges_.push_back(charge);
+ masses_.push_back(mass);
+}
+
+void BuildingBlock::RemoveInteractionsToPrev(){
+ std::vector<String> names;
+ bool has_prev_atom;
+
+ for(uint i = 0; i < bonds_.size(); ++i){
+ has_prev_atom = false;
+ names = bonds_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ bonds_.erase(bonds_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < angles_.size(); ++i){
+ has_prev_atom = false;
+ names = angles_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ angles_.erase(angles_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ has_prev_atom = false;
+ names = dihedrals_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ dihedrals_.erase(dihedrals_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < impropers_.size(); ++i){
+ has_prev_atom = false;
+ names = impropers_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ impropers_.erase(impropers_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ has_prev_atom = false;
+ names = exclusions_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ exclusions_.erase(exclusions_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ has_prev_atom = false;
+ names = cmaps_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ cmaps_.erase(cmaps_.begin()+i);
+ --i;
+ }
+ }
+}
+
+void BuildingBlock::RemoveInteractionsToNext(){
+ std::vector<String> names;
+ bool has_next_atom;
+
+ for(uint i = 0; i < bonds_.size(); ++i){
+ has_next_atom = false;
+ names = bonds_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ bonds_.erase(bonds_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < angles_.size(); ++i){
+ has_next_atom = false;
+ names = angles_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ angles_.erase(angles_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ has_next_atom = false;
+ names = dihedrals_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ dihedrals_.erase(dihedrals_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < impropers_.size(); ++i){
+ has_next_atom = false;
+ names = impropers_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ impropers_.erase(impropers_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ has_next_atom = false;
+ names = exclusions_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ exclusions_.erase(exclusions_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ has_next_atom = false;
+ names = cmaps_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ cmaps_.erase(cmaps_.begin()+i);
+ --i;
+ }
+ }
+}
+
+void BuildingBlock::CheckInteractionToAdd(MMInteractionPtr p) const{
+ if(p->GetNames().empty()){
+ throw ost::Error("Expect interaction to have names properly set!");
+ }
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/buildingblock.hh b/modules/mol/mm/src/buildingblock.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f1cacdb516952ac7fc05f91e4357a9cd5035c7e8
--- /dev/null
+++ b/modules/mol/mm/src/buildingblock.hh
@@ -0,0 +1,248 @@
+#ifndef OST_FORCE_FIELD_BUILDING_BLOCK_HH
+#define OST_FORCE_FIELD_BUILDING_BLOCK_HH
+
+#include <vector>
+#include <limits>
+#include <set>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/message.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/geom/vec3.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class BuildingBlock;
+typedef boost::shared_ptr<BuildingBlock> BuildingBlockPtr;
+
+class BuildingBlock{
+public:
+ BuildingBlock() { }
+
+ //copy constructor needs to be defined explicitely, since the forces
+ //have to be newly created
+ BuildingBlock(const BuildingBlock& block);
+
+ bool Match(const ost::mol::ResidueHandle& handle, bool match_connectivity, String& info) const;
+
+ void Connect(ost::mol::ResidueHandle& handle, ost::mol::XCSEditor& ed);
+
+ //getter functionality for all buildingblock members
+
+ std::vector<String> GetAtoms() const { return atoms_; }
+
+ std::vector<String> GetTypes() const { return types_; }
+
+ std::vector<Real> GetCharges() const { return charges_; }
+
+ std::vector<Real> GetMasses() const { return masses_; }
+
+ String GetType(const String& name) const;
+
+ Real GetCharge(const String& name) const;
+
+ Real GetMass(const String& name) const;
+
+ std::vector<MMInteractionPtr> GetBonds() const { return bonds_; }
+
+ std::vector<MMInteractionPtr> GetAngles() const { return angles_; }
+
+ std::vector<MMInteractionPtr> GetDihedrals() const { return dihedrals_; }
+
+ std::vector<MMInteractionPtr> GetImpropers() const { return impropers_; }
+
+ std::vector<MMInteractionPtr> GetCMaps() const { return cmaps_; }
+
+ std::vector<MMInteractionPtr> GetExclusions() const { return exclusions_; }
+
+ std::vector<MMInteractionPtr> GetConstraints() const { return constraints_;}
+
+ //Add data to building block
+
+ void AddAtom(const String& name, const String& type, Real charge, Real mass = std::numeric_limits<Real>::quiet_NaN());
+
+ void AddBond(MMInteractionPtr p, bool replace_existing = false);
+
+ void AddAngle(MMInteractionPtr p, bool replace_existing = false);
+
+ void AddDihedral(MMInteractionPtr p, bool replace_existing = false);
+
+ void AddImproper(MMInteractionPtr p, bool replace_existing = false);
+
+ void AddExclusion(MMInteractionPtr p, bool replace_existing = false);
+
+ void AddCMap(MMInteractionPtr p, bool replace_existing = false);
+
+ void AddConstraint(MMInteractionPtr p, bool replace_existing = false);
+
+ //modifiers
+
+ //removes atom and all interactions associated to it
+ void RemoveAtom(const String& name);
+
+ //replaces atom in all interactions
+ void ReplaceAtom(const String& name,const String& new_name,
+ const String& new_type, Real new_charge,
+ Real new_mass = std::numeric_limits<Real>::quiet_NaN());
+
+
+ //remove all interactions to previous or next residue
+ void RemoveInteractionsToPrev();
+
+ void RemoveInteractionsToNext();
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ int num_atoms = atoms_.size();
+ ds & num_atoms;
+
+ if(ds.IsSource()){
+ atoms_ = std::vector<String>(num_atoms);
+ types_ = std::vector<String>(num_atoms);
+ charges_ = std::vector<Real>(num_atoms);
+ masses_ = std::vector<Real>(num_atoms);
+ }
+
+ for(unsigned int i = 0; i < num_atoms; ++i){
+ ds & atoms_[i];
+ ds & types_[i];
+ ds & charges_[i];
+ ds & masses_[i];
+ }
+
+ int num_bonds = bonds_.size();
+ int num_angles = angles_.size();
+ int num_dihedrals = dihedrals_.size();
+ int num_impropers = impropers_.size();
+ int num_exclusions = exclusions_.size();
+ int num_cmaps = cmaps_.size();
+ int num_constraints = constraints_.size();
+
+ ds & num_bonds;
+ ds & num_angles;
+ ds & num_dihedrals;
+ ds & num_impropers;
+ ds & num_exclusions;
+ ds & num_cmaps;
+ ds & num_constraints;
+
+ for(unsigned int i = 0; i < num_bonds; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ bonds_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = bonds_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(bonds_[i]);
+ }
+
+ for(unsigned int i = 0; i < num_angles; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ angles_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = angles_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(angles_[i]);
+ }
+
+ for(unsigned int i = 0; i < num_dihedrals; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ dihedrals_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = dihedrals_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(dihedrals_[i]);
+ }
+
+ for(unsigned int i = 0; i < num_impropers; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ impropers_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = impropers_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(impropers_[i]);
+ }
+
+ for(unsigned int i = 0; i < num_exclusions; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ exclusions_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = exclusions_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(exclusions_[i]);
+ }
+
+ for(unsigned int i = 0; i < num_cmaps; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ cmaps_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = cmaps_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(cmaps_[i]);
+ }
+
+ for(unsigned int i = 0; i < num_constraints; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ constraints_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = constraints_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(constraints_[i]);
+ }
+ }
+
+
+private:
+
+ int GetAtomIndex(const String& atom_name) const;
+ void CheckInteractionToAdd(MMInteractionPtr p) const;
+
+ std::vector<String> atoms_;
+ std::vector<String> types_;
+ std::vector<Real> charges_;
+ std::vector<Real> masses_;
+ std::vector<MMInteractionPtr> bonds_;
+ std::vector<MMInteractionPtr> angles_;
+ std::vector<MMInteractionPtr> dihedrals_;
+ std::vector<MMInteractionPtr> impropers_;
+ std::vector<MMInteractionPtr> exclusions_;
+ std::vector<MMInteractionPtr> cmaps_;
+ std::vector<MMInteractionPtr> constraints_;
+};
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/forcefield.cc b/modules/mol/mm/src/forcefield.cc
new file mode 100644
index 0000000000000000000000000000000000000000..93f1c882746f3e33b063657b3bcec8c94fef5a5c
--- /dev/null
+++ b/modules/mol/mm/src/forcefield.cc
@@ -0,0 +1,977 @@
+#include <ost/mol/mm/forcefield.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+ForcefieldPtr Forcefield::Load(const String& filename){
+
+
+ if (!boost::filesystem::exists(filename)) {
+ std::stringstream ss;
+ ss << "Could not open forcefield. File '"
+ << filename << "' does not exist";
+ throw ost::io::IOException(ss.str());
+ }
+
+ std::ifstream stream(filename.c_str(), std::ios_base::binary);
+ ost::io::BinaryDataSource ds(stream);
+ ForcefieldPtr ff_p(new Forcefield);
+
+ bool gen_pairs;
+ Real fudge_LJ;
+ Real fudge_QQ;
+ ds & gen_pairs;
+ ds & fudge_LJ;
+ ds & fudge_QQ;
+
+ ff_p->SetGenPairs(gen_pairs);
+ ff_p->SetFudgeLJ(fudge_LJ);
+ ff_p->SetFudgeQQ(fudge_QQ);
+
+ int num_atom_masses;
+ ds & num_atom_masses;
+
+ String atom_name;
+ Real mass;
+ for(int i = 0; i < num_atom_masses; ++i){
+ ds & atom_name;
+ ds & mass;
+ ff_p->AddMass(atom_name,mass);
+ }
+
+ int num_building_blocks;
+ ds & num_building_blocks;
+ String block_name;
+ for(int i = 0; i < num_building_blocks; ++i){
+ ds & block_name;
+ BuildingBlockPtr p(new BuildingBlock);
+ ds & *p;
+ ff_p->AddBuildingBlock(block_name,p);
+ }
+
+ int func_type;
+ int num_bonds;
+ ds & num_bonds;
+ for(int i = 0; i < num_bonds; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddBond(p);
+ }
+
+ int num_angles;
+ ds & num_angles;
+ for(int i = 0; i < num_angles; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddAngle(p);
+ }
+
+ int num_lj_pairs;
+ ds & num_lj_pairs;
+ for(int i = 0; i < num_lj_pairs; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddLJPair(p);
+ }
+
+ int num_constraints;
+ ds & num_constraints;
+ for(int i = 0; i < num_constraints; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddConstraint(p);
+ }
+
+ int num_cmaps;
+ ds & num_cmaps;
+ for(int i = 0; i < num_cmaps; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddCMap(p);
+ }
+
+ int num_genborn;
+ ds & num_genborn;
+ for(int i = 0; i < num_genborn; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddImplicitGenborn(p);
+ }
+
+ int num_ljs;
+ ds & num_ljs;
+ for(int i = 0; i < num_ljs; ++i){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddLJ(p);
+ }
+
+
+ int num_dihedrals;
+ ds & num_dihedrals;
+ int temp_num;
+ for(int i = 0; i < num_dihedrals; ++i){
+ ds & temp_num;
+ for(int j = 0; j < temp_num; ++j){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddDihedral(p);
+ }
+ }
+
+ int num_impropers;
+ ds & num_impropers;
+ for(int i = 0; i < num_impropers; ++i){
+ ds & temp_num;
+ for(int j = 0; j < temp_num; ++j){
+ ds & func_type;
+ MMInteractionPtr p(new MMInteraction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddImproper(p);
+ }
+ }
+
+ int num_atom_renamings;
+ ds & num_atom_renamings;
+ String res_name, old_name, new_name;
+ for(int i = 0; i < num_atom_renamings; ++i){
+ ds & res_name;
+ ds & temp_num;
+ for(int j = 0; j < temp_num; ++j){
+ ds & old_name;
+ ds & new_name;
+ ff_p->AddAtomRenamingRule(res_name,old_name,new_name);
+ }
+ }
+
+ int num_res_renaming;
+ ds & num_res_renaming;
+ for(int i = 0; i < num_res_renaming; ++i){
+ ds & res_name;
+ ResidueNamesPtr p(new ResidueNames);
+ ds & *p;
+ ff_p->AddResidueRenamingRule(res_name, p->main, p->nter, p->cter, p->twoter);
+ }
+
+ int num_hydrogen_constructors;
+ int block_modifier_type;
+ String block_modifier_name;
+ ds & num_hydrogen_constructors;
+ for(int i = 0; i < num_hydrogen_constructors; ++i){
+ ds & block_modifier_type;
+ ds & block_modifier_name;
+ switch(block_modifier_type){
+ case GromacsBlockModifiers:{
+ GromacsHydrogenConstructorPtr p(new GromacsHydrogenConstructor);
+ ds & *p;
+ ff_p->AddHydrogenConstructor(block_modifier_name,p);
+ break;
+ }
+ default:{
+ throw ost::Error("Invalid Block Modifier type encountered when loading hydrogen constructor!");
+ }
+
+ }
+ }
+
+ int num_block_modifiers;
+ ds & num_block_modifiers;
+ String modifier_name;
+
+ for(int i = 0; i < num_block_modifiers; ++i){
+ ds & block_modifier_type;
+ switch(block_modifier_type){
+ case GromacsBlockModifiers:{
+ GromacsBlockModifierPtr p(new GromacsBlockModifier);
+ ds & modifier_name;
+ ds & *p;
+ ff_p->AddBlockModifier(modifier_name,p);
+ break;
+ }
+ default:{
+ throw ost::Error("Invalid Block Modifier type encountered when loading!");
+ }
+ }
+
+ }
+
+ int num_standard_n_termini;
+ int num_standard_c_termini;
+
+ ds & num_standard_n_termini;
+ ds & num_standard_c_termini;
+
+ for(int i = 0; i < num_standard_n_termini; ++i){
+ ds & res_name;
+ ds & modifier_name;
+ ff_p->SetStandardNTer(res_name,modifier_name);
+ }
+
+ for(int i = 0; i < num_standard_c_termini; ++i){
+ ds & res_name;
+ ds & modifier_name;
+ ff_p->SetStandardCTer(res_name,modifier_name);
+ }
+
+ return ff_p;
+}
+
+void Forcefield::Save(const String& filename){
+ std::ofstream stream(filename.c_str(), std::ios_base::binary);
+ io::BinaryDataSink ds(stream);
+
+
+ ds & gen_pairs_;
+ ds & fudge_LJ_;
+ ds & fudge_QQ_;
+
+ int num_atom_masses = atom_masses_.size();
+ ds & num_atom_masses;
+ for(boost::unordered_map<String,Real>::iterator i = atom_masses_.begin();
+ i != atom_masses_.end(); ++i){
+ ds & i->first;
+ ds & i->second;
+ }
+
+ int num_building_blocks = building_blocks_.size();
+ ds & num_building_blocks;
+ for(boost::unordered_map<String,BuildingBlockPtr>::iterator i = building_blocks_.begin();
+ i != building_blocks_.end(); ++i){
+ ds & i->first;
+ ds & *(i->second);
+ }
+
+
+ int func_type;
+ int num_bonds = bonds_.size();
+ ds & num_bonds;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = bonds_.begin();
+ i != bonds_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_angles = angles_.size();
+ ds & num_angles;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = angles_.begin();
+ i != angles_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_lj_pairs = lj_14_pairs_.size();
+ ds & num_lj_pairs;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = lj_14_pairs_.begin();
+ i != lj_14_pairs_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_constraints = constraints_.size();
+ ds & num_constraints;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = constraints_.begin();
+ i != constraints_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_cmaps = cmaps_.size();
+ ds & num_cmaps;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = cmaps_.begin();
+ i != cmaps_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_genborn = implicit_genborn_.size();
+ ds & num_genborn;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = implicit_genborn_.begin();
+ i != implicit_genborn_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_ljs = ljs_.size();
+ ds & num_ljs;
+ for(boost::unordered_map<String,MMInteractionPtr>::iterator i = ljs_.begin();
+ i != ljs_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_dihedrals = dihedrals_.size();
+ int vector_size;
+ ds & num_dihedrals;
+ for(boost::unordered_map<String,std::vector<MMInteractionPtr> >::iterator i = dihedrals_.begin();
+ i != dihedrals_.end(); ++i){
+ vector_size = i->second.size();
+ ds & vector_size;
+ for(std::vector<MMInteractionPtr>::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ func_type = int((*j)->GetFuncType());
+ ds & func_type;
+ ds & **j;
+ }
+ }
+
+ int num_impropers = improper_dihedrals_.size();
+ ds & num_impropers;
+ for(boost::unordered_map<String,std::vector<MMInteractionPtr> >::iterator i = improper_dihedrals_.begin();
+ i != improper_dihedrals_.end(); ++i){
+ vector_size = i->second.size();
+ ds & vector_size;
+ for(std::vector<MMInteractionPtr>::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ func_type = int((*j)->GetFuncType());
+ ds & func_type;
+ ds & **j;
+ }
+ }
+
+
+ int num_atom_renamings = atom_renaming_ff_specific_.size();
+ ds & num_atom_renamings;
+ for(boost::unordered_map<String,std::vector<std::pair<String,String> > >::iterator i = atom_renaming_ff_specific_.begin();
+ i != atom_renaming_ff_specific_.end(); ++i){
+ ds & i->first;
+ vector_size = i->second.size();
+ ds & vector_size;
+ for(std::vector<std::pair<String,String> >::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ ds & j->first;
+ ds & j->second;
+ }
+ }
+
+ int num_res_renaming = res_renaming_ff_specific_.size();
+ ds & num_res_renaming;
+ for(boost::unordered_map<String,ResidueNamesPtr>::iterator i = res_renaming_ff_specific_.begin();
+ i != res_renaming_ff_specific_.end(); ++i){
+ ds & i->first;
+ ds & *(i->second);
+ }
+
+ int num_hydrogen_constructors = hydrogen_constructors_.size();
+ ds & num_hydrogen_constructors;
+ for(boost::unordered_map<String,HydrogenConstructorPtr>::iterator i = hydrogen_constructors_.begin();
+ i != hydrogen_constructors_.end(); ++i){
+ func_type = int(i->second->GetBlockModifierType());
+ ds & func_type;
+ ds & i->first;
+ i->second->OnSave(ds);
+ }
+
+ int num_block_modifiers = block_modifiers_.size();
+ ds & num_block_modifiers;
+ for(boost::unordered_map<String,BlockModifierPtr>::iterator i = block_modifiers_.begin();
+ i != block_modifiers_.end(); ++i){
+ func_type = int(i->second->GetBlockModifierType());
+ ds & func_type;
+ ds & i->first;
+ i->second->OnSave(ds);
+ }
+
+ int num_standard_n_termini = standard_c_termini_.size();
+ int num_standard_c_termini = standard_n_termini_.size();
+ ds & num_standard_n_termini;
+ ds & num_standard_c_termini;
+
+ for(boost::unordered_map<String, String>::iterator i = standard_n_termini_.begin();
+ i != standard_n_termini_.end(); ++i){
+ ds & i->first;
+ ds & i->second;
+ }
+
+ for(boost::unordered_map<String, String>::iterator i = standard_c_termini_.begin();
+ i != standard_c_termini_.end(); ++i){
+ ds & i->first;
+ ds & i->second;
+ }
+
+}
+
+BuildingBlockPtr Forcefield::GetBuildingBlock(const String& name) const{
+ boost::unordered_map<String,BuildingBlockPtr>::const_iterator i = building_blocks_.find(name);
+ if(i == building_blocks_.end()){
+ std::stringstream ss;
+ ss << "Forcefield does not contain requested building block ";
+ ss << "\"" << name << "\"";
+ throw ost::Error(ss.str());
+ }
+ BuildingBlockPtr ff_p = i->second;
+ //let's create a new building block to avoid messing around with the
+ //force field building blocks
+ BuildingBlockPtr p(new BuildingBlock(*ff_p));
+ return p;
+}
+
+BlockModifierPtr Forcefield::GetBlockModifier(const String& modifier_name) const{
+ boost::unordered_map<String,BlockModifierPtr>::const_iterator i = block_modifiers_.find(modifier_name);
+ if(i == block_modifiers_.end()) return BlockModifierPtr();
+ return i->second;
+}
+
+String Forcefield::GetAtomType(const String& res_name, const String& atom_name) const{
+ BuildingBlockPtr block = this->GetBuildingBlock(res_name);
+ return block->GetType(atom_name);
+}
+
+HydrogenConstructorPtr Forcefield::GetHydrogenConstructor(const String& name) const{
+ boost::unordered_map<String,HydrogenConstructorPtr>::const_iterator i = hydrogen_constructors_.find(name);
+ if(i != hydrogen_constructors_.end()) return i->second;
+ return HydrogenConstructorPtr();
+}
+
+BlockModifierPtr Forcefield::GetNTerModifier(const String& res_name, const String& ter_name) const{
+ String temp = ter_name;
+ if(temp == ""){
+ boost::unordered_map<String,String>::const_iterator it = standard_n_termini_.find(res_name);
+ if(it != standard_n_termini_.end()) temp = it->second;
+ else return BlockModifierPtr();
+ }
+ return this->GetBlockModifier(temp);
+}
+
+BlockModifierPtr Forcefield::GetCTerModifier(const String& res_name, const String& ter_name) const{
+ String temp = ter_name;
+ if(temp == ""){
+ boost::unordered_map<String,String>::const_iterator it = standard_c_termini_.find(res_name);
+ if(it != standard_c_termini_.end()) temp = it->second;
+ else return BlockModifierPtr();
+ }
+ return this->GetBlockModifier(temp);
+}
+
+MMInteractionPtr Forcefield::GetBond(const String& type1, const String& type2) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ bonds_.find(this->AtomTypesToKeyword(types));
+ if(i != bonds_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain bond for requested atom types!");
+}
+
+MMInteractionPtr Forcefield::GetAngle(const String& type1, const String& type2,
+ const String& type3) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ angles_.find(this->AtomTypesToKeyword(types));
+ if(i != angles_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain angle for requested atom types!");
+}
+
+std::vector<MMInteractionPtr> Forcefield::GetDihedrals(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ types.push_back(type4);
+
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator i =
+ dihedrals_.find(this->AtomTypesToKeyword(types));
+
+ if(i != dihedrals_.end()) return i->second;
+
+ //if we reach this point, we have to look for all dihedrals with wildcards...
+ std::vector<MMInteractionPtr> dihedrals;
+ std::vector<String> types_with_wildcards;
+
+ //lets first check single wildcards
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != dihedrals_.end()) dihedrals.insert(dihedrals.end(),j->second.begin(),j->second.end());
+ }
+
+ //we check for two wildcards
+ for(int i = 0; i < 4; ++i){
+ for(int j = i+1; j < 4; ++j){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ types_with_wildcards[j] = "X";
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator k =
+ dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(k != dihedrals_.end()) dihedrals.insert(dihedrals.end(),k->second.begin(),k->second.end());
+ }
+ }
+
+ //as stupid as it may sound, we also look for dihedrals with 3 wildcards
+ std::vector<String> all_wildcards;
+ for(int i = 0; i < 4; ++i){
+ all_wildcards.push_back("X");
+ }
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = all_wildcards;
+ types_with_wildcards[i] = types[i];
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != dihedrals_.end()) dihedrals.insert(dihedrals.end(),j->second.begin(),j->second.end());
+ }
+
+ if(!dihedrals.empty()) return dihedrals;
+ throw ost::Error("Forcefield does not contain any dihedrals for requested atom types!");
+}
+
+std::vector<MMInteractionPtr> Forcefield::GetImpropers(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ types.push_back(type4);
+
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator i =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types));
+
+ if(i != improper_dihedrals_.end()) return i->second;
+
+ //if we reach this point, we have to look for all dihedrals with wildcards...
+ std::vector<MMInteractionPtr> impropers;
+ std::vector<String> types_with_wildcards;
+
+ //lets first check single wildcards
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != improper_dihedrals_.end()) impropers.insert(impropers.end(),j->second.begin(),j->second.end());
+ }
+
+ //we check for two wildcards
+ for(int i = 0; i < 4; ++i){
+ for(int j = i+1; j < 4; ++j){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ types_with_wildcards[j] = "X";
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator k =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(k != improper_dihedrals_.end()) impropers.insert(impropers.end(),k->second.begin(),k->second.end());
+ }
+ }
+
+ //as stupid as it may sound, we also look for dihedrals with 3 wildcards
+ std::vector<String> all_wildcards;
+ for(int i = 0; i < 4; ++i){
+ all_wildcards.push_back("X");
+ }
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = all_wildcards;
+ types_with_wildcards[i] = types[i];
+ boost::unordered_map<String,std::vector<MMInteractionPtr> >::const_iterator j =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != improper_dihedrals_.end()) impropers.insert(impropers.end(),j->second.begin(),j->second.end());
+ }
+
+ if(!impropers.empty()) return impropers;
+
+ throw ost::Error("Forcefield does not contain any impropers for requested atom types!");
+}
+
+MMInteractionPtr Forcefield::GetCMap(const String& type1, const String& type2,
+ const String& type3, const String& type4,
+ const String& type5) const{
+
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ types.push_back(type4);
+ types.push_back(type5);
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ cmaps_.find(this->AtomTypesToKeyword(types,false));
+ if(i != cmaps_.end()) return i->second;
+
+ throw ost::Error("Forcefield does not contain cmap for requested atom types!");
+}
+
+MMInteractionPtr Forcefield::GetImplicitGenborn(const String& type) const{
+
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ implicit_genborn_.find(type);
+ if(i != implicit_genborn_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain implicit genborn parameters for requested atom type!");
+}
+
+MMInteractionPtr Forcefield::GetLJ(const String& type) const{
+
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ ljs_.find(type);
+
+ if(i != ljs_.end()){
+ return i->second;
+ }
+ throw ost::Error("Forcefield does not contain lennard jones parameters for requested atom types!");
+}
+
+MMInteractionPtr Forcefield::GetLJ(const String& type1,
+ const String& type2,
+ bool pair) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+
+ if(pair){
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ lj_14_pairs_.find(this->AtomTypesToKeyword(types));
+ if(i == lj_14_pairs_.end()){
+ if(!gen_pairs_){
+ std::stringstream ss;
+ ss << "was not able to find lj parameters between atoms of type ";
+ ss << type1 << " and " << type2 << " with gen_pairs ";
+ ss << "set to no!";
+ throw ost::Error(ss.str());
+ }
+ }
+ else{
+ return i->second;
+ }
+ }
+
+ MMInteractionPtr temp1, temp2;
+ temp1 = this->GetLJ(type1);
+ temp2 = this->GetLJ(type2);
+ if(temp1 && temp2){
+ MMInteraction* interaction_ptr;
+ if(pair) interaction_ptr = new MMInteraction(LJPair);
+ else interaction_ptr = new MMInteraction(LJ);
+ MMInteractionPtr return_ptr(interaction_ptr);
+ std::vector<Real> param1, param2, param;
+ param1 = temp1->GetParam();
+ param2 = temp2->GetParam();
+ param.push_back(0.5*(param1[0]+param2[0]));
+ param.push_back(sqrt(param1[1]*param2[1]));
+ return_ptr->SetTypes(types);
+ return_ptr->SetParam(param);
+ return return_ptr;
+ }
+
+ throw ost::Error("Forcefield does not contain lennard jones parameters for requested atom types!");
+
+}
+
+MMInteractionPtr Forcefield::GetConstraint(const String& type1,
+ const String& type2){
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ boost::unordered_map<String,MMInteractionPtr>::const_iterator i =
+ constraints_.find(this->AtomTypesToKeyword(types));
+ if(i != constraints_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain constraint for requested atom types!");
+}
+
+Real Forcefield::GetMass(const String& atom_type) const{
+ boost::unordered_map<String,Real>::const_iterator it = atom_masses_.find(atom_type);
+ if(it == atom_masses_.end()){
+ std::stringstream ss;
+ ss << "There is no mass defined for atom of type " << atom_type;
+ throw ost::Error(ss.str());
+ }
+ return it->second;
+}
+
+void Forcefield::AddBond(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"BOND");
+ std::vector<String> types = p->GetTypes();
+ bonds_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddAngle(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"ANGLE");
+ std::vector<String> types = p->GetTypes();
+ angles_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddDihedral(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"DIHEDRAL");
+ std::vector<String> types = p->GetTypes();
+ String keyword = this->AtomTypesToKeyword(types);
+ if(dihedrals_.find(keyword) == dihedrals_.end()){
+ dihedrals_[keyword] = std::vector<MMInteractionPtr>();
+ }
+ dihedrals_[keyword].push_back(p);
+}
+
+void Forcefield::AddImproper(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"IMPROPER");
+ std::vector<String> types = p->GetTypes();
+ String keyword = this->AtomTypesToKeyword(types);
+ if(improper_dihedrals_.find(keyword) == improper_dihedrals_.end()){
+ improper_dihedrals_[keyword] = std::vector<MMInteractionPtr>();
+ }
+ improper_dihedrals_[keyword].push_back(p);
+}
+
+void Forcefield::AddCMap(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"CMAP");
+ std::vector<String> types = p->GetTypes();
+ cmaps_[this->AtomTypesToKeyword(types,false)] = p;
+}
+
+void Forcefield::AddImplicitGenborn(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"IMPLICIT_GENBORN");
+ std::vector<String> types = p->GetTypes();
+ implicit_genborn_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddLJ(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"LJ");
+ std::vector<String> types = p->GetTypes();
+ ljs_[types[0]] = p;
+}
+
+void Forcefield::AddLJPair(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"LJ_PAIR");
+ std::vector<String> types = p->GetTypes();
+ lj_14_pairs_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddConstraint(MMInteractionPtr p){
+ this->CheckInteractionToAdd(p,"CONSTRAINT");
+ std::vector<String> types = p->GetTypes();
+ constraints_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddResidueRenamingRule(const String& name,
+ const String& ff_main_name,
+ const String& ff_n_ter_name,
+ const String& ff_c_ter_name,
+ const String& ff_two_ter_name){
+ ResidueNamesPtr p(new ResidueNames(ff_main_name,
+ ff_n_ter_name,
+ ff_c_ter_name,
+ ff_two_ter_name));
+ res_renaming_ff_specific_[name] = p;
+}
+
+void Forcefield::AddAtomRenamingRule(const String& res_name,
+ const String& old_atom_name,
+ const String& new_atom_name){
+ if(atom_renaming_ff_specific_.find(res_name) == atom_renaming_ff_specific_.end()){
+ std::vector<std::pair<String,String> > new_vec;
+ atom_renaming_ff_specific_[res_name] = new_vec;
+ }
+
+ atom_renaming_ff_specific_[res_name].push_back(std::make_pair(old_atom_name,new_atom_name));
+}
+
+void Forcefield::AssignFFSpecificNames(ost::mol::EntityHandle& handle, bool reverse) const{
+
+ //the whole FF specific renaming procedure assumes a standard naming,
+ //in our case the gromacs defined standard naming
+
+ ost::mol::XCSEditor ed = handle.EditXCS();
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::AtomHandleList atom_list;
+ ost::mol::AtomHandle atom;
+ ost::mol::ResidueHandle residue;
+
+ if(!reverse){
+
+ ost::mol::ResidueHandle next,prev;
+ bool n_ter,c_ter;
+ //ost::mol::AtomHandle peptide_n,peptide_c,nucleotide_p,nucleotide_o;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+
+ if(res_renaming_ff_specific_.find(i->GetName()) == res_renaming_ff_specific_.end()){
+ continue;
+ }
+
+ n_ter = false;
+ c_ter = false;
+
+ //peptide_n = i->FindAtom("N");
+ //nucleotide_p = i->FindAtom("P");
+
+ prev = i->GetPrev();
+ next = i->GetNext();
+
+ if(!prev.IsValid()){
+ n_ter = true;
+ }
+ //else{
+ //peptide_c = prev.FindAtom("C");
+ //nucleotide_o = prev.FindAtom("O3");
+
+ //if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ //n_ter = true;
+ //}
+ //}
+
+ if(!next.IsValid()){
+ c_ter = true;
+ }
+ //else{
+ //peptide_n = next.FindAtom("N");
+ //peptide_c = i->FindAtom("C");
+ //nucleotide_p = next.FindAtom("P");
+ //nucleotide_o = i->FindAtom("O3");
+
+ //if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ //c_ter = true;
+ //}
+ //}
+ if(c_ter && n_ter){
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->twoter);
+ continue;
+ }
+ if(n_ter){
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->nter);
+ continue;
+ }
+ if(c_ter){
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->cter);
+ continue;
+ }
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->main);
+ }
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();i!=res_list.end();++i){
+ boost::unordered_map<String,std::vector<std::pair<String,String> > >::const_iterator map_it = atom_renaming_ff_specific_.find(i->GetName());
+ if(map_it!=atom_renaming_ff_specific_.end()){
+ for(std::vector<std::pair<String,String> >::const_iterator j = map_it->second.begin();
+ j!=map_it->second.end();++j){
+ atom = i->FindAtom(j->first);
+ if(atom.IsValid()) ed.RenameAtom(atom,j->second);
+ }
+ }
+ }
+ return;
+ }
+
+ //it seems, that we have to do the reverse ff renaming => ff specific to gromacs standard
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();i!=res_list.end();++i){
+ boost::unordered_map<String,std::vector<std::pair<String,String> > >::const_iterator map_it = atom_renaming_ff_specific_.find(i->GetName());
+ if(map_it!=atom_renaming_ff_specific_.end()){
+ for(std::vector<std::pair<String,String> >::const_iterator j = map_it->second.begin();
+ j!=map_it->second.end();++j){
+ atom = i->FindAtom(j->second);
+ if(atom.IsValid()) ed.RenameAtom(atom,j->first);
+ }
+ }
+ }
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin(); i != res_list.end(); ++i){
+ for(boost::unordered_map<String,ResidueNamesPtr>::const_iterator j = res_renaming_ff_specific_.begin();
+ j != res_renaming_ff_specific_.end(); ++j){
+ if(j->second->Contains(i->GetName())){
+ ed.RenameResidue(*i,j->first);
+ break;
+ }
+ }
+ }
+}
+
+String Forcefield::AtomTypesToKeyword(std::vector<String>& types, bool allow_reordering) const{
+ bool revert = false;
+ int num_types = types.size();
+
+ int comparisons = num_types/2; //integer division => truncate
+ for(int i = 0; i < comparisons; ++i){
+ //note, that in case of equality the next iteration gets entered
+ if(types[i] < types[num_types - i - 1]) break;
+ else if(types[i] > types[num_types - i - 1]){
+ revert = true;
+ break;
+ }
+ }
+
+ if(revert && allow_reordering) std::reverse(types.begin(),types.end());
+ std::stringstream ss;
+ std::vector<String>::iterator i = types.begin();
+ ss << *i++;
+ for (; i != types.end(); ++i) {
+ ss << "_" << *i;
+ }
+ return ss.str();
+}
+
+void Forcefield::CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const{
+ bool valid = true;
+ if(p->GetTypes().empty()) valid = false;
+ if(!p->IsParametrized()) valid = false;
+ if(!valid){
+ throw ost::Error("Expect interaction to have types and parameters properly set!");
+ }
+ if(interaction_type == "BOND"){
+ if(p->GetFuncType() != HarmonicBond){
+ throw ost::Error("Invalid function type encountered when adding bond!");
+ } return;
+ }
+ if(interaction_type == "ANGLE"){
+ if(p->GetFuncType() != HarmonicAngle && p->GetFuncType() != UreyBradleyAngle){
+ throw ost::Error("Invalid function type encountered when adding angle!");
+ } return;
+ }
+ if(interaction_type == "DIHEDRAL"){
+ if(p->GetFuncType() != PeriodicDihedral){
+ throw ost::Error("Invalid function type encountered when adding dihedral!");
+ } return;
+ }
+ if(interaction_type == "IMPROPER"){
+ if(p->GetFuncType() != PeriodicImproper && p->GetFuncType() != HarmonicImproper){
+ throw ost::Error("Invalid function type encountered when adding improper!");
+ } return;
+ }
+ if(interaction_type == "CMAP"){
+ if(p->GetFuncType() != CMap){
+ throw ost::Error("Invalid function type encountered when adding cmap!");
+ } return;
+ }
+ if(interaction_type == "IMPLICIT_GENBORN"){
+ if(p->GetFuncType() != GBSA){
+ throw ost::Error("Invalid function type encountered when adding implicit genborn!");
+ } return;
+ }
+ if(interaction_type == "LJ"){
+ if(p->GetFuncType() != LJ){
+ throw ost::Error("Invalid function type encountered when adding lj!");
+ } return;
+ }
+ if(interaction_type == "LJ_PAIR"){
+ if(p->GetFuncType() != LJPair){
+ throw ost::Error("Invalid function type encountered when adding lj pair!");
+ } return;
+ }
+ if(interaction_type == "CONSTRAINT"){
+ if(p->GetFuncType() != DistanceConstraint){
+ throw ost::Error("Invalid function type encountered when adding constraint!");
+ } return;
+ }
+
+ std::stringstream ss;
+ ss << "Cannot validate added interaction of type "<< interaction_type << "!";
+ throw ost::Error(ss.str());
+
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/forcefield.hh b/modules/mol/mm/src/forcefield.hh
new file mode 100644
index 0000000000000000000000000000000000000000..e5d39ad321e8774a91388618481396241762a70b
--- /dev/null
+++ b/modules/mol/mm/src/forcefield.hh
@@ -0,0 +1,204 @@
+#ifndef OST_FORCE_FIELD_HH
+#define OST_FORCE_FIELD_HH
+
+#include <vector>
+#include <algorithm>
+
+
+#include <boost/shared_ptr.hpp>
+#include <boost/unordered_map.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+namespace ost { namespace mol{ namespace mm{
+
+struct ResidueNames;
+class Forcefield;
+
+typedef boost::shared_ptr<ResidueNames> ResidueNamesPtr;
+typedef boost::shared_ptr<ost::mol::mm::Forcefield> ForcefieldPtr;
+
+struct ResidueNames{
+
+ ResidueNames() { };
+
+ ResidueNames(String a, String b, String c, String d):
+ main(a),nter(b),cter(c),twoter(d) { }
+
+ String main;
+ String nter;
+ String cter;
+ String twoter;
+
+ bool Contains(const String& name){
+ return name == main || name == nter || name == cter || name == twoter;
+ }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & main;
+ ds & nter;
+ ds & cter;
+ ds & twoter;
+ }
+};
+
+
+class Forcefield {
+public:
+
+ Forcefield(): gen_pairs_(true), fudge_LJ_(1.0),fudge_QQ_(1.0) { }
+
+ static ForcefieldPtr Load(const String& filename);
+
+ void Save(const String& filename);
+
+ //Getter functions
+
+ BuildingBlockPtr GetBuildingBlock(const String& name) const;
+
+ BlockModifierPtr GetBlockModifier(const String& modifier_name) const;
+
+ String GetAtomType(const String& res_name, const String& atom_name) const;
+
+ HydrogenConstructorPtr GetHydrogenConstructor(const String& name) const;
+
+ BlockModifierPtr GetNTerModifier(const String& res_name, const String& ter_name = "") const;
+
+ BlockModifierPtr GetCTerModifier(const String& res_name, const String& ter_name = "") const;
+
+ MMInteractionPtr GetBond(const String& type1,
+ const String& type2) const;
+
+ MMInteractionPtr GetAngle(const String& type1,
+ const String& type2,
+ const String& type3) const;
+
+ std::vector<MMInteractionPtr> GetDihedrals(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const;
+
+ std::vector<MMInteractionPtr> GetImpropers(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const;
+
+ MMInteractionPtr GetCMap(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4,
+ const String& type5) const;
+
+ MMInteractionPtr GetImplicitGenborn(const String& type1) const;
+
+ MMInteractionPtr GetLJ(const String& type1,
+ const String& type2,
+ bool pair=false) const;
+
+ MMInteractionPtr GetLJ(const String& type) const;
+
+ MMInteractionPtr GetConstraint(const String& type1,
+ const String& type2);
+
+ Real GetMass(const String& type) const;
+
+ Real GetFudgeLJ() const { return fudge_LJ_; }
+
+ Real GetFudgeQQ() const { return fudge_QQ_; }
+
+ //functions to add interactions and settings
+
+ void AddBuildingBlock(const String& name, BuildingBlockPtr p) { building_blocks_[name] = p; }
+
+ void AddBond(MMInteractionPtr p);
+
+ void AddAngle(MMInteractionPtr p);
+
+ void AddDihedral(MMInteractionPtr p);
+
+ void AddImproper(MMInteractionPtr p);
+
+ void AddCMap(MMInteractionPtr p);
+
+ void AddImplicitGenborn(MMInteractionPtr p);
+
+ void AddLJ(MMInteractionPtr p);
+
+ void AddLJPair(MMInteractionPtr p);
+
+ void AddConstraint(MMInteractionPtr p);
+
+ void AddMass(const String& type, Real mass) { atom_masses_[type] = mass; }
+
+ void SetFudgeLJ(Real f_lj) { fudge_LJ_ = f_lj; }
+
+ void SetFudgeQQ(Real f_qq) { fudge_QQ_ = f_qq; }
+
+ void SetGenPairs(bool gen_pairs) { gen_pairs_ = gen_pairs; }
+
+ void AddResidueRenamingRule(const String& name,
+ const String& ff_main_name,
+ const String& ff_n_ter_name,
+ const String& ff_c_ter_name,
+ const String& ff_two_ter_name);
+
+ void AddAtomRenamingRule(const String& res_name,
+ const String& old_atom_name,
+ const String& new_atom_name);
+
+ void AddHydrogenConstructor(const String& residue_name, HydrogenConstructorPtr p){
+ hydrogen_constructors_[residue_name] = p;
+ }
+
+ void AddBlockModifier(const String& modifier_name,
+ BlockModifierPtr p) { block_modifiers_[modifier_name] = p; }
+
+ void SetStandardCTer(const String& res_name, const String& ter_name) { standard_c_termini_[res_name] = ter_name; }
+
+ void SetStandardNTer(const String& res_name, const String& ter_name) { standard_n_termini_[res_name] = ter_name; }
+
+
+ //Renaming to the forcefield specific names (residues/atoms)
+ void AssignFFSpecificNames(ost::mol::EntityHandle& handle, bool reverse=false) const;
+
+private:
+
+ String AtomTypesToKeyword(std::vector<String>& types, bool allow_reordering = true) const;
+ void CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const;
+
+ //this is all nonbonded stuff
+ bool gen_pairs_;
+ Real fudge_LJ_;
+ Real fudge_QQ_;
+
+ boost::unordered_map<String, Real> atom_masses_;
+ boost::unordered_map<String, BuildingBlockPtr> building_blocks_;
+ boost::unordered_map<String, BlockModifierPtr> block_modifiers_;
+
+ //the standard interactions
+ boost::unordered_map<String,MMInteractionPtr> bonds_;
+ boost::unordered_map<String,MMInteractionPtr> angles_;
+ boost::unordered_map<String,MMInteractionPtr> lj_14_pairs_;
+ boost::unordered_map<String,MMInteractionPtr> constraints_;
+ boost::unordered_map<String,MMInteractionPtr> cmaps_;
+ boost::unordered_map<String,MMInteractionPtr> implicit_genborn_;
+ boost::unordered_map<String,MMInteractionPtr> ljs_;
+ boost::unordered_map<String,std::vector<MMInteractionPtr> > dihedrals_;
+ boost::unordered_map<String,std::vector<MMInteractionPtr> > improper_dihedrals_;
+
+ boost::unordered_map<String, std::vector<std::pair<String,String> > > atom_renaming_ff_specific_;
+ boost::unordered_map<String, ResidueNamesPtr> res_renaming_ff_specific_;
+
+ boost::unordered_map<String, HydrogenConstructorPtr> hydrogen_constructors_;
+ boost::unordered_map<String, String> standard_n_termini_;
+ boost::unordered_map<String, String> standard_c_termini_;
+};
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.cc b/modules/mol/mm/src/gromacs_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0a8f74c96d19e172a350e55e5fcc99834e9f00b4
--- /dev/null
+++ b/modules/mol/mm/src/gromacs_block_modifiers.cc
@@ -0,0 +1,506 @@
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+std::vector<geom::Vec3> GromacsPositionRuleEvaluator::EvaluatePosRule(int rule,
+ int number,
+ const std::vector<geom::Vec3>& anchors){
+
+ std::vector<geom::Vec3> positions;
+
+ switch(rule){
+
+ case 1:{
+ geom::Vec3 i_j = geom::Normalize(anchors[0]-anchors[1]);
+ geom::Vec3 i_k = geom::Normalize(anchors[0]-anchors[2]);
+ geom::Vec3 temp = geom::Normalize(i_j+i_k);
+ positions.push_back(anchors[0]+temp);
+ break;
+ }
+
+ case 2:{
+ Real x = 0.333806859234;
+ Real y = 0.942641491092;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 3:{
+ Real x = 0.5;
+ Real y = 0.866025403784;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i-y*q);
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 4:{
+ Real x = 0.333313247568;
+ Real y = 0.942816142732;
+ Real z = 0.866025403784;
+
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ geom::Vec3 n1 = i+x*j_i+y*q;
+
+ geom::Vec3 temp = geom::Normalize(geom::Cross(j_i,n1-i));
+
+ geom::Vec3 n2 = i+x*j_i-0.5*q+z*temp;
+ geom::Vec3 n3 = i+x*j_i-0.5*q-z*temp;
+
+ positions.push_back(n1);
+ positions.push_back(n2);
+ if(number==3) positions.push_back(n3);
+ break;
+ }
+
+ case 5:{
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 i_j = geom::Normalize(i-anchors[1]);
+ geom::Vec3 i_k = geom::Normalize(i-anchors[2]);
+ geom::Vec3 i_l = geom::Normalize(i-anchors[3]);
+ geom::Vec3 temp = geom::Normalize(i_j+i_k+i_l);
+ positions.push_back(i+temp);
+ break;
+ }
+
+ case 6:{
+ Real x = 0.81649043092;
+ Real y = 0.577358966516;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 i_j = geom::Normalize(i-anchors[1]);
+ geom::Vec3 i_k = geom::Normalize(i-anchors[2]);
+ geom::Vec3 temp_one = geom::Normalize(i_j+i_k);
+ geom::Vec3 temp_two = geom::Normalize(geom::Cross(i_j,i_k));
+ positions.push_back(i+y*temp_one+x*temp_two);
+ positions.push_back(i+y*temp_one-x*temp_two);
+ break;
+ }
+
+ case 7:{
+ //not implemented yet, do nothing
+ break;
+ }
+
+ case 8:{
+ Real x = 1.36*0.522498564716;
+ Real y = 1.36*0.852640164354;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i-y*q);
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 9:{
+ Real x1 = 1.23*0.51503807491;
+ Real x2 = 1.25*0.422618261741;
+ Real y1 = 1.23*0.857167300702;
+ Real y2 = 1.25*0.906307787037;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x1*j_i-y1*q);
+ positions.push_back(i+x2*j_i+y2*q);
+
+ //we have to construct a third position hanging at the second one...
+
+ Real x = 0.333806859234;
+ Real y = 0.942641491092;
+
+ std::vector<geom::Vec3> new_anchors;
+ new_anchors.push_back(positions[2]);
+ new_anchors.push_back(anchors[0]);
+ new_anchors.push_back(anchors[1]);
+
+ i = new_anchors[0];
+ j = new_anchors[1];
+ k = new_anchors[2];
+
+ j_i = geom::Normalize(i-j);
+ q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 10:{
+ //not implemented yet, do nothing
+ break;
+ }
+
+ case 11:{
+ //not implemented yet, do nothing
+ break;
+ }
+
+ default:{
+ break;
+ }
+ }
+ return positions;
+}
+
+
+void GromacsHydrogenConstructor::ApplyOnBuildingBlock(BuildingBlockPtr p){
+ //we assume, that the hydrogens are already correct in the building block...
+}
+
+void GromacsHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+
+ if(!res.IsValid()) return;
+
+ int number;
+ int method;
+ String prefix;
+
+ std::vector<String> anchor_names;
+ ost::mol::AtomHandleList anchor_atoms;
+
+ std::vector<String> hydrogen_names;
+ std::vector<geom::Vec3> hydrogen_positions;
+ std::vector<geom::Vec3> anchor_positions;
+
+ bool hydrogens_present;
+
+ for(uint a=0;a<add_number_.size();++a){
+
+ hydrogen_names = hydrogen_names_[a];
+
+ /*
+ bool hydrogens_present = true;
+ for(std::vector<String>::iterator i = hydrogen_names.begin();
+ i != hydrogen_names.end(); ++i){
+ if(!res.FindAtom(*i).IsValid()){
+ hydrogens_present = false;
+ break;
+ }
+ }
+
+ if(hydrogens_present) continue;
+ */
+ number = add_number_[a];
+ method = methods_[a];
+ anchor_names = anchor_atom_names_[a];
+
+ hydrogen_positions.clear();
+ anchor_positions.clear();
+ anchor_atoms.clear();
+
+
+
+ String atom_name;
+ ost::mol::ResidueHandle temp_res;
+ ost::mol::AtomHandle atom;
+ bool found_anchors = true;
+
+ for(std::vector<String>::iterator it = anchor_names.begin();it!=anchor_names.end();++it){
+
+ temp_res = res;
+ atom_name = *it;
+
+ if(atom_name[0] == '-'){
+ atom_name.erase(0,1);
+ temp_res = res.GetPrev();
+ if(!temp_res.IsValid()){
+ //happens in case of termini... In this case the adding definitions
+ //are taken from the termini database...
+ found_anchors = false;
+ break;
+ }
+ }
+ if(atom_name[0] == '+'){
+ atom_name.erase(0,1);
+ temp_res = res.GetNext();
+ if(!temp_res.IsValid()){
+ //happens in case of termini... In this case the adding definitions
+ //are taken from the termini database...
+ found_anchors = false;
+ break;
+ }
+ }
+
+ atom = temp_res.FindAtom(atom_name);
+ if(!atom.IsValid()){
+ std::stringstream ss;
+ ss << "cannot find required anchor atom " << atom_name << " in residue ";
+ ss << res.GetQualifiedName() << " to add hydrogen!";
+ throw ost::Error(ss.str());
+ }
+
+ anchor_atoms.push_back(atom);
+ anchor_positions.push_back(atom.GetPos());
+ }
+
+ if(!found_anchors){
+ continue;
+ }
+
+ hydrogen_positions = GromacsPositionRuleEvaluator::EvaluatePosRule(method,
+ number,
+ anchor_positions);
+
+ for(int b=0;b<number;++b){
+ //only add hydrogen if not already present!
+ atom = res.FindAtom(hydrogen_names[b]);
+ if(!atom.IsValid()){
+ atom = ed.InsertAtom(res,hydrogen_names[b],hydrogen_positions[b],"H");
+ }
+ //ed.Connect(atom, anchor_atoms[0]);
+ }
+ }
+}
+
+
+void GromacsHydrogenConstructor::AddHydrogenRule(uint number, int method,
+ const std::vector<String>& hydrogen_names,
+ const std::vector<String>& anchors){
+
+ if(number != hydrogen_names.size()){
+ std::stringstream ss;
+ ss << "Tried to add hydrogen rule to hydrogen constructor with add number ";
+ ss << number << ", but "<< hydrogen_names.size() << "hydrogen names";
+ }
+
+ hydrogen_names_.push_back(hydrogen_names);
+ add_number_.push_back(number);
+ methods_.push_back(method);
+ anchor_atom_names_.push_back(anchors);
+}
+
+void GromacsBlockModifier::AddReplaceRule(const String& name, const String& new_name,
+ const String& new_type, Real new_charge){
+ replace_old_atom_name_.push_back(name);
+ replace_new_atom_name_.push_back(new_name);
+ replace_new_atom_type_.push_back(new_type);
+ replace_new_charge_.push_back(new_charge);
+}
+
+void GromacsBlockModifier::AddAddRule(int number, int method,
+ const std::vector<String>& atom_names,
+ const std::vector<String>& anchors,
+ const String& type, Real charge){
+ add_add_number_.push_back(number);
+ add_methods_.push_back(method);
+ add_atom_names_.push_back(atom_names);
+ add_anchor_atom_names_.push_back(anchors);
+ add_atom_types_.push_back(type);
+ add_charges_.push_back(charge);
+}
+
+void GromacsBlockModifier::ApplyOnBuildingBlock(BuildingBlockPtr p){
+
+ //let's resolve the replace statement
+ for(uint i = 0; i < replace_old_atom_name_.size(); ++i){
+ p->ReplaceAtom(replace_old_atom_name_[i], replace_new_atom_name_[i],
+ replace_new_atom_type_[i], replace_new_charge_[i]);
+
+ }
+ //let's resolve the add statement
+ for(uint i = 0; i < add_add_number_.size(); ++i){
+ String type = add_atom_types_[i];
+ Real charge = add_charges_[i];
+ std::vector<String> anchor_atoms = add_anchor_atom_names_[i];
+ std::vector<String> names = add_atom_names_[i];
+
+ //let's add the stuff to the buildingblock
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ p->AddAtom(*j,type,charge);
+ //the bond, that connects the newly added atom to its anchor is not necessarily
+ //defined. Let's add it here. Note, that nothing happens, if this specific bond
+ //is already part of the building block.
+ MMInteractionPtr b_p(new MMInteraction(p->GetBonds()[0]->GetFuncType()));
+ std::vector<String> bond_names;
+ std::vector<String> bond_types;
+ bond_names.push_back(anchor_atoms[0]);
+ bond_names.push_back(*j);
+ bond_types.push_back(p->GetType(anchor_atoms[0]));
+ bond_types.push_back(type);
+ b_p->SetNames(bond_names);
+ b_p->SetTypes(bond_types);
+ p->AddBond(b_p);
+ }
+ }
+
+ //let's resolve the delete statement
+ for(std::vector<String>::iterator i = delete_atom_names_.begin();
+ i != delete_atom_names_.end(); ++i){
+ p->RemoveAtom(*i);
+ }
+
+ //we simply add the new interactions to the building block
+ for(std::vector<MMInteractionPtr>::iterator i = bonds_.begin();
+ i != bonds_.end(); ++i){
+ p->AddBond(*i, true);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = angles_.begin();
+ i != angles_.end(); ++i){
+ p->AddAngle(*i, true);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = dihedrals_.begin();
+ i != dihedrals_.end(); ++i){
+ p->AddDihedral(*i, true);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = impropers_.begin();
+ i != impropers_.end(); ++i){
+ p->AddImproper(*i, true);
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator i = cmaps_.begin();
+ i != cmaps_.end(); ++i){
+ p->AddCMap(*i, true);
+ }
+}
+
+void GromacsBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+
+ //let's resolve the replace statement
+ for(uint i = 0; i < replace_old_atom_name_.size(); ++i){
+ ost::mol::AtomHandle at = res.FindAtom(replace_old_atom_name_[i]);
+ if(at.IsValid()){
+ ed.RenameAtom(at,replace_new_atom_name_[i]);
+ }
+ }
+
+
+ //let's resolve the add statement
+ for(uint i = 0; i < add_add_number_.size(); ++i){
+ int number = add_add_number_[i];
+ int method = add_methods_[i];
+ std::vector<String> anchor_names = add_anchor_atom_names_[i];
+ //String type = add_atom_types_[i];
+ std::vector<geom::Vec3> anchor_positions;
+ ost::mol::AtomHandleList anchor_atoms;
+ std::vector<String> names = add_atom_names_[i];
+
+ for(std::vector<String>::iterator j = anchor_names.begin();
+ j != anchor_names.end(); ++j){
+ ost::mol::AtomHandle at = res.FindAtom(*j);
+ if(!at.IsValid()){
+ std::stringstream ss;
+ ss << "Cannot find anchor atom required to construct termini";
+ ss << " in provided residue!";
+ throw ost::Error(ss.str());
+ }
+ anchor_positions.push_back(at.GetPos());
+ anchor_atoms.push_back(at);
+ }
+ std::vector<geom::Vec3> positions = GromacsPositionRuleEvaluator::EvaluatePosRule(method,
+ number,
+ anchor_positions);
+
+ String ele = "H";
+ if(method == 8 || method == 9){
+ ele = "O";
+ }
+ for(int j=0; j<number; ++j){
+ ost::mol::AtomHandle at = res.FindAtom(names[j]);
+ if(!at.IsValid()) at = ed.InsertAtom(res,names[j],positions[j],ele);
+ ed.Connect(at, anchor_atoms[0]);
+ }
+ }
+ //let's resolve the delete statement
+ for(std::vector<String>::iterator i = delete_atom_names_.begin();
+ i != delete_atom_names_.end(); ++i){
+ ost::mol::AtomHandle at = res.FindAtom(*i);
+ if(at.IsValid()){
+ ed.DeleteAtom(at);
+ }
+ }
+}
+
+
+void GromacsBlockModifier::CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const{
+ if(p->GetNames().empty()) throw ost::Error("Expect interaction to have names properly set!");
+
+ if(interaction_type == "BOND"){
+ if(p->GetFuncType() != HarmonicBond){
+ throw ost::Error("Invalid function type encountered when adding bond!");
+ } return;
+ }
+ if(interaction_type == "ANGLE"){
+ if(p->GetFuncType() != HarmonicAngle && p->GetFuncType() != UreyBradleyAngle){
+ throw ost::Error("Invalid function type encountered when adding angle!");
+ } return;
+ }
+ if(interaction_type == "DIHEDRAL"){
+ if(p->GetFuncType() != PeriodicDihedral){
+ throw ost::Error("Invalid function type encountered when adding dihedral!");
+ } return;
+ }
+ if(interaction_type == "IMPROPER"){
+ if(p->GetFuncType() != PeriodicImproper && p->GetFuncType() != HarmonicImproper){
+ throw ost::Error("Invalid function type encountered when adding improper!");
+ } return;
+ }
+ if(interaction_type == "CMAP"){
+ if(p->GetFuncType() != CMap){
+ throw ost::Error("Invalid function type encountered when adding cmap!");
+ } return;
+ }
+
+ std::stringstream ss;
+ ss << "Cannot validate added interaction of type "<< interaction_type << "!";
+ throw ost::Error(ss.str());
+
+}
+
+
+
+
+}}}//ns
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.hh b/modules/mol/mm/src/gromacs_block_modifiers.hh
new file mode 100644
index 0000000000000000000000000000000000000000..e5621f9e772b4ea3cf9d9bdb8783302695d9d7e5
--- /dev/null
+++ b/modules/mol/mm/src/gromacs_block_modifiers.hh
@@ -0,0 +1,309 @@
+#ifndef GROMCACS_BLOCK_MODIFIERS
+#define GROMCACS_BLOCK_MODIFIERS
+
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/buildingblock.hh>
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+class GromacsHydrogenConstructor;
+class GromacsTerminiConstructor;
+class GromacsBlockModifier;
+
+typedef boost::shared_ptr<GromacsHydrogenConstructor> GromacsHydrogenConstructorPtr;
+typedef boost::shared_ptr<GromacsTerminiConstructor> GromacsTerminiConstructorPtr;
+typedef boost::shared_ptr<GromacsBlockModifier> GromacsBlockModifierPtr;
+
+class GromacsPositionRuleEvaluator{
+
+public:
+ static std::vector<geom::Vec3> EvaluatePosRule(int rule, int number,
+ const std::vector<geom::Vec3>& anchors);
+};
+
+class GromacsHydrogenConstructor : public HydrogenConstructor{
+
+public:
+
+ GromacsHydrogenConstructor() { }
+
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr);
+
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed);
+
+ void AddHydrogenRule(uint number, int method,
+ const std::vector<String>& hydrogen_names,
+ const std::vector<String>& anchors);
+
+ virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
+
+ virtual BlockModifierType GetBlockModifierType() { return GromacsBlockModifiers; }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ int num_hydrogen_add_rules = add_number_.size();
+ ds & num_hydrogen_add_rules;
+
+ if(ds.IsSource()){
+ add_number_ = std::vector<int>(num_hydrogen_add_rules);
+ methods_ = std::vector<int>(num_hydrogen_add_rules);
+ hydrogen_names_ = std::vector<std::vector<String> >(num_hydrogen_add_rules);
+ anchor_atom_names_ = std::vector<std::vector<String> >(num_hydrogen_add_rules);
+ }
+
+ for(int i = 0; i < num_hydrogen_add_rules; ++i){
+ ds & add_number_[i];
+ ds & methods_[i];
+ int num_hydrogen_names = hydrogen_names_[i].size();
+ int num_anchor_names = anchor_atom_names_[i].size();
+ ds & num_hydrogen_names;
+ ds & num_anchor_names;
+ if(ds.IsSource()){
+ hydrogen_names_[i] = std::vector<String>(num_hydrogen_names);
+ anchor_atom_names_[i] = std::vector<String>(num_anchor_names);
+ }
+
+ for(int j = 0; j < num_hydrogen_names; ++j){
+ ds & hydrogen_names_[i][j];
+ }
+ for(int j = 0; j < num_anchor_names; ++j){
+ ds & anchor_atom_names_[i][j];
+ }
+ }
+ }
+
+private:
+ std::vector<int> add_number_;
+ std::vector<int> methods_;
+ std::vector<std::vector<String> > hydrogen_names_;
+ std::vector<std::vector<String> > anchor_atom_names_;
+};
+
+
+class GromacsBlockModifier : public BlockModifier{
+
+public:
+
+ GromacsBlockModifier() { }
+
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p);
+
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed);
+
+ void AddReplaceRule(const String& name, const String& new_name,
+ const String& new_type, Real new_charge);
+
+ void AddAddRule(int number, int method,
+ const std::vector<String>& atom_names,
+ const std::vector<String>& anchors,
+ const String& type, Real charge);
+
+ void AddBond(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"BOND");
+ bonds_.push_back(p); }
+
+ void AddAngle(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"ANGLE");
+ angles_.push_back(p); }
+
+ void AddDihedral(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"DIHEDRAL");
+ dihedrals_.push_back(p); }
+
+ void AddImproper(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"IMPROPER");
+ impropers_.push_back(p); }
+
+ void AddCMap(MMInteractionPtr p) { this->CheckInteractionToAdd(p,"CMAP");
+ cmaps_.push_back(p); }
+
+ void AddDeleteAtom(const String& atom_name) { delete_atom_names_.push_back(atom_name); }
+
+ virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
+
+ virtual BlockModifierType GetBlockModifierType() { return GromacsBlockModifiers; }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+
+ int num_bonds = bonds_.size();
+ int num_angles = angles_.size();
+ int num_dihedrals = dihedrals_.size();
+ int num_impropers = impropers_.size();
+ int num_cmaps = cmaps_.size();
+
+ ds & num_bonds;
+ ds & num_angles;
+ ds & num_dihedrals;
+ ds & num_impropers;
+ ds & num_cmaps;
+
+ for(int i = 0; i < num_bonds; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ bonds_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = bonds_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(bonds_[i]);
+ }
+
+ for(int i = 0; i < num_angles; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ angles_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = angles_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(angles_[i]);
+ }
+
+ for(int i = 0; i < num_dihedrals; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ dihedrals_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = dihedrals_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(dihedrals_[i]);
+ }
+
+ for(int i = 0; i < num_impropers; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ impropers_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = impropers_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(impropers_[i]);
+ }
+
+ for(int i = 0; i < num_cmaps; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ cmaps_.push_back(MMInteractionPtr(new MMInteraction(FuncType(func_type))));
+ }
+ else{
+ func_type = cmaps_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(cmaps_[i]);
+ }
+
+ int num_replace_atoms = replace_old_atom_name_.size();
+ ds & num_replace_atoms;
+
+ if(ds.IsSource()){
+ replace_old_atom_name_ = std::vector<String>(num_replace_atoms);
+ replace_new_atom_name_ = std::vector<String>(num_replace_atoms);
+ replace_new_atom_type_ = std::vector<String>(num_replace_atoms);
+ replace_new_charge_ = std::vector<Real>(num_replace_atoms);
+ }
+
+ for(int i = 0; i < num_replace_atoms; ++i){
+ ds & replace_old_atom_name_[i];
+ ds & replace_new_atom_name_[i];
+ ds & replace_new_atom_type_[i];
+ ds & replace_new_charge_[i];
+ }
+
+ int num_add_atoms = add_add_number_.size();
+ ds & num_add_atoms;
+
+ if(ds.IsSource()){
+ add_add_number_ = std::vector<int>(num_add_atoms);
+ add_methods_ = std::vector<int>(num_add_atoms);
+ add_atom_names_ = std::vector<std::vector<String> >(num_add_atoms);
+ add_anchor_atom_names_ = std::vector<std::vector<String> >(num_add_atoms);
+ add_atom_types_ = std::vector<String>(num_add_atoms);
+ add_charges_ = std::vector<Real>(num_add_atoms);
+ }
+
+ for(int i = 0; i < num_add_atoms; ++i){
+ ds & add_add_number_[i];
+ ds & add_methods_[i];
+ ds & add_atom_types_[i];
+ ds & add_charges_[i];
+ int num_add_atom_names = add_atom_names_[i].size();
+ int num_add_anchor_atom_names = add_anchor_atom_names_[i].size();
+ ds & num_add_atom_names;
+ ds & num_add_anchor_atom_names;
+ if(ds.IsSource()){
+ add_atom_names_[i] = std::vector<String>(num_add_atom_names);
+ add_anchor_atom_names_[i] = std::vector<String>(num_add_anchor_atom_names);
+ }
+ for(int j = 0; j < num_add_atom_names; ++j){
+ ds & add_atom_names_[i][j];
+ }
+ for(int j = 0; j < num_add_anchor_atom_names; ++j){
+ ds & add_anchor_atom_names_[i][j];
+ }
+ }
+
+ int num_delete_atoms = delete_atom_names_.size();
+ ds & num_delete_atoms;
+ if(ds.IsSource()){
+ delete_atom_names_ = std::vector<String>(num_delete_atoms);
+ }
+ for(int i = 0; i < num_delete_atoms; ++i){
+ ds & delete_atom_names_[i];
+ }
+ }
+
+private:
+
+ void CheckInteractionToAdd(MMInteractionPtr p, const String& interaction_type) const;
+
+ //Atoms, that will be added to the building block
+
+ //Interactions, that will be added to the building block
+ std::vector<MMInteractionPtr> bonds_;
+ std::vector<MMInteractionPtr> angles_;
+ std::vector<MMInteractionPtr> dihedrals_;
+ std::vector<MMInteractionPtr> impropers_;
+ std::vector<MMInteractionPtr> cmaps_;
+
+ //paramters we need for the replace statement
+ std::vector<String> replace_old_atom_name_;
+ std::vector<String> replace_new_atom_name_;
+ std::vector<String> replace_new_atom_type_;
+ std::vector<Real> replace_new_charge_;
+
+ //parameters we need for the add statement => gromacs dependent rules!
+ std::vector<int> add_add_number_;
+ std::vector<int> add_methods_;
+ std::vector<std::vector<String> > add_atom_names_;
+ std::vector<std::vector<String> > add_anchor_atom_names_;
+ std::vector<String> add_atom_types_;
+ std::vector<Real> add_charges_;
+
+ //parameters we need for the delete statement
+ std::vector<String> delete_atom_names_;
+};
+
+
+
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/gromacs_reader.cc b/modules/mol/mm/src/gromacs_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e6fed54ac29ceef9bc77c325183b44d8fb54020f
--- /dev/null
+++ b/modules/mol/mm/src/gromacs_reader.cc
@@ -0,0 +1,2073 @@
+#include <ost/mol/mm/gromacs_reader.hh>
+
+
+namespace ost { namespace mol{ namespace mm {
+
+
+GromacsData::GromacsData(){
+ keyword_map_["atoms"] = 0;
+ keyword_map_["bonds"] = 1;
+ keyword_map_["angles"] = 2;
+ keyword_map_["impropers"] = 3;
+ keyword_map_["dihedrals"] = 4;
+ keyword_map_["exclusions"] = 5;
+ keyword_map_["cmap"] = 6;
+ keyword_map_["replace"] = 7;
+ keyword_map_["moleculetype"] = 8;
+ keyword_map_["add"] = 9;
+ keyword_map_["delete"] = 10;
+ keyword_map_["bondtypes"] = 11;
+ keyword_map_["constrainttypes"] = 12;
+ keyword_map_["angletypes"] = 13;
+ keyword_map_["dihedraltypes"] = 14;
+ keyword_map_["atomtypes"] = 15;
+ keyword_map_["implicit_genborn_params"] = 16;
+ keyword_map_["pairtypes"] = 17;
+ keyword_map_["nonbond_params"] = 18;
+ keyword_map_["defaults"] = 19;
+ keyword_map_["cmaptypes"] = 20;
+ keyword_map_["pairs"] = 21;
+ keyword_map_["settles"] = 22;
+
+
+ renaming_to_standard_["ILE"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HOH"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HO4"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HO5"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HEME"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["protein"] = std::vector<std::pair<String,String> >();
+
+ renaming_to_standard_["ILE"].push_back(std::make_pair("CD1","CD"));
+ renaming_to_standard_["ILE"].push_back(std::make_pair("HD11","HD1"));
+ renaming_to_standard_["ILE"].push_back(std::make_pair("HD12","HD2"));
+ renaming_to_standard_["ILE"].push_back(std::make_pair("HD13","HD3"));
+
+ renaming_to_standard_["HOH"].push_back(std::make_pair("O","OW"));
+ renaming_to_standard_["HOH"].push_back(std::make_pair("OW1","OW"));
+ renaming_to_standard_["HO4"].push_back(std::make_pair("O","OW"));
+ renaming_to_standard_["HO4"].push_back(std::make_pair("OW1","OW"));
+ renaming_to_standard_["HO5"].push_back(std::make_pair("O","OW"));
+ renaming_to_standard_["HO5"].push_back(std::make_pair("OW1","OW"));
+
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_A","NA"));
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_B","NB"));
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_C","NC"));
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_D","ND"));
+
+ renaming_to_standard_["protein"].push_back(std::make_pair("O1","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("O2","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OT1","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OT2","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OT","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("O'","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("O''","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OC1","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OC2","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HN","H"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HT1","H1"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HT2","H2"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HT3","H3"));
+}
+
+int GromacsData::GetKeywordIndex(const String& keyword){
+ String lowercase_keyword = keyword;
+ boost::algorithm::to_lower(lowercase_keyword);
+ if(keyword_map_.find(lowercase_keyword) == keyword_map_.end()) return -1;
+ else return keyword_map_[lowercase_keyword];
+}
+
+String GromacsData::ConvertToStandard(const String& res_name, const String& atom_name){
+
+ if(renaming_to_standard_.find(res_name) == renaming_to_standard_.end()) return atom_name;
+ for(std::vector<std::pair<String,String> >::iterator i = renaming_to_standard_[res_name].begin();
+ i != renaming_to_standard_[res_name].end(); ++i){
+ if(i->first == atom_name) return i->second;
+ }
+ return atom_name;
+}
+
+bool GromacsData::ConversionExists(const String& res_name){
+ return renaming_to_standard_.find(res_name) != renaming_to_standard_.end();
+}
+
+GromacsDataPtr GromacsData::Instance(){
+ if(!instance_){
+ instance_ = GromacsDataPtr(new GromacsData);
+ }
+ return instance_;
+}
+
+GromacsDataPtr GromacsData::instance_ = GromacsDataPtr();
+
+CHARMMData::CHARMMData() {
+
+ keyword_map_["atoms"] = 0;
+ keyword_map_["bonds"] = 1;
+ keyword_map_["angles"] = 2;
+ keyword_map_["dihedrals"] = 3;
+ keyword_map_["improper"] = 4;
+ keyword_map_["cmap"] = 5;
+ keyword_map_["nonbonded"] = 6;
+ keyword_map_["hbond"] = 7;
+ keyword_map_["end"] = 8;
+ keyword_map_["mass"] = 9;
+ keyword_map_["decl"] = 10;
+ keyword_map_["defa"] = 11;
+ keyword_map_["auto"] = 12;
+ keyword_map_["resi"] = 13;
+ keyword_map_["pres"] = 14;
+ keyword_map_["atom"] = 15;
+ keyword_map_["group"] = 16;
+ keyword_map_["bond"] = 17;
+ keyword_map_["angle"] = 18;
+ keyword_map_["dihe"] = 19;
+ keyword_map_["impr"] = 20;
+ keyword_map_["donor"] = 21;
+ keyword_map_["acceptor"] = 22;
+ keyword_map_["ic"] = 23;
+ keyword_map_["patching"] = 24;
+ keyword_map_["print"] = 25;
+ keyword_map_["double"] = 26;
+}
+
+int CHARMMData::GetKeywordIndex(const String& keyword){
+ String lowercase_keyword = keyword;
+ boost::algorithm::to_lower(lowercase_keyword);
+ if(keyword_map_.find(lowercase_keyword) == keyword_map_.end()) return -1;
+ else return keyword_map_[lowercase_keyword];
+}
+
+
+CHARMMDataPtr CHARMMData::Instance(){
+ if(!instance_){
+ instance_ = CHARMMDataPtr(new CHARMMData);
+ }
+ return instance_;
+}
+
+CHARMMDataPtr CHARMMData::instance_ = CHARMMDataPtr();
+
+
+
+
+
+std::vector<std::vector<String> > MMPreprocessor::Process(const String& filename){
+
+ std::vector<std::vector<String> > file_content = this->ReadFile(filename);
+ std::vector<std::vector<String> > temp;
+ std::vector<std::vector<String> > return_file;
+
+ //we first resolve all include statements
+ String include_file_name;
+ for(uint i = 0; i<file_content.size(); ++i){
+ if(file_content[i][0] == "#include"){
+ if(file_content[i].size() != 2){
+ std::stringstream ss;
+ ss<<"Can only evaluate include statement in combination with a filename.";
+ ss<<"Also more stuff in the same line blows the thing up...";
+ throw ost::io::IOException(ss.str());
+ }
+ String include_filename = file_content[i][1].substr(1,file_content[i][1].size()-2);
+ temp = this->ReadFile(include_filename);
+ //directly delete the line with the
+ //include statement and fill in the full content
+ file_content.insert(file_content.erase(file_content.begin()+i), temp.begin(), temp.end());
+ }
+ }
+
+ //let's resolve all definitions
+ std::map<String,std::vector<String> >::iterator definitions_it;
+ for(uint i=0; i<file_content.size(); ++i){
+ //resolve definition
+ if(file_content[i][0] == "#define"){
+ if(file_content[i].size()==2){
+ defines_.insert(file_content[i][1]);
+ file_content.erase(file_content.begin()+i);
+ if(i == file_content.size()) break;
+ --i;
+ continue;
+ }
+ definitions_[file_content[i][1]] = std::vector<String>(file_content[i].begin()+2,file_content[i].end());
+ file_content.erase(file_content.begin()+i);
+ if(i == file_content.size()) break;
+ --i;
+ continue;
+ }
+ //resolve ifdef
+ if(file_content[i][0] == "#ifdef" || file_content[i][0] == "#ifndef"){
+ this->ResolveIFDEF(file_content,i);
+ --i;
+ continue;
+ }
+ //check whether a word in current line corresponds to a found definition
+ for(uint j = 0; j<file_content[i].size(); ++j){
+ definitions_it = definitions_.find(file_content[i][j]);
+ if(definitions_it!=definitions_.end()){
+ file_content[i].insert(file_content[i].erase(file_content[i].begin()+j),definitions_it->second.begin(),definitions_it->second.end());
+ }
+ }
+ }
+ return file_content;
+}
+
+void MMPreprocessor::ResolveIFDEF(std::vector<std::vector<String> >& file_content, int line_counter){
+
+ String ifdef_statement = file_content[line_counter][1];
+ bool logical_outcome;
+ if(file_content[line_counter][0] == "#ifdef"){
+ logical_outcome = defines_.find(ifdef_statement) != defines_.end();
+ }
+ else if(file_content[line_counter][0] == "#ifndef"){
+ logical_outcome = defines_.find(ifdef_statement) == defines_.end();
+ }
+ else{
+ throw ost::Error("Invalid preprocessor statement observed in ResolveIFDEF function!");
+ }
+
+ bool has_else = true;
+ uint else_position = line_counter+1;
+ while(true){
+ if(else_position >= file_content.size()){
+ throw ost::io::IOException("Invalid ifdef statement encountered!");
+ }
+ if(file_content[else_position][0] == "#ifdef" || file_content[else_position][0] == "#ifndef"){
+ this->ResolveIFDEF(file_content,else_position);
+ }
+ if(file_content[else_position][0] == "#else") break;
+ if(file_content[else_position][0] == "#endif"){
+ has_else = false;
+ break;
+ }
+ ++else_position;
+ }
+
+ uint endif_position = else_position+1;
+ while(true && has_else){
+ if(endif_position >= file_content.size()){
+ throw ost::io::IOException("Invalid ifdef statement encountered!");
+ }
+ if(file_content[endif_position][0] == "#ifdef" || file_content[endif_position][0] == "#ifndef"){
+ this->ResolveIFDEF(file_content,endif_position);
+ }
+ if(file_content[endif_position][0] == "#endif") break;
+ ++endif_position;
+ }
+
+ if(has_else){
+ if(logical_outcome){
+ //delete part after else
+ file_content.erase(file_content.begin()+else_position, file_content.begin()+endif_position+1);
+ file_content.erase(file_content.begin()+line_counter);
+ }
+ else{
+ //delete part before else
+ file_content.erase(file_content.begin()+line_counter,file_content.begin()+else_position+1);
+ file_content.erase(file_content.begin()+line_counter+(endif_position-else_position)-1);
+ }
+ }
+ else{
+ if(logical_outcome){//only delete ifdef and endif
+ file_content.erase(file_content.begin()+else_position);
+ file_content.erase(file_content.begin()+line_counter);
+ }
+ else{//it's not defined => delete whole block
+ file_content.erase(file_content.begin()+line_counter,file_content.begin()+else_position+1);
+ }
+ }
+}
+
+std::vector<std::vector<String> > MMPreprocessor::ReadFile(const String& filename){
+
+ boost::filesystem::path file_path = basepath_ / filename;
+ std::ifstream file;
+ file.open((file_path.string()).c_str());
+
+ if(!file){
+ std::stringstream ss;
+ ss<<"Could not read file. File '";
+ ss<<filename<<"' does not exist!";
+ throw ost::io::IOException(ss.str());
+ }
+
+ std::vector<String> file_content;
+ std::vector<std::vector<String> > split_file_content;
+ String string_line;
+ ost::StringRef stringref_line;
+ std::vector<ost::StringRef> data;
+ std::vector<String> fill_data;
+
+ while(file.good()){
+ std::getline(file,string_line);
+ file_content.push_back(string_line);
+ }
+
+ //splitting the stuff up. Everything in a line coming after an element starting
+ //with a colon or exclamation mark, is neglected. (wont neglect anything of:
+ //ab! c, but will neglect the second item of: ab !c)
+ for(std::vector<String>::iterator i = file_content.begin();
+ i!=file_content.end(); ++i){
+ stringref_line = ost::StringRef(i->c_str(),i->length());
+ data = stringref_line.split();
+ if(data.empty()) continue;
+ fill_data.clear();
+ for(std::vector<ost::StringRef>::iterator j = data.begin();
+ j!=data.end(); ++j){
+ //if(*(j->begin()) == ';' || *(j->begin()) == '*'){
+ if(*(j->begin()) == ';' || *(j->begin()) == '!'){
+ break;
+ }
+ fill_data.push_back(j->str());
+ }
+ if(fill_data.empty()) continue;
+ split_file_content.push_back(fill_data);
+ }
+
+ //handling linebreaks ("\")
+ for(uint i = 0; i != split_file_content.size(); ++i){
+ if(*split_file_content[i].back().rbegin() == '\\'){
+ if(i < split_file_content.size() - 1){
+ if(split_file_content[i].back() == "\\"){
+ split_file_content[i].pop_back();
+ }
+ else{
+ split_file_content[i].back() = split_file_content[i].back().substr(0,split_file_content[i].back().size()-1);
+ }
+ if(split_file_content[i].empty()){
+ throw io::IOException("Observed single linebreak (\\) in one line of input file!");
+ }
+ for(std::vector<String>::iterator j = split_file_content[i+1].begin();
+ j != split_file_content[i+1].end(); ++j){
+ split_file_content[i].push_back(*j);
+ }
+ split_file_content.erase(split_file_content.begin()+i+1);
+ --i;
+ }
+ }
+ }
+
+ return split_file_content;
+}
+
+GromacsReader::GromacsReader(const String& base_dir): preprocessor_(base_dir),
+ ff_(new Forcefield)
+{
+ for(int i = 0; i < 4; ++i){
+ ff_bonded_types_.push_back(Invalid);
+ bonded_types_.push_back(Invalid);
+ }
+}
+
+void GromacsReader::ReadGromacsForcefield(){
+
+ //read in the forcefield
+ if(!boost::filesystem::exists(preprocessor_.GetBasedir() / "forcefield.itp")){
+ throw io::IOException("directory must contain forcefield.itp file!");
+ }
+ if(!boost::filesystem::exists(preprocessor_.GetBasedir() / "atomtypes.atp")){
+ throw io::IOException("directory must contain atomtypes.atp file!");
+ }
+ std::vector<std::vector<String> > content = preprocessor_.Process("forcefield.itp");
+ this->ParseForcefield(content);
+ content = preprocessor_.Process("atomtypes.atp");
+ this->ParseAtomTypes(content);
+}
+
+void GromacsReader::ReadResidueDatabase(const String& basename){
+ std::vector<std::vector<String> > data = preprocessor_.Process(basename+".rtp");
+ this->ParseRTP(data);
+
+ try{
+ data = preprocessor_.Process(basename+".arn");
+ this->ParseARN(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".hdb");
+ this->ParseHDB(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".n.tdb");
+ this->ParseNTDB(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".c.tdb");
+ this->ParseCTDB(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".vsd");
+ this->ParseVSD(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".r2b");
+ this->ParseRtoB(data);
+ }catch(ost::io::IOException e) { }
+}
+
+void GromacsReader::ReadCHARMMPRM(const String& filename){
+ std::vector<std::vector<String> > data = preprocessor_.Process(filename);
+ this->ParseCHARMMPRM(data);
+}
+
+void GromacsReader::ReadCHARMMRTF(const String& filename){
+ std::vector<std::vector<String> > data = preprocessor_.Process(filename);
+ this->ParseCHARMMRTF(data);
+}
+
+void GromacsReader::ParseForcefield(std::vector<std::vector<String> >& content){
+
+ int keyword_id = -1;
+ std::vector<String> current_line;
+
+ for(uint line_counter = 0; line_counter<content.size(); ++line_counter){
+ current_line = content[line_counter];
+ if(current_line[0] == "["){
+ keyword_id = GromacsData::Instance()->GetKeywordIndex(current_line[1]);
+ if(keyword_id == -1){
+ std::stringstream ss;
+ ss << "Unknown keyword '"<<current_line[1];
+ ss << "' in forcefield file."<<std::endl;
+ throw io::IOException(ss.str());
+ }
+ continue;
+ }
+
+ switch(keyword_id){
+ case 11:{
+ MMInteractionPtr bond = this->ParseBond(current_line,true);
+ ff_->AddBond(bond);
+ ff_bonded_types_[0] = bond->GetFuncType();
+ break;
+ }
+ case 12:{
+ MMInteractionPtr constraint = this->ParseConstraint(current_line,true);
+ ff_->AddConstraint(constraint);
+ break;
+ }
+ case 13:{
+ MMInteractionPtr angle = this->ParseAngle(current_line,true);
+ ff_->AddAngle(angle);
+ ff_bonded_types_[1] = angle->GetFuncType();
+ break;
+ }
+ case 14:{
+
+ MMInteractionPtr p = this->ParseDihedral(current_line,true);
+ FuncType functype = p->GetFuncType();
+
+ if(functype == PeriodicDihedral){
+ ff_->AddDihedral(p);
+ ff_bonded_types_[2] = functype;
+ }
+ else if(functype == PeriodicImproper || functype == HarmonicImproper){
+ ff_->AddImproper(p);
+ ff_bonded_types_[3] = functype;
+ }
+ break;
+ }
+ case 15:{
+ MMInteractionPtr lj = this->ParseLJ(current_line,true);
+ ff_->AddLJ(lj);
+ break;
+ }
+ case 16:{
+ MMInteractionPtr genborn = this->ParseGenborn(current_line,true);
+ ff_->AddImplicitGenborn(genborn);
+ break;
+ }
+ case 17:{
+ MMInteractionPtr lj_pair = this->ParseLJPair(current_line,true);
+ ff_->AddLJPair(lj_pair);
+ break;
+ }
+ case 18:{
+ std::stringstream ss;
+ ss << "Observerd nonbond_params in forcefield file. Only forcefields with ";
+ ss << "combining rules for sigma epsilon calculations are supported!"<<std::endl;
+ throw ost::Error(ss.str());
+ break;
+ }
+ case 19:{
+ bool gen_pairs;
+ Real fudge_lj, fudge_qq;
+ if(current_line[2] == "yes") gen_pairs = true;
+ else if(current_line[2] == "no") gen_pairs = false;
+ else throw io::IOException("Only \"yes\" and \"no\" are supported for gen_pairs parameter!");
+
+ fudge_lj = boost::lexical_cast<Real>(current_line[3]);
+ fudge_qq = boost::lexical_cast<Real>(current_line[4]);
+
+ ff_->SetGenPairs(gen_pairs);
+ ff_->SetFudgeLJ(fudge_lj);
+ ff_->SetFudgeQQ(fudge_qq);
+ break;
+ }
+ case 20:{
+ MMInteractionPtr cmap = this->ParseCMap(current_line,true);
+ ff_->AddCMap(cmap);
+ break;
+ }
+ default: break;
+ }
+ }
+}
+
+void GromacsReader::ParseAtomTypes(std::vector<std::vector<String> >& content){
+ for(std::vector<std::vector<String> >::iterator i = content.begin();
+ i!=content.end(); ++i){
+ ff_->AddMass((*i)[0],boost::lexical_cast<Real>((*i)[1]));
+ }
+}
+
+void GromacsReader::ParseRTP(std::vector<std::vector<String> >& content){
+
+ read_residues_.clear();
+
+ //we assume, that at the beginning is the keyword 'bondedtypes'
+ //we neglect anything before that...
+ uint line_counter = 0;
+ for(; line_counter<content.size(); ++line_counter){
+ if(content[line_counter].size()>1){
+ if(content[line_counter][1] == "bondedtypes"){
+ ++line_counter;
+ //we're interested in the next line
+ if(content[line_counter].size() < 4){
+ throw ost::Error("Error in parsing bondedtypes section of RTP file!");
+ }
+ int gromacs_functype;
+ //first element defines the bonds
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][0]);
+ if(gromacs_functype == 1){
+ bonded_types_[0] = HarmonicBond;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for bond in bondedtypes section of rtp file!";
+ throw ost::Error(ss.str());
+ }
+ //second element defines angle
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][1]);
+ if(gromacs_functype == 5) bonded_types_[1] = UreyBradleyAngle;
+ else if(gromacs_functype == 1) bonded_types_[1] = HarmonicAngle;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for angle in bondedtypes section of rtp file!";
+ throw ost::Error(ss.str());
+ }
+ //third element defines the dihedral
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][2]);
+ if(gromacs_functype == 9 || gromacs_functype == 1) bonded_types_[2] = PeriodicDihedral;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for dihedral in bondedtypes section of rtp file!";
+ throw ost::Error(ss.str());
+ }
+ //fourth elemend defines improper dihedral
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][3]);
+ if(gromacs_functype == 4) bonded_types_[3] = PeriodicImproper;
+ else if(gromacs_functype == 2) bonded_types_[3] = HarmonicImproper;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for dihedral!";
+ throw ost::Error(ss.str());
+ }
+ ++line_counter;
+ break;
+ }
+ }
+ }
+
+ //data for specific residue will be filled in here and passed
+ //in the residue_building block Parse function
+ std::vector<std::vector<String> > residue_data;
+ String residue_name;
+ for(; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ //I there is a keyword (start with [) not defined above,
+ //we assume, that it is a new residue
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == -1){
+ //parse the old residue and set new residue name
+ if(!residue_data.empty()){
+ ff_->AddBuildingBlock(residue_name, this->BlockFromRTP(residue_data));
+ read_residues_.push_back(residue_name);
+ }
+ residue_data.clear();
+ residue_name = content[line_counter][1];
+ continue;
+ }
+ }
+ residue_data.push_back(content[line_counter]);
+ }
+ //we probably missed the last residue
+ if(!residue_data.empty()){
+ ff_->AddBuildingBlock(residue_name, this->BlockFromRTP(residue_data));
+ read_residues_.push_back(residue_name);
+ }
+
+
+ //It could be, that certain bondedtypes in the forcefield are not defined yet,
+ //since all forces are defined in the building blocks...
+ //We assume, that the whole stuff is consistent across all forcefield and rtp
+ //files... If not, you'll get errors when setting up your system
+ for(int i = 0; i < 4; ++i){
+ if(ff_bonded_types_[i] == Invalid) ff_bonded_types_[i] = bonded_types_[i];
+ }
+
+}
+
+void GromacsReader::ParseARN(std::vector<std::vector<String> >& content){
+ String res_name, a_one, a_two;
+
+ for(std::vector<std::vector<String> >::iterator i = content.begin();
+ i!=content.end(); ++i){
+ res_name = (*i)[0];
+ a_one = (*i)[1];
+ a_two = (*i)[2];
+ if(res_name == "*"){
+ // * is wildcard... valid for all residues in the previously read rtp file
+ for(std::vector<String>::iterator j = read_residues_.begin();
+ j != read_residues_.end(); ++j){
+ ff_->AddAtomRenamingRule(*j,a_one,a_two);
+ }
+ }
+ else{
+ ff_->AddAtomRenamingRule(res_name, a_one, a_two);
+ }
+ }
+}
+
+void GromacsReader::ParseHDB(std::vector<std::vector<String> >& content){
+
+ std::vector<std::vector<String> > residue_data;
+ String residue_name;
+ for(uint line_counter = 0; line_counter<content.size(); ++line_counter){
+ if(content[line_counter].size() == 2){
+ if(!residue_data.empty()){
+ GromacsHydrogenConstructor* p = new GromacsHydrogenConstructor;
+ for(std::vector<std::vector<String> >::iterator i = residue_data.begin();
+ i != residue_data.end(); ++i){
+ this->ParseHydrogenRule(*i,*p);
+ }
+ ff_->AddHydrogenConstructor(residue_name,HydrogenConstructorPtr(p));
+ }
+ residue_data.clear();
+ residue_name = content[line_counter][0];
+ continue;
+ }
+ residue_data.push_back(content[line_counter]);
+ }
+ //we probably missed the last residue
+ if(!residue_data.empty()){
+ GromacsHydrogenConstructor* p = new GromacsHydrogenConstructor;
+ for(std::vector<std::vector<String> >::iterator i = residue_data.begin();
+ i != residue_data.end(); ++i){
+ this->ParseHydrogenRule(*i,*p);
+ }
+ ff_->AddHydrogenConstructor(residue_name,HydrogenConstructorPtr(p));
+ }
+}
+
+void GromacsReader::ParseHydrogenRule(const std::vector<String>& data,
+ GromacsHydrogenConstructor& constructor){
+
+ if(data.size() < 4){
+ throw ost::Error("Require at least four items when parsing hydrogen rule!");
+ }
+
+ int number = boost::lexical_cast<int>(data[0]);
+ int method = boost::lexical_cast<int>(data[1]);
+ String prefix = data[2];
+ std::vector<String> anchors;
+ std::vector<String> hydrogen_names;
+
+ for(uint i=3; i<data.size(); ++i){
+ anchors.push_back(data[i]);
+ }
+
+ switch(number){
+ case 1:{
+ hydrogen_names.push_back(prefix);
+ break;
+ }
+ case 2:{
+ hydrogen_names.push_back(prefix+"1");
+ hydrogen_names.push_back(prefix+"2");
+ break;
+ }
+ case 3:{
+ hydrogen_names.push_back(prefix+"1");
+ hydrogen_names.push_back(prefix+"2");
+ hydrogen_names.push_back(prefix+"3");
+ break;
+ }
+ default:{
+ break;
+ }
+ }
+
+ constructor.AddHydrogenRule(number,method,hydrogen_names, anchors);
+}
+
+
+void GromacsReader::ParseTerminiReplaceRule(const std::vector<String>& data,
+ GromacsBlockModifier& modifier){
+
+ String name;
+ String new_name;
+ String new_type;
+ Real new_charge;
+ if(data.size() == 5 && data.back() != "0"){
+ name = data[0];
+ new_name = data[1];
+ new_type = data[2];
+ new_charge = boost::lexical_cast<Real>(data[4]);
+ }
+ else{
+ name = data[0];
+ new_name = name;
+ new_type = data[1];
+ new_charge = boost::lexical_cast<Real>(data[3]);
+ }
+
+ modifier.AddReplaceRule(name, new_name, new_type, new_charge);
+ //we neglect the mass! This will be read from the forcefield itself!
+}
+
+void GromacsReader::ParseTerminiAddRule(const std::vector<String>& data1,
+ const std::vector<String>& data2,
+ GromacsBlockModifier& modifier){
+
+ int number = boost::lexical_cast<int>(data1[0]);
+ int method = boost::lexical_cast<int>(data1[1]);
+ String prefix = data1[2];
+
+ std::vector<String> anchors;
+ for(uint i = 3; i < data1.size(); ++i){
+ anchors.push_back(data1[i]);
+ }
+
+ String type = data2[0];
+ Real charge = boost::lexical_cast<Real>(data2[2]);
+ //we again neglect the masses...
+
+ std::vector<String> names;
+
+ switch(number){
+ case 1:{
+ names.push_back(prefix);
+ break;
+ }
+ case 2:{
+ names.push_back(prefix+"1");
+ names.push_back(prefix+"2");
+ break;
+ }
+ case 3:{
+ names.push_back(prefix+"1");
+ names.push_back(prefix+"2");
+ names.push_back(prefix+"3");
+ break;
+ }
+ default:{
+ std::stringstream ss;
+ ss<<"Can only add one, two or three atoms at one position.";
+ ss<<"The provided force field file seems to tell something different";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ modifier.AddAddRule(number, method, names, anchors, type, charge);
+
+}
+
+
+void GromacsReader::ParseNTDB(std::vector<std::vector<String> >& content){
+
+ //Besided general termini constructors, there are also residue
+ //specific constructors => custom constructors
+ std::vector<String> termini;
+ std::map<String,std::vector<String> > custom_termini;
+
+ std::vector<std::vector<String> > data;
+ String name;
+
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ //I there is a keyword (start with [) not defined above,
+ //we assume, that it is a new residue
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == -1){
+ //parse the old residue and set new residue name
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+ data.clear();
+ name = content[line_counter][1];
+ continue;
+ }
+ }
+ data.push_back(content[line_counter]);
+ }
+
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+
+ for(std::vector<String>::iterator i = read_residues_.begin();
+ i != read_residues_.end(); ++i){
+ if(custom_termini.find(*i) != custom_termini.end()){
+ if(!custom_termini[*i].empty()) ff_->SetStandardNTer(*i,custom_termini[*i][0]);
+ continue;
+ }
+ if(!termini.empty()) ff_->SetStandardNTer(*i,termini[0]);
+ }
+}
+
+void GromacsReader::ParseCTDB(std::vector<std::vector<String> >& content){
+
+ //Besided general termini constructors, there are also residue
+ //specific constructors => custom constructors
+ std::vector<String> termini;
+ std::map<String,std::vector<String> > custom_termini;
+
+ std::vector<std::vector<String> > data;
+ String name;
+
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ //I there is a keyword (start with [) not defined above,
+ //we assume, that it is a new residue
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == -1){
+ //parse the old residue and set new residue name
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+ data.clear();
+ name = content[line_counter][1];
+ continue;
+ }
+ }
+ data.push_back(content[line_counter]);
+ }
+
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+
+ for(std::vector<String>::iterator i = read_residues_.begin();
+ i != read_residues_.end(); ++i){
+ if(custom_termini.find(*i) != custom_termini.end()){
+ if(!custom_termini[*i].empty()) ff_->SetStandardCTer(*i,custom_termini[*i][0]);
+ continue;
+ }
+ if(!termini.empty()) ff_->SetStandardCTer(*i,termini[0]);
+ }
+}
+
+void GromacsReader::ParseVSD(std::vector<std::vector<String> >& content){
+
+}
+
+void GromacsReader::ParseRtoB(std::vector<std::vector<String> >& content){
+
+ //there are two versions of this file, either with two or five
+ //columns further instructions can be found in the gromacs manual
+
+ String res_name, main, n_ter, c_ter, two_ter;
+
+ for(std::vector<std::vector<String> >::iterator i = content.begin();
+ i != content.end(); ++i){
+ if((*i).size() == 2){
+ res_name = (*i)[0];
+ main = (*i)[1];
+ n_ter = main;
+ c_ter = main;
+ two_ter = main;
+ ff_->AddResidueRenamingRule(res_name,main,n_ter,c_ter,two_ter);
+ continue;
+ }
+ if((*i).size() == 5){
+ res_name = (*i)[0];
+ main = (*i)[1];
+ n_ter = (*i)[2];
+ c_ter = (*i)[3];
+ two_ter = (*i)[4];
+ ff_->AddResidueRenamingRule(res_name,main,n_ter,c_ter,two_ter);
+ continue;
+ }
+ throw io::IOException("Entries in r2b files must contain 2 or 5 columns");
+ }
+}
+
+void GromacsReader::ReadITP(const String& basename){
+ std::vector<std::vector<String> > content = preprocessor_.Process(basename + ".itp");
+ this->ParseITP(content);
+}
+
+void GromacsReader::ParseITP(std::vector<std::vector<String> >& content){
+
+ std::vector<std::vector<String> > residue_data;
+ String residue_name;
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == 8){
+ //parse the old residue and set new residue name
+ if(!residue_data.empty()){
+ BuildingBlockPtr p = this->BlockFromITP(residue_data);
+ ff_->AddBuildingBlock(residue_name, p);
+ }
+ residue_data.clear();
+ residue_name = content[++line_counter][0];
+ continue;
+ }
+ }
+ residue_data.push_back(content[line_counter]);
+ }
+ //we probably missed the last residue
+ if(!residue_data.empty()){
+ BuildingBlockPtr p = this->BlockFromITP(residue_data);
+ ff_->AddBuildingBlock(residue_name, p);
+ }
+}
+
+BuildingBlockPtr GromacsReader::BlockFromRTP(const std::vector<std::vector<String> >& data){
+
+ if(bonded_types_.size()<4){
+ std::stringstream ss;
+ ss << "There must be at least 4 parameters in the bondedtypes section of";
+ ss << ".rtp file";
+ throw io::IOException(ss.str());
+ }
+
+ if(data[0][1] != "atoms"){
+ std::stringstream ss;
+ ss << "Expect residue definition to start with the atom keyword!";
+ throw io::IOException(ss.str());
+ }
+
+ int keyword_index = 0;
+ BuildingBlockPtr p(new BuildingBlock);
+
+ for(uint i=1;i<data.size(); ++i){
+ if(data[i].size()>1){
+ if(data[i][0]=="["){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[i][1]);
+ continue;
+ }
+ }
+
+ switch(keyword_index){
+ case 0:{
+ p->AddAtom(data[i][0],
+ data[i][1],
+ boost::lexical_cast<Real>(data[i][2]));
+ break;
+ }
+ case 1:{
+ p->AddBond(this->ParseBond(data[i],false,bonded_types_[0]));
+ break;
+ }
+ case 2:{
+ p->AddAngle(this->ParseAngle(data[i],false,bonded_types_[1]));
+ break;
+ }
+ case 3:{
+ p->AddImproper(this->ParseDihedral(data[i],false,bonded_types_[3]));
+ break;
+ }
+ case 4:{
+ p->AddDihedral(this->ParseDihedral(data[i],false,bonded_types_[2]));
+ break;
+ }
+ case 5:{
+ p->AddExclusion(this->ParseExclusion(data[i],false));
+ break;
+ }
+ case 6:{
+ p->AddCMap(this->ParseCMap(data[i],false));
+ break;
+ }
+ default:{
+ std::stringstream ss;
+ ss << "Encountered invalid keyword while parsing rtp file: " << data[i-1][1];
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+ return p;
+}
+
+BuildingBlockPtr GromacsReader::BlockFromITP(const std::vector<std::vector<String> >& data){
+
+ int keyword_index;
+
+ if(data[0][1] != "atoms"){
+ std::stringstream ss;
+ ss << "Expect residue definition to start with the atom keyword!";
+ throw io::IOException(ss.str());
+ }
+
+ std::map<int,String> index_name_mapper;
+ keyword_index = 0;
+ BuildingBlockPtr p(new BuildingBlock);
+ std::vector<String> current_line;
+
+ for(uint i=1;i<data.size(); ++i){
+ if(data[i].size()>1){
+ if(data[i][0]=="["){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[i][1]);
+ continue;
+ }
+ }
+ current_line = data[i];
+ switch(keyword_index){
+ case 0:{
+ p->AddAtom(current_line[4],
+ current_line[1],
+ boost::lexical_cast<Real>(current_line[6]));
+ index_name_mapper[boost::lexical_cast<int>(current_line[0])] = current_line[4];
+ break;
+ }
+ case 1:{
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ p->AddBond(this->ParseBond(current_line,false));
+ break;
+ }
+ case 2:{
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
+ p->AddAngle(this->ParseAngle(current_line,false));
+ break;
+ }
+ case 4:{
+ //there must be a function type, otherwise we can't distinguish
+ //between dihedrals and impropers
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
+ current_line[3] = index_name_mapper[boost::lexical_cast<int>(current_line[3])];
+
+ MMInteractionPtr int_ptr = this->ParseDihedral(current_line,false);
+ FuncType functype = int_ptr->GetFuncType();
+
+ if(functype == PeriodicDihedral){
+ p->AddDihedral(int_ptr);
+ }
+ else if(functype == PeriodicImproper || functype == HarmonicImproper){
+ p->AddImproper(int_ptr);
+ }
+ break;
+ }
+ case 5:{
+ //current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ //current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ //p->exclusions_.push_back(MMInteraction::ParseExclusion(current_line,false));
+ break;
+ }
+ case 6:{
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
+ current_line[3] = index_name_mapper[boost::lexical_cast<int>(current_line[3])];
+ current_line[4] = index_name_mapper[boost::lexical_cast<int>(current_line[4])];
+ p->AddCMap(this->ParseCMap(current_line,false));
+ break;
+ }
+ case 21:{
+ //we extract pairs manually...
+ break;
+ }
+ case 22:{
+ std::vector<String> block_atom_names = p->GetAtoms();
+ if(block_atom_names.size() < 3){
+ throw ost::Error("Molecule with settles keyword must contain at least 3 atoms!");
+ }
+ std::vector<Real> parameters;
+ std::vector<String> names;
+
+
+ MMInteractionPtr p1(new MMInteraction(DistanceConstraint));
+ MMInteractionPtr p2(new MMInteraction(DistanceConstraint));
+ MMInteractionPtr p3(new MMInteraction(DistanceConstraint));
+
+ //first constraint dist => O - H
+ parameters.push_back(boost::lexical_cast<Real>(current_line[2]));
+ names.push_back(block_atom_names[0]);
+ names.push_back(block_atom_names[1]);
+ p1->SetNames(names);
+ p1->SetParam(parameters);
+ p->AddConstraint(p1);
+
+ //second constraint dist => O - H
+ names[1] = block_atom_names[2];
+ p2->SetNames(names);
+ p2->SetParam(parameters);
+ p->AddConstraint(p2);
+
+ //third constraint dist => H - H
+ names[0] = block_atom_names[1];
+ parameters[0] = boost::lexical_cast<Real>(current_line[3]);
+ p3->SetNames(names);
+ p3->SetParam(parameters);
+ p->AddConstraint(p3);
+
+ break;
+ }
+ default:{
+ std::stringstream ss;
+ ss << "Encountered invalid keyword while parsing itp file: " << data[i-1][1];
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+ return p;
+}
+
+
+BlockModifierPtr GromacsReader::ParseBlockModifier(const std::vector<std::vector<String> >& data){
+
+
+ int keyword_index = -1;
+
+ if(data[0].size() > 0){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[0][1]);
+ if(keyword_index == -1){
+ throw ost::io::IOException("Expect termini data to start with a valid keyword!");
+ }
+ }
+
+ GromacsBlockModifier* p = new GromacsBlockModifier;
+
+ for(uint i = 1; i < data.size(); ++i){
+ if(data[i].size()>1){
+ if(data[i][0] == "["){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[i][1]);
+ continue;
+ }
+ }
+ switch(keyword_index){
+ case 7:{
+ this->ParseTerminiReplaceRule(data[i],*p);
+ break;
+ }
+ case 9:{
+ std::vector<String> line1 = data[i];
+ std::vector<String> line2 = data[++i];
+ this->ParseTerminiAddRule(line1, line2, *p);
+ break;
+ }
+ case 10:{
+ p->AddDeleteAtom(data[i][0]);
+ break;
+ }
+ case 1:{
+ p->AddBond(this->ParseBond(data[i],false,bonded_types_[0]));
+ break;
+ }
+ case 2:{
+ p->AddAngle(this->ParseAngle(data[i],false,bonded_types_[1]));
+ break;
+ }
+ case 4:{
+ p->AddDihedral(this->ParseDihedral(data[i],false,bonded_types_[2]));
+ break;
+ }
+ case 3:{
+ p->AddImproper(this->ParseDihedral(data[i],false,bonded_types_[3]));
+ break;
+ }
+ case 6:{
+ p->AddCMap(this->ParseCMap(data[i],false));
+ break;
+ }
+
+ default:{
+ std::stringstream ss;
+ ss << "Encountered invalid keyword while parsing termini: " << data[i-1][1];
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+
+ return BlockModifierPtr(p);
+}
+
+
+MMInteractionPtr GromacsReader::ParseBond(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 arguments in parsing bond!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 2){
+ throw ost::Error("Error in determining bond function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[2]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing bond!");
+ }
+ if(gromacs_functype == 1){
+ functype = HarmonicBond;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for bond!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 3){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ return p;
+}
+
+MMInteractionPtr GromacsReader::ParseAngle(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 3){
+ throw ost::io::IOException("Require at least 3 arguments in parsing angle!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 3){
+ throw ost::Error("Error in determining angle function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[3]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing angle!");
+ }
+ if(gromacs_functype == 5) functype = UreyBradleyAngle;
+ else if(gromacs_functype == 1) functype = HarmonicAngle;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for angle!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+ atom_definition.push_back(data[2]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 4){
+ std::vector<Real> parameters;
+ if(functype == UreyBradleyAngle){
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-4])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-3]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+
+ }
+ else{
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ }
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast angle parameters into real type!");
+ }
+ return p;
+}
+
+MMInteractionPtr GromacsReader::ParseDihedral(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+ if(data.size() < 4){
+ throw ost::io::IOException("Require at least 4 arguments in parsing dihedral/improper!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 4){
+ throw ost::Error("Error in determining angle function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[4]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing dihedral!");
+ }
+ if(gromacs_functype == 9 || gromacs_functype == 1) functype = PeriodicDihedral;
+ else if(gromacs_functype == 4) functype = PeriodicImproper;
+ else if(gromacs_functype == 2) functype = HarmonicImproper;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for dihedral!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+ atom_definition.push_back(data[2]);
+ atom_definition.push_back(data[3]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 5){
+ std::vector<Real> parameters;
+ if(functype == HarmonicImproper){
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ }
+ else{
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-3])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ }
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast dihedral/improper parameters into real type!");
+ }
+ return p;
+}
+
+MMInteractionPtr GromacsReader::ParseCMap(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+ if(data.size() < 5){
+ throw ost::io::IOException("Require at least 5 arguments in parsing cmap!");
+ }
+
+ if(functype == Invalid){
+ functype = CMap; //well, there is only this possibility
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+ atom_definition.push_back(data[2]);
+ atom_definition.push_back(data[3]);
+ atom_definition.push_back(data[4]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ if(data.size() > 6){
+ uint a,b;
+ try{
+ a = boost::lexical_cast<uint>(data[6]);
+ b = boost::lexical_cast<uint>(data[7]);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Failed to parse size of the cmap!");
+ }
+ if(a != b){
+ throw ost::io::IOException("Expect cmap to have equal extension into both dimensions!");
+ }
+
+ if((8+a*b) > data.size()){
+ throw ost::io::IOException("Expected more data to fill cmap!");
+ }
+ try{
+ std::vector<Real> parameters;
+ parameters.push_back(Real(a));
+ for(uint i = 0; i < a*a; ++i){
+ parameters.push_back(boost::lexical_cast<Real>(data[8+i]));
+ }
+ p->SetParam(parameters);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Failed to cast cmap values into real type!");
+ }
+ }
+ return p;
+}
+
+
+MMInteractionPtr GromacsReader::ParseLJ(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 1){
+ throw ost::io::IOException("Require at least 1 arguments in parsing LJ!");
+ }
+
+ if(functype == Invalid){
+ functype = LJ; //well, there is only this possibility
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 2){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast atomtype parameters into real type!");
+ }
+ return p;
+}
+
+
+MMInteractionPtr GromacsReader::ParseLJPair(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 arguments in parsing nonbonded parameters!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 2){
+ throw ost::Error("Error in determining LJ Pair function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[2]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing lj pair!");
+ }
+ if(gromacs_functype == 1){
+ functype = LJPair;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for LJ Pair!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 3){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast nonbonded parameters into real type!");
+ }
+ return p;
+}
+
+MMInteractionPtr GromacsReader::ParseConstraint(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 arguments in parsing nonbonded parameters!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 2){
+ throw ost::Error("Error in determining constraint function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[2]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing constraint!");
+ }
+ if(gromacs_functype == 1 || gromacs_functype == 2){
+ functype = DistanceConstraint;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for constraint!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 3){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast constraint parameters into real type!");
+ }
+ return p;
+}
+
+MMInteractionPtr GromacsReader::ParseGenborn(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+
+ if(data.size() < 1){
+ throw ost::io::IOException("Require at least 1 argument in parsing genborn parameters!");
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+
+ functype = GBSA; //bit hacky, I know, but there is only one type for gbsa anyway....
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 1){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[4]));
+ parameters.push_back(boost::lexical_cast<Real>(data[5]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast genborn parameters into real type!");
+ }
+ return p;
+}
+
+
+MMInteractionPtr GromacsReader::ParseExclusion(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 argument in parsing exclusion parameters!");
+ }
+
+ functype = Exclusion; //bit hacky, I know, but there is only one type for exclusion anyway....
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ MMInteractionPtr p(new MMInteraction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ return p;
+}
+
+void GromacsReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
+
+
+ int keyword_id = -1;
+ std::vector<String> current_line;
+
+ //will be used to calculate all pairwise 1,4 lj parameters later on
+ std::vector<String> lj_14_types;
+ std::vector<Real> lj_14_sigmas;
+ std::vector<Real> lj_14_epsilons;
+ std::vector<String> lj_types;
+ std::vector<Real> lj_sigmas;
+ std::vector<Real> lj_epsilons;
+
+ for(uint line_counter = 0; line_counter<content.size(); ++line_counter){
+ current_line = content[line_counter];
+ if(CHARMMData::Instance()->GetKeywordIndex(current_line[0]) != -1){
+ keyword_id = CHARMMData::Instance()->GetKeywordIndex(current_line[0]);
+ continue;
+ }
+
+ if(keyword_id == 8) break;
+
+ switch(keyword_id){
+ case 0:{ //atoms keyword
+ ff_->AddMass(current_line[2],boost::lexical_cast<Real>(current_line[3]));
+ break;
+ }
+ case 1:{ //bonds
+ MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ try{
+ parameters.push_back(0.1 * boost::lexical_cast<Real>(current_line[3]));
+ parameters.push_back(418.4*2 * boost::lexical_cast<Real>(current_line[2]));
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddBond(p);
+ break;
+ }
+ case 2:{ //angles
+ MMInteractionPtr p(new MMInteraction(UreyBradleyAngle));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[4])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[3])*4.184*2);
+ if(current_line.size() > 5){
+ parameters.push_back(boost::lexical_cast<Real>(current_line[6])*0.1);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[5])*418.4*2);
+ }
+ else{
+ parameters.push_back(0.0);
+ parameters.push_back(0.0);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast angle parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddAngle(p);
+ break;
+ }
+ case 3:{ //diherals
+ MMInteractionPtr p(new MMInteraction(PeriodicDihedral));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ types.push_back(current_line[3]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[5]));
+ parameters.push_back(boost::lexical_cast<Real>(current_line[6])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[4])*4.184);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddDihedral(p);
+ break;
+ }
+ case 4:{ //improper
+ MMInteractionPtr p(new MMInteraction(HarmonicImproper));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ types.push_back(current_line[3]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[6])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[4])*4.184*2);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddImproper(p);
+ break;
+ }
+ case 5:{ //cmap
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ types.push_back(current_line[3]);
+ types.push_back(current_line[7]);
+ uint dim = boost::lexical_cast<uint>(current_line[8]);
+ parameters.push_back(Real(dim));
+
+ ++line_counter;
+
+ while(true){
+ if(line_counter >= content.size()){
+ throw ost::io::IOException("Not enough data to fill cmap!");
+ }
+ if(parameters.size() > dim*dim+1){
+ std::stringstream ss;
+ ss << "Expect cmap values to fit exactly into a grid with dim ";
+ ss << dim << " x " << dim;
+ throw ost::io::IOException(ss.str());
+ }
+ if(parameters.size() == dim*dim+1){
+ MMInteractionPtr p(new MMInteraction(CMap));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddCMap(p);
+ --line_counter;
+ break;
+ }
+
+ for(std::vector<String>::iterator i = content[line_counter].begin();
+ i != content[line_counter].end(); ++i){
+ parameters.push_back(boost::lexical_cast<Real>(*i)*4.184);
+ }
+ ++line_counter;
+ }
+
+ break;
+ }
+ case 6:{ //nonbonded
+ if(current_line[0] == "cutnb") break;
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[3])*0.1/(std::pow(2,1.0/6.0))*2);
+ parameters.push_back(std::abs(boost::lexical_cast<Real>(current_line[2])*4.184));
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast LJ parameters into real type!");
+ }
+ MMInteractionPtr p(new MMInteraction(LJ));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddLJ(p);
+
+ if(current_line.size() >= 7){
+ try{
+ lj_14_types.push_back(current_line[0]);
+ lj_14_sigmas.push_back(boost::lexical_cast<Real>(current_line[6])*0.1/(std::pow(2,1.0/6.0))*2);
+ lj_14_epsilons.push_back(std::abs(boost::lexical_cast<Real>(current_line[5])*4.184));
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast LJ parameters into real type!");
+ }
+ }else{
+ lj_types.push_back(types[0]);
+ lj_sigmas.push_back(parameters[0]);
+ lj_epsilons.push_back(parameters[1]);
+ }
+
+ break;
+ }
+ case 7:{ //hbond
+ //we don't implement any things regarding hbonds in CHARMM
+ break;
+ }
+ }
+ }
+ //let's add all possible pairwise 1,4 interactions, where both interaction partners
+ //have explicitely defined 1,4 interactions
+ for(uint i = 0; i < lj_14_types.size(); ++i){
+ for(uint j = i; j < lj_14_types.size(); ++j){
+ MMInteractionPtr p(new MMInteraction(LJPair));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(lj_14_types[i]);
+ types.push_back(lj_14_types[j]);
+ parameters.push_back(0.5 * (lj_14_sigmas[i] + lj_14_sigmas[j]));
+ parameters.push_back(sqrt(lj_14_epsilons[i] * lj_14_epsilons[j]));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddLJPair(p);
+ }
+ }
+ //let's add all pairwise 1,4 interactions, where only one partner has explicitely defined 1,4 interactions
+ for(uint i = 0; i < lj_14_types.size(); ++i){
+ for(uint j = 0; j < lj_types.size(); ++j){
+ MMInteractionPtr p(new MMInteraction(LJPair));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(lj_14_types[i]);
+ types.push_back(lj_types[j]);
+ parameters.push_back(0.5 * (lj_14_sigmas[i] + lj_sigmas[j]));
+ parameters.push_back(sqrt(lj_14_epsilons[i] * lj_epsilons[j]));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddLJPair(p);
+ }
+ }
+
+
+}
+
+void GromacsReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
+
+ bool in_block = false;
+
+ BuildingBlockPtr actual_block;
+
+ String actual_block_name = "";
+
+ int keyword_id = -1;
+ std::vector<String> current_line;
+ bool line_read = false;
+
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ current_line = content[line_counter];
+ std::cerr<<current_line[0]<<std::endl;
+ if(CHARMMData::Instance()->GetKeywordIndex(current_line[0]) != -1){
+ keyword_id = CHARMMData::Instance()->GetKeywordIndex(current_line[0]);
+ }
+ if(keyword_id == -1) continue;
+
+
+
+ if(in_block){
+ line_read = false;
+ switch(keyword_id){
+ case 15:{ //atom
+ actual_block->AddAtom(current_line[1],current_line[2],boost::lexical_cast<Real>(current_line[3]));
+ line_read=true;
+ break;
+ }
+ case 16:{//group
+ line_read=true;
+ break;
+ }
+ case 17:{//bond
+ int num_bonds = (current_line.size()-1) / 2;
+ for(int i = 0; i < num_bonds; ++i){
+ MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ std::vector<String> names;
+ names.push_back(current_line[i*2+1]);
+ names.push_back(current_line[i*2+2]);
+ p->SetNames(names);
+ actual_block->AddBond(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 18:{//angle
+ int num_angles = (current_line.size()-1) / 3;
+ for(int i = 0; i < num_angles; ++i){
+ MMInteractionPtr p(new MMInteraction(UreyBradleyAngle));
+ std::vector<String> names;
+ names.push_back(current_line[i*3+1]);
+ names.push_back(current_line[i*3+2]);
+ names.push_back(current_line[i*3+3]);
+ p->SetNames(names);
+ actual_block->AddAngle(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 19:{//dihedral
+ int num_dihedrals = (current_line.size()-1) / 4;
+ for(int i = 0; i < num_dihedrals; ++i){
+ MMInteractionPtr p(new MMInteraction(PeriodicDihedral));
+ std::vector<String> names;
+ names.push_back(current_line[i*4+1]);
+ names.push_back(current_line[i*4+2]);
+ names.push_back(current_line[i*4+3]);
+ names.push_back(current_line[i*4+4]);
+ p->SetNames(names);
+ actual_block->AddDihedral(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 20:{//improper
+ int num_impropers = (current_line.size()-1) / 4;
+ for(int i = 0; i < num_impropers; ++i){
+ MMInteractionPtr p(new MMInteraction(HarmonicImproper));
+ std::vector<String> names;
+ names.push_back(current_line[i*4+1]);
+ names.push_back(current_line[i*4+2]);
+ names.push_back(current_line[i*4+3]);
+ names.push_back(current_line[i*4+4]);
+ p->SetNames(names);
+ actual_block->AddImproper(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 5:{//cmap
+ int num_cmaps = (current_line.size()-1) / 8;
+ for(int i = 0; i < num_cmaps; ++i){
+ MMInteractionPtr p(new MMInteraction(CMap));
+ std::vector<String> names;
+ names.push_back(current_line[i*4+1]);
+ names.push_back(current_line[i*4+2]);
+ names.push_back(current_line[i*4+3]);
+ names.push_back(current_line[i*4+4]);
+ names.push_back(current_line[i*4+8]);
+ p->SetNames(names);
+ actual_block->AddCMap(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 21:{ //donor
+ line_read=true;
+ break; //I don't think. that this will ever be read...
+ }
+ case 22:{//acceptor
+ line_read=true;
+ break; //I don't think. that this will ever be read...
+ }
+ case 23:{// ic
+ line_read=true;
+ break;
+ }
+ case 24:{ //patching
+ line_read=true;
+ break;
+ }
+ case 25:{ //print
+ line_read=true;
+ break;
+ }
+ case 26:{ //double =>basically a bond
+ int num_bonds = (current_line.size()-1) / 2;
+ for(int i = 0; i < num_bonds; ++i){
+ MMInteractionPtr p(new MMInteraction(HarmonicBond));
+ std::vector<String> names;
+ names.push_back(current_line[i*2+1]);
+ names.push_back(current_line[i*2+2]);
+ p->SetNames(names);
+ actual_block->AddBond(p);
+ }
+ line_read=true;
+ break;
+ }
+ }
+ }
+
+ if(line_read) continue;
+
+ switch(keyword_id){
+ case 9:{
+ try {ff_->AddMass(current_line[2],boost::lexical_cast<Real>(current_line[3]));}
+ catch(std::exception& e){
+ throw ost::io::IOException("Could not cast mass into real type!");
+ }
+ break;
+ }
+ case 10:{
+ break; //we don't read that for now....
+ }
+ case 11:{//we don't allow patches for now
+ break;
+ }
+ case 12:{
+ break; //we don't read that for now
+ }
+ case 13:{
+ //check, whether there is an "open block"
+ if(in_block){
+ ff_->AddBuildingBlock(actual_block_name,actual_block);
+ std::cerr<<"added building block: "<<actual_block_name<<std::endl;
+ }
+ actual_block_name = current_line[1];
+ actual_block = BuildingBlockPtr(new BuildingBlock);
+ in_block = true;
+ std::cerr<<actual_block_name<<std::endl;
+ break;
+ }
+ case 14:{
+ //check, whether there is an "open block"
+ if(in_block){
+ ff_->AddBuildingBlock(actual_block_name,actual_block);
+ in_block = false;
+ }
+ break;
+ }
+
+
+ }
+
+ }
+
+ //add last building block if necessary
+ if(in_block) ff_->AddBuildingBlock(actual_block_name,actual_block);
+
+}
+
+}}}
diff --git a/modules/mol/mm/src/gromacs_reader.hh b/modules/mol/mm/src/gromacs_reader.hh
new file mode 100644
index 0000000000000000000000000000000000000000..89a2e20a45edbbb2e63c860800a80f704339eefc
--- /dev/null
+++ b/modules/mol/mm/src/gromacs_reader.hh
@@ -0,0 +1,194 @@
+#ifndef OST_GROMACS_READER_HH
+#define OST_GROMACS_READER_HH
+
+#include <fstream>
+
+#include <boost/filesystem.hpp>
+#include <boost/algorithm/string.hpp>
+#include <boost/lexical_cast.hpp>
+#include <boost/unordered_map.hpp>
+
+#include <ost/base.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class GromacsData;
+class CHARMMData;
+class GromacsReader;
+typedef boost::shared_ptr<GromacsData> GromacsDataPtr;
+typedef boost::shared_ptr<GromacsReader> GromacsReaderPtr;
+typedef boost::shared_ptr<CHARMMData> CHARMMDataPtr;
+
+class GromacsData{
+public:
+ static GromacsDataPtr Instance();
+ int GetKeywordIndex(const String& keyword);
+ String ConvertToStandard(const String& res_name, const String& atom_name);
+ bool ConversionExists(const String& res_name);
+
+private:
+ GromacsData();
+ GromacsData(const GromacsData&);
+ GromacsDataPtr operator=(const GromacsDataPtr&);
+ static GromacsDataPtr instance_;
+ boost::unordered_map<String,int> keyword_map_;
+ boost::unordered_map<String, std::vector<std::pair<String,String> > > renaming_to_standard_;
+
+};
+
+class CHARMMData{
+public:
+ static CHARMMDataPtr Instance();
+ int GetKeywordIndex(const String& keyword);
+
+private:
+ CHARMMData();
+ CHARMMData(const CHARMMData&);
+ CHARMMDataPtr operator=(const CHARMMDataPtr&);
+ static CHARMMDataPtr instance_;
+ boost::unordered_map<String,int> keyword_map_;
+};
+
+class MMPreprocessor{
+
+public:
+
+ MMPreprocessor(const String& basepath): basepath_(basepath) { }
+
+ std::vector<std::vector<String> > Process(const String& filename);
+
+ void SetDefinition(const String& def) { defines_.insert(def); }
+
+ boost::filesystem::path GetBasedir() { return basepath_; }
+
+private:
+
+ //function, that can recursively resolve ifdef / ifndef statements
+ void ResolveIFDEF(std::vector<std::vector<String> >& file_content, int line_counter);
+
+ //simply reads a file, cuts it into pieces and removes comments marked by '*' and ';'
+ std::vector<std::vector<String> > ReadFile(const String& filename);
+
+ std::map<String,std::vector<String> > definitions_;
+ std::set<String> defines_;
+ boost::filesystem::path basepath_;
+};
+
+
+class GromacsReader {
+public:
+
+ GromacsReader(const String& base_dir);
+
+ void SetPreprocessorDefinition(const String& def) { preprocessor_.SetDefinition(def); }
+
+ void ReadGromacsForcefield();
+
+ ForcefieldPtr GetForcefield() { return ff_;}
+
+ void SetForcefield(ForcefieldPtr ff) { ff_ = ff; }
+
+ void ReadResidueDatabase(const String& basename);
+
+ void ReadITP(const String& basename);
+
+ void ReadCHARMMPRM(const String& basename);
+
+ void ReadCHARMMRTF(const String& basename);
+
+private:
+
+ MMInteractionPtr ParseBond(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseAngle(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseDihedral(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseCMap(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseLJ(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseLJPair(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseConstraint(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseGenborn(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ MMInteractionPtr ParseExclusion(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ BuildingBlockPtr BlockFromRTP(const std::vector<std::vector<String> >& data);
+
+ BuildingBlockPtr BlockFromITP(const std::vector<std::vector<String> >& data);
+
+ TerminiConstructorPtr ParseTermini(const std::vector<std::vector<String> >& data);
+
+ BlockModifierPtr ParseBlockModifier(const std::vector<std::vector<String> >& data);
+
+ void ParseHydrogenRule(const std::vector<String>& data, GromacsHydrogenConstructor& constructor);
+
+ void ParseTerminiReplaceRule(const std::vector<String>& data, GromacsBlockModifier& constructor);
+
+ void ParseTerminiAddRule(const std::vector<String>& data1, const std::vector<String>& data2,
+ GromacsBlockModifier& constructor);
+
+ //Reader functions for the mandatory forcefield files
+ void ParseForcefield(std::vector<std::vector<String> >& content);
+ void ParseAtomTypes(std::vector<std::vector<String> >& content);
+
+ //Reader functions for CHARMM stuff
+ void ParseCHARMMPRM(std::vector<std::vector<String> >& content);
+
+ void ParseCHARMMRTF(std::vector<std::vector<String> >& content);
+
+ //Reader functions for all different residue database files
+ void ParseRTP(std::vector<std::vector<String> >& content);
+ void ParseARN(std::vector<std::vector<String> >& content);
+ void ParseHDB(std::vector<std::vector<String> >& content);
+ void ParseNTDB(std::vector<std::vector<String> >& content);
+ void ParseCTDB(std::vector<std::vector<String> >& content);
+ void ParseVSD(std::vector<std::vector<String> >& content);
+ void ParseRtoB(std::vector<std::vector<String> >& content);
+ //Reader function for single molecule itp files
+ void ParseITP(std::vector<std::vector<String> >& content);
+
+ boost::unordered_map<String, std::vector<std::pair<String,String> > > atom_renaming_ff_specific_;
+ boost::unordered_map<String, ResidueNamesPtr> res_renaming_ff_specific_;
+
+ std::vector<FuncType> ff_bonded_types_;
+
+ MMPreprocessor preprocessor_;
+ ForcefieldPtr ff_;
+
+ //following part is ugly...
+ //data that is read during the residue datababase parsing process gets stored in there
+ std::vector<FuncType> bonded_types_;
+ std::vector<String> read_residues_;
+};
+
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/src/index.hh b/modules/mol/mm/src/index.hh
new file mode 100644
index 0000000000000000000000000000000000000000..055ad73a23ca22b4f53b02cf78ccefd2aa7421d4
--- /dev/null
+++ b/modules/mol/mm/src/index.hh
@@ -0,0 +1,173 @@
+#ifndef OST_MM_INDEX_HH
+#define OST_MM_INDEX_HH
+
+/*
+ Author: Marco Biasini
+ */
+
+#include <algorithm>
+
+#include <cstring>
+
+namespace ost { namespace mol{ namespace mm{
+
+namespace impl {
+template <uint D>
+class IndexBase {
+public:
+ enum { Dimension = D };
+ IndexBase(const IndexBase& rhs) {
+ memcpy(data_, rhs.data_, sizeof(uint[D]));
+ }
+ IndexBase() {
+ memset(data_, 0, sizeof(uint[D]));
+ }
+
+ IndexBase& operator=(const IndexBase& rhs) {
+ memcpy(data_, rhs.data_, sizeof(uint[D]));
+ return *this;
+ }
+ uint operator[](uint idx) const {
+ assert(idx < D);
+ return data_[idx];
+ }
+ uint& operator[](uint idx) {
+ assert(idx < D);
+ return data_[idx];
+ }
+ //allows index to be inserted into set
+ inline bool operator < (const IndexBase<D>& rhs) const{
+ return std::lexicographical_compare(data_, data_+D, rhs.data_, rhs.data_+D);
+ }
+
+ inline bool operator==(const IndexBase<D>& rhs) const{
+ return std::equal(data_,data_+D,rhs.data_);
+ }
+
+ inline bool operator!=(const IndexBase<D>& rhs) const{
+ return !(*this == rhs);
+ }
+
+private:
+ uint data_[D];
+};
+
+} // namespace impl
+
+template <uint D>
+class Index;
+
+template <>
+class Index<1> : public impl::IndexBase<1> {
+public:
+ Index() : impl::IndexBase<1>() {}
+ Index(uint a) {
+ (*this)[0]=a;
+ }
+};
+template <>
+class Index<2> : public impl::IndexBase<2> {
+public:
+ Index() : impl::IndexBase<2>() {}
+ Index(uint a, uint b) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ }
+};
+template <>
+class Index<3> : public impl::IndexBase<3> {
+public:
+ Index() : impl::IndexBase<3>() {}
+ Index(uint a, uint b, uint c) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ }
+};
+template <>
+class Index<4> : public impl::IndexBase<4> {
+public:
+ Index() : impl::IndexBase<4>() {}
+ Index(uint a, uint b, uint c, uint d) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ }
+};
+template <>
+class Index<5> : public impl::IndexBase<5> {
+public:
+ Index() : impl::IndexBase<5>() {}
+ Index(uint a, uint b, uint c, uint d, uint e) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ (*this)[4]=e;
+ }
+};
+template <>
+class Index<6> : public impl::IndexBase<6> {
+public:
+ Index() : impl::IndexBase<6>() {}
+ Index(uint a, uint b, uint c, uint d, uint e, uint f) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ (*this)[4]=e;
+ (*this)[5]=f;
+ }
+};
+template <>
+class Index<7> : public impl::IndexBase<7> {
+public:
+ Index() : impl::IndexBase<7>() {}
+ Index(uint a, uint b, uint c, uint d, uint e, uint f, uint g) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ (*this)[4]=e;
+ (*this)[5]=f;
+ (*this)[6]=g;
+ }
+};
+template<uint D>
+class IndexIterator {
+public:
+ typedef Index<D> IndexType;
+ IndexIterator(const IndexType& s, const IndexType& e)
+ : start_(s), end_(e), current_(s) {
+
+ }
+
+ IndexIterator<D>& operator++() {
+ uint current_it=0;
+ while (++current_[current_it] > end_[current_it]) {
+ current_it++;
+ if (current_it < D) {
+ current_[current_it-1] = start_[current_it-1];
+ } else {
+ break;
+ }
+ }
+ return *this;
+ }
+ const IndexType& operator *() const {
+ return current_;
+ }
+ bool AtEnd() {
+ return current_[D-1] > end_[D-1];
+ }
+private:
+ IndexType start_;
+ IndexType end_;
+ IndexType current_;
+
+};
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/mm_interaction.cc b/modules/mol/mm/src/mm_interaction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..093e2d122e43773e786c1afa5b3440e109d65c2d
--- /dev/null
+++ b/modules/mol/mm/src/mm_interaction.cc
@@ -0,0 +1,194 @@
+#include <ost/mol/mm/mm_interaction.hh>
+
+namespace ost { namespace mol{ namespace mm{
+
+MMInteraction::MMInteraction(FuncType func_type): func_type_(func_type),
+ set_parameters_(false),
+ has_type_wildcard_(false),
+ has_name_wildcard_(false){ }
+
+
+void MMInteraction::SetTypes(std::vector<String> types){
+ if(!this->CheckSetNamesTypes(types)){
+ throw ost::Error("Tried to set invalid number of types to interaction!");
+ }
+ atom_types_ = types;
+ if(std::find(atom_types_.begin(),atom_types_.end(),"X") != atom_types_.end()){
+ has_type_wildcard_ = true;
+ }
+ else has_type_wildcard_ = false;
+}
+
+void MMInteraction::SetNames(std::vector<String> names){
+ if(!this->CheckSetNamesTypes(names)){
+ throw ost::Error("Tried to set invalid number of names to interaction!");
+ }
+ atom_names_ = names;
+ if(std::find(atom_names_.begin(),atom_names_.end(),"X") != atom_names_.end()){
+ has_name_wildcard_ = true;
+ }
+ else has_name_wildcard_ = false;
+}
+
+void MMInteraction::SetParam(std::vector<Real>& parameters){
+ if(!this->CheckSetParam(parameters)){
+ throw ost::Error("Tried to set invalid number of parameters to interaction!");
+ }
+ parameters_ = parameters;
+ set_parameters_ = true;
+}
+
+ost::mol::AtomHandleList MMInteraction::GetAtoms(const ost::mol::ResidueHandle& res) const{
+
+ ost::mol::AtomHandleList return_list;
+ ost::mol::ResidueHandle prev = res.GetPrev();
+ ost::mol::ResidueHandle next = res.GetNext();
+ String atom_name;
+ ost::mol::AtomHandle atom;
+
+ for(std::vector<String>::const_iterator i = atom_names_.begin();
+ i != atom_names_.end(); ++i){
+ atom_name = (*i);
+ if(atom_name[0] == '+'){
+ atom_name = atom_name.substr(1);
+ if(!next.IsValid()){
+ throw ost::Error("Access to nonexistent next residue requested!");
+ }
+ atom = next.FindAtom(atom_name);
+ if(atom.IsValid()){
+ return_list.push_back(atom);
+ continue;
+ }
+ throw ost::Error("Could not find required atom "+*i+"!");
+ }
+ if(atom_name[0] == '-'){
+ atom_name = atom_name.substr(1);
+ if(!prev.IsValid()){
+ throw ost::Error("Access to nonexistent previous residue requested!");
+ }
+ atom = prev.FindAtom(atom_name);
+ if(atom.IsValid()){
+ return_list.push_back(atom);
+ continue;
+ }
+ throw ost::Error("Could not find required atom "+*i+"!");
+ }
+ atom = res.FindAtom(atom_name);
+ if(atom.IsValid()){
+ return_list.push_back(atom);
+ continue;
+ }
+ throw ost::Error("Could not find required atom "+*i+"!");
+ }
+
+ return return_list;
+}
+
+bool MMInteraction::MatchTypes(const std::vector<String>& atom_types) const {
+
+ if(atom_types_.size() == 0) return false;
+ if(atom_types.size() != atom_types_.size()) return false;
+
+ bool match = true;
+ bool reverse_match = true;
+
+ uint i,j;
+
+ for(i = 0, j = atom_types_.size()-1; i < atom_types_.size(); ++i,--j){
+ if((atom_types[i] != atom_types_[i]) && (atom_types_[i] != "X")) match = false;
+ if((atom_types[i] != atom_types_[j]) && (atom_types_[j] != "X")) reverse_match = false;
+ }
+
+ return match || reverse_match;
+}
+
+bool MMInteraction::MatchNames(const std::vector<String>& atom_names) const {
+
+ if(atom_names_.size() == 0) return false;
+ if(atom_names.size() != atom_names_.size()) return false;
+
+ bool match = true;
+ bool r_match = true;
+
+ uint i,j;
+
+ for(i = 0, j = atom_names_.size()-1; i < atom_names_.size(); ++i,--j){
+ if((atom_names[i] != atom_names_[i]) && (atom_names_[i] != "X")) match = false;
+ if((atom_names[i] != atom_names_[j]) && (atom_names_[j] != "X")) r_match = false;
+ }
+
+ return match || r_match;
+}
+
+bool MMInteraction::ReplaceAtom(const String& name, const String& new_name, const String& new_type){
+
+ for(uint i = 0; i < atom_names_.size(); ++i){
+ if(atom_names_[i] == name){
+ atom_names_[i] = new_name;
+ if(i < atom_types_.size()) atom_types_[i] = new_type;
+ //it could be, that wildcard stuff has changed
+ has_type_wildcard_ = std::find(atom_types_.begin(),atom_types_.end(),"X") != atom_types_.end();
+ has_name_wildcard_ = std::find(atom_names_.begin(),atom_names_.end(),"X") != atom_names_.end();
+ return true;
+ }
+ }
+ return false;
+}
+
+bool MMInteraction::HasName(const String& name) const{
+ return std::find(atom_names_.begin(),atom_names_.end(),name) != atom_names_.end();
+}
+
+bool MMInteraction::HasType(const String& type) const{
+ return std::find(atom_types_.begin(),atom_types_.end(),type) != atom_types_.end();
+}
+
+bool MMInteraction::CheckSetNamesTypes(std::vector<String>& types){
+
+ switch(func_type_){
+ case HarmonicBond: return types.size() == 2;
+ case HarmonicAngle: return types.size() == 3;
+ case UreyBradleyAngle: return types.size() == 3;
+ case PeriodicDihedral: return types.size() == 4;
+ case PeriodicImproper: return types.size() == 4;
+ case HarmonicImproper: return types.size() == 4;
+ case CMap: return types.size() == 5;
+ case LJ: return types.size() == 1;
+ case LJPair: return types.size() == 2;
+ case GBSA: return types.size() == 1;
+ case DistanceConstraint: return types.size() == 2;
+ case Exclusion: return types.size() == 2;
+ case HarmonicPositionRestraint: return types.size() == 1;
+ case HarmonicDistanceRestraint: return types.size() == 2;
+ default: return false;
+ }
+}
+
+bool MMInteraction::CheckSetParam(std::vector<Real>& param){
+
+ switch(func_type_){
+ case HarmonicBond: return param.size() == 2;
+ case HarmonicAngle: return param.size() == 2;
+ case UreyBradleyAngle: return param.size() == 4;
+ case PeriodicDihedral: return param.size() == 3;
+ case PeriodicImproper: return param.size() == 3;
+ case HarmonicImproper: return param.size() == 2;
+ case CMap:{
+ int num_param = param.size();
+ if(num_param < 1) return false;
+ int x = param[0];
+ return num_param == (x*x + 1);
+ }
+ case LJ: return param.size() == 2;
+ case LJPair: return param.size() == 2;
+ case GBSA: return param.size() == 2;
+ case DistanceConstraint: return param.size() == 1;
+ case Exclusion: return param.empty();
+ case HarmonicPositionRestraint: return param.size() == 7;
+ case HarmonicDistanceRestraint: return param.size() == 2;
+ default: return false;
+ }
+
+}
+
+}}} //ns
\ No newline at end of file
diff --git a/modules/mol/mm/src/mm_interaction.hh b/modules/mol/mm/src/mm_interaction.hh
new file mode 100644
index 0000000000000000000000000000000000000000..edc8afc21e6ab660b279275267db9ac4fccd2273
--- /dev/null
+++ b/modules/mol/mm/src/mm_interaction.hh
@@ -0,0 +1,147 @@
+#ifndef OST_MM_INTERACTION_HH
+#define OST_MM_INTERACTION_HH
+
+#include <vector>
+#include <fstream>
+
+#include <boost/shared_ptr.hpp>
+#include <boost/filesystem.hpp>
+
+#include <ost/io/binary_data_source.hh>
+#include <ost/io/binary_data_sink.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/message.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/residue_handle.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class MMInteraction;
+typedef boost::shared_ptr<MMInteraction> MMInteractionPtr;
+
+enum FuncType{
+ Invalid,
+ HarmonicBond,
+ HarmonicAngle,
+ UreyBradleyAngle,
+ PeriodicDihedral,
+ PeriodicImproper,
+ HarmonicImproper,
+ CMap,
+ LJ,
+ LJPair,
+ GBSA,
+ DistanceConstraint,
+ Exclusion,
+ HarmonicPositionRestraint,
+ HarmonicDistanceRestraint
+};
+
+class MMInteraction{
+
+public:
+ MMInteraction(FuncType func_type);
+
+ void SetTypes(std::vector<String> types);
+
+ void SetNames(std::vector<String> names);
+
+ void SetParam(std::vector<Real>& parameters);
+
+ std::vector<String> GetTypes() const { return atom_types_; }
+
+ std::vector<String> GetNames() const { return atom_names_; }
+
+ std::vector<Real> GetParam() const { return parameters_; }
+
+ ost::mol::AtomHandleList GetAtoms(const ost::mol::ResidueHandle& res) const;
+
+ FuncType GetFuncType() const { return func_type_; }
+
+ bool ReplaceAtom(const String& name, const String& new_name, const String& new_type);
+
+ bool MatchTypes(const std::vector<String>& atom_types) const;
+
+ bool MatchNames(const std::vector<String>& atom_names) const;
+
+ bool HasName(const String& name) const;
+
+ bool HasType(const String& type) const;
+
+ bool IsParametrized() const { return set_parameters_; }
+
+ bool HasTypeWildcard() const { return has_type_wildcard_; }
+
+ bool HasNameWildcard() const { return has_name_wildcard_; }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & set_parameters_;
+ ds & has_type_wildcard_;
+ ds & has_name_wildcard_;
+
+ if(ds.IsSource()){
+ int num_types;
+ int num_names;
+ int num_param;
+ ds & num_types;
+ ds & num_names;
+ ds & num_param;
+ for(int i = 0; i < num_types; ++i){
+ String type;
+ ds & type;
+ atom_types_.push_back(type);
+ }
+ for(int i = 0; i < num_names; ++i){
+ String name;
+ ds & name;
+ atom_names_.push_back(name);
+ }
+ for(int i = 0; i < num_param; ++i){
+ Real param;
+ ds & param;
+ parameters_.push_back(param);
+ }
+ }
+ else{
+ int atom_types_size = atom_types_.size();
+ int atom_names_size = atom_names_.size();
+ int parameters_size = parameters_.size();
+ ds & atom_types_size;
+ ds & atom_names_size;
+ ds & parameters_size;
+
+ for(std::vector<String>::iterator i = atom_types_.begin();
+ i != atom_types_.end(); ++i){
+ ds & *i;
+ }
+ for(std::vector<String>::iterator i = atom_names_.begin();
+ i != atom_names_.end(); ++i){
+ ds & *i;
+ }
+ for(std::vector<Real>::iterator i = parameters_.begin();
+ i != parameters_.end(); ++i){
+ ds & *i;
+ }
+ }
+ }
+
+private:
+
+ bool CheckSetNamesTypes(std::vector<String>& types);
+ bool CheckSetParam(std::vector<Real>& param);
+
+ FuncType func_type_;
+ bool set_parameters_;
+ bool has_type_wildcard_;
+ bool has_name_wildcard_;
+ std::vector<Real> parameters_;
+ std::vector<String> atom_types_;
+ std::vector<String> atom_names_;
+};
+
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/mm_modeller.cc b/modules/mol/mm/src/mm_modeller.cc
new file mode 100644
index 0000000000000000000000000000000000000000..893e1a2702757464e4d1e0e0ce8671b6ce3b5edb
--- /dev/null
+++ b/modules/mol/mm/src/mm_modeller.cc
@@ -0,0 +1,322 @@
+#include <ost/mol/mm/mm_modeller.hh>
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+void MMModeller::GenerateDisulfidBonds(ost::mol::EntityHandle& handle){
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(i->GetName() == "CYS" || i->GetName() == "CYX" || i->GetName() == "CYS2" || i->GetName() == "CYM"){
+ ost::mol::AtomHandle s = i->FindAtom("SG");
+ if(s.IsValid()){
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(s.GetPos(),2.5);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if(j->GetName() == "SG" && j->GetResidue() != *i){
+ if(!ost::mol::BondExists(s,*j)){
+ ed.Connect(s,*j);
+ }
+ ed.RenameResidue(*i,"CYS2");
+ ed.RenameResidue(j->GetResidue(),"CYS2");
+ }
+ }
+ }
+ }
+ }
+}
+
+void MMModeller::GenerateCYSHEMEBonds(ost::mol::EntityHandle& handle){
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(i->GetName() == "HEM" || i->GetName() == "HEME"){
+ ost::mol::AtomHandle fe = i->FindAtom("FE");
+ if(fe.IsValid()){
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(fe.GetPos(), 3.0);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if( j->GetName() == "SG"){
+ if(!ost::mol::BondExists(fe,*j)){
+ ed.Connect(fe,*j);
+ }
+ ed.RenameResidue(*i,"HEME");
+ ed.RenameResidue(j->GetResidue(),"CYS2");
+ }
+ }
+ }
+ ost::mol::AtomHandle cab = i->FindAtom("CAB");
+ if(cab.IsValid()){
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(cab.GetPos(), 0.23);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if(j->GetName() == "SG"){
+ if(!BondExists(cab,*j)){
+ ed.Connect(cab,*j);
+ }
+ ed.RenameResidue(*i,"HEME");
+ ed.RenameResidue(j->GetResidue(),"CYS2");
+ }
+ }
+ }
+ ost::mol::AtomHandle cac = i->FindAtom("CAC");
+ if(cac.IsValid()){
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(cac.GetPos(),0.23);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if(j->GetName() == "SG"){
+ if(!BondExists(cac,*j)){
+ ed.Connect(cac,*j);
+ }
+ ed.RenameResidue(*i,"HEME");
+ ed.RenameResidue(j->GetResidue(),"CYS2");
+ }
+ }
+ }
+ }
+ }
+}
+
+void MMModeller::GenerateHISHEMEBonds(ost::mol::EntityHandle& handle){
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(i->GetName() == "HEM" || i->GetName() == "HEME"){
+ ost::mol::AtomHandle fe = i->FindAtom("FE");
+ if(fe.IsValid()){
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(fe.GetPos(),2.5);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if(j->GetName() == "NE2" && j->GetResidue().GetName() == "HIS"){
+ if(!ost::mol::BondExists(fe,*j)){
+ ed.Connect(fe,*j);
+ }
+ ed.RenameResidue(*i,"HEME");
+ ed.RenameResidue(j->GetResidue(),"HIS1");
+ }
+ }
+ }
+ }
+ }
+}
+
+void MMModeller::GenerateMETHEMEBonds(ost::mol::EntityHandle& handle){
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(i->GetName() == "HEM" || i->GetName() == "HEME"){
+ ost::mol::AtomHandle fe = i->FindAtom("FE");
+ if(fe.IsValid()){
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(fe.GetPos(),2.9);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if(j->GetName() == "SD" && j->GetResidue().GetName() == "MET"){
+ if(!ost::mol::BondExists(fe,*j)){
+ ed.Connect(fe,*j);
+ }
+ ed.RenameResidue(*i,"HEME");
+ }
+ }
+ }
+ }
+ }
+}
+
+void MMModeller::LowerPrecision(ost::mol::EntityHandle& handle){
+
+ ost::mol::AtomHandleList atom_list = handle.GetAtomList();
+ ost::mol::XCSEditor ed = handle.EditXCS(ost::mol::BUFFERED_EDIT);
+ geom::Vec3 pos;
+ geom::Vec3 truncated_pos;
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i != atom_list.end(); ++i){
+ pos = i->GetPos();
+ truncated_pos[0] = Real(round(pos[0]*100))/100;
+ truncated_pos[1] = Real(round(pos[1]*100))/100;
+ truncated_pos[2] = Real(round(pos[2]*100))/100;
+ ed.SetAtomPos(*i,truncated_pos);
+ }
+ ed.UpdateICS();
+}
+
+void MMModeller::AssignPDBNaming(ost::mol::EntityHandle& handle){
+
+ std::map<String,String> gromacs_to_pdb;
+ gromacs_to_pdb["ARGN"] = "ARG";
+ gromacs_to_pdb["ASPH"] = "ASP";
+ gromacs_to_pdb["CYS2"] = "CYS";
+ gromacs_to_pdb["GLUH"] = "GLU";
+ gromacs_to_pdb["HISD"] = "HIS";
+ gromacs_to_pdb["HISE"] = "HIS";
+ gromacs_to_pdb["HISH"] = "HIS";
+ gromacs_to_pdb["HIS1"] = "HIS";
+ gromacs_to_pdb["LYSN"] = "LYS";
+ gromacs_to_pdb["HEME"] = "HEM";
+
+ ost::mol::XCSEditor ed = handle.EditXCS();
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ String res_name;
+ ost::mol::AtomHandle atom;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ res_name = i->GetName();
+ if(gromacs_to_pdb.find(res_name) != gromacs_to_pdb.end()){
+ ed.RenameResidue(*i,gromacs_to_pdb[res_name]);
+ }
+ //this is nasty hardcoded stuff
+ //in case of ILE gromacs seems to define wrong standard naming
+ //we have to keep this wrong standard naming to remain consistent
+ //with the namings in the forcefields.
+ //to avoid errors in loading a pdb structure with these namings
+ //we have to hardcode a correct conversion
+ if(res_name == "ILE"){
+ atom = i->FindAtom("CD");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"CD1");
+ }
+ atom = i->FindAtom("HD1");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"HD11");
+ }
+ atom = i->FindAtom("HD2");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"HD12");
+ }
+ atom = i->FindAtom("HD3");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"HD13");
+ }
+ }
+ }
+}
+
+void MMModeller::AssignGromacsNaming(ost::mol::EntityHandle& handle){
+
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ //Let's first rename as much as possible to the gromacs standard
+ std::map<String,String> residue_renaming;
+
+ //a proper solution should be found for that (assign proper protonation)
+ residue_renaming["HIS"] = "HISE";
+ //this is awful....
+
+
+ residue_renaming["HID"] = "HISD";
+ residue_renaming["HIE"] = "HISE";
+ residue_renaming["HSP"] = "HISH";
+ residue_renaming["LSN"] = "LYSN";
+ residue_renaming["ASPP"] = "ASPH";
+ residue_renaming["GLUP"] = "GLUH";
+ residue_renaming["HOH"] = "SOL";
+ residue_renaming["TIP3"] = "SOL";
+ residue_renaming["HOH"] = "SOL";
+ residue_renaming["HEME"] = "HEM";
+ //following stuff are required to rename the charmm names that are different,
+ //as it for example comes from CHARMM GUI
+ residue_renaming["POT"] = "K";
+ residue_renaming["CLA"] = "CL";
+ residue_renaming["SOD"] = "NA";
+ residue_renaming["CAL"] = "CA";
+ residue_renaming["CES"] = "CS";
+ residue_renaming["ZN2"] = "ZN";
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(residue_renaming.find(i->GetName()) != residue_renaming.end()){
+ ed.RenameResidue(*i,residue_renaming[i->GetName()]);
+ }
+ }
+
+ //this data is taken from the gromacs xlateat.dat file
+ std::map<String, std::map<String, String> > renaming_to_standard;
+ renaming_to_standard["ILE"] = std::map<String,String>();
+ renaming_to_standard["HOH"] = std::map<String,String>();
+ renaming_to_standard["HO4"] = std::map<String,String>();
+ renaming_to_standard["HO5"] = std::map<String,String>();
+ renaming_to_standard["HEME"] = std::map<String,String>();
+ renaming_to_standard["protein"] = std::map<String,String>();
+
+ renaming_to_standard["ILE"]["CD1"] = "CD";
+ renaming_to_standard["ILE"]["HD11"] = "HD1";
+ renaming_to_standard["ILE"]["HD12"] = "HD2";
+ renaming_to_standard["ILE"]["HD13"] = "HD3";
+
+ renaming_to_standard["SOL"]["O"] = "OW";
+ renaming_to_standard["SOL"]["OW1"] = "OW";
+ renaming_to_standard["SOL"]["OH2"] = "OW"; //specific for CHARMM-GUI
+ renaming_to_standard["SOL"]["H1"] = "HW1"; //specific for CHARMM-GUI
+ renaming_to_standard["SOL"]["H2"] = "HW2"; //specific for CHARMM-GUI
+
+ renaming_to_standard["HEM"]["N_A"] = "NA";
+ renaming_to_standard["HEM"]["N_B"] = "NB";
+ renaming_to_standard["HEM"]["N_C"] = "NC";
+ renaming_to_standard["HEM"]["N_D"] = "ND";
+
+ renaming_to_standard["protein"]["O1"] = "O";
+ renaming_to_standard["protein"]["O2"] = "OXT";
+ renaming_to_standard["protein"]["OT1"] = "O";
+ renaming_to_standard["protein"]["OT2"] = "OXT";
+ renaming_to_standard["protein"]["OT"] = "OXT";
+ renaming_to_standard["protein"]["O'"] = "O";
+ renaming_to_standard["protein"]["O''"] = "OXT";
+ renaming_to_standard["protein"]["OC1"] = "O";
+ renaming_to_standard["protein"]["OC2"] = "OXT";
+ renaming_to_standard["protein"]["HN"] = "H";
+ renaming_to_standard["protein"]["HT1"] = "H1";
+ renaming_to_standard["protein"]["HT2"] = "H2";
+ renaming_to_standard["protein"]["HT3"] = "H3";
+
+ //again CHARMM specific stuff
+ renaming_to_standard["K"]["POT"] = "K";
+ renaming_to_standard["CL"]["CLA"] = "CL";
+ renaming_to_standard["NA"]["SOD"] = "NA";
+ renaming_to_standard["CA"]["CAL"] = "CA";
+ renaming_to_standard["CS"]["CES"] = "CS";
+
+
+
+ //let's apply the explicit residue names definition of aboves weird data structure
+ ost::mol::AtomHandleList renaming_atom_list;
+ String res_name;
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ res_name = i->GetName();
+ if(renaming_to_standard.find(res_name) == renaming_to_standard.end()) continue;
+ renaming_atom_list = i->GetAtomList();
+ for(ost::mol::AtomHandleList::iterator j = renaming_atom_list.begin();
+ j != renaming_atom_list.end(); ++j){
+ if(renaming_to_standard[res_name].find(j->GetName()) == renaming_to_standard[res_name].end()) continue;
+ ed.RenameAtom(*j,renaming_to_standard[res_name][j->GetName()]);
+ }
+ }
+
+ //entries with of name protein have to be applied on all peptide residues
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(!i->IsPeptideLinking()) continue;
+ renaming_atom_list = i->GetAtomList();
+ for(ost::mol::AtomHandleList::iterator j = renaming_atom_list.begin();
+ j != renaming_atom_list.end(); ++j){
+ if(renaming_to_standard["protein"].find(j->GetName()) == renaming_to_standard["protein"].end()) continue;
+ ed.RenameAtom(*j,renaming_to_standard["protein"][j->GetName()]);
+ }
+ }
+}
+
+}}}
diff --git a/modules/mol/mm/src/mm_modeller.hh b/modules/mol/mm/src/mm_modeller.hh
new file mode 100644
index 0000000000000000000000000000000000000000..682f5a885ba37e829e96a35c410923350c7081d1
--- /dev/null
+++ b/modules/mol/mm/src/mm_modeller.hh
@@ -0,0 +1,61 @@
+#ifndef OST_MMMODELLER_HH
+#define OST_MMMODELLER_HH
+
+
+#include <vector>
+#include <set>
+
+#include <ost/platform.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/geom/composite.hh>
+#include <ost/geom/transform.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/message.hh>
+//#include <ost/mol/mm/gromacs_data.hh>
+#include <ost/mol/bounding_box.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/topology.hh>
+#include <ost/conop/heuristic.hh>
+#include <ost/mol/spatial_organizer.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class MMModeller{
+public:
+
+ static void GenerateDisulfidBonds(ost::mol::EntityHandle& handle);
+
+ static void GenerateCYSHEMEBonds(ost::mol::EntityHandle& handle);
+
+ static void GenerateHISHEMEBonds(ost::mol::EntityHandle& handle);
+
+ static void GenerateMETHEMEBonds(ost::mol::EntityHandle& handle);
+
+ //may sound pretty stupid...
+ //But this is necessary if we want to compare our energies with
+ //the energies calculated by gromacs. When ost writes and entity
+ //down to disk, it uses 3 digits precision.
+ //If we feed this into gromacs, it also produces a topology
+ //with three digits precision. The problem is, that gromacs
+ //uses nm, therefore the precision gets lowered tenfold.
+ //To take care of that it is necessary to lower our precision...
+ static void LowerPrecision(ost::mol::EntityHandle& handle);
+
+ static void AssignPDBNaming(ost::mol::EntityHandle& handle);
+
+ static void AssignGromacsNaming(ost::mol::EntityHandle& handle);
+};
+
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/mm_observer.cc b/modules/mol/mm/src/mm_observer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..ed1f14b7a9396f3765ede452b2d26d7c37bec101
--- /dev/null
+++ b/modules/mol/mm/src/mm_observer.cc
@@ -0,0 +1,180 @@
+#include <ost/mol/mm/mm_observer.hh>
+
+namespace ost { namespace mol{ namespace mm{
+
+void TrajObserver::Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top){
+
+ if(registered_){
+ throw ost::Error("Can register observer to only one simulation!");
+ }
+
+ registered_ = true;
+
+ context_ = c;
+ ost::mol::EntityHandle ent = top->GetEntity().Copy();
+ MMModeller::AssignPDBNaming(ent);
+ c_group_ = ost::mol::CreateCoordGroup(ent.GetAtomList());
+}
+
+void TrajObserver::Notify(){
+
+ geom::Vec3List positions;
+ StateExtractor::ExtractPositions(context_,positions,true);
+ c_group_.AddFrame(positions);
+}
+
+
+void TrajWriter::Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top){
+
+ if(registered_){
+ throw ost::Error("Can register observer to only one simulation!");
+ }
+
+ registered_ = true;
+
+ context_ = c;
+ ost::io::IOProfile profile("CHARMM",false,false,false,false,false);
+ ost::io::PDBWriter writer(pdb_filename_, profile);
+ writer.Write(top->GetEntity().GetAtomList());
+
+ stream_.open(dcd_filename_.c_str(), std::ios::binary);
+
+ x.resize(top->GetNumAtoms());
+ y.resize(top->GetNumAtoms());
+ z.resize(top->GetNumAtoms());
+
+
+ // size of first header block in bytes
+ int32_t magic_number=84;
+ stream_.write(reinterpret_cast<char*>(&magic_number), 4);
+
+ // magic string
+ char crd[]={'C', 'O', 'R', 'D'};
+ stream_.write(crd, 4);
+
+ // icntrl[0], NSET, number of frames
+ // we don't know the number of frames yet, will be written
+ // when the finalize function is called.
+ int32_t zero=0;
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+
+ // icntrl[1], ISTART, starting timestep
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+
+ // icntrl[2], NSAVC, timesteps between DCD saves
+ int32_t one=1;
+ stream_.write(reinterpret_cast<char*>(&one), 4);
+
+ // icntrl[3] to icntrl[7], unused
+ for (int i=3; i<=7; ++i) {
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+ }
+
+ // icntrl[8], NAMNF, number of fixed atoms
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+
+ // icntrl[9], DELTA, timestep as float for CHARMM format
+ float delta=1.0;
+ stream_.write(reinterpret_cast<char*>(&delta), 4);
+
+ // icntrl[10], CHARMM format: ucell per frame
+ stream_.write(reinterpret_cast<char*>(&one), 4);
+
+ // icntrl[11] to icntrl[18], unused
+ for (int i=11; i<=18; ++i) {
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+ }
+
+ // icntrl[19], charmm version
+ int32_t charmm_version=24;
+ stream_.write(reinterpret_cast<char*>(&charmm_version), 4);
+ // bracket first header block
+ stream_.write(reinterpret_cast<char*>(&magic_number), 4);
+
+ // no titles in title block
+ int32_t four=4;
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+
+ // atom count block
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+ int32_t atom_count=top->GetNumAtoms();
+ stream_.write(reinterpret_cast<char*>(&atom_count), 4);
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+}
+
+void TrajWriter::Notify(){
+
+ if(!registered_){
+ throw ost::Error("Trajectory writer is not registered to any simulation!");
+ }
+
+ if(!stream_){
+ throw ost::Error("Trajectory writer does not contain open filestream. Did you already call the finalize funciton before?");
+ }
+
+ geom::Vec3List positions;
+ StateExtractor::ExtractPositions(context_,positions,true,true);
+ OpenMM::State openmm_state = context_->getState(0); //create minimal state
+ //to only extract periodic
+ //box information
+ openmm_state.getPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+
+ int32_t out_n=positions.size()*4;
+
+ // ucell
+ int32_t bsize=48; // ucell block size, 6 doubles
+ //context_->getSystem().getDefaultPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+
+ // a,alpha,b,beta,gamma,c (don't ask)
+ // OpenMM only supports rectangular boxes, since we have to add
+ // the cosines of the angles, we can directly set the values to 0.0
+
+ double ucell[]={10 * sqrt(ucell_a.dot(ucell_a)),
+ 0.0,
+ 10 * sqrt(ucell_b.dot(ucell_b)),
+ 0.0,
+ 0.0,
+ 10 * sqrt(ucell_c.dot(ucell_c))};
+ stream_.write(reinterpret_cast<char*>(&bsize),4);
+ stream_.write(reinterpret_cast<char*>(ucell),bsize);
+ stream_.write(reinterpret_cast<char*>(&bsize),4);
+
+ int k=0;
+ for (geom::Vec3List::iterator i=positions.begin();
+ i!=positions.end(); ++i, ++k) {
+ x[k]=float((*i)[0]);
+ y[k]=float((*i)[1]);
+ z[k]=float((*i)[2]);
+ }
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&x[0]), out_n);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&y[0]), out_n);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&z[0]), out_n);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+
+ ++frames_;
+
+ stream_.seekp(8,std::ios_base::beg);
+ stream_.write(reinterpret_cast<char*>(&frames_),4);
+ stream_.seekp(0,std::ios_base::end);
+}
+
+void TrajWriter::Finalize(){
+ if(!registered_){
+ throw ost::Error("Trajectory writer is not registered to any simulation!");
+ }
+ if(!stream_){
+ throw ost::Error("Trajectory writer does not contain open filestream. Did you already call the finalize function before?");
+ }
+ stream_.close();
+}
+
+}}}// ns
diff --git a/modules/mol/mm/src/mm_observer.hh b/modules/mol/mm/src/mm_observer.hh
new file mode 100644
index 0000000000000000000000000000000000000000..92b52971a4c5b60f3fef5d3e60620e8b9c067588
--- /dev/null
+++ b/modules/mol/mm/src/mm_observer.hh
@@ -0,0 +1,109 @@
+#ifndef OST_MM_OBSERVER_HH
+#define OST_MM_OBSERVER_HH
+
+
+#include <OpenMM.h>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/io/mol/io_profile.hh>
+#include <ost/io/mol/pdb_writer.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/coord_frame.hh>
+#include <ost/mol/coord_group.hh>
+#include <ost/mol/mm/state_extractor.hh>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/mm_modeller.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class MMObserver;
+class TrajObserver;
+class TrajWriter;
+typedef boost::shared_ptr<MMObserver> MMObserverPtr;
+typedef boost::shared_ptr<TrajObserver> TrajObserverPtr;
+typedef boost::shared_ptr<TrajWriter> TrajWriterPtr;
+
+class MMObserver{
+public:
+
+ virtual void Notify() = 0;
+
+ virtual void Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top) = 0;
+
+ virtual int Rythm() = 0;
+
+};
+
+
+class TrajObserver : public MMObserver{
+
+public:
+
+ TrajObserver(int rythm): rythm_(rythm), registered_(false) { }
+
+ void Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top);
+
+ void Notify();
+
+ int Rythm() { return rythm_; }
+
+ CoordGroupHandle GetTraj() { return c_group_; }
+
+private:
+
+ ost::mol::CoordGroupHandle c_group_;
+ boost::shared_ptr<OpenMM::Context> context_;
+ int rythm_;
+ bool registered_;
+};
+
+class TrajWriter : public MMObserver{
+
+//Note, that this code is highly redundant to the code in io/mol/dcd_io.hh!!!
+
+public:
+
+ TrajWriter(int rythm, const String& pdb_filename, const String& dcd_filename): rythm_(rythm),
+ pdb_filename_(pdb_filename),
+ dcd_filename_(dcd_filename),
+ stream_(),
+ registered_(false),
+ frames_(0) { }
+
+ void Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top);
+
+ void Notify();
+
+ int Rythm() { return rythm_; }
+
+ void Finalize();
+
+private:
+
+ TrajWriter(const TrajWriter& writer) { } //output filestream is unique!
+
+
+ boost::shared_ptr<OpenMM::Context> context_;
+ int rythm_;
+ String pdb_filename_;
+ String dcd_filename_;
+ std::ofstream stream_;
+ bool registered_;
+ uint32_t frames_;
+ std::vector<float> x;
+ std::vector<float> y;
+ std::vector<float> z;
+ OpenMM::Vec3 ucell_a;
+ OpenMM::Vec3 ucell_b;
+ OpenMM::Vec3 ucell_c;
+};
+
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/src/mm_settings.hh b/modules/mol/mm/src/mm_settings.hh
new file mode 100644
index 0000000000000000000000000000000000000000..45fac0b7205cdf17f0895dff1e611f60deb90709
--- /dev/null
+++ b/modules/mol/mm/src/mm_settings.hh
@@ -0,0 +1,153 @@
+#ifndef OST_MM_SETTINGS_HH
+#define OST_MM_SETTINGS_HH
+
+#include <OpenMM.h>
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+#include <limits>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/mm/forcefield.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+struct MMSettings;
+class TerminiExceptions;
+typedef boost::shared_ptr<MMSettings> MMSettingsPtr;
+typedef boost::shared_ptr<TerminiExceptions> TerminiExceptionsPtr;
+
+enum Platform{
+ Reference,
+ OpenCL,
+ CUDA,
+ CPU
+};
+
+
+class TerminiExceptions{
+
+public:
+
+ TerminiExceptions(){ }
+
+ void SetException(const ost::mol::ResidueHandle& res, const String& exception_name){
+ exceptions_[res.GetQualifiedName()] = exception_name;
+ }
+
+ bool HasException(const ost::mol::ResidueHandle& res) const{
+ return exceptions_.find(res.GetQualifiedName()) != exceptions_.end();
+ }
+
+ String GetException(const ost::mol::ResidueHandle& res) const {
+ if(!this->HasException(res)){
+ std::stringstream ss;
+ ss<<"Tried to get termini exceptions of res "<<res<<" without defined exception!";
+ throw ost::Error(ss.str());
+ }
+ std::map<String, String>::const_iterator i = exceptions_.find(res.GetQualifiedName());
+ return i->second;
+ }
+private:
+ std::map<String, String> exceptions_;
+
+};
+
+struct MMSettings{
+
+ MMSettings(): add_bonds(true),
+ add_angles(true),
+ add_dihedrals(true),
+ add_impropers(true),
+ add_cmaps(true),
+ add_exclusions(true),
+ add_nonbonded(true),
+ add_gbsa(false),
+ constrain_hbonds(false),
+ constrain_hangles(false),
+ constrain_bonds(false),
+ rigid_water(false),
+ strict_interactions(true),
+ ideal_bond_length_constraints(true),
+ fix_heavy_atoms(false),
+ kill_electrostatics(false),
+ generate_disulfid_bonds(true),
+ nonbonded_method(OpenMM::NonbondedForce::NoCutoff),
+ nonbonded_cutoff(10.0),
+ remove_cmm_motion(true),
+ cmm_frequency(1),
+ periodic_box_extents(0,0,0),
+ init_temperature(0.0),
+ forcefield(), //note, that we don't create an empty forcefield at this point =>force the user
+ //to assign a forcefield
+ termini_exceptions(new TerminiExceptions),
+ platform(Reference),
+ add_thermostat(false),
+ thermostat_temperature(std::numeric_limits<Real>::quiet_NaN()),
+ thermostat_collision_frequency(std::numeric_limits<Real>::quiet_NaN()),
+ add_barostat(false),
+ barostat_temperature(std::numeric_limits<Real>::quiet_NaN()),
+ barostat_pressure(std::numeric_limits<Real>::quiet_NaN()),
+ barostat_frequency(25),
+ integrator(),
+ solvent_dielectric(78.3), //this is for GBSA
+ solute_dielectric(1.0), //this is for GBSA
+ reaction_field_dielectric(78.3),
+ use_dispersion_correction(true),
+ openmm_plugin_directory(OpenMM::Platform::getDefaultPluginsDirectory()),
+ custom_plugin_directory(OpenMM::Platform::getDefaultPluginsDirectory())
+
+ { }
+
+ //
+ bool add_bonds;
+ bool add_angles;
+ bool add_dihedrals;
+ bool add_impropers;
+ bool add_cmaps;
+ bool add_exclusions;
+ bool add_nonbonded;
+ bool add_gbsa;
+ bool constrain_hbonds;
+ bool constrain_hangles;
+ bool constrain_bonds;
+ bool rigid_water;
+ bool strict_interactions;
+ bool ideal_bond_length_constraints;
+ bool fix_heavy_atoms;
+ //set all charges to zero
+ bool kill_electrostatics;
+ //automatically generate disulfid bonds
+ bool generate_disulfid_bonds;
+ //see export_openmm.cc for all possibilities
+ OpenMM::NonbondedForce::NonbondedMethod nonbonded_method;
+ Real nonbonded_cutoff;
+ bool remove_cmm_motion;
+ int cmm_frequency;
+ //currently only boxes defined by base vectors are supported
+ geom::Vec3 periodic_box_extents;
+ //at the beginning of the simulation, the initial velociities are
+ //randomly set according to a boltzmann distribution
+ Real init_temperature;
+ ForcefieldPtr forcefield;
+ TerminiExceptionsPtr termini_exceptions;
+ Platform platform;
+ bool add_thermostat;
+ Real thermostat_temperature;
+ Real thermostat_collision_frequency;
+ bool add_barostat;
+ Real barostat_temperature;
+ Real barostat_pressure;
+ int barostat_frequency;
+ boost::shared_ptr<OpenMM::Integrator> integrator;
+ Real solvent_dielectric;
+ Real solute_dielectric;
+ Real reaction_field_dielectric;
+ bool use_dispersion_correction;
+ String openmm_plugin_directory;
+ String custom_plugin_directory;
+};
+
+}}} //namespace
+
+#endif
\ No newline at end of file
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..410c9bc41c268ee366ea91e938a61b6539fde092
--- /dev/null
+++ b/modules/mol/mm/src/simulation.cc
@@ -0,0 +1,591 @@
+#include <ost/mol/mm/simulation.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+Simulation::Simulation(const ost::mol::EntityHandle& handle,
+ const MMSettingsPtr settings):
+ settings_(settings){
+
+ //note, that ent_ will be "completed" inside this function!
+ //(hydrogens and shit)
+
+ TopologyPtr top = TopologyCreator::Create(handle,settings);
+ this->Init(top);
+}
+
+Simulation::Simulation(const TopologyPtr top,
+ const MMSettingsPtr settings):
+ settings_(settings){
+
+ this->Init(top);
+}
+
+void Simulation::Init(const TopologyPtr top){
+
+
+ top_ = top;
+ integrator_ = settings_->integrator;
+ if(!integrator_){
+ throw ost::Error("Settings must have a valid integrator attached to set up a simulation!");
+ }
+ system_ = SystemCreator::Create(top_,settings_,system_force_mapper_);
+ ost::mol::EntityHandle ent = top_->GetEntity();
+ original_masses_ = top_->GetMasses();
+
+ //setting up the context, which combines the system with an integrator
+ //to proceed in time, but first we have to load the proper platform
+
+ OpenMM::Platform::loadPluginsFromDirectory (settings_->openmm_plugin_directory);
+ OpenMM::Platform* platform;
+
+ switch(settings_->platform){
+ case Reference:{
+ platform = &OpenMM::Platform::getPlatformByName("Reference");
+ break;
+ }
+ case OpenCL:{
+ platform = &OpenMM::Platform::getPlatformByName("OpenCL");
+ break;
+ }
+ case CUDA:{
+ platform = &OpenMM::Platform::getPlatformByName("CUDA");
+ break;
+ }
+ case CPU:{
+ platform = &OpenMM::Platform::getPlatformByName("CPU");
+ break;
+ }
+ }
+
+ context_ = ContextPtr(new OpenMM::Context(*system_,*integrator_,*platform));
+
+ ost::mol::AtomHandleList atom_list = ent.GetAtomList();
+ std::vector<OpenMM::Vec3> positions;
+ geom::Vec3 ost_vec;
+ OpenMM::Vec3 open_mm_vec;
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i!=atom_list.end();++i){
+ ost_vec = i->GetPos();
+ open_mm_vec[0] = ost_vec[0]/10;
+ open_mm_vec[1] = ost_vec[1]/10;
+ open_mm_vec[2] = ost_vec[2]/10;
+ positions.push_back(open_mm_vec);
+ }
+ context_->setPositions(positions);
+
+ //make sure the context satisfies the distance constraints
+ context_->applyConstraints(0.00001);
+
+ if(settings_->init_temperature > 0.0){
+ context_->setVelocitiesToTemperature(settings_->init_temperature);
+ }
+}
+
+ost::mol::EntityHandle Simulation::GetEntityStandardNaming(){
+ ost::mol::EntityHandle ent = top_->GetEntity();
+ ent = ent.Copy();
+ settings_->forcefield->AssignFFSpecificNames(ent,true);
+ MMModeller::AssignPDBNaming(ent);
+ return ent;
+}
+
+geom::Vec3List Simulation::GetPositions(bool enforce_periodic_box, bool in_angstrom){
+ geom::Vec3List return_vec;
+ StateExtractor::ExtractPositions(context_,return_vec, enforce_periodic_box, in_angstrom);
+ return return_vec;
+}
+
+geom::Vec3List Simulation::GetVelocities(){
+ geom::Vec3List return_vec;
+ StateExtractor::ExtractVelocities(context_, return_vec);
+ return return_vec;
+}
+
+geom::Vec3List Simulation::GetForces(){
+ geom::Vec3List return_vec;
+ StateExtractor::ExtractForces(context_, return_vec);
+ return return_vec;
+}
+
+void Simulation::SetPositions(geom::Vec3List& positions, bool in_angstrom){
+ if(top_->GetNumAtoms() != positions.size()){
+ throw ost::Error("Number of positions does not correspond to number of atoms in topology!");
+ }
+ if(in_angstrom) positions /= 10;
+ std::vector<OpenMM::Vec3> openmm_positions;
+ OpenMM::Vec3 open_mm_vec;
+ for(geom::Vec3List::iterator i = positions.begin();
+ i != positions.end(); ++i){
+ open_mm_vec[0] = (*i)[0];
+ open_mm_vec[1] = (*i)[1];
+ open_mm_vec[2] = (*i)[2];
+ openmm_positions.push_back(open_mm_vec);
+ }
+ context_->setPositions(openmm_positions);
+}
+
+void Simulation::SetVelocities(geom::Vec3List& velocities){
+ if(top_->GetNumAtoms() != velocities.size()){
+ throw ost::Error("Number of velocities does not correspond to number of atoms in topology!");
+ }
+ std::vector<OpenMM::Vec3> openmm_velocities;
+ OpenMM::Vec3 open_mm_vec;
+ for(geom::Vec3List::iterator i = velocities.begin();
+ i != velocities.end(); ++i){
+ open_mm_vec[0] = (*i)[0];
+ open_mm_vec[1] = (*i)[1];
+ open_mm_vec[2] = (*i)[2];
+ openmm_velocities.push_back(open_mm_vec);
+ }
+ context_->setVelocities(openmm_velocities);
+}
+
+void Simulation::UpdateTopologyPositions(bool enforce_periodic_box){
+ geom::Vec3List positions = this->GetPositions(enforce_periodic_box);
+ top_->SetEntityPositions(positions);
+}
+
+void Simulation::MinimizeEnergy(const String& type, Real tolerance, int max_iterations){
+ if(type == "lbfgs") OpenMM::LocalEnergyMinimizer::minimize(*context_, tolerance, max_iterations);
+ else if(type == "steep") Steep::Minimize(*context_,tolerance, max_iterations);
+ else{
+ std::stringstream ss;
+ ss << "Unknown minimization function type \""<< type <<"\" observed";
+ throw ost::Error(ss.str());
+ }
+}
+
+void Simulation::Steps(int steps){
+
+ int time_to_next_notification;
+
+ while(steps > 0){
+ time_to_next_notification = this->TimeToNextNotification();
+ //we can just do the remaining steps and subtract them from
+ //time_to_notify_
+ if(steps < time_to_next_notification){
+ integrator_->step(steps);
+ for(std::vector<int>::iterator i = time_to_notify_.begin();
+ i != time_to_notify_.end(); ++i){
+ (*i) -= steps;
+ }
+ steps = 0;
+ }else{
+ integrator_->step(time_to_next_notification);
+ for(std::vector<int>::iterator i = time_to_notify_.begin();
+ i != time_to_notify_.end(); ++i){
+ (*i) -= time_to_next_notification;
+ }
+ for(uint i = 0; i < time_to_notify_.size(); ++i){
+ if(time_to_notify_[i] == 0){
+ observers_[i]->Notify();
+ time_to_notify_[i] = observers_[i]->Rythm();
+ }
+ }
+ steps -= time_to_next_notification;
+ }
+ }
+}
+
+Real Simulation::GetEnergy(){
+ Real energy;
+ StateExtractor::ExtractEnergy(context_,energy);
+ return energy;
+}
+
+Real Simulation::GetKineticEnergy(){
+ Real energy;
+ StateExtractor::ExtractKineticEnergy(context_,energy);
+ return energy;
+}
+
+Real Simulation::GetPotentialEnergy(){
+ Real energy;
+ StateExtractor::ExtractPotentialEnergy(context_,energy);
+ return energy;
+}
+
+void Simulation::Register(MMObserverPtr o){
+ observers_.push_back(o);
+ time_to_notify_.push_back(o->Rythm());
+ o->Init(context_,top_);
+}
+
+int Simulation::TimeToNextNotification(){
+ if(observers_.empty()){
+ return std::numeric_limits<int>::max();
+ }
+ int minimal_time = std::numeric_limits<int>::max();
+ for(std::vector<int>::iterator i = time_to_notify_.begin();
+ i != time_to_notify_.end(); ++i){
+ if(*i < minimal_time){
+ minimal_time = *i;
+ }
+ }
+ return minimal_time;
+}
+
+void Simulation::ResetHarmonicBond(uint index, Real bond_length, Real force_constant){
+ if(system_force_mapper_.find(HarmonicBond) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic bond force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicBond];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::HarmonicBondForce* bond_force_ptr = reinterpret_cast<OpenMM::HarmonicBondForce*>(&force);
+ if(index >= uint(bond_force_ptr->getNumBonds())){
+ throw ost::Error("Provided bond index exceeds number of bonds!");
+ }
+ double dummy_one, dummy_two;
+ int particle1, particle2;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ bond_force_ptr->getBondParameters(index,particle1,particle2,dummy_one,dummy_two);
+ bond_force_ptr->setBondParameters(index,particle1,particle2,bond_length,force_constant);
+ bond_force_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicBondParameters(index,bond_length,force_constant);
+}
+
+void Simulation::ResetHarmonicAngle(uint index, Real angle, Real force_constant){
+ if(system_force_mapper_.find(HarmonicAngle) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic angle force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicAngle];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::HarmonicAngleForce* angle_force_ptr = reinterpret_cast<OpenMM::HarmonicAngleForce*>(&force);
+ if(index >= uint(angle_force_ptr->getNumAngles())){
+ throw ost::Error("Provided angle index exceeds number of angles!");
+ }
+ double dummy_one, dummy_two;
+ int particle1, particle2, particle3;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ angle_force_ptr->getAngleParameters(index,particle1,particle2,particle3,dummy_one,dummy_two);
+ angle_force_ptr->setAngleParameters(index,particle1,particle2,particle3,angle,force_constant);
+ angle_force_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicAngleParameters(index, angle, force_constant);
+}
+
+void Simulation::ResetUreyBradleyAngle(uint index, Real angle, Real angle_force_constant, Real bond_length, Real bond_force_constant){
+ if(system_force_mapper_.find(UreyBradleyAngle) == system_force_mapper_.end()){
+ throw ost::Error("There is no urey bradley angle force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[UreyBradleyAngle];
+ OpenMM::Force& angle_force = system_->getForce(force_index);
+ OpenMM::Force& bond_force = system_->getForce(force_index+1);
+
+ OpenMM::HarmonicAngleForce* angle_force_ptr = reinterpret_cast<OpenMM::HarmonicAngleForce*>(&angle_force);
+ OpenMM::HarmonicBondForce* bond_force_ptr = reinterpret_cast<OpenMM::HarmonicBondForce*>(&bond_force);
+ if(index >= uint(angle_force_ptr->getNumAngles())){
+ throw ost::Error("Provided angle index exceeds number of angles!");
+ }
+ double dummy_one, dummy_two;
+ int particle1, particle2, particle3;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ angle_force_ptr->getAngleParameters(index,particle1,particle2,particle3,dummy_one,dummy_two);
+ angle_force_ptr->setAngleParameters(index,particle1,particle2,particle3,angle,angle_force_constant);
+ bond_force_ptr->setBondParameters(index,particle1,particle3,bond_length,bond_force_constant);
+ angle_force_ptr->updateParametersInContext(*context_);
+ bond_force_ptr->updateParametersInContext(*context_);
+ top_->SetUreyBradleyAngleParameters(index,angle,angle_force_constant,bond_length,bond_force_constant);
+}
+
+void Simulation::ResetPeriodicDihedral(uint index, int multiplicity, Real phase, Real force_constant){
+ if(system_force_mapper_.find(PeriodicDihedral) == system_force_mapper_.end()){
+ throw ost::Error("There is no periodic dihedral force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[PeriodicDihedral];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::PeriodicTorsionForce* dihedral_force_ptr = reinterpret_cast<OpenMM::PeriodicTorsionForce*>(&force);
+ if(index >= uint(dihedral_force_ptr->getNumTorsions())){
+ throw ost::Error("Provided dihedral index exceeds number of dihedrals!");
+ }
+ int dummy_one;
+ double dummy_two, dummy_three;
+ int particle1, particle2, particle3, particle4;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ dihedral_force_ptr->getTorsionParameters(index,particle1,particle2,particle3,particle4,dummy_one,dummy_two,dummy_three);
+ dihedral_force_ptr->setTorsionParameters(index,particle1,particle2,particle3,particle4,multiplicity,phase,force_constant);
+ dihedral_force_ptr->updateParametersInContext(*context_);
+ top_->SetPeriodicDihedralParameters(index, multiplicity, phase, force_constant);
+}
+
+void Simulation::ResetPeriodicImproper(uint index, int multiplicity, Real phase, Real force_constant){
+ if(system_force_mapper_.find(PeriodicImproper) == system_force_mapper_.end()){
+ throw ost::Error("There is no periodic improper force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[PeriodicImproper];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::PeriodicTorsionForce* improper_ptr = reinterpret_cast<OpenMM::PeriodicTorsionForce*>(&force);
+ if(index >= uint(improper_ptr->getNumTorsions())){
+ throw ost::Error("Provided improper index exceeds number of impropers!");
+ }
+ int dummy_one;
+ double dummy_two, dummy_three;
+ int particle1, particle2, particle3, particle4;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ improper_ptr->getTorsionParameters(index,particle1,particle2,particle3,particle4,dummy_one,dummy_two,dummy_three);
+ improper_ptr->setTorsionParameters(index,particle1,particle2,particle3,particle4,multiplicity,phase,force_constant);
+ improper_ptr->updateParametersInContext(*context_);
+ top_->SetPeriodicImproperParameters(index, multiplicity, phase, force_constant);
+}
+
+void Simulation::ResetHarmonicImproper(uint index, Real phase, Real force_constant){
+ if(system_force_mapper_.find(HarmonicImproper) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic improper force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicImproper];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::CustomTorsionForce* improper_ptr = reinterpret_cast<OpenMM::CustomTorsionForce*>(&force);
+ if(index >= uint(improper_ptr->getNumTorsions())){
+ throw ost::Error("Provided improper index exceeds number of impropers!");
+ }
+ std::vector<double> parameters;
+ parameters.push_back(0.0);
+ parameters.push_back(0.0);
+ int particle1, particle2, particle3, particle4;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ improper_ptr->getTorsionParameters(index,particle1,particle2,particle3,particle4,parameters);
+ parameters[0] = phase;
+ parameters[1] = force_constant;
+ improper_ptr->setTorsionParameters(index,particle1,particle2,particle3,particle4,parameters);
+ improper_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicImproperParameters(index, phase, force_constant);
+}
+
+void Simulation::ResetLJPair(uint index, Real sigma, Real epsilon){
+ if(system_force_mapper_.find(LJ) == system_force_mapper_.end()){
+ throw ost::Error("There is no nonbonded force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[LJ];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::NonbondedForce* nonbonded_ptr = reinterpret_cast<OpenMM::NonbondedForce*>(&force);
+ if(index >= uint(nonbonded_ptr->getNumExceptions())){
+ throw ost::Error("Provided index exceeds number of defined pairs!");
+ }
+ double charge_prod, dummy_one, dummy_two;
+ int particle1, particle2;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ nonbonded_ptr->getExceptionParameters(index,particle1,particle2,charge_prod,dummy_one,dummy_two);
+ nonbonded_ptr->setExceptionParameters(index,particle1,particle2,charge_prod,sigma,epsilon);
+ nonbonded_ptr->updateParametersInContext(*context_);
+ top_->SetLJPairParameters(index, sigma, epsilon);
+}
+
+void Simulation::ResetDistanceConstraint(uint index, Real constraint_length){
+ if(index >= uint(system_->getNumConstraints())){
+ throw ost::Error("Provided index exceeds number of defined constraints!");
+ }
+ double dummy;
+ int particle1, particle2;
+ system_->getConstraintParameters(index,particle1,particle2,dummy);
+ system_->setConstraintParameters(index,particle1,particle2,constraint_length);
+ context_->reinitialize();
+ top_->SetDistanceConstraintParameters(index, constraint_length);
+}
+
+void Simulation::AddPositionConstraint(uint index){
+ if(index >= top_->GetNumAtoms()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ system_->setParticleMass(index,0.0);
+ context_->reinitialize();
+ top_->AddPositionConstraint(index);
+}
+
+void Simulation::AddPositionConstraints(const std::vector<uint>& index){
+
+ for(std::vector<uint>::const_iterator i = index.begin();
+ i != index.end(); ++i){
+ if(*i >= top_->GetNumAtoms()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ system_->setParticleMass(*i,0.0);
+ top_->AddPositionConstraint(*i);
+ }
+ context_->reinitialize();
+}
+
+void Simulation::ResetPositionConstraints(){
+ for(uint i = 0; i < original_masses_.size(); ++i){
+ system_->setParticleMass(i,original_masses_[i]);
+ }
+ top_->ResetPositionConstraints();
+ context_->reinitialize();
+}
+
+void Simulation::ResetHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale, Real y_scale, Real z_scale){
+ if(index >= uint(top_->GetNumHarmonicPositionRestraints())){
+ throw ost::Error("Provided index exceeds number of defined harmonic position restraints!");
+ }
+ if(system_force_mapper_.find(HarmonicPositionRestraint) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic position restraint in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicPositionRestraint];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::CustomExternalForce* restraint_ptr = reinterpret_cast<OpenMM::CustomExternalForce*>(&force);
+ if(index >= uint(restraint_ptr->getNumParticles())){
+ throw ost::Error("Provided index exceeds number of defined harmonic position restraints!");
+ }
+ int particle;
+ std::vector<double> parameters;
+ restraint_ptr->getParticleParameters(index,particle,parameters);
+ parameters[0] = ref_position[0];
+ parameters[1] = ref_position[1];
+ parameters[2] = ref_position[2];
+ parameters[3] = k;
+ parameters[4] = x_scale;
+ parameters[5] = y_scale;
+ parameters[6] = z_scale;
+ restraint_ptr->setParticleParameters(index,particle,parameters);
+ restraint_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicPositionRestraintParameters(index,ref_position,k,x_scale,y_scale,z_scale);
+}
+
+void Simulation::ResetHarmonicDistanceRestraint(uint index, Real length, Real force_constant){
+ if(index >= top_->GetNumHarmonicDistanceRestraints()){
+ throw ost::Error("Provided index exceeds number of defined harmonic distance restraints!");
+ }
+ if(system_force_mapper_.find(HarmonicDistanceRestraint) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic distance restraint in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicDistanceRestraint];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::HarmonicBondForce* restraint_ptr = reinterpret_cast<OpenMM::HarmonicBondForce*>(&force);
+ if(index >= uint(restraint_ptr->getNumBonds())){
+ throw ost::Error("Provided index exceeds number of defined harmonic distance restraints!");
+ }
+ int particle_one,particle_two;
+ double dummy_one, dummy_two;
+ restraint_ptr->getBondParameters(int(index),particle_one,particle_two,dummy_one,dummy_two);
+ restraint_ptr->setBondParameters(int(index),particle_one,particle_two,length,2*force_constant);
+ restraint_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicDistanceRestraintParameters(index,length,force_constant);
+}
+
+void Simulation::ResetLJ(uint index, Real sigma, Real epsilon){
+ if(index >= top_->GetNumAtoms()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ if(system_force_mapper_.find(LJ) == system_force_mapper_.end()){
+ throw ost::Error("There is no nonbonded force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[LJ];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::NonbondedForce* nonbonded_ptr = reinterpret_cast<OpenMM::NonbondedForce*>(&force);
+
+ double charge, dummy_one, dummy_two;
+
+ nonbonded_ptr->getParticleParameters(index,charge,dummy_one,dummy_two);
+ nonbonded_ptr->setParticleParameters(index,charge,sigma,epsilon);
+ nonbonded_ptr->updateParametersInContext(*context_);
+ top_->SetSigma(index, sigma);
+ top_->SetEpsilon(index, epsilon);
+}
+
+void Simulation::ResetGBSA(uint index, Real radius, Real scaling){
+ if(index >= top_->GetNumAtoms()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ if(system_force_mapper_.find(GBSA) == system_force_mapper_.end()){
+ throw ost::Error("There is no gbsa force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[GBSA];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::GBSAOBCForce* gbsa_ptr = reinterpret_cast<OpenMM::GBSAOBCForce*>(&force);
+
+ double charge, dummy_one, dummy_two;
+
+ gbsa_ptr->getParticleParameters(index,charge,dummy_one,dummy_two);
+ gbsa_ptr->setParticleParameters(index,charge,radius,scaling);
+ gbsa_ptr->updateParametersInContext(*context_);
+ top_->SetGBSARadius(index, radius);
+ top_->SetOBCScaling(index, scaling);
+}
+
+void Simulation::ResetCharge(uint index, Real charge){
+ if(index >= top_->GetNumAtoms()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ if(system_force_mapper_.find(LJ) == system_force_mapper_.end()){
+ throw ost::Error("There is no nonbonded force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[LJ];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::NonbondedForce* nonbonded_ptr = reinterpret_cast<OpenMM::NonbondedForce*>(&force);
+
+ double dummy, sigma, epsilon;
+
+ //first update the parameters of the single particle
+ nonbonded_ptr->getParticleParameters(index,dummy,sigma,epsilon);
+ nonbonded_ptr->setParticleParameters(index,charge,sigma,epsilon);
+
+ //the charge product has to be updated in the exceptions (1,4 interactions)
+ std::vector<uint> lj_pair_indices = top_->GetLJPairIndices(index);
+ Real old_charge = top_->GetCharge(index);
+ double charge_prod;
+ Real new_charge_prod;
+ int particle_one, particle_two;
+
+ for(std::vector<uint>::iterator i = lj_pair_indices.begin();
+ i != lj_pair_indices.end(); ++i){
+ nonbonded_ptr->getExceptionParameters(*i,particle_one,particle_two,charge_prod,sigma,epsilon);
+ new_charge_prod = charge_prod/old_charge*charge; // fudge_qq * q1 * q2
+ nonbonded_ptr->setExceptionParameters(*i,particle_one,particle_two,new_charge_prod,sigma,epsilon);
+ }
+
+ nonbonded_ptr->updateParametersInContext(*context_);
+ top_->SetCharge(index, charge);
+
+ //the charge also affects gbsa force...
+ if(system_force_mapper_.find(GBSA) != system_force_mapper_.end()){
+ force_index = system_force_mapper_[GBSA];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::GBSAOBCForce* gbsa_ptr = reinterpret_cast<OpenMM::GBSAOBCForce*>(&force);
+
+ double radius,scaling;
+
+ gbsa_ptr->getParticleParameters(index,dummy,radius,scaling);
+ gbsa_ptr->setParticleParameters(index,charge,radius,scaling);
+ gbsa_ptr->updateParametersInContext(*context_);
+ }
+}
+
+void Simulation::ResetMass(uint index, Real mass){
+ if(index >= top_->GetNumAtoms()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ system_->setParticleMass(index,mass);
+ context_->reinitialize();
+ top_->SetMass(index,mass);
+}
+
+geom::Vec3 Simulation::GetPeriodicBoxExtents(){
+ geom::Vec3 vec;
+ OpenMM::Vec3 ucell_a, ucell_b, ucell_c;
+ OpenMM::State openmm_state = context_->getState(0); //create minimal state
+ //to only extract periodic
+ //box information
+ openmm_state.getPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+ vec[0] = 10 * sqrt(ucell_a.dot(ucell_a));
+ vec[1] = 10 * sqrt(ucell_a.dot(ucell_b));
+ vec[2] = 10 * sqrt(ucell_a.dot(ucell_c));
+ return vec;
+}
+
+void Simulation::SetPeriodicBoxExtents(geom::Vec3& vec){
+ OpenMM::Vec3 ucell_a(vec[0]/10.0,0.0,0.0);
+ OpenMM::Vec3 ucell_b(0.0,vec[1]/10.0,0.0);
+ OpenMM::Vec3 ucell_c(0.0,0.0,vec[2]/10.0);
+ context_->setPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+}
+
+
+
+}}}
+
diff --git a/modules/mol/mm/src/simulation.hh b/modules/mol/mm/src/simulation.hh
new file mode 100644
index 0000000000000000000000000000000000000000..5712b6d5cfab786e65265d9a5a6dfd6b861d1bf3
--- /dev/null
+++ b/modules/mol/mm/src/simulation.hh
@@ -0,0 +1,138 @@
+#ifndef OST_SIMULATION_HH
+#define OST_SIMULATION_HH
+
+#include <OpenMM.h>
+
+#include <vector>
+#include <map>
+
+#include <ost/mol/mol.hh>
+#include <ost/mol/mm/system_creator.hh>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/mol/mm/mm_observer.hh>
+#include <ost/mol/mm/state_extractor.hh>
+#include <ost/mol/mm/steep.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+
+
+#include <time.h>
+
+namespace ost { namespace mol{ namespace mm{
+
+class Simulation;
+
+typedef boost::shared_ptr<OpenMM::Integrator> IntegratorPtr;
+typedef boost::shared_ptr<OpenMM::VerletIntegrator> VerletIntegratorPtr;
+typedef boost::shared_ptr<OpenMM::BrownianIntegrator> BrownianIntegratorPtr;
+typedef boost::shared_ptr<OpenMM::LangevinIntegrator> LangevinIntegratorPtr;
+typedef boost::shared_ptr<OpenMM::VariableVerletIntegrator> VariableVerletIntegratorPtr;
+typedef boost::shared_ptr<OpenMM::VariableLangevinIntegrator> VariableLangevinIntegratorPtr;
+typedef boost::shared_ptr<OpenMM::Context> ContextPtr;
+typedef boost::shared_ptr<OpenMM::AndersenThermostat> AndersenThermostatPtr;
+typedef boost::shared_ptr<OpenMM::MonteCarloBarostat> MonteCarloBarostatPtr;
+
+typedef boost::shared_ptr<Simulation> SimulationPtr;
+
+class Simulation {
+
+public:
+
+ Simulation(const ost::mol::EntityHandle& handle,
+ const MMSettingsPtr settings);
+
+ Simulation(const ost::mol::mm::TopologyPtr top,
+ const MMSettingsPtr settings);
+
+
+ ost::mol::EntityHandle GetEntity() { return top_->GetEntity(); }
+
+ ost::mol::EntityHandle GetEntityStandardNaming();
+
+ geom::Vec3List GetPositions(bool enforce_periodic_box = false, bool in_angstrom = true);
+
+ geom::Vec3List GetVelocities();
+
+ geom::Vec3List GetForces();
+
+ void SetPositions(geom::Vec3List& positions, bool in_angstrom = true);
+
+ void SetVelocities(geom::Vec3List& velocities);
+
+ void UpdateTopologyPositions(bool enforce_periodic_box = false);
+
+ void MinimizeEnergy(const String& type = "steep", Real tolerance = 1.0, int max_iterations = 1000);
+
+ Real GetEnergy();
+
+ Real GetPotentialEnergy();
+
+ Real GetKineticEnergy();
+
+ TopologyPtr GetTopology() { return top_; }
+
+ void Steps(int steps);
+
+ void Register(MMObserverPtr o);
+
+ void ResetHarmonicBond(uint index, Real bond_length, Real force_constant);
+
+ void ResetHarmonicAngle(uint index, Real angle, Real force_constant);
+
+ void ResetUreyBradleyAngle(uint index, Real angle, Real angle_force_constant, Real bond_length, Real bond_force_constant);
+
+ void ResetPeriodicDihedral(uint index, int multiplicity, Real phase, Real force_constant);
+
+ void ResetPeriodicImproper(uint index, int multiplicity, Real phase, Real force_constant);
+
+ void ResetHarmonicImproper(uint index, Real phase, Real force_constant);
+
+ void ResetLJPair(uint index, Real sigma, Real epsilon);
+
+ void ResetDistanceConstraint(uint index, Real constraint_length);
+
+ void ResetHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);
+
+ void ResetHarmonicDistanceRestraint(uint index, Real length, Real force_constant);
+
+ void ResetLJ(uint index, Real sigma, Real epsilon);
+
+ void ResetGBSA(uint index, Real radius, Real scaling);
+
+ void ResetCharge(uint index, Real charge);
+
+ void ResetMass(uint index, Real mass);
+
+ void AddPositionConstraint(uint index);
+
+ void AddPositionConstraints(const std::vector<uint>& index);
+
+ void ResetPositionConstraints();
+
+ geom::Vec3 GetPeriodicBoxExtents();
+
+ void SetPeriodicBoxExtents(geom::Vec3& vec);
+
+private:
+ void Init(const ost::mol::mm::TopologyPtr top);
+
+ int TimeToNextNotification();
+
+ SystemPtr system_;
+ IntegratorPtr integrator_;
+ ContextPtr context_;
+ MMSettingsPtr settings_;
+ TopologyPtr top_;
+ std::vector<MMObserverPtr> observers_;
+ std::vector<int> time_to_notify_;
+ std::map<FuncType,unsigned int> system_force_mapper_;
+ std::vector<Real> original_masses_;
+};
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/state_extractor.cc b/modules/mol/mm/src/state_extractor.cc
new file mode 100644
index 0000000000000000000000000000000000000000..3bb36f7a7b3b143bba9f446c4e0f70c4acf837ae
--- /dev/null
+++ b/modules/mol/mm/src/state_extractor.cc
@@ -0,0 +1,62 @@
+#include <ost/mol/mm/state_extractor.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+void StateExtractor::ExtractPotentialEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy){
+
+ OpenMM::State s = context->getState(OpenMM::State::Energy);
+ energy = s.getPotentialEnergy();
+}
+
+void StateExtractor::ExtractKineticEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy){
+
+ OpenMM::State s = context->getState(OpenMM::State::Energy);
+ energy = s.getKineticEnergy();
+}
+
+void StateExtractor::ExtractEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy){
+
+ OpenMM::State s = context->getState(OpenMM::State::Energy);
+ energy = s.getKineticEnergy() + s.getPotentialEnergy();
+}
+
+void StateExtractor::ExtractPositions(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& positions, bool enforce_periodic_box, bool in_angstrom){
+
+ positions.clear();
+ OpenMM::State s = context->getState(OpenMM::State::Positions, enforce_periodic_box);
+ std::vector<OpenMM::Vec3> p = s.getPositions();
+ for(std::vector<OpenMM::Vec3>::iterator i = p.begin(); i != p.end(); ++i){
+ positions.push_back(geom::Vec3((*i)[0],(*i)[1],(*i)[2]));
+ }
+ if(in_angstrom) positions*=10.0;
+}
+
+void StateExtractor::ExtractVelocities(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& velocities){
+
+ velocities.clear();
+ OpenMM::State s = context->getState(OpenMM::State::Velocities);
+ std::vector<OpenMM::Vec3> v = s.getVelocities();
+ for(std::vector<OpenMM::Vec3>::iterator i = v.begin(); i != v.end(); ++i){
+ velocities.push_back(geom::Vec3((*i)[0],(*i)[1],(*i)[2]));
+ }
+}
+
+void StateExtractor::ExtractForces(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& forces){
+
+ forces.clear();
+ OpenMM::State s = context->getState(OpenMM::State::Forces);
+ std::vector<OpenMM::Vec3> f = s.getForces();
+ for(std::vector<OpenMM::Vec3>::iterator i = f.begin(); i != f.end(); ++i){
+ forces.push_back(geom::Vec3((*i)[0],(*i)[1],(*i)[2]));
+ }
+}
+
+
+}}} //ns
diff --git a/modules/mol/mm/src/state_extractor.hh b/modules/mol/mm/src/state_extractor.hh
new file mode 100644
index 0000000000000000000000000000000000000000..6b77c554ef53d9b3228e2beb421e044e7e09b288
--- /dev/null
+++ b/modules/mol/mm/src/state_extractor.hh
@@ -0,0 +1,43 @@
+#ifndef OST_STATE_EXTRACTOR_HH
+#define OST_STATE_EXTRACTOR_HH
+
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+#include <OpenMM.h>
+#include <ost/geom/vec3.hh>
+
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class StateExtractor{
+
+public:
+
+ static void ExtractPotentialEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy);
+
+ static void ExtractKineticEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy);
+
+ static void ExtractEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy);
+
+ static void ExtractPositions(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& positions,
+ bool enforce_periodic_box = false,
+ bool in_angstrom = true);
+
+ static void ExtractVelocities(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& velocities);
+
+ static void ExtractForces(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& forces);
+
+};
+
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/steep.cc b/modules/mol/mm/src/steep.cc
new file mode 100644
index 0000000000000000000000000000000000000000..d201c010ad519dc1e1c7234461c043540d4c530e
--- /dev/null
+++ b/modules/mol/mm/src/steep.cc
@@ -0,0 +1,65 @@
+#include <ost/mol/mm/steep.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+void Steep::Minimize(OpenMM::Context& context, double tolerance, uint max_iterations) {
+ const OpenMM::System& system = context.getSystem();
+ if(system.getNumConstraints() > 0){
+ throw ost::Error("Cannot handle constraints in steepest descent, use lbgfs instead!");
+ }
+ if( tolerance < 0.0 ){
+ throw ost::Error("tolerance value must be greater 0.0!"); //also important to avoid zero division error when calculating normalization factor for forces
+ }
+ OpenMM::State state = context.getState(OpenMM::State::Energy | OpenMM::State::Forces | OpenMM::State::Positions);
+ std::vector<OpenMM::Vec3> positions = state.getPositions();
+ std::vector<OpenMM::Vec3> new_positions = positions;
+ std::vector<OpenMM::Vec3> normalized_forces = state.getForces();
+ double energy = state.getPotentialEnergy();
+ double h = 0.01;
+ double new_energy,max_length,factor;
+ bool normalize_forces = true;
+ std::vector<uint> non_zero_mass_particles;
+ for(int i = 0; i < system.getNumParticles(); ++i){
+ if(system.getParticleMass(i) != 0){
+ non_zero_mass_particles.push_back(i);
+ }
+ }
+ for(uint i = 0; i < max_iterations; ++i){
+ if(normalize_forces){
+ const std::vector<OpenMM::Vec3>& forces = state.getForces();
+ max_length = 0.0;
+ for(std::vector<uint>::iterator j = non_zero_mass_particles.begin();
+ j != non_zero_mass_particles.end(); ++j){
+ normalized_forces[*j] = forces[*j];
+ max_length = std::max(max_length,forces[*j].dot(forces[*j]));
+ }
+ max_length = sqrt(max_length);
+ if(max_length <= tolerance) break;
+ factor = 1.0/max_length;
+ for(std::vector<uint>::iterator j = non_zero_mass_particles.begin();
+ j != non_zero_mass_particles.end(); ++j){
+ normalized_forces[*j] *= factor;
+ }
+ }
+ for(std::vector<uint>::iterator j = non_zero_mass_particles.begin();
+ j != non_zero_mass_particles.end(); ++j){
+ new_positions[*j] = positions[*j] + normalized_forces[*j] * h;
+ }
+ context.setPositions(new_positions);
+ //context.computeVirtualSites();
+ state = context.getState(OpenMM::State::Forces | OpenMM::State::Energy);
+ new_energy = state.getPotentialEnergy();
+ if(new_energy < energy){
+ std::swap(positions,new_positions);
+ energy = new_energy;
+ h *= 1.2;
+ normalize_forces = true;
+ }
+ else {
+ h *= 0.5;
+ normalize_forces = false;
+ }
+ }
+ context.setPositions(positions);
+}
+}}}//ns
diff --git a/modules/mol/mm/src/steep.hh b/modules/mol/mm/src/steep.hh
new file mode 100644
index 0000000000000000000000000000000000000000..cc6ca3af627ed61269cdc2aa4cb552a098315e2a
--- /dev/null
+++ b/modules/mol/mm/src/steep.hh
@@ -0,0 +1,26 @@
+#ifndef OST_STEEP_H_
+#define OST_STEEP_H_
+
+#include <OpenMM.h>
+#include <ost/base.hh>
+#include <cmath>
+#include <sstream>
+#include <vector>
+#include <iostream>
+#include <cstdio>
+#include <ctime>
+
+#include <ost/message.hh>
+
+
+namespace ost { namespace mol { namespace mm{
+
+
+class Steep {
+public:
+ static void Minimize(OpenMM::Context& context, double tolerance = 100, uint maxIterations = 1000);
+};
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/system_creator.cc b/modules/mol/mm/src/system_creator.cc
new file mode 100644
index 0000000000000000000000000000000000000000..84b592a39d4b17cf1f1c3d4fe284ae840a60be5d
--- /dev/null
+++ b/modules/mol/mm/src/system_creator.cc
@@ -0,0 +1,341 @@
+#include <ost/mol/mm/system_creator.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+SystemPtr SystemCreator::Create(const TopologyPtr top,
+ const MMSettingsPtr settings,
+ std::map<FuncType,uint>& mapper){
+
+ uint mapper_index = 0;
+
+ SystemPtr sys(new OpenMM::System);
+
+ //add particles to the system
+ std::vector<Real> masses = top->GetMasses();
+
+ //set masses of position constraints to zero
+ const std::vector<uint>& position_constraints = top->GetPositionConstraints();
+ if(!position_constraints.empty()){
+ for(std::vector<uint>::const_iterator i = position_constraints.begin();
+ i != position_constraints.end(); ++i){
+ masses[*i] = 0.0;
+ }
+ }
+
+ for(std::vector<Real>::iterator i = masses.begin(); i != masses.end(); ++i){
+ sys->addParticle(*i);
+ }
+
+ //parameters of all added interactions will temporarily be stored in here
+ std::vector<Real> parameters;
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& harmonic_bonds = top->GetHarmonicBonds();
+ if(!harmonic_bonds.empty()){
+ OpenMM::HarmonicBondForce& harmonic_bond_force = *new OpenMM::HarmonicBondForce();
+ sys->addForce(&harmonic_bond_force);
+ mapper[HarmonicBond] = mapper_index++;
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = harmonic_bonds.begin();
+ i != harmonic_bonds.end(); ++i){
+ harmonic_bond_force.addBond(i->first[0],i->first[1],i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& harmonic_angles = top->GetHarmonicAngles();
+ if(!harmonic_angles.empty()){
+ OpenMM::HarmonicAngleForce& harmonic_angle_force = *new OpenMM::HarmonicAngleForce();
+ sys->addForce(&harmonic_angle_force);
+ mapper[HarmonicAngle] = mapper_index++;
+ for(std::vector<std::pair<Index<3>,std::vector<Real> > >::const_iterator i = harmonic_angles.begin();
+ i != harmonic_angles.end(); ++i){
+ harmonic_angle_force.addAngle(i->first[0],i->first[1],i->first[2],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>,std::vector<Real> > >& urey_bradley_angles = top->GetUreyBradleyAngles();
+ if(!urey_bradley_angles.empty()){
+ //urey bradley is a mixture between a harmonic angle and harmonic bond term,
+ //that gets split up
+ OpenMM::HarmonicAngleForce& urey_angle_force = *new OpenMM::HarmonicAngleForce();
+ OpenMM::HarmonicBondForce& urey_bond_force = *new OpenMM::HarmonicBondForce();
+ sys->addForce(&urey_angle_force);
+ sys->addForce(&urey_bond_force);
+ mapper[UreyBradleyAngle] = mapper_index++;
+ ++mapper_index;
+ for(std::vector<std::pair<Index<3>,std::vector<Real> > >::const_iterator i = urey_bradley_angles.begin();
+ i != urey_bradley_angles.end(); ++i){
+ urey_angle_force.addAngle(i->first[0],i->first[1],i->first[2],
+ i->second[0],i->second[1]);
+ urey_bond_force.addBond(i->first[0],i->first[2],i->second[2],i->second[3]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>,std::vector<Real> > >& periodic_dihedrals = top->GetPeriodicDihedrals();
+ if(!periodic_dihedrals.empty()){
+ OpenMM::PeriodicTorsionForce& periodic_torsion_force = *new OpenMM::PeriodicTorsionForce();
+ sys->addForce(&periodic_torsion_force);
+ mapper[PeriodicDihedral] = mapper_index++;
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::const_iterator i = periodic_dihedrals.begin();
+ i != periodic_dihedrals.end(); ++i){
+ periodic_torsion_force.addTorsion(i->first[0],i->first[1],i->first[2],i->first[3],
+ i->second[0],i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>,std::vector<Real> > >& periodic_impropers = top->GetPeriodicImpropers();
+ if(!periodic_impropers.empty()){
+ OpenMM::PeriodicTorsionForce& periodic_improper_force = *new OpenMM::PeriodicTorsionForce();
+ sys->addForce(&periodic_improper_force);
+ mapper[PeriodicImproper] = mapper_index++;
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::const_iterator i = periodic_impropers.begin();
+ i != periodic_impropers.end(); ++i){
+ periodic_improper_force.addTorsion(i->first[0],i->first[1],i->first[2],i->first[3],
+ i->second[0],i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>,std::vector<Real> > >& harmonic_impropers = top->GetHarmonicImpropers();
+ if(!harmonic_impropers.empty()){
+ std::vector<double> custom_parameters;
+ custom_parameters.push_back(0.0);
+ custom_parameters.push_back(0.0);
+ OpenMM::CustomTorsionForce& harmonic_improper_force = *new OpenMM::CustomTorsionForce("0.5*k*(theta-b)^2");
+ harmonic_improper_force.addPerTorsionParameter("b");
+ harmonic_improper_force.addPerTorsionParameter("k");
+ sys->addForce(&harmonic_improper_force);
+ mapper[HarmonicImproper] = mapper_index++;
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::const_iterator i = harmonic_impropers.begin();
+ i != harmonic_impropers.end(); ++i){
+ custom_parameters[0] = i->second[0];
+ custom_parameters[1] = i->second[1];
+ harmonic_improper_force.addTorsion(i->first[0],i->first[1],i->first[2],i->first[3],
+ custom_parameters);
+ }
+ }
+
+ const std::vector<std::pair<Index<5>,std::vector<Real> > >& cmaps = top->GetCMaps();
+ if(!cmaps.empty()){
+ std::vector<std::vector<Real> > unique_cmap_parameters;
+ std::vector<Real> current_parameters;
+ std::vector<int> map_indices;
+ bool cmap_present;
+
+ for(std::vector<std::pair<Index<5>,std::vector<Real> > >::const_iterator i = cmaps.begin();
+ i != cmaps.end(); ++i){
+ cmap_present = false;
+ current_parameters = i->second;
+ for(uint j = 0; j < unique_cmap_parameters.size(); ++j){
+ if(current_parameters == unique_cmap_parameters[j]){
+ cmap_present = true;
+ map_indices.push_back(j);
+ break;
+ }
+ }
+ if(!cmap_present){
+ unique_cmap_parameters.push_back(current_parameters);
+ map_indices.push_back(unique_cmap_parameters.size()-1);
+ }
+ }
+
+ OpenMM::CMAPTorsionForce& cmap_force = *new OpenMM::CMAPTorsionForce();
+ sys->addForce(&cmap_force);
+ mapper[CMap] = mapper_index++;
+
+ for(std::vector<std::vector<Real> >::iterator u_cmap = unique_cmap_parameters.begin();
+ u_cmap != unique_cmap_parameters.end(); ++u_cmap){
+ uint size = sqrt(u_cmap->size());
+ if(size * size != u_cmap->size()){
+ throw ost::Error("Expect cmap to be quadratic!");
+ }
+
+ //in charmm/gromacs the cmap has the following order regarding angle bins:
+ //(phi1,psi1),(phi1,psi2)...
+ //openmm requires following order:
+ //(phi1,psi1),(phi2,psi1)...
+
+ //in charmm/gromacs the range of the angles in the map is [-180,180],[-pi,pi]
+ //respectively
+ //openmm requires the range to be [0,2pi], the map has to be shifted...
+
+ //=>we need basically two "transformation"
+
+ std::vector<double> transformed_map;
+ for(uint i = 0; i < size; ++i){
+ for(uint j = 0; j < size; ++j){
+ transformed_map.push_back((*u_cmap)[size*((j+size/2)%size) + ((i+size/2)%size)]);
+ }
+ }
+ cmap_force.addMap(size, transformed_map);
+ }
+
+ //add the cmaps
+ int atom1,atom2,atom3,atom4,atom5;
+ for(uint i = 0; i < cmaps.size(); ++i){
+ atom1 = cmaps[i].first[0];
+ atom2 = cmaps[i].first[1];
+ atom3 = cmaps[i].first[2];
+ atom4 = cmaps[i].first[3];
+ atom5 = cmaps[i].first[4];
+ cmap_force.addTorsion(map_indices[i],atom1,atom2,atom3,atom4,atom2,atom3,atom4,atom5);
+ }
+ }
+
+ const std::vector<std::pair<Index<1>,std::vector<Real> > >& harmonic_position_restraints = top->GetHarmonicPositionRestraints();
+ if(!harmonic_position_restraints.empty()){
+ OpenMM::CustomExternalForce& position_restraint_force = *new OpenMM::CustomExternalForce("k_force*(x_scale*(x-x0)^2+y_scale*(y-y0)^2+z_scale*(z-z0)^2)");
+ position_restraint_force.addPerParticleParameter("x0");
+ position_restraint_force.addPerParticleParameter("y0");
+ position_restraint_force.addPerParticleParameter("z0");
+ position_restraint_force.addPerParticleParameter("k_force");
+ position_restraint_force.addPerParticleParameter("x_scale");
+ position_restraint_force.addPerParticleParameter("y_scale");
+ position_restraint_force.addPerParticleParameter("z_scale");
+ sys->addForce(&position_restraint_force);
+ mapper[HarmonicPositionRestraint] = mapper_index++;
+ for(std::vector<std::pair<Index<1>,std::vector<Real> > >::const_iterator i = harmonic_position_restraints.begin();
+ i != harmonic_position_restraints.end(); ++i){
+ //stupid cast
+ std::vector<double> parameters;
+ for(std::vector<Real>::const_iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ parameters.push_back(*j);
+ }
+ position_restraint_force.addParticle(i->first[0], parameters);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > > harmonic_distance_restraints = top->GetHarmonicDistanceRestraints();
+ if(!harmonic_distance_restraints.empty()){
+ OpenMM::HarmonicBondForce& harmonic_distance_restraint_force = *new OpenMM::HarmonicBondForce();
+ sys->addForce(&harmonic_distance_restraint_force);
+ mapper[HarmonicDistanceRestraint] = mapper_index++;
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = harmonic_distance_restraints.begin();
+ i != harmonic_distance_restraints.end(); ++i){
+ //note, that the restraint formula is k(b-b0)^2 instead of 1/2*k(b-b0)^2 => multiply by two!
+ harmonic_distance_restraint_force.addBond(i->first[0],i->first[1],i->second[0],2*i->second[1]);
+ }
+ }
+
+ std::vector<Real> sigmas = top->GetSigmas();
+ std::vector<Real> epsilons = top->GetEpsilons();
+ std::vector<Real> charges = top->GetCharges();
+ if(!sigmas.empty() && !epsilons.empty() && !charges.empty()){
+ OpenMM::NonbondedForce& nonbonded_force = *new OpenMM::NonbondedForce();
+ nonbonded_force.setNonbondedMethod(settings->nonbonded_method);
+ //we can set the cutoff in any case, since it will have no effect when
+ //nonbonded method is NoCutoff
+ nonbonded_force.setCutoffDistance(settings->nonbonded_cutoff/10.0);
+ nonbonded_force.setReactionFieldDielectric(settings->reaction_field_dielectric);
+ nonbonded_force.setUseDispersionCorrection(settings->use_dispersion_correction);
+ sys->addForce(&nonbonded_force);
+ mapper[LJ] = mapper_index++;
+
+ //we first add all single particles to the force
+ for(uint i = 0; i < charges.size(); ++i){
+ nonbonded_force.addParticle(charges[i], sigmas[i], epsilons[i]);
+ }
+ //take care of the 1-4 interactions
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& lj_pairs = top->GetLJPairs();
+ if(!lj_pairs.empty()){
+ Real fudge_lj = top->GetFudgeLJ();
+ Real fudge_qq = top->GetFudgeQQ();
+ Real charge;
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = lj_pairs.begin();
+ i != lj_pairs.end(); ++i){
+ charge = fudge_qq * charges[i->first[0]] * charges[i->first[1]];
+ nonbonded_force.addException(i->first[0],i->first[1],charge,
+ i->second[0],fudge_lj*i->second[1]);
+ }
+ }
+ //take care of the exclusions
+ const std::vector<Index<2> >& exclusions = top->GetExclusions();
+ if(!exclusions.empty()){
+ for(std::vector<Index<2> >::const_iterator i = exclusions.begin(); i != exclusions.end(); ++i){
+ nonbonded_force.addException((*i)[0],(*i)[1],0.0,1.0,0.0);
+ }
+ }
+ }
+ std::vector<Real> gbsa_radii = top->GetGBSARadii();
+ std::vector<Real> gbsa_scaling = top->GetOBCScalings();
+ if(!gbsa_radii.empty() && !gbsa_scaling.empty()){
+ std::vector<Real> charges = top->GetCharges();
+ if(charges.empty())
+ throw ost::Error("GBSA force requires atom charges to be set!");
+ OpenMM::GBSAOBCForce& gbsa_force = *new OpenMM::GBSAOBCForce();
+ sys->addForce(&gbsa_force);
+ if(settings->nonbonded_method == OpenMM::NonbondedForce::NoCutoff){
+ gbsa_force.setNonbondedMethod(OpenMM::GBSAOBCForce::NoCutoff);
+ }
+ else if(settings->nonbonded_method == OpenMM::NonbondedForce::CutoffNonPeriodic){
+ gbsa_force.setNonbondedMethod(OpenMM::GBSAOBCForce::CutoffNonPeriodic);
+ }
+ else if(settings->nonbonded_method == OpenMM::NonbondedForce::CutoffPeriodic){
+ gbsa_force.setNonbondedMethod(OpenMM::GBSAOBCForce::CutoffPeriodic);
+ }
+ else{
+ throw ost::Error("Can only use Nonbonded methods NoCutoff, CutoffNonPeriodic,CutoffPeriodic when using GBSA");
+ }
+ mapper[GBSA] = mapper_index++;
+ gbsa_force.setCutoffDistance(settings->nonbonded_cutoff/10);
+ gbsa_force.setSolventDielectric(settings->solvent_dielectric);
+ gbsa_force.setSoluteDielectric(settings->solute_dielectric);
+ //it should be guaranteed from the topology object, that the vectors have the same size
+ for(uint i = 0; i < gbsa_radii.size(); ++i){
+ gbsa_force.addParticle(charges[i],
+ gbsa_radii[i],
+ gbsa_scaling[i]);
+ }
+ }
+ //set constraints
+ std::vector<std::pair<Index<2>,std::vector<Real> > > distance_constraints = top->GetDistanceConstraints();
+ if(!distance_constraints.empty()){
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = distance_constraints.begin();
+ i != distance_constraints.end(); ++i){
+ sys->addConstraint(i->first[0],i->first[1],i->second[0]);
+ }
+ }
+ //set periodic box extents
+ if(geom::Length(settings->periodic_box_extents) > 0){
+ OpenMM::Vec3 x_vec(settings->periodic_box_extents[0]/10,0.0,0.0);
+ OpenMM::Vec3 y_vec(0.0,settings->periodic_box_extents[1]/10,0.0);
+ OpenMM::Vec3 z_vec(0.0,0.0,settings->periodic_box_extents[2]/10);
+ sys->setDefaultPeriodicBoxVectors(x_vec,y_vec,z_vec);
+ }
+ else if(settings->add_nonbonded &&
+ !(settings->nonbonded_method == OpenMM::NonbondedForce::NoCutoff ||
+ settings->nonbonded_method == OpenMM::NonbondedForce::CutoffNonPeriodic)){
+ throw ost::Error("Chosen nonbonded method requires to define the periodic box extents!");
+ }
+ //set the CMMMotion removing force if required
+ if(settings->remove_cmm_motion){
+ if(settings->cmm_frequency != settings->cmm_frequency){
+ throw ost::Error("Cannot set CMM Remover without valid cmm_frequency set!");
+ }
+ sys->addForce(new OpenMM::CMMotionRemover(settings->cmm_frequency));
+ }
+ if(settings->add_thermostat){
+ if(settings->thermostat_temperature != settings->thermostat_temperature ||
+ settings->thermostat_collision_frequency != settings->thermostat_collision_frequency){
+ throw ost::Error("Cannot set thermostat without defined temperature and collision frequency!");
+ }
+ OpenMM::AndersenThermostat& thermostat = *new OpenMM::AndersenThermostat(settings->thermostat_temperature,
+ settings->thermostat_collision_frequency);
+ sys->addForce(&thermostat);
+ }
+ if(settings->add_barostat){
+ if(geom::Length(settings->periodic_box_extents) == 0){
+ throw ost::Error("If you set a barostat, you also have to set nonzero periodic box extents!");
+ }
+ if(settings->barostat_temperature != settings->barostat_temperature ||
+ settings->barostat_pressure != settings->barostat_pressure ||
+ settings->barostat_frequency != settings->barostat_frequency){
+ throw ost::Error("Cannot set barostat without defined temperature, pressure, and frequency parameters!");
+ }
+ OpenMM::MonteCarloBarostat& barostat = *new OpenMM::MonteCarloBarostat(settings->barostat_pressure,
+ settings->barostat_temperature,
+ settings->barostat_frequency);
+ sys->addForce(&barostat);
+ }
+ return sys;
+}
+}}} //ns
diff --git a/modules/mol/mm/src/system_creator.hh b/modules/mol/mm/src/system_creator.hh
new file mode 100644
index 0000000000000000000000000000000000000000..d7fce8408530c205a11f7671fb395fd9fb5f1722
--- /dev/null
+++ b/modules/mol/mm/src/system_creator.hh
@@ -0,0 +1,42 @@
+#ifndef OST_SYSTEM_CREATOR_HH
+#define OST_SYSTEM_CREATOR_HH
+
+#include <OpenMM.h>
+
+#include <vector>
+#include <map>
+#include <set>
+
+#include <ost/message.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/topology.hh>
+
+
+#include <time.h>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+typedef boost::shared_ptr<OpenMM::System> SystemPtr;
+
+class SystemCreator {
+public:
+ static SystemPtr Create(const TopologyPtr top,
+ const MMSettingsPtr settings,
+ std::map<FuncType,uint>& mapper);
+
+};
+
+
+}}}//ns
+
+#endif
\ No newline at end of file
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e31859803ef132227832f869c1d3c79083dd67f4
--- /dev/null
+++ b/modules/mol/mm/src/topology.cc
@@ -0,0 +1,1336 @@
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/mm_modeller.hh>
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+
+
+Topology::Topology(const ost::mol::EntityHandle& ent, const std::vector<Real>& masses){
+
+ num_atoms_ = ent.GetAtomCount();
+ if(num_atoms_ != masses.size()){
+ throw ost::Error("Number of atoms in entity and number of masses do not match when creating topology!");
+ }
+ ent_ = ent.Copy();
+ num_residues_ = ent_.GetResidueCount();
+ atom_list_ = ent_.GetAtomList();
+ res_list_ = ent_.GetResidueList();
+ atom_masses_ = masses;
+ fudge_lj_ = 1.0;
+ fudge_qq_ = 1.0;
+
+ for(uint i = 0; i < atom_list_.size(); ++i){
+ atom_index_mapper_[atom_list_[i].GetHashCode()] = i;
+ }
+
+ for(uint i = 0; i < res_list_.size(); ++i){
+ residue_index_mapper_[res_list_[i].GetHashCode()] = i;
+ }
+
+ std::map<String,uint> per_residue_mapper;
+ ost::mol::AtomHandleList residue_atom_list;
+ for(uint i = 0; i < num_residues_; ++i){
+ per_residue_mapper.clear();
+ residue_atom_list = res_list_[i].GetAtomList();
+ for(ost::mol::AtomHandleList::iterator j = residue_atom_list.begin();
+ j != residue_atom_list.end(); ++j){
+ per_residue_mapper[j->GetName()] = atom_index_mapper_[j->GetHashCode()];
+ }
+ atom_name_mapper_.push_back(per_residue_mapper);
+ }
+}
+
+uint Topology::AddHarmonicBond(uint index_one,
+ uint index_two,
+ Real bond_length,
+ Real force_constant){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_){
+ throw ost::Error("Index of bond atom exceeds number of atoms present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ std::vector<Real> parameters;
+ parameters.push_back(bond_length);
+ parameters.push_back(force_constant);
+ harmonic_bonds_.push_back(std::make_pair(index,parameters));
+ return harmonic_bonds_.size()-1;
+}
+
+uint Topology::AddHarmonicAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real force_constant){
+
+ if(uint(index_one) >= num_atoms_ || uint(index_two) >= num_atoms_ ||
+ uint(index_three) >= num_atoms_){
+ throw ost::Error("Index of angle atom exceeds number of atoms present in topology!");
+ }
+ Index<3> index(index_one,index_two,index_three);
+ std::vector<Real> parameters;
+ parameters.push_back(angle);
+ parameters.push_back(force_constant);
+ harmonic_angles_.push_back(std::make_pair(index,parameters));
+ return harmonic_angles_.size()-1;
+}
+
+uint Topology::AddUreyBradleyAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real angle_force_constant,
+ Real bond_length,
+ Real bond_force_constant){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_ ||
+ index_three >= num_atoms_){
+ throw ost::Error("Index of angle atom exceeds number of atoms present in topology!");
+ }
+ Index<3> index(index_one,index_two,index_three);
+ std::vector<Real> parameters;
+ parameters.push_back(angle);
+ parameters.push_back(angle_force_constant);
+ parameters.push_back(bond_length);
+ parameters.push_back(bond_force_constant);
+ urey_bradley_angles_.push_back(std::make_pair(index,parameters));
+ return urey_bradley_angles_.size()-1;
+}
+
+uint Topology::AddPeriodicDihedral(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_||
+ index_three >= num_atoms_ || index_four >= num_atoms_){
+ throw ost::Error("Index of dihedral atom exceeds number of atoms present in topology!");
+ }
+ Index<4> index(index_one,index_two,index_three,index_four);
+ std::vector<Real> parameters;
+ parameters.push_back(multiplicity);
+ parameters.push_back(phase);
+ parameters.push_back(force_constant);
+ periodic_dihedrals_.push_back(std::make_pair(index,parameters));
+ return periodic_dihedrals_.size()-1;
+}
+
+uint Topology::AddPeriodicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_||
+ index_three >= num_atoms_ || index_four >= num_atoms_){
+ throw ost::Error("Index of improper atom exceeds number of atoms present in topology!");
+ }
+ Index<4> index(index_one,index_two,index_three,index_four);
+ std::vector<Real> parameters;
+ parameters.push_back(multiplicity);
+ parameters.push_back(phase);
+ parameters.push_back(force_constant);
+ periodic_impropers_.push_back(std::make_pair(index,parameters));
+ return periodic_impropers_.size()-1;
+}
+
+uint Topology::AddHarmonicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ Real angle,
+ Real force_constant){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_||
+ index_three >= num_atoms_ || index_four >= num_atoms_){
+ throw ost::Error("Index of improper atom exceeds number of atoms present in topology!");
+ }
+ Index<4> index(index_one,index_two,index_three,index_four);
+ std::vector<Real> parameters;
+ parameters.push_back(angle);
+ parameters.push_back(force_constant);
+ harmonic_impropers_.push_back(std::make_pair(index,parameters));
+ return harmonic_impropers_.size()-1;
+}
+
+uint Topology::AddCMap(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five,
+ int dimension,
+ std::vector<Real> values){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_ ||
+ index_three >= num_atoms_ || index_four >= num_atoms_ ||
+ index_five >= num_atoms_){
+ throw ost::Error("Index of cmap atom exceeds number of atoms present in topology!");
+ }
+ if(uint(dimension * dimension) != values.size()){
+ throw ost::Error("Dimension of CMap is inconsistent with its values!");
+ }
+ Index<5> index(index_one,index_two,index_three,index_four,index_five);
+ cmaps_.push_back(std::make_pair(index,values));
+ return cmaps_.size()-1;
+}
+
+uint Topology::AddLJPair(uint index_one,
+ uint index_two,
+ Real sigma,
+ Real epsilon){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_){
+ throw ost::Error("Index of lj pair atom exceeds number of atoms present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ if(added_lj_pairs_.find(index) != added_lj_pairs_.end() || added_lj_pairs_.find(reverse_index) != added_lj_pairs_.end()){
+ throw ost::Error("This particular lj 1,4-interaction is already parametrized!");
+ }
+ added_lj_pairs_.insert(index);
+ std::vector<Real> parameters;
+ parameters.push_back(sigma);
+ parameters.push_back(epsilon);
+ lj_pairs_.push_back(std::make_pair(index,parameters));
+ return lj_pairs_.size()-1;
+}
+
+uint Topology::AddExclusion(uint index_one,
+ uint index_two){
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ if(index_one >= num_atoms_ || index_two >= num_atoms_){
+ throw ost::Error("Index of exclusion atom exceeds number of atoms present in topology!");
+ }
+ if(added_exclusions_.find(index) != added_exclusions_.end() || added_exclusions_.find(reverse_index) != added_exclusions_.end()){
+ throw ost::Error("This particular exclusion has already been set!");
+ }
+ added_exclusions_.insert(index);
+ exclusions_.push_back(index);
+ return exclusions_.size()-1;
+}
+
+uint Topology::AddDistanceConstraint(uint index_one,
+ uint index_two,
+ Real distance){
+
+ if(index_one >= num_atoms_ || index_two >= num_atoms_){
+ throw ost::Error("Index of distance constraint atom exceeds number of atoms present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ if(added_distance_constraints_.find(index) != added_distance_constraints_.end() || added_distance_constraints_.find(reverse_index) != added_distance_constraints_.end()){
+ throw ost::Error("This particular distance constraint is already parametrized!");
+ }
+ added_distance_constraints_.insert(index);
+ std::vector<Real> parameters;
+ parameters.push_back(distance);
+ distance_constraints_.push_back(std::make_pair(index,parameters));
+ return distance_constraints_.size()-1;
+}
+
+void Topology::AddPositionConstraint(uint index){
+ if(index >= num_atoms_){
+ throw ost::Error("Index of position constraint exceeds number of atoms present in topology!");
+ }
+ std::vector<uint>::iterator it = std::find(position_constraints_.begin(),position_constraints_.end(),index);
+ if(it != position_constraints_.end()) return; //already present
+ position_constraints_.push_back(index);
+}
+
+uint Topology::AddHarmonicPositionRestraint(uint ind, const geom::Vec3& ref_position, Real k,
+ Real x_scale, Real y_scale, Real z_scale){
+ if(ind >= num_atoms_){
+ throw ost::Error("Index of harmonic distance constraint exceeds number of atoms present in topology!");
+ }
+ Index<1> index(ind);
+ std::vector<Real> parameters;
+ parameters.push_back(ref_position[0]);
+ parameters.push_back(ref_position[1]);
+ parameters.push_back(ref_position[2]);
+ parameters.push_back(k);
+ parameters.push_back(x_scale);
+ parameters.push_back(y_scale);
+ parameters.push_back(z_scale);
+
+ harmonic_position_restraints_.push_back(std::make_pair(index,parameters));
+ return harmonic_position_restraints_.size()-1;
+}
+
+uint Topology::AddHarmonicDistanceRestraint(uint index_one, uint index_two,
+ Real length, Real force_constant){
+ if(index_one >= num_atoms_ || index_two >= num_atoms_){
+ throw ost::Error("Index of distance restraint atom exceeds number of atoms present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ std::vector<Real> parameters;
+ parameters.push_back(length);
+ parameters.push_back(force_constant);
+ harmonic_distance_restraints_.push_back(std::make_pair(index,parameters));
+ return harmonic_distance_restraints_.size()-1;
+}
+
+void Topology::SetSigmas(const std::vector<Real>& sigmas){
+ if(sigmas.size() != num_atoms_){
+ throw ost::Error("Expect the same number of sigma parameters than atoms!");
+ }
+ sigmas_ = sigmas;
+}
+
+void Topology::SetSigma(uint index, Real sigma){
+ if(sigmas_.empty()){
+ throw ost::Error("Modification of sigma parameter requires initial assignment of sigma parameters in globo!");
+ }
+ if(index >= num_atoms_){
+ throw ost::Error("Given atom index exceeds number off available atoms!");
+ }
+ sigmas_[index] = sigma;
+}
+
+void Topology::SetEpsilons(const std::vector<Real>& epsilons){
+ if(epsilons.size() != num_atoms_){
+ throw ost::Error("Expect the same number of epsilon parameters than atoms!");
+ }
+ epsilons_ = epsilons;
+}
+
+void Topology::SetEpsilon(uint index, Real epsilon){
+ if(epsilons_.empty()){
+ throw ost::Error("Modification of epsilon parameter requires initial assignment of epsilon parameters in globo!");
+ }
+ if(index >= num_atoms_){
+ throw ost::Error("Given atom index exceeds number off available atoms!");
+ }
+ epsilons_[index] = epsilon;
+}
+
+void Topology::SetGBSARadii(const std::vector<Real>& gbsa_radii){
+ if(gbsa_radii.size() != num_atoms_){
+ throw ost::Error("Expect the same number of gbsa parameters than atoms!");
+ }
+ gbsa_radii_ = gbsa_radii;
+}
+
+void Topology::SetGBSARadius(uint index, Real radius){
+ if(gbsa_radii_.empty()){
+ throw ost::Error("Modification of gbsa radius requires initial assignment of gbsa radii in globo!");
+ }
+ if(index >= num_atoms_){
+ throw ost::Error("Given atom index exceeds number off available atoms!");
+ }
+ gbsa_radii_[index] = radius;
+}
+
+void Topology::SetOBCScalings(const std::vector<Real>& obc_scaling){
+ if(obc_scaling.size() != num_atoms_){
+ throw ost::Error("Expect the same number of gbsa parameters than atoms!");
+ }
+ obc_scaling_ = obc_scaling;
+}
+
+void Topology::SetOBCScaling(uint index, Real scaling){
+ if(obc_scaling_.empty()){
+ throw ost::Error("Modification of obc scaling parameter requires initial assignment of obc scaling parameters in globo!");
+ }
+ if(index >= num_atoms_){
+ throw ost::Error("Given atom index exceeds number off available atoms!");
+ }
+ obc_scaling_[index] = scaling;
+}
+
+void Topology::SetCharges(const std::vector<Real>& charges){
+ if(charges.size() != num_atoms_){
+ throw ost::Error("Expect the same number of charges than atoms!");
+ }
+ charges_ = charges;
+}
+
+void Topology::SetCharge(uint index, Real charge){
+ if(charges_.empty()){
+ throw ost::Error("Modification of charge parameter requires initial assignment of charges in globo!");
+ }
+ if(index >= num_atoms_){
+ throw ost::Error("Given atom index exceeds number off available atoms!");
+ }
+ charges_[index] = charge;
+}
+
+void Topology::SetMasses(const std::vector<Real>& masses){
+ if(masses.size() != num_atoms_){
+ throw ost::Error("Expect masses vector to have the same number of elements than atoms in the topologies entity!");
+ }
+ atom_masses_ = masses;
+}
+
+void Topology::SetMass(uint index, Real mass){
+ if(atom_masses_.empty()){
+ throw ost::Error("Modification of mass parameter requires initial assignment of masses in globo!");
+ }
+ if(index >= num_atoms_){
+ throw ost::Error("Given atom index exceeds number off available atoms!");
+ }
+ atom_masses_[index] = mass;
+
+}
+
+
+void Topology::GetHarmonicBondParameters(uint index, uint& index_one, uint& index_two,
+ Real& bond_length, Real& force_constant) const{
+ if(index >= harmonic_bonds_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic bonds present in topology!");
+ }
+ bond_length = harmonic_bonds_[index].second[0];
+ force_constant = harmonic_bonds_[index].second[1];
+ index_one = harmonic_bonds_[index].first[0];
+ index_two = harmonic_bonds_[index].first[1];
+}
+
+void Topology::GetHarmonicAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& force_constant) const{
+ if(index >= harmonic_angles_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic angles present in topology!");
+ }
+ angle = harmonic_angles_[index].second[0];
+ force_constant = harmonic_angles_[index].second[1];
+ index_one = harmonic_angles_[index].first[0];
+ index_two = harmonic_angles_[index].first[1];
+ index_three = harmonic_angles_[index].first[2];
+}
+
+void Topology::GetUreyBradleyAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& angle_force_constant, Real& bond_length, Real& bond_force_constant) const{
+ if(index >= urey_bradley_angles_.size()){
+ throw ost::Error("Provided index exceeds number of urey_bradley angles present in topology!");
+ }
+ angle = urey_bradley_angles_[index].second[0];
+ angle_force_constant = urey_bradley_angles_[index].second[1];
+ bond_length = urey_bradley_angles_[index].second[2];
+ bond_force_constant = urey_bradley_angles_[index].second[3];
+ index_one = urey_bradley_angles_[index].first[0];
+ index_two = urey_bradley_angles_[index].first[1];
+ index_three = urey_bradley_angles_[index].first[2];
+}
+
+void Topology::GetPeriodicDihedralParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const{
+ if(index >= periodic_dihedrals_.size()){
+ throw ost::Error("Provided index exceeds number of periodic dihedrals present in topology!");
+ }
+ multiplicity = int(periodic_dihedrals_[index].second[0]);
+ phase = periodic_dihedrals_[index].second[1];
+ force_constant = periodic_dihedrals_[index].second[2];
+ index_one = periodic_dihedrals_[index].first[0];
+ index_two = periodic_dihedrals_[index].first[1];
+ index_three = periodic_dihedrals_[index].first[2];
+ index_four = periodic_dihedrals_[index].first[3];
+}
+
+void Topology::GetPeriodicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const{
+ if(index >= periodic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of periodic impropers present in topology!");
+ }
+ multiplicity = int(periodic_impropers_[index].second[0]);
+ phase = periodic_impropers_[index].second[1];
+ force_constant = periodic_impropers_[index].second[2];
+ index_one = periodic_impropers_[index].first[0];
+ index_two = periodic_impropers_[index].first[1];
+ index_three = periodic_impropers_[index].first[2];
+ index_four = periodic_impropers_[index].first[3];
+}
+
+void Topology::GetHarmonicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ Real& angle, Real& force_constant) const{
+ if(index >= harmonic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic impropers present in topology!");
+ }
+ angle = harmonic_impropers_[index].second[0];
+ force_constant = harmonic_impropers_[index].second[1];
+ index_one = harmonic_impropers_[index].first[0];
+ index_two = harmonic_impropers_[index].first[1];
+ index_three = harmonic_impropers_[index].first[2];
+ index_four = harmonic_impropers_[index].first[3];
+}
+
+void Topology::GetCMapParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four, uint& index_five,
+ int& dimension, std::vector<Real>& map) const{
+ if(index >= cmaps_.size()){
+ throw ost::Error("Provided index exceeds number of cmaps present in topology!");
+ }
+ dimension = int(sqrt(cmaps_[index].second.size()));
+ map = cmaps_[index].second;
+ index_one = cmaps_[index].first[0];
+ index_two = cmaps_[index].first[1];
+ index_three = cmaps_[index].first[2];
+ index_four = cmaps_[index].first[3];
+ index_five = cmaps_[index].first[4];
+
+}
+
+void Topology::GetLJPairParameters(uint index, uint& index_one, uint& index_two,
+ Real& sigma, Real& epsilon) const{
+ if(index >= lj_pairs_.size()){
+ throw ost::Error("Provided index exceeds number of lj pairs present in topology!");
+ }
+ sigma = lj_pairs_[index].second[0];
+ epsilon = lj_pairs_[index].second[1];
+ index_one = lj_pairs_[index].first[0];
+ index_two = lj_pairs_[index].first[1];
+}
+
+void Topology::GetDistanceConstraintParameters(uint index, uint& index_one, uint& index_two,
+ Real& distance) const{
+ if(index >= distance_constraints_.size()){
+ throw ost::Error("Provided index exceeds number of distance_constraints present in topology!");
+ }
+ distance = distance_constraints_[index].second[0];
+ index_one = distance_constraints_[index].first[0];
+ index_two = distance_constraints_[index].first[1];
+}
+
+void Topology::GetHarmonicPositionRestraintParameters(uint index, uint& atom_index, geom::Vec3& ref_position,
+ Real& k, Real& x_scale, Real& y_scale, Real& z_scale) const{
+ if(index >= harmonic_position_restraints_.size()){
+ throw ost::Error("Provided index exceeds numnber of harmonic position constraints present in topology!");
+ }
+ atom_index = harmonic_position_restraints_[index].first[0];
+ ref_position[0] = harmonic_position_restraints_[index].second[0];
+ ref_position[1] = harmonic_position_restraints_[index].second[1];
+ ref_position[2] = harmonic_position_restraints_[index].second[2];
+ k = harmonic_position_restraints_[index].second[3];
+ x_scale = harmonic_position_restraints_[index].second[4];
+ y_scale = harmonic_position_restraints_[index].second[5];
+ z_scale = harmonic_position_restraints_[index].second[6];
+}
+
+void Topology::GetHarmonicDistanceRestraintParameters(uint index, uint& atom_one, uint& atom_two, Real& length,
+ Real& force_constant) const{
+ if(index >= harmonic_distance_restraints_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic distance restraints present in topology!");
+ }
+ atom_one = harmonic_distance_restraints_[index].first[0];
+ atom_two = harmonic_distance_restraints_[index].first[1];
+ length = harmonic_distance_restraints_[index].second[0];
+ force_constant = harmonic_distance_restraints_[index].second[1];
+}
+
+
+void Topology::SetHarmonicBondParameters(uint index, const Real& bond_length, const Real& force_constant){
+ if(index >= harmonic_bonds_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic bonds present in topology!");
+ }
+ harmonic_bonds_[index].second[0] = bond_length;
+ harmonic_bonds_[index].second[1] = force_constant;
+}
+
+void Topology::SetHarmonicAngleParameters(uint index, const Real& angle, const Real& force_constant){
+ if(index >= harmonic_angles_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic angles present in topology!");
+ }
+ harmonic_angles_[index].second[0] = angle;
+ harmonic_angles_[index].second[1] = force_constant;
+}
+
+void Topology::SetUreyBradleyAngleParameters(uint index, const Real& angle, const Real& angle_force_constant, const Real& bond_length, const Real& bond_force_constant){
+ if(index >= urey_bradley_angles_.size()){
+ throw ost::Error("Provided index exceeds number of urey_bradley angles present in topology!");
+ }
+ urey_bradley_angles_[index].second[0] = angle;
+ urey_bradley_angles_[index].second[1] = angle_force_constant;
+ urey_bradley_angles_[index].second[2] = bond_length;
+ urey_bradley_angles_[index].second[3] = bond_force_constant;
+}
+
+void Topology::SetPeriodicDihedralParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant){
+ if(index >= periodic_dihedrals_.size()){
+ throw ost::Error("Provided index exceeds number of periodic dihedrals present in topology!");
+ }
+ periodic_dihedrals_[index].second[0] = multiplicity;
+ periodic_dihedrals_[index].second[1] = phase;
+ periodic_dihedrals_[index].second[2] = force_constant;
+}
+
+void Topology::SetPeriodicImproperParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant){
+ if(index >= periodic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of periodic impropers present in topology!");
+ }
+ periodic_impropers_[index].second[0] = multiplicity;
+ periodic_impropers_[index].second[1] = phase;
+ periodic_impropers_[index].second[2] = force_constant;
+}
+
+void Topology::SetHarmonicImproperParameters(uint index, const Real& angle, const Real& force_constant){
+ if(index >= harmonic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic impropers present in topology!");
+ }
+ harmonic_impropers_[index].second[0] = angle;
+ harmonic_impropers_[index].second[1] = force_constant;
+}
+
+void Topology::SetCMapParameters(uint index, const int& dimension, const std::vector<Real>& map){
+ if(index >= cmaps_.size()){
+ throw ost::Error("Provided index exceeds number of cmaps present in topology!");
+ }
+ if(uint(dimension * dimension) != map.size()){
+ throw ost::Error("Provided dimension and map are inconsistent!");
+ }
+ cmaps_[index].second = map;
+}
+
+void Topology::SetLJPairParameters(uint index, const Real& sigma, const Real& epsilon){
+ if(index >= lj_pairs_.size()){
+ throw ost::Error("Provided index exceeds number of lj pairs present in topology!");
+ }
+ lj_pairs_[index].second[0] = sigma;
+ lj_pairs_[index].second[1] = epsilon;
+}
+
+void Topology::SetDistanceConstraintParameters(uint index, const Real& distance){
+ if(index >= distance_constraints_.size()){
+ throw ost::Error("Provided index exceeds number of distance_constraints present in topology!");
+ }
+ distance_constraints_[index].second[0] = distance;
+}
+
+void Topology::SetHarmonicPositionRestraintParameters(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale, Real y_scale, Real z_scale){
+ if(index >= harmonic_position_restraints_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic position restraints present in topology!");
+ }
+ harmonic_position_restraints_[index].second[0] = ref_position[0];
+ harmonic_position_restraints_[index].second[1] = ref_position[1];
+ harmonic_position_restraints_[index].second[2] = ref_position[2];
+ harmonic_position_restraints_[index].second[3] = k;
+ harmonic_position_restraints_[index].second[4] = x_scale;
+ harmonic_position_restraints_[index].second[5] = y_scale;
+ harmonic_position_restraints_[index].second[6] = z_scale;
+}
+
+void Topology::SetHarmonicDistanceRestraintParameters(uint index, Real length,
+ Real force_constant){
+ if(index >= harmonic_distance_restraints_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic distance restraints present in topology!");
+ }
+ harmonic_distance_restraints_[index].second[0] = length;
+ harmonic_distance_restraints_[index].second[1] = force_constant;
+
+}
+
+uint Topology::GetAtomIndex(const ost::mol::AtomHandle& at) const{
+ std::map<long,uint>::const_iterator i = atom_index_mapper_.find(at.GetHashCode());
+ if(i == atom_index_mapper_.end()){
+ throw ost::Error("Could not find atom in attached entity!");
+ }
+ return i->second;
+}
+
+
+uint Topology::GetResidueIndex(const ost::mol::ResidueHandle& res) const{
+ std::map<long,uint>::const_iterator i = residue_index_mapper_.find(res.GetHashCode());
+ if(i == residue_index_mapper_.end()){
+ throw ost::Error("Could not find residue in attached entity!");
+ }
+ return i->second;
+}
+
+uint Topology::GetAtomIndex(uint residue_index, const String& atom_name) const{
+ if(residue_index < 0 || residue_index >= num_residues_){
+ throw ost::Error("Residue index out of bounds");
+ }
+ if(atom_name[0] == '+'){
+ ost::mol::ResidueHandle actual_res = res_list_[residue_index];
+ ost::mol::ResidueHandle next_residue = actual_res.GetNext();
+ if(!next_residue){
+ throw ost::Error("Could not get next residue!");
+ }
+ String next_atom_name = atom_name.substr(1);
+ std::map<String,uint>::const_iterator it = atom_name_mapper_[this->GetResidueIndex(next_residue)].find(next_atom_name);
+ if(it == atom_name_mapper_[this->GetResidueIndex(next_residue)].end()){
+ std::stringstream ss;
+ ss << "Could not find required atom " << next_atom_name;
+ ss << " from residue " << next_residue.GetQualifiedName();
+ }
+ return it->second;
+ }
+ if(atom_name[0] == '-'){
+ ost::mol::ResidueHandle actual_res = res_list_[residue_index];
+ ost::mol::ResidueHandle prev_residue = actual_res.GetPrev();
+ if(!prev_residue){
+ throw ost::Error("Could not get prev residue!");
+ }
+ String prev_atom_name = atom_name.substr(1);
+ std::map<String,uint>::const_iterator it = atom_name_mapper_[this->GetResidueIndex(prev_residue)].find(prev_atom_name);
+ if(it == atom_name_mapper_[this->GetResidueIndex(prev_residue)].end()){
+ std::stringstream ss;
+ ss << "Could not find required atom " << prev_atom_name;
+ ss << " from residue " << prev_residue.GetQualifiedName();
+ }
+ return it->second;
+ }
+ std::map<String,uint>::const_iterator it = atom_name_mapper_[residue_index].find(atom_name);
+ if(it == atom_name_mapper_[residue_index].end()){
+ std::stringstream ss;
+ ss << "Could not find required atom " << atom_name;
+ ss << " from residue " << res_list_[residue_index].GetQualifiedName();
+ }
+ return it->second;
+}
+
+Real Topology::GetMass(uint index) const{
+ if(index >= num_atoms_) throw ost::Error("Provided index exceeds number of atoms present in topology!");
+ return atom_masses_[index];
+}
+
+Real Topology::GetSigma(uint index) const{
+ if(index >= num_atoms_) throw ost::Error("Provided index exceeds number of atoms present in topology!");
+ if(sigmas_.empty()) throw ost::Error("No sigmas set!");
+ return sigmas_[index];
+}
+
+Real Topology::GetEpsilon(uint index) const{
+ if(index >= num_atoms_) throw ost::Error("Provided index exceeds number of atoms present in topology!");
+ if(epsilons_.empty()) throw ost::Error("No epsilons set!");
+ return epsilons_[index];
+}
+
+Real Topology::GetGBSARadius(uint index) const{
+ if(index >= num_atoms_) throw ost::Error("Provided index exceeds number of atoms present in topology!");
+ if(gbsa_radii_.empty()) throw ost::Error("No gbsa radii set!");
+ return gbsa_radii_[index];
+}
+
+Real Topology::GetOBCScaling(uint index) const{
+ if(index >= num_atoms_) throw ost::Error("Provided index exceeds number of atoms present in topology!");
+ if(obc_scaling_.empty()) throw ost::Error("No obc scalings set!");
+ return obc_scaling_[index];
+}
+
+
+Real Topology::GetCharge(uint index) const{
+ if(index >= num_atoms_) throw ost::Error("Provided index exceeds number of atoms present in topology!");
+ if(charges_.empty()) throw ost::Error("No charges set!");
+ return charges_[index];
+}
+
+
+void Topology::SetEntityPositions(const geom::Vec3List& positions){
+ if(positions.size() != num_atoms_){
+ throw ost::Error("Expect positions vector to have the same number of elements than atoms in the topologies entity!");
+ }
+ ost::mol::XCSEditor ed = ent_.EditXCS(ost::mol::BUFFERED_EDIT);
+ for(uint i = 0; i < num_atoms_; ++i){
+ ed.SetAtomPos(atom_list_[i],positions[i]);
+ }
+ ed.UpdateICS();
+}
+
+std::vector<uint> Topology::GetHarmonicBondIndices(uint index_one,
+ uint index_two) const{
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_bonds_.size(); ++i){
+ if(index == harmonic_bonds_[i].first || reverse_index == harmonic_bonds_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const{
+ Index<3> index(index_one,index_two,index_three);
+ Index<3> reverse_index(index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_angles_.size(); ++i){
+ if(index == harmonic_angles_[i].first || reverse_index == harmonic_angles_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetUreyBradleyAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const{
+ Index<3> index(index_one,index_two,index_three);
+ Index<3> reverse_index(index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < urey_bradley_angles_.size(); ++i){
+ if(index == urey_bradley_angles_[i].first || reverse_index == urey_bradley_angles_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicDihedralIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const{
+ Index<4> index(index_one,index_two,index_three,index_four);
+ Index<4> reverse_index(index_four,index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_dihedrals_.size(); ++i){
+ if(index == periodic_dihedrals_[i].first || reverse_index == periodic_dihedrals_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const{
+ Index<4> index(index_one,index_two,index_three,index_four);
+ Index<4> reverse_index(index_four,index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_impropers_.size(); ++i){
+ if(index == periodic_impropers_[i].first || reverse_index == periodic_impropers_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const{
+ Index<4> index(index_one,index_two,index_three,index_four);
+ Index<4> reverse_index(index_four,index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_impropers_.size(); ++i){
+ if(index == harmonic_impropers_[i].first || reverse_index == harmonic_impropers_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetCMapIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five) const{
+ //note, that in case of cmaps the order of the atoms matters
+ Index<5> index(index_one,index_two,index_three,index_four,index_five);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(index == cmaps_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+int Topology::GetLJPairIndex(uint index_one,
+ uint index_two) const{
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ for(uint i = 0; i < lj_pairs_.size(); ++i){
+ if(index == lj_pairs_[i].first || reverse_index == lj_pairs_[i].first){
+ return i;
+ }
+ }
+ return -1;
+}
+
+int Topology::GetDistanceConstraintIndex(uint index_one,
+ uint index_two) const{
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ for(uint i = 0; i < distance_constraints_.size(); ++i){
+ if(index == distance_constraints_[i].first || reverse_index == distance_constraints_[i].first){
+ return i;
+ }
+ }
+ return -1;
+}
+
+std::vector<uint> Topology::GetHarmonicPositionRestraintIndices(uint atom_index) const{
+ Index<1> index(atom_index);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_position_restraints_.size(); ++i){
+ if(index == harmonic_position_restraints_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicDistanceRestraintIndices(uint index_one, uint index_two) const{
+
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_distance_restraints_.size(); ++i){
+ if(index == harmonic_distance_restraints_[i].first || reverse_index == harmonic_distance_restraints_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicBondIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_bonds_.size(); ++i){
+ if(harmonic_bonds_[i].first[0] == atom_index || harmonic_bonds_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicAngleIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_angles_.size(); ++i){
+ if(harmonic_angles_[i].first[0] == atom_index || harmonic_angles_[i].first[1] == atom_index ||
+ harmonic_angles_[i].first[2] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetUreyBradleyAngleIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < urey_bradley_angles_.size(); ++i){
+ if(urey_bradley_angles_[i].first[0] == atom_index || urey_bradley_angles_[i].first[1] == atom_index ||
+ urey_bradley_angles_[i].first[2] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicDihedralIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_dihedrals_.size(); ++i){
+ if(periodic_dihedrals_[i].first[0] == atom_index || periodic_dihedrals_[i].first[1] == atom_index ||
+ periodic_dihedrals_[i].first[2] == atom_index || periodic_dihedrals_[i].first[3] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicImproperIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_impropers_.size(); ++i){
+ if(periodic_impropers_[i].first[0] == atom_index || periodic_impropers_[i].first[1] == atom_index ||
+ periodic_impropers_[i].first[2] == atom_index || periodic_impropers_[i].first[3] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicImproperIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_impropers_.size(); ++i){
+ if(harmonic_impropers_[i].first[0] == atom_index || harmonic_impropers_[i].first[1] == atom_index ||
+ harmonic_impropers_[i].first[2] == atom_index || harmonic_impropers_[i].first[3] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetCMapIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(cmaps_[i].first[0] == atom_index || cmaps_[i].first[1] == atom_index ||
+ cmaps_[i].first[2] == atom_index || cmaps_[i].first[3] == atom_index ||
+ cmaps_[i].first[4] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetLJPairIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < lj_pairs_.size(); ++i){
+ if(lj_pairs_[i].first[0] == atom_index || lj_pairs_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetDistanceConstraintIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < distance_constraints_.size(); ++i){
+ if(distance_constraints_[i].first[0] == atom_index || distance_constraints_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicDistanceRestraintIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_distance_restraints_.size(); ++i){
+ if(harmonic_distance_restraints_[i].first[0] == atom_index || harmonic_distance_restraints_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+void Topology::Merge(TopologyPtr p){
+ //check whether there is chain from the new entity is already present in the actual entity
+ ost::mol::EntityHandle source_ent = p->GetEntity();
+ ost::mol::ChainHandleList source_chains = source_ent.GetChainList();
+ for(ost::mol::ChainHandleList::iterator i = source_chains.begin();
+ i != source_chains.end(); ++i){
+ if(ent_.FindChain(i->GetName()).IsValid()){
+ std::stringstream ss;
+ ss << "Chain with name \"" << i->GetName() << "\" from source topology";
+ ss << "is already present in destination topology!";
+ throw ost::Error(ss.str());
+ }
+ }
+ //check whether the fudge parameters are consistent
+ if(p->GetFudgeLJ() != fudge_lj_ || p->GetFudgeQQ() != fudge_qq_){
+ throw ost::Error("Expect the fudge parameters of source topology to consistent with the fudge parameters from the destination topology!");
+ }
+
+ //mapper of hashcode from source atom to index in added_atom list
+ std::map<long,int> index_mapper;
+ ost::mol::AtomHandleList added_atoms;
+
+ //let's create an editor to copy over all chains, residues and atoms
+ //from the source topologies entity
+ ost::mol::XCSEditor ed = ent_.EditXCS(ost::mol::BUFFERED_EDIT);
+ for(ost::mol::ChainHandleList::iterator i = source_chains.begin();
+ i != source_chains.end(); ++i){
+ ost::mol::ResidueHandleList res_list = i->GetResidueList();
+ ost::mol::ChainHandle added_chain = ed.InsertChain(i->GetName());
+
+ for(ost::mol::ResidueHandleList::iterator j = res_list.begin();
+ j != res_list.end(); ++j){
+ ost::mol::AtomHandleList atom_list = j->GetAtomList();
+ ost::mol::ResidueHandle added_residue = ed.AppendResidue(added_chain,*j);
+
+ for(ost::mol::AtomHandleList::iterator k = atom_list.begin();
+ k != atom_list.end(); ++k){
+ index_mapper[k->GetHashCode()] = added_atoms.size();
+ added_atoms.push_back(ed.InsertAtom(added_residue,*k));
+ }
+ }
+ }
+
+ //let's rebuild the connectivity
+ ost::mol::BondHandleList bond_list = source_ent.GetBondList();
+ for(ost::mol::BondHandleList::iterator i = bond_list.begin();
+ i != bond_list.end(); ++i){
+ ed.Connect(added_atoms[index_mapper[i->GetFirst().GetHashCode()]],
+ added_atoms[index_mapper[i->GetSecond().GetHashCode()]]);
+ }
+ ed.UpdateICS();
+
+ //let's update the remaining structural data
+ atom_list_ = ent_.GetAtomList();
+ res_list_ = ent_.GetResidueList();
+ num_atoms_ = atom_list_.size();
+ num_residues_ = res_list_.size();
+
+ //let's update the index mappers
+ for(uint i = 0; i < num_atoms_; ++i){
+ if(atom_index_mapper_.find(atom_list_[i].GetHashCode()) == atom_index_mapper_.end()){
+ atom_index_mapper_[atom_list_[i].GetHashCode()] = i;
+ continue;
+ }
+ //indices of atoms that have already been there must not be changed
+ if(atom_index_mapper_[atom_list_[i].GetHashCode()] != i){
+ throw ost::Error("Updating indices during merging process went horribly wrong!");
+ }
+ }
+
+ for(uint i = 0; i != num_residues_; ++i){
+ if(residue_index_mapper_.find(res_list_[i].GetHashCode()) == residue_index_mapper_.end()){
+ residue_index_mapper_[res_list_[i].GetHashCode()] = i;
+ continue;
+ }
+ //indices of residues that have already been there must not be changed
+ if(residue_index_mapper_[res_list_[i].GetHashCode()] != i){
+ throw ost::Error("Updating indices during merging process went horribly wrong!");
+ }
+ }
+
+ atom_name_mapper_.clear(); //let's rebuild from scratch
+ std::map<String,uint> per_residue_mapper;
+ ost::mol::AtomHandleList residue_atom_list;
+ for(uint i = 0; i < num_residues_; ++i){
+ per_residue_mapper.clear();
+ residue_atom_list = res_list_[i].GetAtomList();
+ for(ost::mol::AtomHandleList::iterator j = residue_atom_list.begin();
+ j != residue_atom_list.end(); ++j){
+ per_residue_mapper[j->GetName()] = atom_index_mapper_[j->GetHashCode()];
+ }
+ atom_name_mapper_.push_back(per_residue_mapper);
+ }
+
+ //let's first generate an index mapper from source atom indices to the indices in
+ //the destination entity
+ ost::mol::AtomHandleList source_atoms = source_ent.GetAtomList();
+ std::map<int,int> final_index_mapper;
+ for(uint i = 0; i < source_atoms.size(); ++i){
+ final_index_mapper[i] = atom_index_mapper_[added_atoms[index_mapper[source_atoms[i].GetHashCode()]].GetHashCode()];
+ }
+
+ //let's map over masses
+ std::vector<Real> source_masses = p->GetMasses();
+
+ for(uint i = 0; i < source_atoms.size(); ++i){
+ atom_masses_.push_back(0.0);
+ }
+ for(uint i = 0; i < source_atoms.size(); ++i){
+ atom_masses_[final_index_mapper[i]] = source_masses[i];
+ }
+
+ //let's map over the other per atom parameters if they're defined in the destination topology
+ if(!charges_.empty()){
+ std::vector<Real> source_charges = p->GetCharges();
+ if(source_charges.empty()){
+ throw ost::Error("Cannot merge topology without charges into a topology with defined charges!");
+ }
+ for(uint i = 0; i < source_charges.size(); ++i){
+ charges_.push_back(0.0);
+ }
+ for(uint i = 0; i < source_charges.size(); ++i){
+ charges_[final_index_mapper[i]] = source_charges[i];
+ }
+ }
+
+ if(!sigmas_.empty()){
+ std::vector<Real> source_sigmas = p->GetSigmas();
+ if(source_sigmas.empty()){
+ throw ost::Error("Cannot merge topology without lj sigmas into a topology with defined sigmas!");
+ }
+ for(uint i = 0; i < source_sigmas.size(); ++i){
+ sigmas_.push_back(0.0);
+ }
+ for(uint i = 0; i < source_sigmas.size(); ++i){
+ sigmas_[final_index_mapper[i]] = source_sigmas[i];
+ }
+ }
+
+ if(!epsilons_.empty()){
+ std::vector<Real> source_epsilons= p->GetEpsilons();
+ if(source_epsilons.empty()){
+ throw ost::Error("Cannot merge topology without lj epsilons into a topology with defined epsilons!");
+ }
+ for(uint i = 0; i < source_epsilons.size(); ++i){
+ epsilons_.push_back(0.0);
+ }
+ for(uint i = 0; i < source_epsilons.size(); ++i){
+ epsilons_[final_index_mapper[i]] = source_epsilons[i];
+ }
+ }
+
+ if(!gbsa_radii_.empty()){
+ std::vector<Real> source_radii= p->GetGBSARadii();
+ if(source_radii.empty()){
+ throw ost::Error("Cannot merge topology without gbsa radii into a topology with defined radii!");
+ }
+ for(uint i = 0; i < source_radii.size(); ++i){
+ gbsa_radii_.push_back(0.0);
+ }
+ for(uint i = 0; i < source_radii.size(); ++i){
+ gbsa_radii_[final_index_mapper[i]] = source_radii[i];
+ }
+ }
+
+ if(!obc_scaling_.empty()){
+ std::vector<Real> source_scaling= p->GetOBCScalings();
+ if(source_scaling.empty()){
+ throw ost::Error("Cannot merge topology without obc scaling into a topology with defined scaling!");
+ }
+ for(uint i = 0; i < source_scaling.size(); ++i){
+ obc_scaling_.push_back(0.0);
+ }
+ for(uint i = 0; i < source_scaling.size(); ++i){
+ obc_scaling_[final_index_mapper[i]] = source_scaling[i];
+ }
+ }
+
+ //finally, all the interactions get mapped over
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& harmonic_bonds = p->GetHarmonicBonds();
+ if(!harmonic_bonds.empty()){
+ for(std::vector<std::pair<Index<2>, std::vector<Real> > >::const_iterator i = harmonic_bonds.begin();
+ i != harmonic_bonds.end(); ++i){
+ this->AddHarmonicBond(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& harmonic_angles = p->GetHarmonicAngles();
+ if(!harmonic_angles.empty()){
+ for(std::vector<std::pair<Index<3>, std::vector<Real> > >::const_iterator i = harmonic_angles.begin();
+ i != harmonic_angles.end(); ++i){
+ this->AddHarmonicAngle(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ final_index_mapper[i->first[2]],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& urey_bradley_angles = p->GetUreyBradleyAngles();
+ if(!urey_bradley_angles.empty()){
+ for(std::vector<std::pair<Index<3>, std::vector<Real> > >::const_iterator i = urey_bradley_angles.begin();
+ i != urey_bradley_angles.end(); ++i){
+ this->AddUreyBradleyAngle(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ final_index_mapper[i->first[2]],
+ i->second[0],i->second[1],
+ i->second[2],i->second[3]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& periodic_dihedrals = p->GetPeriodicDihedrals();
+ if(!periodic_dihedrals.empty()){
+ for(std::vector<std::pair<Index<4>, std::vector<Real> > >::const_iterator i = periodic_dihedrals.begin();
+ i != periodic_dihedrals.end(); ++i){
+ this->AddPeriodicDihedral(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ final_index_mapper[i->first[2]],
+ final_index_mapper[i->first[3]],
+ int(i->second[0]),i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& periodic_impropers = p->GetPeriodicImpropers();
+ if(!periodic_impropers.empty()){
+ for(std::vector<std::pair<Index<4>, std::vector<Real> > >::const_iterator i = periodic_impropers.begin();
+ i != periodic_impropers.end(); ++i){
+ this->AddPeriodicImproper(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ final_index_mapper[i->first[2]],
+ final_index_mapper[i->first[3]],
+ int(i->second[0]),i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& harmonic_impropers = p->GetHarmonicImpropers();
+ if(!harmonic_impropers.empty()){
+ for(std::vector<std::pair<Index<4>, std::vector<Real> > >::const_iterator i = harmonic_impropers.begin();
+ i != harmonic_impropers.end(); ++i){
+ this->AddHarmonicImproper(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ final_index_mapper[i->first[2]],
+ final_index_mapper[i->first[3]],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<5>, std::vector<Real> > >& cmaps = p->GetCMaps();
+ if(!cmaps.empty()){
+ for(std::vector<std::pair<Index<5>, std::vector<Real> > >::const_iterator i = cmaps.begin();
+ i != cmaps.end(); ++i){
+ uint dimension = sqrt(i->second.size());
+ this->AddCMap(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ final_index_mapper[i->first[2]],
+ final_index_mapper[i->first[3]],
+ final_index_mapper[i->first[4]],
+ dimension,i->second);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& ljpairs = p->GetLJPairs();
+ if(!ljpairs.empty()){
+ for(std::vector<std::pair<Index<2>, std::vector<Real> > >::const_iterator i = ljpairs.begin();
+ i != ljpairs.end(); ++i){
+ this->AddLJPair(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ i->second[0],i->second[1]);
+ }
+ }
+
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& distance_constraints = p->GetDistanceConstraints();
+ if(!distance_constraints.empty()){
+ for(std::vector<std::pair<Index<2>, std::vector<Real> > >::const_iterator i = distance_constraints.begin();
+ i != distance_constraints.end(); ++i){
+ this->AddDistanceConstraint(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ i->second[0]);
+ }
+ }
+
+ const std::vector<Index<2> >& exclusions = p->GetExclusions();
+ if(!exclusions.empty()){
+ for(std::vector<Index<2> >::const_iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ this->AddExclusion(final_index_mapper[(*i)[0]],
+ final_index_mapper[(*i)[1]]);
+ }
+ }
+
+ const std::vector<std::pair<Index<1>,std::vector<Real> > >& harmonic_position_restraints = p->GetHarmonicPositionRestraints();
+ if(!harmonic_position_restraints.empty()){
+ for(std::vector<std::pair<Index<1>,std::vector<Real> > >::const_iterator i = harmonic_position_restraints.begin();
+ i != harmonic_position_restraints.end(); ++i){
+ geom::Vec3 ref_pos(i->second[0],i->second[1],i->second[2]);
+ this->AddHarmonicPositionRestraint(final_index_mapper[i->first[0]],
+ ref_pos,
+ i->second[3],
+ i->second[4],
+ i->second[5],
+ i->second[6]);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& harmonic_distance_restraints = p->GetHarmonicDistanceRestraints();
+ if(!harmonic_distance_restraints.empty()){
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = harmonic_distance_restraints.begin();
+ i != harmonic_distance_restraints.end(); ++i){
+ this->AddHarmonicDistanceRestraint(final_index_mapper[i->first[0]],
+ final_index_mapper[i->first[1]],
+ i->second[0],
+ i->second[1]);
+ }
+ }
+
+ const std::vector<uint>& position_constraints = p->GetPositionConstraints();
+ if(!position_constraints.empty()){
+ for(std::vector<uint>::const_iterator i = position_constraints.begin();
+ i != position_constraints.end(); ++i){
+ this->AddPositionConstraint(final_index_mapper[*i]);
+ }
+ }
+
+ for(std::set<Index<2> >::iterator i = p->added_lj_pairs_.begin();
+ i != p->added_lj_pairs_.end(); ++i){
+ added_lj_pairs_.insert(Index<2>(final_index_mapper[(*i)[0]],
+ final_index_mapper[(*i)[1]]));
+ }
+
+ for(std::set<Index<2> >::iterator i = p->added_distance_constraints_.begin();
+ i != p->added_distance_constraints_.end(); ++i){
+ added_distance_constraints_.insert(Index<2>(final_index_mapper[(*i)[0]],
+ final_index_mapper[(*i)[1]]));
+ }
+
+ for(std::set<Index<2> >::iterator i = p->added_exclusions_.begin();
+ i != p->added_exclusions_.end(); ++i){
+ added_exclusions_.insert(Index<2>(final_index_mapper[(*i)[0]],
+ final_index_mapper[(*i)[1]]));
+ }
+
+}
+
+
+}}}//ns
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
new file mode 100644
index 0000000000000000000000000000000000000000..dbe67e60d48f07cb918d3145e8f7f852da9e3c5d
--- /dev/null
+++ b/modules/mol/mm/src/topology.hh
@@ -0,0 +1,414 @@
+#ifndef OST_MM_TOPOLOGY_HH
+#define OST_MM_TOPOLOGY_HH
+
+#include <vector>
+#include <map>
+#include <set>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/bond_handle.hh>
+
+#include <time.h>
+
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class Topology;
+typedef boost::shared_ptr<Topology> TopologyPtr;
+
+
+class Topology{
+
+public:
+
+ Topology(const ost::mol::EntityHandle& ent, const std::vector<Real>& masses);
+
+ uint AddHarmonicBond(uint index_one,
+ uint index_two,
+ Real bond_length,
+ Real force_constant);
+
+ uint AddHarmonicAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real force_constant);
+
+ uint AddUreyBradleyAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real angle_force_constant,
+ Real bond_length,
+ Real bond_force_constant);
+
+ uint AddPeriodicDihedral(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant);
+
+ uint AddPeriodicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant);
+
+ uint AddHarmonicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ Real angle,
+ Real force_constant);
+
+ uint AddCMap(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five,
+ int dimension,
+ std::vector<Real> values);
+
+ uint AddLJPair(uint index_one,
+ uint index_two,
+ Real sigma,
+ Real epsilon);
+
+
+ uint AddDistanceConstraint(uint index_one,
+ uint index_two,
+ Real distance);
+
+ uint AddExclusion(uint index_one,
+ uint index_two);
+
+ void AddPositionConstraint(uint index);
+
+ void ResetPositionConstraints() { position_constraints_.clear(); }
+
+ void ResetExclusions() { exclusions_.clear(); }
+
+ uint AddHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);
+
+ uint AddHarmonicDistanceRestraint(uint index_one, uint index_two,
+ Real length, Real force_constant);
+
+ //Single atom parameters are expected to be set at once...
+ void SetSigmas(const std::vector<Real>& sigmas);
+
+ void SetSigma(uint index, Real sigma);
+
+ void SetEpsilons(const std::vector<Real>& epsilons);
+
+ void SetEpsilon(uint index, Real epsilon);
+
+ void SetGBSARadii(const std::vector<Real>& gbsa_radii);
+
+ void SetGBSARadius(uint index, Real radius);
+
+ void SetOBCScalings(const std::vector<Real>& obc_scaling);
+
+ void SetOBCScaling(uint index, Real scaling);
+
+ void SetCharges(const std::vector<Real>& charges);
+
+ void SetCharge(uint index, Real charge);
+
+ void SetMasses(const std::vector<Real>& masses);
+
+ void SetMass(uint index, Real mass);
+
+ void SetFudgeQQ(Real fudge) { fudge_qq_ = fudge; }
+
+ void SetFudgeLJ(Real fudge) { fudge_lj_ = fudge;}
+
+
+ void GetHarmonicBondParameters(uint index, uint& index_one, uint& index_two,
+ Real& bond_length, Real& force_constant) const;
+
+ void GetHarmonicAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& force_constant) const;
+
+ void GetUreyBradleyAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& angle_force_constant, Real& bond_length, Real& bond_force_constant) const;
+
+ void GetPeriodicDihedralParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const;
+
+ void GetPeriodicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const;
+
+ void GetHarmonicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ Real& angle, Real& force_constant) const;
+
+ void GetCMapParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four, uint& index_five,
+ int& dimension, std::vector<Real>& map) const;
+
+ void GetLJPairParameters(uint index, uint& index_one, uint& index_two,
+ Real& sigma, Real& epsilon) const;
+
+ void GetDistanceConstraintParameters(uint index, uint& index_one, uint& index_two,
+ Real& distance) const;
+
+ void GetHarmonicPositionRestraintParameters(uint index, uint& atom_index, geom::Vec3& ref_position,
+ Real& k, Real& x_scale, Real& y_scale, Real& z_scale) const;
+
+ void GetHarmonicDistanceRestraintParameters(uint index, uint& atom_one, uint& atom_two, Real& length,
+ Real& force_constant) const;
+
+ void SetHarmonicBondParameters(uint index, const Real& bond_length, const Real& force_constant);
+
+ void SetHarmonicAngleParameters(uint index, const Real& angle, const Real& force_constant);
+
+ void SetUreyBradleyAngleParameters(uint index, const Real& angle, const Real& angle_force_constant, const Real& bond_length, const Real& bond_force_constant);
+
+ void SetPeriodicDihedralParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant);
+
+ void SetPeriodicImproperParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant);
+
+ void SetHarmonicImproperParameters(uint index, const Real& angle, const Real& force_constant);
+
+ void SetCMapParameters(uint index, const int& dimension, const std::vector<Real>& map);
+
+ void SetLJPairParameters(uint index, const Real& sigma, const Real& epsilon);
+
+ void SetDistanceConstraintParameters(uint index, const Real& distance);
+
+ void SetHarmonicPositionRestraintParameters(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);
+
+ void SetHarmonicDistanceRestraintParameters(uint index, Real length, Real force_constant);
+
+ ost::mol::EntityHandle GetEntity() const { return ent_; };
+
+ uint GetAtomIndex(const ost::mol::AtomHandle& at) const;
+
+ uint GetAtomIndex(uint residue_index, const String& atom_name) const;
+
+ uint GetResidueIndex(const ost::mol::ResidueHandle& res) const;
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicBonds() const { return harmonic_bonds_; }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetHarmonicAngles() const { return harmonic_angles_; }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetUreyBradleyAngles() const { return urey_bradley_angles_; }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicDihedrals() const { return periodic_dihedrals_; }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicImpropers() const { return periodic_impropers_; }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetHarmonicImpropers() const { return harmonic_impropers_; }
+
+ const std::vector<std::pair<Index<5>, std::vector<Real> > >& GetCMaps() const { return cmaps_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetLJPairs() const { return lj_pairs_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetDistanceConstraints() const { return distance_constraints_; }
+
+ const std::vector<std::pair<Index<1>, std::vector<Real> > >&GetHarmonicPositionRestraints() const { return harmonic_position_restraints_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >&GetHarmonicDistanceRestraints() const{ return harmonic_distance_restraints_; }
+
+ const std::vector<Index<2> >& GetExclusions() const { return exclusions_; }
+
+ const std::vector<uint>& GetPositionConstraints() const { return position_constraints_; }
+
+ std::vector<Real> GetSigmas() const { return sigmas_; }
+
+ std::vector<Real> GetEpsilons() const { return epsilons_; }
+
+ std::vector<Real> GetGBSARadii() const { return gbsa_radii_; }
+
+ std::vector<Real> GetOBCScalings() const { return obc_scaling_; }
+
+ std::vector<Real> GetCharges() const { return charges_; }
+
+ Real GetCharge(uint index) const;
+
+ Real GetMass(uint index) const;
+
+ Real GetSigma(uint index) const;
+
+ Real GetEpsilon(uint index) const;
+
+ Real GetGBSARadius(uint index) const;
+
+ Real GetOBCScaling(uint index) const;
+
+ std::vector<Real> GetMasses() const { return atom_masses_; }
+
+ Real GetFudgeQQ() const { return fudge_qq_; }
+
+ Real GetFudgeLJ() const { return fudge_lj_; }
+
+ std::vector<uint> GetHarmonicBondIndices(uint index_one,
+ uint index_two) const;
+
+ std::vector<uint> GetHarmonicAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const;
+
+ std::vector<uint> GetUreyBradleyAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const;
+
+ std::vector<uint> GetPeriodicDihedralIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const;
+
+ std::vector<uint> GetPeriodicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const;
+
+ std::vector<uint> GetHarmonicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const;
+
+ std::vector<uint> GetCMapIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five) const;
+
+ int GetLJPairIndex(uint index_one,
+ uint index_two) const;
+
+ int GetDistanceConstraintIndex(uint index_one,
+ uint index_two) const;
+
+
+
+ std::vector<uint> GetHarmonicDistanceRestraintIndices(uint index_one,
+ uint index_two) const;
+
+
+ std::vector<uint> GetHarmonicBondIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicAngleIndices(uint atom_index) const;
+
+ std::vector<uint> GetUreyBradleyAngleIndices(uint atom_index) const;
+
+ std::vector<uint> GetPeriodicDihedralIndices(uint atom_index) const;
+
+ std::vector<uint> GetPeriodicImproperIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicImproperIndices(uint atom_index) const;
+
+ std::vector<uint> GetCMapIndices(uint atom_index) const;
+
+ std::vector<uint> GetLJPairIndices(uint atom_index) const;
+
+ std::vector<uint> GetDistanceConstraintIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicPositionRestraintIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicDistanceRestraintIndices(uint atom_index) const;
+
+ uint GetNumAtoms() { return num_atoms_; }
+
+ uint GetNumResidues() { return num_residues_; }
+
+ uint GetNumHarmonicBonds() { return harmonic_bonds_.size(); }
+
+ uint GetNumHarmonicAngles() { return harmonic_angles_.size(); }
+
+ uint GetNumUreyBradleyAngles() { return urey_bradley_angles_.size(); }
+
+ uint GetNumPeriodicDihedrals() { return periodic_dihedrals_.size(); }
+
+ uint GetNumPeriodicImpropers() { return periodic_impropers_.size(); }
+
+ uint GetNumHarmonicImpropers() { return harmonic_impropers_.size(); }
+
+ uint GetNumCMaps() { return cmaps_.size(); }
+
+ uint GetNumLJPairs() { return lj_pairs_.size(); }
+
+ uint GetNumDistanceConstraints() { return distance_constraints_.size(); }
+
+ uint GetNumPositionConstraints() { return position_constraints_.size(); }
+
+ uint GetNumHarmonicPositionRestraints() { return harmonic_position_restraints_.size(); }
+
+ uint GetNumHarmonicDistanceRestraints() { return harmonic_distance_restraints_.size();}
+
+ uint GetNumExclusions() { return exclusions_.size(); }
+
+ void Merge(TopologyPtr p);
+
+ void SetEntityPositions(const geom::Vec3List& positions);
+
+private:
+
+ ost::mol::EntityHandle ent_;
+ ost::mol::AtomHandleList atom_list_;
+ ost::mol::ResidueHandleList res_list_;
+
+ uint num_atoms_;
+ uint num_residues_;
+
+ std::map<long,uint> atom_index_mapper_;
+ std::map<long,uint> residue_index_mapper_;
+ std::vector<std::map<String,uint> > atom_name_mapper_;
+
+ //fudge parameters for lj 1,4 pairs
+ Real fudge_qq_;
+ Real fudge_lj_;
+
+ //single atom parameters
+ std::vector<Real> atom_masses_;
+ std::vector<Real> sigmas_;
+ std::vector<Real> epsilons_;
+ std::vector<Real> gbsa_radii_;
+ std::vector<Real> obc_scaling_;
+ std::vector<Real> charges_;
+ std::vector<uint> position_constraints_;
+
+ //interactions with multiple atoms involved
+ std::vector<std::pair<Index<2>,std::vector<Real> > > harmonic_bonds_;
+ std::vector<std::pair<Index<3>,std::vector<Real> > > harmonic_angles_;
+ std::vector<std::pair<Index<3>,std::vector<Real> > > urey_bradley_angles_;
+ std::vector<std::pair<Index<4>,std::vector<Real> > > periodic_dihedrals_;
+ std::vector<std::pair<Index<4>,std::vector<Real> > > periodic_impropers_;
+ std::vector<std::pair<Index<4>,std::vector<Real> > > harmonic_impropers_;
+ std::vector<std::pair<Index<5>,std::vector<Real> > > cmaps_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > lj_pairs_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > distance_constraints_;
+ std::vector<Index<2> > exclusions_;
+ std::vector<std::pair<Index<1>,std::vector<Real> > > harmonic_position_restraints_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > harmonic_distance_restraints_;
+
+ //the atoms of the interactions, that should be unique get tracked in here
+ //note, that this is waste of memory, needs better implementation
+ std::set<Index<2> > added_lj_pairs_;
+ std::set<Index<2> > added_distance_constraints_;
+ std::set<Index<2> > added_exclusions_;
+
+};
+
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
new file mode 100644
index 0000000000000000000000000000000000000000..71401b50b14f3873690f2227214fd32b51ad68d0
--- /dev/null
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -0,0 +1,937 @@
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/mm/mm_modeller.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
+ const MMSettingsPtr settings){
+
+ if(settings->constrain_hangles == true && settings->constrain_hbonds == false){
+ throw ost::Error("If hangles is true, hbonds must also be true in settings object!");
+ }
+
+ //make sure the input gets not modified
+ ost::mol::EntityHandle ent = handle.Copy();
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
+ ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
+
+
+ //rename all the stuff to the gromacs naming...
+ MMModeller::AssignGromacsNaming(ent);
+
+
+ //even if not reconnected yet, it gets assumed, that
+ //peptide or nucleotide bonds are correctly set in the input entity
+ //to allow the identification and tagging of terminal residues
+ //note, that only nucleotides or aminoacids are allowed to build termini...
+ //this should be enough for most needs
+
+ ost::mol::ResidueHandle next,prev;
+ bool n_ter,c_ter;
+ ost::mol::AtomHandle peptide_n,peptide_c,nucleotide_p,nucleotide_o;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+
+ n_ter = false;
+ c_ter = false;
+
+ peptide_n = i->FindAtom("N");
+ nucleotide_p = i->FindAtom("P");
+
+ if(!peptide_n.IsValid() && !nucleotide_p.IsValid()) continue;
+ //in this case the residue is neither a peptide nor a nucleotide.
+ //There won't be a termini anyway...
+
+ prev = i->GetPrev();
+ next = i->GetNext();
+
+ if(!prev.IsValid()){
+ n_ter = true;
+ }
+ else{
+ peptide_c = prev.FindAtom("C");
+ nucleotide_o = prev.FindAtom("O3");
+
+ if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ n_ter = true;
+ }
+ }
+
+ if(!next.IsValid()){
+ c_ter = true;
+ }
+ else{
+ peptide_n = next.FindAtom("N");
+ peptide_c = i->FindAtom("C");
+ nucleotide_p = next.FindAtom("P");
+ nucleotide_o = i->FindAtom("O3");
+
+ if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ c_ter = true;
+ }
+ }
+
+ if(n_ter) i->SetBoolProp("n_ter",true);
+ if(c_ter) i->SetBoolProp("c_ter",true);
+ }
+
+
+ ForcefieldPtr ff = settings->forcefield;
+ if(!ff){
+ throw ost::Error("You have to assign a valid forcefield to the settings object when creating a topology!");
+ }
+ //The full parametrization procedure relies on the naming, that is force field specific
+
+ ost::mol::BondHandleList bond_list = ent.GetBondList();
+ ed.DeleteBonds(bond_list);
+ ed.UpdateICS();
+
+ if(settings->generate_disulfid_bonds){
+ MMModeller::GenerateDisulfidBonds(ent);
+ }
+
+ ff->AssignFFSpecificNames(ent);
+
+ //we first generate the building blocks and directly construct hydrogens/termini and stuff
+ std::vector<BuildingBlockPtr> building_blocks;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ BuildingBlockPtr block = ff->GetBuildingBlock(i->GetName());
+ HydrogenConstructorPtr hc = ff->GetHydrogenConstructor(i->GetName());
+ if(hc){
+ hc->ApplyOnBuildingBlock(block);
+ hc->ApplyOnResidue(*i,ed);
+ }
+ //check for n terminus
+ if(i->HasProp("n_ter")){
+ String exception_name = "";
+ if(settings->termini_exceptions->HasException(*i)){
+ exception_name = settings->termini_exceptions->GetException(*i);
+ }
+ BlockModifierPtr bm = ff->GetNTerModifier(i->GetName(), exception_name);
+ if(bm){
+ bm->ApplyOnBuildingBlock(block);
+ bm->ApplyOnResidue(*i,ed);
+ block->RemoveInteractionsToPrev();
+ }
+ }
+ if(i->HasProp("c_ter")){
+ String exception_name = "";
+ if(settings->termini_exceptions->HasException(*i)){
+ exception_name = settings->termini_exceptions->GetException(*i);
+ }
+ BlockModifierPtr bm = ff->GetCTerModifier(i->GetName(), exception_name);
+ if(bm){
+ bm->ApplyOnBuildingBlock(block);
+ bm->ApplyOnResidue(*i,ed);
+ block->RemoveInteractionsToNext();
+ }
+ }
+ block->Connect(*i,ed);
+ building_blocks.push_back(block);
+ }
+
+ //The editor won't be needed anymore, let's update the internal coordinate system
+ ed.UpdateICS();
+
+
+ String match_fail_info;
+ for(unsigned int i = 0; i < building_blocks.size(); ++i){
+ if(!building_blocks[i]->Match(res_list[i], false, match_fail_info)){
+ std::stringstream ss;
+ ss << "Residue "<< res_list[i].GetQualifiedName() << " does not match the force field ";
+ ss << "definition. "<<match_fail_info;
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<Real> initial_masses(ent.GetAtomCount());
+
+ TopologyPtr top = TopologyPtr(new Topology(ent,initial_masses));
+ ent = top->GetEntity();
+
+ //note, that we have to get the residue list again, since there is a new entity handle
+ //created when initializing the topology
+ res_list = ent.GetResidueList();
+ ost::mol::AtomHandleList atom_list = ent.GetAtomList();
+
+ //let's extract atom specific informations
+ //extract information about single atoms
+ std::vector<std::vector<uint> > bound_to;
+ std::vector<String> atom_types;
+ std::vector<Real> atom_charges;
+ std::vector<String> atom_names;
+ std::vector<Real> atom_masses;
+ std::vector<String> atom_elements;
+ std::vector<String> residue_names_of_atoms;
+ ost::mol::AtomHandleList bonded_atoms;
+ std::vector<uint> temp;
+ //extract masses, types, charges and bondpartners
+
+ ost::mol::ResidueHandle temp_res;
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i!=atom_list.end();++i){
+ temp_res = i->GetResidue();
+ residue_names_of_atoms.push_back(temp_res.GetName());
+ atom_elements.push_back(i->GetElement());
+ atom_types.push_back(building_blocks[top->GetResidueIndex(temp_res)]->GetType(i->GetName()));
+ atom_charges.push_back(building_blocks[top->GetResidueIndex(temp_res)]->GetCharge(i->GetName()));
+ //atom_masses.push_back(building_blocks[top->GetResidueIndex(temp_res)]->GetMass(i->GetName()));
+ //if( atom_masses.back() != atom_masses.back() ){
+ // atom_masses.back() = ff->GetMass(atom_types.back());
+ //}
+ atom_masses.push_back(ff->GetMass(atom_types.back()));
+ bonded_atoms = i->GetBondPartners();
+ temp.clear();
+ for(ost::mol::AtomHandleList::iterator j = bonded_atoms.begin();
+ j!=bonded_atoms.end();++j){
+ temp.push_back(top->GetAtomIndex(*j));
+ }
+ bound_to.push_back(temp);
+ }
+
+
+ //let's set the proper masses
+ top->SetMasses(atom_masses);
+
+
+ //we simply set all charges to zero if we want to kill the electrostatics
+ if(settings->kill_electrostatics){
+ for(std::vector<Real>::iterator i = atom_charges.begin();
+ i != atom_charges.end(); ++i){
+ *i = 0;
+ }
+ }
+
+ top->SetCharges(atom_charges);
+
+ //the interaction read from the structure will be stored in here
+ std::set<Index<2> > bonds;
+ std::set<Index<3> > angles;
+ std::set<Index<4> > dihedrals;
+ std::set<Index<4> > impropers;
+ std::set<Index<5> > cmaps;
+ std::set<Index<2> > exclusions;
+ std::set<Index<2> > pairs_14;
+ std::set<Index<2> > distance_constraints;
+ //per atom parameters
+ std::vector<MMInteractionPtr> ljs;
+ std::vector<MMInteractionPtr> gbsa;
+ //extract all bonded interactions directly from the structure itself,
+ //except the impropers, cmaps and exclusions. Those two get read from the building
+ //blocks.
+ //Note, that the bonds build the basis to build angles and the angles
+ //build the basis to build dihedrals... so we have to extract bonds
+ //even when only dihedrals have to be added.
+ //Another special case is when nonbonded terms have to be added.
+ //They often exclude interactions originating from closely bonded
+ //atoms. We will use the bonds, angles and dihedrals later on to
+ //define these closely bonded atoms, so if nonbonded terms have to
+ //added, we also need to get the bonds, angles and dihedrals.
+ if(settings->add_bonds || settings->add_angles ||
+ settings->add_dihedrals || settings->add_nonbonded){
+ //build all bonds
+ for(uint i=0 ; i<bound_to.size() ;++i){
+ for(uint j = 0; j<bound_to[i].size(); ++j){
+ bonds.insert(Index<2>(std::min(i,bound_to[i][j]),std::max(i,bound_to[i][j])));
+ }
+ }
+ }
+ if(settings->add_angles || settings->add_dihedrals ||
+ settings->add_nonbonded){
+ //build all angles
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i!=bonds.end();++i){
+ uint atom_1 = (*i)[0];
+ uint atom_2 = (*i)[1];
+
+ for(std::vector<uint>::iterator j = bound_to[atom_1].begin();
+ j!=bound_to[atom_1].end(); ++j){
+ if((*j) != atom_2){
+ angles.insert(Index<3>(std::min((*j),atom_2),atom_1,std::max((*j),atom_2)));
+ }
+ }
+ for(std::vector<uint>::iterator j = bound_to[atom_2].begin();
+ j!=bound_to[atom_2].end(); ++j){
+ if((*j) != atom_1){
+ angles.insert(Index<3>(std::min((*j),atom_1),atom_2,std::max((*j),atom_1)));
+ }
+ }
+ }
+ }
+ if(settings->add_dihedrals || settings->add_nonbonded){
+ //build all dihedrals
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i!=angles.end();++i){
+ uint atom_1 = (*i)[0];
+ uint atom_2 = (*i)[1];
+ uint atom_3 = (*i)[2];
+ for(std::vector<uint>::iterator j = bound_to[atom_1].begin();
+ j!=bound_to[atom_1].end();++j){
+ if((*j)!=atom_2){
+ if((*j)<atom_3) dihedrals.insert(Index<4>(*j,atom_1,atom_2,atom_3));
+ else dihedrals.insert(Index<4>(atom_3,atom_2,atom_1,*j));
+ }
+ }
+ for(std::vector<uint>::iterator j = bound_to[atom_3].begin();
+ j!=bound_to[atom_3].end();++j){
+ if((*j)!=atom_2){
+ if((*j)<atom_1) dihedrals.insert(Index<4>(*j,atom_3,atom_2,atom_1));
+ else dihedrals.insert(Index<4>(atom_1,atom_2,atom_3,*j));
+ }
+ }
+ }
+ }
+ //impropers exclusions and cmaps get read from residuetemplates!
+ std::vector<MMInteractionPtr> interaction_list;
+ std::vector<String> interaction_atom_names;
+
+ if(settings->add_impropers){
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetImpropers();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ Index<4> improper_index;
+ for(uint k = 0; k < 4; ++k){
+ improper_index[k] = top->GetAtomIndex(i,interaction_atom_names[k]);
+ }
+ impropers.insert(improper_index);
+ }
+ }
+ }
+
+ if(settings->add_cmaps){
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetCMaps();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ Index<5> cmap_index;
+ for(uint k = 0; k < 5; ++k){
+ cmap_index[k] = top->GetAtomIndex(i,interaction_atom_names[k]);
+ }
+ cmaps.insert(cmap_index);
+ }
+ }
+ }
+
+ if(settings->add_nonbonded && settings->add_exclusions){
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetExclusions();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i,interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i,interaction_atom_names[1]);
+ exclusions.insert(Index<2>(std::min(one,two),std::max(one,two)));
+ }
+ }
+ }
+ if(settings->add_nonbonded){
+
+ //find exclusions and excpetions based on connectivity
+ //add exclusions using previously extracted bonds => 1,2 interactions
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i!=bonds.end(); ++i){
+ exclusions.insert(*i);
+ }
+ //add exclusions using previously extracted angles => 1,3 interactions
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i!=angles.end(); ++i){
+ exclusions.insert(Index<2>((*i)[0],(*i)[2]));
+ }
+ //add exclusions using previously extracted dihedrals => 1,4 interactions
+ for(std::set<Index<4> >::iterator i = dihedrals.begin();
+ i!=dihedrals.end(); ++i){
+ pairs_14.insert(Index<2>((*i)[0],(*i)[3]));
+ }
+
+ //remove all exclusions from the 1,4 interactions
+ for(std::set<Index<2> >::iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ pairs_14.erase(*i);
+ }
+ }
+
+ //we will need this goddamn variable in a lot of places...
+ std::vector<Real> parameters;
+
+
+ //add constraints from building blocks
+ //note, that the constraints are in some cases parametrized.
+ //If there is no constraint distance specified, the actual distance
+ //between the corresponding atoms is taken.
+ //if there are several constraints on the same atom pair,
+ //only the first is added to avoid contradicting constraints
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetConstraints();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i, interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i, interaction_atom_names[1]);
+ Index<2> index(std::min(one,two),std::max(one,two));
+ //we don't want contradicting constraints!
+ if(distance_constraints.find(index) != distance_constraints.end()) continue;
+ distance_constraints.insert(index);
+ Real distance;
+ if((*j)->IsParametrized()){
+ parameters = (*j)->GetParam();
+ distance = parameters[0];
+ }
+ else distance = geom::Distance(atom_list[one].GetPos(),atom_list[two].GetPos())/10;
+ top->AddDistanceConstraint(one,two,distance);
+ }
+ }
+
+ //add distance constrains given the corresponding settings
+ if(settings->constrain_bonds || settings->constrain_hbonds || settings->rigid_water){
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i != bonds.end(); ++i){
+ if(settings->constrain_bonds){
+ if(distance_constraints.find(*i) != distance_constraints.end()) continue;
+ distance_constraints.insert(*i);
+ Real distance;
+ if(settings->ideal_bond_length_constraints){
+ MMInteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ parameters = bond_ptr->GetParam();
+ distance = parameters[0];
+ }
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[1]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[1],distance);
+ continue;
+ }
+ if(settings->constrain_hbonds){
+ //if(atom_elements[(*i)[0]] == "H" || atom_elements[(*i)[1]] == "H"){
+ if(atom_masses[(*i)[0]] < 1.1 || atom_masses[(*i)[1]] < 1.1){
+ if(distance_constraints.find(*i) != distance_constraints.end()) continue;
+ distance_constraints.insert(*i);
+ Real distance;
+ if(settings->ideal_bond_length_constraints){
+ MMInteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ parameters = bond_ptr->GetParam();
+ distance = parameters[0];
+ }
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[1]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[1],distance);
+ continue;
+ }
+ }
+ if(settings->rigid_water){
+ if(residue_names_of_atoms[(*i)[0]] == "SOL" || residue_names_of_atoms[(*i)[1]] == "SOL"){
+ if(distance_constraints.find(*i) != distance_constraints.end()) continue;
+ distance_constraints.insert(*i);
+ Real distance;
+ if(settings->ideal_bond_length_constraints) distance = 0.09572; //OH bond length in water in CHARMM forcefield...
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[1]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[1],distance);
+ continue;
+ }
+ }
+ }
+ }
+
+ //set angle constraints given the corresponding settings
+ std::set<Index<3> > constrained_angles;
+ if(settings->rigid_water){
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i != angles.end(); ++i){
+ if(residue_names_of_atoms[(*i)[0]] == "SOL" || residue_names_of_atoms[(*i)[0]] == "SOL" ||
+ residue_names_of_atoms[(*i)[2]] == "SOL"){
+ //even for ideal_bond_length_constraints, we calculate the ideal angle every time...
+ //could be replaced...
+ Real distance;
+ if(settings->ideal_bond_length_constraints) distance = 0.15139; //HH distance taken from CHARMM
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[2],distance);
+ constrained_angles.insert(*i);
+ }
+ }
+ }
+
+ if(settings->constrain_hangles){
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i != angles.end(); ++i){
+ if(atom_masses[(*i)[0]] < 1.1 && atom_masses[(*i)[2]] < 1.1){
+ //two hydrogens...
+ if(constrained_angles.find(*i) != constrained_angles.end()) continue;
+ Real distance;
+ if(settings->ideal_bond_length_constraints){
+ MMInteractionPtr bond_one = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ MMInteractionPtr bond_two = ff->GetBond(atom_types[(*i)[1]],atom_types[(*i)[2]]);
+ MMInteractionPtr angle = ff->GetAngle(atom_types[(*i)[0]],atom_types[(*i)[1]],atom_types[(*i)[2]]);
+ std::vector<Real> parameters;
+ Real l1,l2,a;
+ parameters = bond_one->GetParam();
+ l1 = parameters[0];
+ parameters = bond_two->GetParam();
+ l2 = parameters[0];
+ parameters = angle->GetParam();
+ a = parameters[0];
+ distance = sqrt(l1*l1+l2*l2-2*l1*l2*cos(a));
+ }
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[2],distance);
+ constrained_angles.insert(*i);
+ continue;
+ }
+
+ if(atom_masses[(*i)[1]] > 15.0 && atom_masses[(*i)[1]] < 17.0){
+ //central atom is an oxygen
+ if(atom_masses[(*i)[0]] < 1.1 || atom_masses[(*i)[2]] < 1.1){
+ //a hydrogen is attached to the oxygen...
+ if(constrained_angles.find(*i) != constrained_angles.end()) continue;
+ Real distance;
+ if(settings->ideal_bond_length_constraints){
+ MMInteractionPtr bond_one = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ MMInteractionPtr bond_two = ff->GetBond(atom_types[(*i)[1]],atom_types[(*i)[2]]);
+ MMInteractionPtr angle = ff->GetAngle(atom_types[(*i)[0]],atom_types[(*i)[1]],atom_types[(*i)[2]]);
+ std::vector<Real> parameters;
+ Real l1,l2,a;
+ parameters = bond_one->GetParam();
+ l1 = parameters[0];
+ parameters = bond_two->GetParam();
+ l2 = parameters[0];
+ parameters = angle->GetParam();
+ a = parameters[0];
+ distance = sqrt(l1*l1+l2*l2-2*l1*l2*cos(a));
+ }
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[2],distance);
+ constrained_angles.insert(*i);
+ continue;
+ }
+ }
+ }
+ }
+
+ //remove all constraints from the bonds and angles
+ for(std::set<Index<2> >::iterator i = distance_constraints.begin();
+ i != distance_constraints.end(); ++i){
+ bonds.erase(*i);
+ }
+
+ for(std::set<Index<3> >::iterator i = constrained_angles.begin();
+ i!= constrained_angles.end(); ++i){
+ angles.erase(*i);
+ }
+
+
+ //the force definitions from the forcefield can be overwritten by parameters
+ //defined in the residue building blocks.
+ //We therefore check which forces have been defined in the building blocks
+ //and don't search them any more in the forcefield forces.
+ std::vector<String> types;
+ if(settings->add_bonds){
+ //handle bonds
+ for(uint i = 0; i < top->GetNumResidues(); ++i){
+ interaction_list = building_blocks[i]->GetBonds();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i, interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i, interaction_atom_names[1]);
+ Index<2> bond_index(std::min(one,two),std::max(one,two));
+ bonds.erase(bond_index);
+ //There are only harmonic bonds supported
+ parameters = (*j)->GetParam();
+ top->AddHarmonicBond(one,two,parameters[0],parameters[1]);
+ }
+ }
+ }
+ //add pointers of bond definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i!=bonds.end(); ++i){
+
+ MMInteractionPtr bond_ptr;
+ try{
+ bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize bond between: " << atom_list[(*i)[0]];
+ ss << " and "<<atom_list[(*i)[1]] << ". ";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ parameters = bond_ptr->GetParam();
+ top->AddHarmonicBond((*i)[0],(*i)[1],parameters[0],parameters[1]);
+ }
+ }
+
+ if(settings->add_angles){
+ //handle angles
+ for(uint i = 0; i < top->GetNumResidues(); ++i){
+ interaction_list = building_blocks[i]->GetAngles();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i, interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i, interaction_atom_names[1]);
+ uint three = top->GetAtomIndex(i, interaction_atom_names[2]);
+ Index<3> angle_index(std::min(one,three),two,std::max(one,three));
+ if(angles.find(angle_index) == angles.end()){
+ std::stringstream ss;
+ ss << "Building block for residue " << res_list[i].GetQualifiedName();
+ ss << " defines angle, that doesn't exist!";
+ throw ost::Error(ss.str());
+ }
+ angles.erase(angle_index);
+ parameters = (*j)->GetParam();
+ switch((*j)->GetFuncType()){
+ case HarmonicAngle:{
+ top->AddHarmonicAngle(angle_index[0],angle_index[1],angle_index[2],
+ parameters[0], parameters[1]);
+ break;
+ }
+ case UreyBradleyAngle:{
+ top->AddUreyBradleyAngle(angle_index[0],angle_index[1],angle_index[2],
+ parameters[0], parameters[1], parameters[2],
+ parameters[3]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed unknown function type for angle interaction!");
+ }
+ }
+ }
+ }
+ }
+ //add pointers of angle definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i!=angles.end(); ++i){
+
+ MMInteractionPtr angle_ptr;
+ try{
+ angle_ptr = ff->GetAngle(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize angle between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << " and " << atom_list[(*i)[2]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ parameters = angle_ptr->GetParam();
+ switch(angle_ptr->GetFuncType()){
+ case HarmonicAngle:{
+ top->AddHarmonicAngle((*i)[0],(*i)[1],(*i)[2],
+ parameters[0],parameters[1]);
+ break;
+ }
+ case UreyBradleyAngle:{
+ top->AddUreyBradleyAngle((*i)[0],(*i)[1],(*i)[2],
+ parameters[0],parameters[1],
+ parameters[2],parameters[3]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed invalid function type for angle interaction!");
+ }
+ }
+ }
+ }
+
+ if(settings->add_dihedrals){
+ //handle dihedrals
+ for(uint i = 0; i < top->GetNumResidues(); ++i){
+ interaction_list = building_blocks[i]->GetDihedrals();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i, interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i, interaction_atom_names[1]);
+ uint three = top->GetAtomIndex(i, interaction_atom_names[2]);
+ uint four = top->GetAtomIndex(i, interaction_atom_names[3]);
+ Index<4> dihedral_index;
+ if(one<four){
+ dihedral_index[0] = one;
+ dihedral_index[1] = two;
+ dihedral_index[2] = three;
+ dihedral_index[3] = four;
+ }
+ else{
+ dihedral_index[0] = four;
+ dihedral_index[1] = three;
+ dihedral_index[2] = two;
+ dihedral_index[3] = one;
+ }
+ if(dihedrals.find(dihedral_index) == dihedrals.end()){
+ std::stringstream ss;
+ ss << "Building block for residue " << res_list[i].GetQualifiedName();
+ ss << "defines dihedral, that doesn't exist!";
+ throw ost::Error(ss.str());
+ }
+ dihedrals.erase(dihedral_index);
+ //only periodic dihedrals are supported...
+ parameters = (*j)->GetParam();
+ top->AddPeriodicDihedral(one,two,three,four,
+ parameters[0],parameters[1],parameters[2]);
+ }
+ }
+ }
+
+ //add pointers of dihedrals definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<4> >::iterator i = dihedrals.begin();
+ i!=dihedrals.end(); ++i){
+
+ std::vector<MMInteractionPtr> dihedral_ptr;
+
+ try{
+ dihedral_ptr = ff->GetDihedrals(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]],
+ atom_types[(*i)[3]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize dihedral between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << ", " << atom_list[(*i)[2]] << " and ";
+ ss << atom_list[(*i)[3]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator j = dihedral_ptr.begin();
+ j != dihedral_ptr.end(); ++j){
+ parameters = (*j)->GetParam();
+ top->AddPeriodicDihedral((*i)[0],(*i)[1],(*i)[2],(*i)[3],
+ parameters[0],parameters[1],parameters[2]);
+ }
+ }
+ }
+
+ if(settings->add_impropers){
+ //handle impropers
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetImpropers();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ //we do not have to care about the ordering, since we extracted the
+ //impropers from the building block => they will have the same ordering
+ //anyway (or at least hopefully ;)
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i, interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i, interaction_atom_names[1]);
+ uint three = top->GetAtomIndex(i, interaction_atom_names[2]);
+ uint four = top->GetAtomIndex(i, interaction_atom_names[3]);
+ Index<4> improper_index(one,two,three,four);
+ impropers.erase(improper_index);
+ parameters = (*j)->GetParam();
+ switch((*j)->GetFuncType()){
+ case PeriodicImproper:{
+ top->AddPeriodicImproper(one,two,three,four,
+ parameters[0],parameters[1],parameters[2]);
+ break;
+ }
+ case HarmonicImproper:{
+ top->AddHarmonicImproper(one,two,three,four,
+ parameters[0],parameters[1]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed invalid function type when adding improper interaction!");
+ }
+ }
+ }
+ }
+ }
+ //add pointers of improper definitions, that are not already parametrized
+ //in the building blocks
+
+ for(std::set<Index<4> >::iterator i = impropers.begin();
+ i!=impropers.end(); ++i){
+
+ std::vector<MMInteractionPtr> improper_ptr;
+
+ try{
+ improper_ptr = ff->GetImpropers(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]],
+ atom_types[(*i)[3]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize improper between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << ", " << atom_list[(*i)[2]] << " and ";
+ ss << atom_list[(*i)[3]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ for(std::vector<MMInteractionPtr>::iterator j = improper_ptr.begin();
+ j != improper_ptr.end(); ++j){
+ parameters = (*j)->GetParam();
+ switch((*j)->GetFuncType()){
+ case PeriodicImproper:{
+ top->AddPeriodicImproper((*i)[0],(*i)[1],(*i)[2],(*i)[3],
+ parameters[0],parameters[1],parameters[2]);
+ break;
+ }
+ case HarmonicImproper:{
+ top->AddHarmonicImproper((*i)[0],(*i)[1],(*i)[2],(*i)[3],
+ parameters[0],parameters[1]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed invalid function type when adding improper interaction!");
+ }
+ }
+ }
+ }
+ }
+
+ if(settings->add_cmaps){
+ //handle cmaps
+ for(uint i = 0; i < top->GetNumResidues(); ++i){
+ interaction_list = building_blocks[i]->GetCMaps();
+ for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ //we do not have to care about the ordering, since we extracted the
+ //cmaps from the building block => they will have the same ordering
+ //anyway
+ interaction_atom_names = (*j)->GetNames();
+ uint one = top->GetAtomIndex(i, interaction_atom_names[0]);
+ uint two = top->GetAtomIndex(i, interaction_atom_names[1]);
+ uint three = top->GetAtomIndex(i, interaction_atom_names[2]);
+ uint four = top->GetAtomIndex(i, interaction_atom_names[3]);
+ uint five = top->GetAtomIndex(i, interaction_atom_names[4]);
+ Index<5> cmap_index(one,two,three,four,five);
+ cmaps.erase(cmap_index);
+ parameters = (*j)->GetParam();
+ int dimension = int(parameters[0]);
+ parameters.erase(parameters.begin());
+ top->AddCMap(cmap_index[0],cmap_index[1],cmap_index[2],cmap_index[3],
+ cmap_index[4],dimension,parameters);
+ }
+ }
+ }
+
+ //add pointers of cmap definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<5> >::iterator i = cmaps.begin();
+ i!=cmaps.end(); ++i){
+
+ MMInteractionPtr cmap_ptr;
+
+ try{
+ cmap_ptr = ff->GetCMap(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]],
+ atom_types[(*i)[3]],
+ atom_types[(*i)[4]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize cmap between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << ", " << atom_list[(*i)[2]] << ", ";
+ ss << atom_list[(*i)[3]] << " and " << atom_list[(*i)[4]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+ parameters = cmap_ptr->GetParam();
+ int dimension = int(parameters[0]);
+ parameters.erase(parameters.begin());
+ top->AddCMap((*i)[0],(*i)[1],(*i)[2],(*i)[3],(*i)[4],dimension,parameters);
+ }
+ }
+
+ if(settings->add_nonbonded){
+
+ MMInteractionPtr lj_interaction;
+ std::vector<Real> sigmas;
+ std::vector<Real> epsilons;
+
+ for(std::vector<String>::iterator i = atom_types.begin();
+ i != atom_types.end(); ++i){
+ lj_interaction = ff->GetLJ(*i);
+ if(!lj_interaction){
+ std::stringstream ss;
+ ss << "Failed to find LJ parametrization for type \""<<*i<<"\"";
+ ss << " in given forcefield!";
+ throw ost::Error(ss.str());
+ }
+ parameters = lj_interaction->GetParam();
+ sigmas.push_back(parameters[0]);
+ epsilons.push_back(parameters[1]);
+ }
+ top->SetSigmas(sigmas);
+ top->SetEpsilons(epsilons);
+ //take care of the 1-4 interactions
+ for(std::set<Index<2> >::iterator i = pairs_14.begin();
+ i != pairs_14.end(); ++i){
+ //we can be sure, that the parameters are valid, since we found all single
+ //parameters. The forcefield can therefore build the new parametrization with
+ //the combination rules... Except: gen_pairs_ is set to no, but then an error
+ // is thrown anyway
+ lj_interaction = ff->GetLJ(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ true);
+ parameters = lj_interaction->GetParam();
+ top->AddLJPair((*i)[0],(*i)[1],parameters[0],parameters[1]);
+ }
+ //take care of the exclusions
+ for(std::set<Index<2> >::iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ top->AddExclusion((*i)[0],(*i)[1]);
+ }
+ }
+ if(settings->add_gbsa){
+ std::vector<Real> radii;
+ std::vector<Real> scaling;
+ for(uint i = 0; i < top->GetNumAtoms(); ++i){
+ MMInteractionPtr gbsa_ptr = ff->GetImplicitGenborn(atom_types[i]);
+ if(!gbsa_ptr){
+ std::stringstream ss;
+ ss << "Structure contains atom of type " << types[i] << " which is not";
+ ss << "parametrized in the forcefield!"<<std::endl;
+ throw ost::Error(ss.str());
+ }
+ parameters = gbsa_ptr->GetParam();
+ radii.push_back(parameters[0]);
+ scaling.push_back(parameters[1]);
+ }
+ top->SetGBSARadii(radii);
+ top->SetOBCScalings(scaling);
+ }
+
+ top->SetFudgeQQ(ff->GetFudgeQQ());
+ top->SetFudgeLJ(ff->GetFudgeLJ());
+
+
+ return top;
+
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/topology_creator.hh b/modules/mol/mm/src/topology_creator.hh
new file mode 100644
index 0000000000000000000000000000000000000000..1d719a4144b7a3571e8bb2e2764bf4327a2d06e2
--- /dev/null
+++ b/modules/mol/mm/src/topology_creator.hh
@@ -0,0 +1,40 @@
+#ifndef OST_TOPOLOGY_CREATOR_HH
+#define OST_TOPOLOGY_CREATOR_HH
+
+#include <OpenMM.h>
+
+#include <vector>
+#include <map>
+#include <set>
+#include <math.h>
+
+#include <ost/message.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/mm_modeller.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/topology.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class TopologyCreator;
+typedef boost::shared_ptr<TopologyCreator> TopologyCreatorPtr;
+
+class TopologyCreator {
+public:
+ static TopologyPtr Create(const ost::mol::EntityHandle& ent,
+ const MMSettingsPtr settings);
+
+};
+
+
+}}}//ns
+
+#endif
\ No newline at end of file
diff --git a/modules/mol/mm/tests/1CRN.pdb b/modules/mol/mm/tests/1CRN.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..13ca618d438ae60a55a8ce1c532cd23bf545e200
--- /dev/null
+++ b/modules/mol/mm/tests/1CRN.pdb
@@ -0,0 +1,329 @@
+ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
+ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
+ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
+ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
+ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C
+ATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N
+ATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C
+ATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C
+ATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O
+ATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C
+ATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C
+ATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C
+ATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S
+ATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C
+ATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C
+ATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S
+ATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C
+ATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C
+ATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C
+ATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N
+ATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C
+ATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C
+ATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O
+ATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C
+ATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O
+ATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C
+ATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C
+ATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C
+ATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C
+ATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C
+ATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C
+ATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C
+ATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C
+ATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C
+ATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C
+ATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C
+ATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N
+ATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N
+ATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C
+ATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C
+ATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O
+ATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C
+ATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O
+ATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C
+ATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C
+ATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N
+ATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N
+ATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C
+ATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C
+ATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C
+ATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C
+ATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C
+ATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C
+ATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N
+ATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C
+ATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C
+ATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C
+ATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C
+ATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C
+ATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O
+ATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S
+ATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C
+ATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C
+ATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N
+ATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C
+ATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C
+ATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C
+ATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C
+ATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C
+ATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C
+ATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C
+ATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C
+ATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O
+ATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N
+ATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C
+ATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C
+ATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O
+ATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C
+ATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C
+ATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C
+ATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C
+ATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C
+ATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C
+ATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C
+ATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
+ATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C
+ATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C
+ATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C
+ATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N
+ATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C
+ATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C
+ATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O
+ATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C
+ATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C
+ATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C
+ATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C
+ATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N
+ATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C
+ATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C
+ATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O
+ATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C
+ATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S
+ATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N
+ATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C
+ATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C
+ATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O
+ATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C
+ATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N
+ATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C
+ATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C
+ATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O
+ATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C
+ATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O
+ATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C
+ATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N
+ATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C
+ATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C
+ATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O
+ATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C
+ATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C
+ATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C
+ATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C
+ATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C
+ATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C
+ATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C
+ATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O
+ATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N
+ATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C
+ATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C
+ATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O
+ATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C
+ATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O
+ATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C
+ATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N
+ATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C
+ATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C
+ATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O
+ATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C
+ATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C
+ATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S
+ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
+ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
+ATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C
+ATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C
+ATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C
+ATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O
+ATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C
+ATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C
+ATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C
+ATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C
+ATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C
+ATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C
+ATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C
+ATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N
+ATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C
+ATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C
+ATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O
+ATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C
+ATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C
+ATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C
+ATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N
+ATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C
+ATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C
+ATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O
+ATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C
+ATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C
+ATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C
+ATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S
+ATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C
+ATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C
+ATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C
+ATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C
+ATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C
+ATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O
+ATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C
+ATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C
+ATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O
+ATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C
+ATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C
+ATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O
+ATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C
+ATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C
+ATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C
+ATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C
+ATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C
+ATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O
+TER 328 ASN A 46
+END
diff --git a/modules/mol/mm/tests/AMBER03.dat b/modules/mol/mm/tests/AMBER03.dat
new file mode 100644
index 0000000000000000000000000000000000000000..69e7d22171f447229ce354d731773876fcba7bd4
Binary files /dev/null and b/modules/mol/mm/tests/AMBER03.dat differ
diff --git a/modules/mol/mm/tests/CHARMM27.dat b/modules/mol/mm/tests/CHARMM27.dat
new file mode 100644
index 0000000000000000000000000000000000000000..9a9459fb0c9882ff4db05a70560389124a73f2e6
Binary files /dev/null and b/modules/mol/mm/tests/CHARMM27.dat differ
diff --git a/modules/mol/mm/tests/CMakeLists.txt b/modules/mol/mm/tests/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99f2c4575dbc77849567d5d9e08a0497dfc9118d
--- /dev/null
+++ b/modules/mol/mm/tests/CMakeLists.txt
@@ -0,0 +1,12 @@
+set(OST_MOL_MM_UNIT_TESTS
+ test_interaction.cc
+ test_block.cc
+ test_block_modifiers.cc
+ test_topology.cc
+ test_forcefield.cc
+ test_simulation.cc
+ tests.cc
+)
+
+ost_unittest(MODULE mol_mm SOURCES "${OST_MOL_MM_UNIT_TESTS}")
+
diff --git a/modules/mol/mm/tests/test.ff b/modules/mol/mm/tests/test.ff
new file mode 100644
index 0000000000000000000000000000000000000000..a9dfffe15ebe5915d3daba9c199e01cef5645e0c
Binary files /dev/null and b/modules/mol/mm/tests/test.ff differ
diff --git a/modules/mol/mm/tests/test_block.cc b/modules/mol/mm/tests/test_block.cc
new file mode 100644
index 0000000000000000000000000000000000000000..45732b4131e3d4732ef2cba57169ee8ed294ccb8
--- /dev/null
+++ b/modules/mol/mm/tests/test_block.cc
@@ -0,0 +1,211 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+
+
+#include <ost/message.hh>
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_block_basics)
+{
+ BuildingBlock block = BuildingBlock();
+ block.AddAtom("A","a",0.5);
+ block.AddAtom("B","b",1.0);
+ MMInteractionPtr bond(new MMInteraction(HarmonicBond));
+ std::vector<String> names;
+ names.push_back("A");
+ names.push_back("B");
+ bond->SetNames(names);
+ block.AddBond(bond);
+ BOOST_CHECK_THROW(block.GetCharge("C"),ost::Error);
+ BOOST_CHECK_THROW(block.GetType("C"),ost::Error);
+ BOOST_CHECK(block.GetCharge("A") == 0.5);
+ BOOST_CHECK(block.GetType("A") == "a");
+ block.ReplaceAtom("A","X","x",42.0);
+ BOOST_CHECK(block.GetType("X") == "x");
+ BOOST_CHECK(block.GetCharge("X")==42.0);
+ BOOST_CHECK(block.GetAtoms().size() == 2);
+ std::vector<MMInteractionPtr> bonds = block.GetBonds();
+ BOOST_CHECK(bonds[0]->HasName("X"));
+ block.RemoveAtom("X");
+ BOOST_CHECK_THROW(block.GetType("X"),ost::Error);
+ BOOST_CHECK_NO_THROW(block.GetType("B"));
+ BOOST_CHECK(block.GetAtoms().size()==1);
+ BOOST_CHECK(block.GetCharges().size()==1);
+ BOOST_CHECK(block.GetBonds().size()==0);
+ std::vector<Real> param_one,param_two;
+ param_one.push_back(1.0);
+ param_one.push_back(1.0);
+ param_two.push_back(2.0);
+ param_two.push_back(2.0);
+ MMInteractionPtr bond_one(new MMInteraction(HarmonicBond));
+ MMInteractionPtr bond_two(new MMInteraction(HarmonicBond));
+ bond_one->SetNames(names);
+ bond_one->SetParam(param_one);
+ bond_two->SetNames(names);
+ bond_two->SetParam(param_two);
+ block.AddBond(bond_one);
+ BOOST_CHECK(block.GetBonds()[0]->GetParam() == param_one);
+ block.AddBond(bond_two,true);
+ BOOST_CHECK(block.GetBonds()[0]->GetParam() == param_two);
+ block.RemoveAtom("A");
+
+ names[0] = "-A";
+ bond_one->SetNames(names);
+ names[0] = "A";
+ names[1] = "+B";
+ bond_two->SetNames(names);
+ block.AddBond(bond_one);
+ block.AddBond(bond_two);
+ BOOST_CHECK(block.GetBonds().size() == 2);
+ block.RemoveInteractionsToPrev();
+ BOOST_CHECK(block.GetBonds().size() == 1);
+ BOOST_CHECK(block.GetBonds()[0]->HasName("+B"));
+ block.RemoveInteractionsToNext();
+ BOOST_CHECK(block.GetBonds().size() == 0);
+}
+
+BOOST_AUTO_TEST_CASE(test_connect)
+{
+ ost::mol::EntityHandle e = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(1,1,1))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(2,2,2))
+ .Atom("B",geom::Vec3(3,3,3))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(4,4,4))
+ .Atom("B",geom::Vec3(5,5,5));
+
+ ost::mol::XCSEditor ed = e.EditXCS();
+ ed.DeleteBonds(e.GetBondList());
+
+ BuildingBlock block = BuildingBlock();
+ block.AddAtom("A","a",0.0);
+ block.AddAtom("B","b",0.0);
+
+ MMInteractionPtr bond_one(new MMInteraction(HarmonicBond));
+ MMInteractionPtr bond_two(new MMInteraction(HarmonicBond));
+ MMInteractionPtr bond_three(new MMInteraction(HarmonicBond));
+ std::vector<String> two_string;
+ two_string.push_back("A");
+ two_string.push_back("B");
+ bond_one->SetNames(two_string);
+ two_string[0] = "-B";
+ two_string[1] = "A";
+ bond_two->SetNames(two_string);
+ two_string[0] = "B";
+ two_string[1] = "+A";
+ bond_three->SetNames(two_string);
+ block.AddBond(bond_one);
+ block.AddBond(bond_two);
+ block.AddBond(bond_three);
+
+ ost::mol::ResidueHandleList res_list = e.GetResidueList();
+ ost::mol::AtomHandleList atoms_one = res_list[0].GetAtomList();
+ ost::mol::AtomHandleList atoms_two = res_list[1].GetAtomList();
+ ost::mol::AtomHandleList atoms_three = res_list[2].GetAtomList();
+
+ block.Connect(res_list[1],ed);
+ BOOST_CHECK(ost::mol::BondExists(atoms_one[1],atoms_two[0]));
+ BOOST_CHECK(ost::mol::BondExists(atoms_two[0],atoms_two[1]));
+ BOOST_CHECK(ost::mol::BondExists(atoms_two[1],atoms_three[0]));
+
+ ed.DeleteBonds(e.GetBondList());
+
+ BOOST_CHECK_THROW(block.Connect(res_list[0],ed),ost::Error);
+ BOOST_CHECK_THROW(block.Connect(res_list[2],ed),ost::Error);
+
+ MMInteractionPtr bond_four(new MMInteraction(HarmonicBond));
+ two_string[1] = "X";
+ bond_four->SetNames(two_string);
+ block.AddBond(bond_four);
+
+ BOOST_CHECK_THROW(block.Connect(res_list[1],ed),ost::Error);
+}
+
+BOOST_AUTO_TEST_CASE(test_match)
+{
+
+ ost::mol::EntityHandle e = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(1,1,1))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(2,2,2))
+ .Atom("B",geom::Vec3(3,3,3))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(4,4,4))
+ .Atom("B",geom::Vec3(5,5,5))
+ .Residue("FOUR")
+ .Atom("A",geom::Vec3(6,6,6))
+ .Atom("B",geom::Vec3(7,7,7));
+
+ ost::mol::ResidueHandleList res_list = e.GetResidueList();
+ ost::mol::XCSEditor ed = e.EditXCS();
+
+ ed.Connect(res_list[0].FindAtom("A"),res_list[0].FindAtom("B"));
+ ed.Connect(res_list[0].FindAtom("B"),res_list[1].FindAtom("A"));
+ ed.Connect(res_list[1].FindAtom("A"),res_list[1].FindAtom("B"));
+ ed.Connect(res_list[1].FindAtom("B"),res_list[2].FindAtom("A"));
+ ed.Connect(res_list[2].FindAtom("A"),res_list[2].FindAtom("B"));
+ //ed.Connect(atoms_two[1],atoms_four[1]);
+
+ BuildingBlock block = BuildingBlock();
+ String info_string;
+ BOOST_CHECK(!block.Match(res_list[1],true,info_string));
+
+ block.AddAtom("A","a",0.0);
+ block.AddAtom("B","b",0.0);
+
+ BOOST_CHECK(!block.Match(res_list[1],true,info_string));
+
+ MMInteractionPtr bond_one(new MMInteraction(HarmonicBond));
+ MMInteractionPtr bond_two(new MMInteraction(HarmonicBond));
+ MMInteractionPtr bond_three(new MMInteraction(HarmonicBond));
+
+ std::vector<String> names_one;
+ names_one.push_back("A");
+ names_one.push_back("B");
+ std::vector<String> names_two;
+ names_two.push_back("-B");
+ names_two.push_back("A");
+ std::vector<String> names_three;
+ names_three.push_back("B");
+ names_three.push_back("+A");
+
+ bond_one->SetNames(names_one);
+ bond_two->SetNames(names_two);
+ bond_three->SetNames(names_three);
+
+ block.AddBond(bond_one);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+
+ block.AddBond(bond_two);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+
+ block.AddBond(bond_three);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+
+ //let's remove the central bond and replace it with a constraint
+
+ block.RemoveAtom("A");
+ block.AddAtom("A","a",0.0);
+ MMInteractionPtr constraint(new MMInteraction(DistanceConstraint));
+ constraint->SetNames(names_one);
+ BOOST_CHECK(!block.Match(res_list[1],true,info_string));
+ block.AddConstraint(constraint);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_block_modifiers.cc b/modules/mol/mm/tests/test_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..901ae4c6fa8e30a26f632a97475d7da6a50f820b
--- /dev/null
+++ b/modules/mol/mm/tests/test_block_modifiers.cc
@@ -0,0 +1,97 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+
+#include <ost/message.hh>
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_gromacs_block_modifier_basics){
+
+ GromacsBlockModifier mod;
+
+ //let's create some interactions
+ MMInteractionPtr harmonic_bond(new MMInteraction(HarmonicBond));
+ MMInteractionPtr urey_bradley_angle(new MMInteraction(UreyBradleyAngle));
+ MMInteractionPtr harmonic_angle(new MMInteraction(HarmonicAngle));
+ MMInteractionPtr periodic_dihedral(new MMInteraction(PeriodicDihedral));
+ MMInteractionPtr periodic_improper(new MMInteraction(PeriodicImproper));
+ MMInteractionPtr harmonic_improper(new MMInteraction(HarmonicImproper));
+ MMInteractionPtr cmap(new MMInteraction(CMap));
+
+ //check whether error gets thrown, when names of interactions are not set
+ BOOST_CHECK_THROW(mod.AddBond(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(mod.AddAngle(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(mod.AddDihedral(periodic_dihedral),ost::Error);
+ BOOST_CHECK_THROW(mod.AddImproper(periodic_improper),ost::Error);
+ BOOST_CHECK_THROW(mod.AddCMap(cmap),ost::Error);
+
+ std::vector<String> two_string, three_string, four_string, five_string;
+
+ two_string.push_back("one");
+ three_string.push_back("one");
+ four_string.push_back("one");
+ five_string.push_back("one");
+
+ two_string.push_back("two");
+ three_string.push_back("two");
+ four_string.push_back("two");
+ five_string.push_back("two");
+
+ three_string.push_back("three");
+ four_string.push_back("three");
+ five_string.push_back("three");
+
+ four_string.push_back("four");
+ five_string.push_back("four");
+
+ five_string.push_back("five");
+
+ harmonic_bond->SetNames(two_string);
+ harmonic_angle->SetNames(three_string);
+ urey_bradley_angle->SetNames(three_string);
+ periodic_dihedral->SetNames(four_string);
+ periodic_improper->SetNames(four_string);
+ harmonic_improper->SetNames(four_string);
+ cmap->SetNames(five_string);
+
+ BOOST_CHECK_NO_THROW(mod.AddBond(harmonic_bond));
+ BOOST_CHECK_NO_THROW(mod.AddAngle(harmonic_angle));
+ BOOST_CHECK_NO_THROW(mod.AddAngle(urey_bradley_angle));
+ BOOST_CHECK_NO_THROW(mod.AddDihedral(periodic_dihedral));
+ BOOST_CHECK_NO_THROW(mod.AddImproper(periodic_improper));
+ BOOST_CHECK_NO_THROW(mod.AddImproper(harmonic_improper));
+ BOOST_CHECK_NO_THROW(mod.AddCMap(cmap));
+
+ //check whether error get thrown when wrong interactions get added
+
+ BOOST_CHECK_THROW(mod.AddBond(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(mod.AddAngle(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(mod.AddDihedral(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(mod.AddImproper(periodic_dihedral),ost::Error);
+ BOOST_CHECK_THROW(mod.AddCMap(periodic_improper),ost::Error);
+
+
+
+
+
+
+
+
+
+
+
+}
+
+
+
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_forcefield.cc b/modules/mol/mm/tests/test_forcefield.cc
new file mode 100644
index 0000000000000000000000000000000000000000..a2fec9865249a2f2ba9a629352516824ad3542e1
--- /dev/null
+++ b/modules/mol/mm/tests/test_forcefield.cc
@@ -0,0 +1,271 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+#include <ost/message.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_forcefield_basics){
+ Forcefield ff;
+
+ //if a building block doesn't exist, it should throw an error
+ //this is not the case for hydrogen constructors and block modifiers
+ BOOST_CHECK_THROW(ff.GetBuildingBlock("IDoNotExist"),ost::Error);
+
+ //add some atom types
+ ff.AddMass("one",1.0);
+ ff.AddMass("two",2.0);
+ ff.AddMass("three",3.0);
+ ff.AddMass("four",4.0);
+ ff.AddMass("five",5.0);
+
+ BOOST_CHECK_THROW(ff.GetBond("one","two"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetAngle("one","two","three"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetDihedrals("one","two","three","four"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetImpropers("one","two","three","four"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetCMap("one","two","three","four","five"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetImplicitGenborn("one"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetLJ("one"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetLJ("one","two"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetConstraint("one","two"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetMass("i_do_not_exist"),ost::Error);
+
+ //let's add some interactions
+ std::vector<String> one_string, two_string, three_string, four_string, five_string;
+ std::vector<Real> one_real, two_real, three_real, four_real, five_real;
+
+ one_string.push_back("one");
+ two_string.push_back("one");
+ three_string.push_back("one");
+ four_string.push_back("one");
+ five_string.push_back("one");
+
+ two_string.push_back("two");
+ three_string.push_back("two");
+ four_string.push_back("two");
+ five_string.push_back("two");
+
+ three_string.push_back("three");
+ four_string.push_back("three");
+ five_string.push_back("three");
+
+ four_string.push_back("four");
+ five_string.push_back("four");
+
+ five_string.push_back("five");
+
+
+ one_real.push_back(1.0);
+ two_real.push_back(1.0);
+ three_real.push_back(1.0);
+ four_real.push_back(1.0);
+ five_real.push_back(1.0);
+
+ two_real.push_back(2.0);
+ three_real.push_back(2.0);
+ four_real.push_back(2.0);
+ five_real.push_back(2.0);
+
+ three_real.push_back(3.0);
+ four_real.push_back(3.0);
+ five_real.push_back(3.0);
+
+ four_real.push_back(4.0);
+ five_real.push_back(4.0);
+
+ five_real.push_back(5.0);
+
+
+ MMInteractionPtr harmonic_bond(new MMInteraction(HarmonicBond));
+ MMInteractionPtr urey_bradley_angle(new MMInteraction(UreyBradleyAngle));
+ MMInteractionPtr harmonic_angle(new MMInteraction(HarmonicAngle));
+ MMInteractionPtr periodic_dihedral(new MMInteraction(PeriodicDihedral));
+ MMInteractionPtr periodic_improper(new MMInteraction(PeriodicImproper));
+ MMInteractionPtr harmonic_improper(new MMInteraction(HarmonicImproper));
+ MMInteractionPtr cmap(new MMInteraction(CMap));
+ MMInteractionPtr lj(new MMInteraction(LJ));
+ MMInteractionPtr lj_pair(new MMInteraction(LJPair));
+ MMInteractionPtr gbsa(new MMInteraction(GBSA));
+ MMInteractionPtr distance_constraint(new MMInteraction(DistanceConstraint));
+
+
+ //check whether errors get thrown when incorrectly parametrized interactions are added
+ BOOST_CHECK_THROW(ff.AddBond(harmonic_bond),ost::Error);
+ harmonic_bond->SetTypes(two_string);
+ BOOST_CHECK_THROW(ff.AddBond(harmonic_bond),ost::Error);
+ harmonic_angle->SetParam(two_real);
+ BOOST_CHECK_THROW(ff.AddAngle(harmonic_angle),ost::Error);
+ harmonic_bond->SetParam(two_real);
+ BOOST_CHECK_NO_THROW(ff.AddBond(harmonic_bond));
+ harmonic_angle->SetTypes(three_string);
+
+ //parametrize the rest
+ urey_bradley_angle->SetTypes(three_string);
+ urey_bradley_angle->SetParam(four_real);
+ periodic_dihedral->SetTypes(four_string);
+ periodic_dihedral->SetParam(three_real);
+ periodic_improper->SetTypes(four_string);
+ periodic_improper->SetParam(three_real);
+ harmonic_improper->SetTypes(four_string);
+ harmonic_improper->SetParam(two_real);
+ std::vector<Real> cmap_param = five_real;
+ cmap_param[0] = 2.0;
+ cmap->SetTypes(five_string);
+ cmap->SetParam(cmap_param);
+ lj->SetTypes(one_string);
+ lj->SetParam(two_real);
+ lj_pair->SetTypes(two_string);
+ lj_pair->SetParam(two_real);
+ gbsa->SetTypes(one_string);
+ gbsa->SetParam(two_real);
+ distance_constraint->SetTypes(two_string);
+ distance_constraint->SetParam(one_real);
+
+ //check whether errors get thrown when wrong interactions get added
+
+ BOOST_CHECK_THROW(ff.AddBond(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddAngle(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(ff.AddDihedral(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddImproper(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddCMap(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddImplicitGenborn(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddLJ(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddLJPair(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddConstraint(harmonic_angle),ost::Error);
+
+ BOOST_CHECK_NO_THROW(ff.AddBond(harmonic_bond));
+ BOOST_CHECK_NO_THROW(ff.AddAngle(harmonic_angle));
+ BOOST_CHECK_NO_THROW(ff.AddDihedral(periodic_dihedral));
+ BOOST_CHECK_NO_THROW(ff.AddImproper(periodic_improper));
+ BOOST_CHECK_NO_THROW(ff.AddImproper(harmonic_improper));
+ BOOST_CHECK_NO_THROW(ff.AddCMap(cmap));
+ BOOST_CHECK_NO_THROW(ff.AddImplicitGenborn(gbsa));
+ BOOST_CHECK_NO_THROW(ff.AddLJ(lj));
+ BOOST_CHECK_NO_THROW(ff.AddLJPair(lj_pair));
+ BOOST_CHECK_NO_THROW(ff.AddConstraint(distance_constraint));
+
+
+ //add a building block
+ BuildingBlockPtr block(new BuildingBlock);
+ block->AddAtom("a","one",0.5);
+ block->AddAtom("b","two",1.0);
+ ff.AddBuildingBlock("im_so_sexy",block);
+
+ //add block modifier
+ BlockModifierPtr modifier(new GromacsBlockModifier);
+ ff.AddBlockModifier("el_modificator",modifier);
+
+ //add hydrogen constructor
+ HydrogenConstructorPtr hydrogen_constructor(new GromacsHydrogenConstructor);
+ ff.AddHydrogenConstructor("death_metal",hydrogen_constructor);
+
+ //add some renaming rules
+ ff.AddResidueRenamingRule("im_so_sexy","even_sexier","sexy_n","sexy_c","sexy_two");
+ ff.AddAtomRenamingRule("even_sexier","a","z");
+ ff.AddAtomRenamingRule("sexy_two","a","z");
+
+ //save and load it again, before we check parameters
+ ff.Save("test.ff");
+ ForcefieldPtr loaded_ff = Forcefield::Load("test.ff");
+
+
+ //check the parameters
+ BOOST_CHECK(loaded_ff->GetBond("one","two")->GetParam() == two_real);
+ BOOST_CHECK(loaded_ff->GetBond("two","one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetAngle("one","two","three")->GetParam() == two_real);
+ BOOST_CHECK(loaded_ff->GetAngle("three","two","one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetDihedrals("one","two","three","four")[0]->GetParam() == three_real);
+ BOOST_CHECK(loaded_ff->GetDihedrals("four","three","two","one")[0]->GetParam() == three_real);
+
+ BOOST_CHECK(loaded_ff->GetImpropers("one","two","three","four")[0]->GetParam() == three_real);
+ BOOST_CHECK(loaded_ff->GetImpropers("four","three","two","one")[0]->GetParam() == three_real);
+
+ BOOST_CHECK(loaded_ff->GetDihedrals("one","two","three","four")[0]->GetParam() == three_real);
+ BOOST_CHECK(loaded_ff->GetDihedrals("four","three","two","one")[0]->GetParam() == three_real);
+
+ BOOST_CHECK(loaded_ff->GetCMap("one","two","three","four","five")->GetParam() == cmap_param);
+ //cmaps are directional...
+ BOOST_CHECK_THROW(loaded_ff->GetCMap("five","four","three","two","one"),ost::Error);
+
+ BOOST_CHECK(loaded_ff->GetImplicitGenborn("one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetLJ("one","two",true)->GetParam() == two_real);
+ BOOST_CHECK(loaded_ff->GetLJ("two","one",true)->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetLJ("one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetConstraint("one","two")->GetParam() == one_real);
+ BOOST_CHECK(loaded_ff->GetConstraint("two","one")->GetParam() == one_real);
+
+ BOOST_CHECK(loaded_ff->GetMass("two") == 2.0);
+
+ BOOST_CHECK(loaded_ff->GetAtomType("im_so_sexy","a") == "one");
+
+ //check whether the modifiers are still there
+ BOOST_CHECK(loaded_ff->GetHydrogenConstructor("death_metal"));
+ BOOST_CHECK(loaded_ff->GetBlockModifier("el_modificator"));
+
+
+ //check the renaming stuff
+
+
+ ost::mol::EntityHandle new_ent = ost::mol::Builder()
+ .Chain("A")
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(0,0,0))
+ .Atom("b",geom::Vec3(1,1,1))
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(2,2,2))
+ .Atom("b",geom::Vec3(3,3,3))
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(4,4,4))
+ .Atom("b",geom::Vec3(5,5,5));
+
+ ost::mol::XCSEditor ed = new_ent.EditXCS();
+
+
+ loaded_ff->AssignFFSpecificNames(new_ent);
+ ost::mol::ResidueHandleList res_list = new_ent.GetResidueList();
+ ost::mol::AtomHandleList atom_list = new_ent.GetAtomList();
+
+ BOOST_CHECK(res_list[0].GetName() == "sexy_n");
+ BOOST_CHECK(res_list[1].GetName() == "even_sexier");
+ BOOST_CHECK(res_list[2].GetName() == "sexy_c");
+ BOOST_CHECK(atom_list[2].GetName() == "z");
+
+ loaded_ff->AssignFFSpecificNames(new_ent,true);
+
+ BOOST_CHECK(res_list[0].GetName() == "im_so_sexy");
+ BOOST_CHECK(res_list[1].GetName() == "im_so_sexy");
+ BOOST_CHECK(res_list[2].GetName() == "im_so_sexy");
+ BOOST_CHECK(atom_list[2].GetName() == "a");
+
+ ost::mol::EntityHandle new_ent_two = ost::mol::Builder()
+ .Chain("A")
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(0,0,0))
+ .Atom("b",geom::Vec3(1,1,1));
+
+ loaded_ff->AssignFFSpecificNames(new_ent_two);
+ res_list = new_ent_two.GetResidueList();
+ atom_list = new_ent_two.GetAtomList();
+ BOOST_CHECK(res_list[0].GetName() == "sexy_two");
+ BOOST_CHECK(atom_list[0].GetName() == "z");
+ loaded_ff->AssignFFSpecificNames(new_ent_two,true);
+ BOOST_CHECK(res_list[0].GetName() == "im_so_sexy");
+ BOOST_CHECK(atom_list[0].GetName() == "a");
+
+}
+
+BOOST_AUTO_TEST_SUITE_END();
\ No newline at end of file
diff --git a/modules/mol/mm/tests/test_interaction.cc b/modules/mol/mm/tests/test_interaction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..b30080e8c0e924efbe102c3ecd0389bc2489dcc7
--- /dev/null
+++ b/modules/mol/mm/tests/test_interaction.cc
@@ -0,0 +1,273 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/builder.hh>
+
+#include <ost/message.hh>
+
+using namespace ost::mol::mm;
+
+
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_set_stuff)
+{
+ MMInteraction harmonic_bond = MMInteraction(HarmonicBond);
+ MMInteraction harmonic_angle = MMInteraction(HarmonicAngle);
+ MMInteraction urey_bradley = MMInteraction(UreyBradleyAngle);
+ MMInteraction periodic_dihedral = MMInteraction(PeriodicDihedral);
+ MMInteraction periodic_improper = MMInteraction(PeriodicImproper);
+ MMInteraction harmonic_improper = MMInteraction(HarmonicImproper);
+ MMInteraction cmap = MMInteraction(CMap);
+ MMInteraction lj = MMInteraction(LJ);
+ MMInteraction lj_pair = MMInteraction(LJPair);
+ MMInteraction gbsa = MMInteraction(GBSA);
+ MMInteraction distance_constraint = MMInteraction(DistanceConstraint);
+ MMInteraction exclusion = MMInteraction(Exclusion);
+ MMInteraction harmonic_distance_restraint = MMInteraction(HarmonicDistanceRestraint);
+ MMInteraction harmonic_position_restraint = MMInteraction(HarmonicPositionRestraint);
+
+ //std::vector<String> one_string, two_string, three_string, four_string, five_string;
+ //std::vector<Real> one_real, two_real, three_real, four_real, five_real, zero_real;
+
+ std::vector<Real> one_real(1);
+ std::vector<Real> two_real(2);
+ std::vector<Real> three_real(3);
+ std::vector<Real> four_real(4);
+ std::vector<Real> five_real(5);
+ std::vector<Real> seven_real(7);
+ std::vector<Real> zero_real(0);
+
+ std::vector<String> one_string(1);
+ std::vector<String> two_string(2);
+ std::vector<String> three_string(3);
+ std::vector<String> four_string(4);
+ std::vector<String> five_string(5);
+
+
+ BOOST_CHECK(!harmonic_bond.IsParametrized());
+
+ BOOST_CHECK_THROW(harmonic_bond.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_angle.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(urey_bradley.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_dihedral.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_improper.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_improper.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(cmap.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(lj.SetNames(two_string),ost::Error);
+ BOOST_CHECK_THROW(lj_pair.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(gbsa.SetNames(two_string),ost::Error);
+ BOOST_CHECK_THROW(distance_constraint.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(exclusion.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_distance_restraint.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_position_restraint.SetNames(two_string),ost::Error);
+
+
+ BOOST_CHECK_THROW(harmonic_bond.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_angle.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(urey_bradley.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_dihedral.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_improper.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_improper.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(cmap.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(lj.SetTypes(two_string),ost::Error);
+ BOOST_CHECK_THROW(lj_pair.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(gbsa.SetTypes(two_string),ost::Error);
+ BOOST_CHECK_THROW(distance_constraint.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(exclusion.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_distance_restraint.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_position_restraint.SetTypes(two_string),ost::Error);
+
+ BOOST_CHECK_THROW(harmonic_bond.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_angle.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(urey_bradley.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(periodic_dihedral.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(periodic_improper.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_improper.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(cmap.SetParam(two_real),ost::Error);
+ BOOST_CHECK_THROW(lj.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(lj_pair.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(gbsa.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(distance_constraint.SetParam(two_real),ost::Error);
+ BOOST_CHECK_THROW(exclusion.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_distance_restraint.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_position_restraint.SetParam(one_real),ost::Error);
+
+
+
+ BOOST_CHECK_NO_THROW(harmonic_bond.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_angle.SetNames(three_string));
+ BOOST_CHECK_NO_THROW(urey_bradley.SetNames(three_string));
+ BOOST_CHECK_NO_THROW(periodic_dihedral.SetNames(four_string));
+ BOOST_CHECK_NO_THROW(periodic_improper.SetNames(four_string));
+ BOOST_CHECK_NO_THROW(harmonic_improper.SetNames(four_string));
+ BOOST_CHECK_NO_THROW(cmap.SetNames(five_string));
+ BOOST_CHECK_NO_THROW(lj.SetNames(one_string));
+ BOOST_CHECK_NO_THROW(lj_pair.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(gbsa.SetNames(one_string));
+ BOOST_CHECK_NO_THROW(distance_constraint.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(exclusion.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetNames(one_string));
+
+
+ BOOST_CHECK_NO_THROW(harmonic_bond.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_angle.SetTypes(three_string));
+ BOOST_CHECK_NO_THROW(urey_bradley.SetTypes(three_string));
+ BOOST_CHECK_NO_THROW(periodic_dihedral.SetTypes(four_string));
+ BOOST_CHECK_NO_THROW(periodic_improper.SetTypes(four_string));
+ BOOST_CHECK_NO_THROW(harmonic_improper.SetTypes(four_string));
+ BOOST_CHECK_NO_THROW(cmap.SetTypes(five_string));
+ BOOST_CHECK_NO_THROW(lj.SetTypes(one_string));
+ BOOST_CHECK_NO_THROW(lj_pair.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(gbsa.SetTypes(one_string));
+ BOOST_CHECK_NO_THROW(distance_constraint.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(exclusion.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetTypes(one_string));
+
+ BOOST_CHECK_NO_THROW(harmonic_bond.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(harmonic_angle.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(urey_bradley.SetParam(four_real));
+ BOOST_CHECK_NO_THROW(periodic_dihedral.SetParam(three_real));
+ BOOST_CHECK_NO_THROW(periodic_improper.SetParam(three_real));
+ BOOST_CHECK_NO_THROW(harmonic_improper.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(lj.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(lj_pair.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(gbsa.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(distance_constraint.SetParam(one_real));
+ BOOST_CHECK_NO_THROW(exclusion.SetParam(zero_real));
+ BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetParam(seven_real));
+
+ std::vector<Real> valid_cmap_parameters;
+ valid_cmap_parameters.push_back(2.0);
+ valid_cmap_parameters.push_back(0.0);
+ valid_cmap_parameters.push_back(0.0);
+ valid_cmap_parameters.push_back(0.0);
+ valid_cmap_parameters.push_back(0.0);
+
+ BOOST_CHECK_NO_THROW(cmap.SetParam(valid_cmap_parameters));
+ BOOST_CHECK(harmonic_bond.IsParametrized());
+
+ MMInteraction new_bond = MMInteraction(HarmonicBond);
+ std::vector<String> with_wildcard, without_wildcard;
+ with_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ with_wildcard.push_back("X");
+ without_wildcard.push_back("A");
+
+ //should be initialized with false
+ BOOST_CHECK(!new_bond.HasNameWildcard());
+ BOOST_CHECK(!new_bond.HasTypeWildcard());
+
+ new_bond.SetNames(without_wildcard);
+ new_bond.SetTypes(without_wildcard);
+ BOOST_CHECK(!new_bond.HasNameWildcard());
+ BOOST_CHECK(!new_bond.HasTypeWildcard());
+
+ new_bond.SetNames(with_wildcard);
+ new_bond.SetTypes(with_wildcard);
+ BOOST_CHECK(new_bond.HasNameWildcard());
+ BOOST_CHECK(new_bond.HasTypeWildcard());
+
+ //Check hasname/hastype
+ BOOST_CHECK(new_bond.HasType("A"));
+ BOOST_CHECK(!new_bond.HasType("B"));
+ BOOST_CHECK(new_bond.HasName("A"));
+ BOOST_CHECK(!new_bond.HasType("B"));
+
+}
+
+BOOST_AUTO_TEST_CASE(test_match_stuff)
+{
+ MMInteraction dihedral = MMInteraction(PeriodicDihedral);
+
+ std::vector<String> with_wildcard, without_wildcard;
+ with_wildcard.push_back("X");
+ with_wildcard.push_back("A");
+ with_wildcard.push_back("A");
+ with_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+
+ dihedral.SetTypes(with_wildcard);
+ BOOST_CHECK(dihedral.MatchTypes(with_wildcard));
+ BOOST_CHECK(dihedral.MatchTypes(without_wildcard));
+ dihedral.SetTypes(without_wildcard);
+ BOOST_CHECK(dihedral.MatchTypes(without_wildcard));
+ BOOST_CHECK(!dihedral.MatchTypes(with_wildcard));
+
+ dihedral.SetNames(with_wildcard);
+ BOOST_CHECK(dihedral.MatchNames(with_wildcard));
+ BOOST_CHECK(dihedral.MatchNames(without_wildcard));
+ dihedral.SetNames(without_wildcard);
+ BOOST_CHECK(dihedral.MatchNames(without_wildcard));
+ BOOST_CHECK(!dihedral.MatchNames(with_wildcard));
+
+}
+
+BOOST_AUTO_TEST_CASE(test_replace_atom){
+ MMInteraction bond = MMInteraction(HarmonicBond);
+ std::vector<String> strings;
+ strings.push_back("A");
+ strings.push_back("B");
+ bond.SetNames(strings);
+ bond.ReplaceAtom("A","X","X");
+ std::vector<String> new_names = bond.GetNames();
+ BOOST_CHECK(new_names != strings);
+ bond.SetTypes(strings);
+ bond.ReplaceAtom("X","A","X");
+ std::vector<String> new_types = bond.GetTypes();
+ BOOST_CHECK(new_types == new_names);
+
+}
+
+BOOST_AUTO_TEST_CASE(test_getatoms){
+ ost::mol::EntityHandle e = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(-5,-5,-5))
+ .Atom("B",geom::Vec3(-5, 5,-5))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(1,1,1))
+ .Atom("B",geom::Vec3(2,2,2))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(3,3,3))
+ .Atom("B",geom::Vec3(4,4,4));
+
+ ost::mol::ResidueHandleList res_list = e.GetResidueList();
+ ost::mol::AtomHandleList atom_list_one = res_list[0].GetAtomList();
+ ost::mol::AtomHandleList atom_list_two = res_list[1].GetAtomList();
+ ost::mol::AtomHandleList atom_list_three = res_list[2].GetAtomList();
+
+ MMInteraction bond = MMInteraction(HarmonicBond);
+ std::vector<String> strings;
+ strings.push_back("A");
+ strings.push_back("B");
+ bond.SetNames(strings);
+ ost::mol::AtomHandleList bond_atom_list = bond.GetAtoms(res_list[0]);
+ BOOST_CHECK(atom_list_one[0] == bond_atom_list[0]);
+ BOOST_CHECK(atom_list_one[1] == bond_atom_list[1]);
+ strings[1] = "X";
+ bond.SetNames(strings);
+ BOOST_CHECK_THROW(bond.GetAtoms(res_list[0]),ost::Error);
+ strings[0] = "-A";
+ strings[1] = "B";
+ bond.SetNames(strings);
+ BOOST_CHECK_THROW(bond.GetAtoms(res_list[0]),ost::Error);
+ bond_atom_list = bond.GetAtoms(res_list[1]);
+ BOOST_CHECK(bond_atom_list[0] == atom_list_one[0]);
+ BOOST_CHECK(bond_atom_list[1] == atom_list_two[1]);
+ strings[1]="+B";
+ bond.SetNames(strings);
+ BOOST_CHECK_THROW(bond.GetAtoms(res_list[2]),ost::Error);
+ bond_atom_list = bond.GetAtoms(res_list[1]);
+ BOOST_CHECK(bond_atom_list[0] == atom_list_one[0]);
+ BOOST_CHECK(bond_atom_list[1] == atom_list_three[1]);
+}
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_simulation.cc b/modules/mol/mm/tests/test_simulation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..6d1351972639d9042dc8cf5e0b2c85fa9f600432
--- /dev/null
+++ b/modules/mol/mm/tests/test_simulation.cc
@@ -0,0 +1,242 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/mm_interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+#include <ost/message.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/mol/mm/simulation.hh>
+#include <ost/mol/mm/topology.hh>
+
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_simulation_basics){
+
+ String pdb_name = "1CRN.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ MMSettingsPtr settings(new MMSettings);
+ ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
+ settings->forcefield = forcefield;
+ settings->add_gbsa = true;
+
+ TopologyPtr top = TopologyCreator::Create(test_ent,settings);
+ //lets add interactions, that are not set when using charmm
+ top->AddHarmonicAngle(1,2,3,10.0,10.0);
+ top->AddPeriodicImproper(1,2,3,4,2,10.0,10.0);
+ top->AddDistanceConstraint(1,2,10.0);
+ top->AddHarmonicPositionRestraint(1,geom::Vec3(0.0,0.0,0.0),10.0);
+ top->AddHarmonicDistanceRestraint(1,2,10.0,10.0);
+
+ //try to set up simulation without an integrator
+ BOOST_CHECK_THROW(Simulation sim(test_ent,settings),ost::Error);
+
+ settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+
+ Simulation sim(top, settings);
+
+
+ //we check, wether the reset functions have the desired effect on the topology
+ //we cannot really check the effect on the openmm system...
+ sim.ResetHarmonicBond(42,5.0,6.0);
+ sim.ResetHarmonicAngle(0,8.0,9.0);
+ sim.ResetUreyBradleyAngle(42,5.0,6.0,7.0,8.0);
+ sim.ResetPeriodicDihedral(42,4,5.0,6.0);
+ sim.ResetPeriodicImproper(0,5,8.0,9.0);
+ sim.ResetHarmonicImproper(42,5.0,6.0);
+ sim.ResetLJPair(42,5.0,6.0);
+ sim.ResetDistanceConstraint(0,10.0);
+ sim.ResetHarmonicPositionRestraint(0,geom::Vec3(1.0,1.0,1.0),5.0);
+ sim.ResetHarmonicDistanceRestraint(0,5.0,10.0);
+ sim.ResetLJ(42,2.0,3.0);
+ sim.ResetGBSA(42,5.0,6.0);
+ sim.ResetCharge(42,100.0);
+ sim.ResetMass(42,200.0);
+
+ uint ui1,ui2,ui3,ui4;
+ int i1;
+ Real r1,r2,r3,r4;
+ geom::Vec3 pos;
+
+
+ top->GetHarmonicBondParameters(42,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
+
+ top->GetHarmonicAngleParameters(0,ui1,ui2,ui3,r1,r2);
+ BOOST_CHECK(r1 == 8.0 && r2 == 9.0);
+
+ top->GetUreyBradleyAngleParameters(42,ui1,ui2,ui3,r1,r2,r3,r4);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0 && r3 == 7.0 && r4 == 8.0);
+
+ top->GetPeriodicDihedralParameters(42,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK(i1 == 4 && r1 == 5.0 && r2 == 6.0);
+
+ top->GetPeriodicImproperParameters(0,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK(i1 == 5 && r1 == 8.0 && r2 == 9.0);
+
+ top->GetLJPairParameters(42,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
+
+ top->GetDistanceConstraintParameters(0,ui1,ui2,r1);
+ BOOST_CHECK(r1 == 10.0);
+
+ top->GetHarmonicPositionRestraintParameters(0, ui1, pos,r1, r2, r3, r3);
+ BOOST_CHECK(pos == geom::Vec3(1.0,1.0,1.0) && r1 == 5.0);
+
+ top->GetHarmonicDistanceRestraintParameters(0,ui1,ui2, r1, r2);
+ BOOST_CHECK(r1 == 5.0 && r2 == 10.0);
+
+ r1 = top->GetSigma(42);
+ r2 = top->GetEpsilon(42);
+ BOOST_CHECK(r1 == 2.0 && r2 == 3.0);
+
+ r1 = top->GetGBSARadius(42);
+ r2 = top->GetOBCScaling(42);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
+
+ r1 = top->GetCharge(42);
+ r2 = top->GetMass(42);
+ BOOST_CHECK(r1 == 100.0 && r2 == 200.0);
+}
+
+
+BOOST_AUTO_TEST_CASE(test_simulation_energy_calculations){
+
+
+ String pdb_name = "1CRN.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ MMSettingsPtr settings(new MMSettings);
+ ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
+ settings->forcefield = forcefield;
+
+ TopologyPtr top = TopologyCreator::Create(test_ent,settings);
+ //lets add interactions, that are not set when using charmm
+
+ settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+
+ Simulation sim(top, settings);
+
+ sim.MinimizeEnergy("steep",1.0,200);
+ sim.UpdateTopologyPositions();
+
+ ost::mol::EntityHandle minimized_ent = sim.GetEntity();
+
+ MMSettingsPtr harmonic_bond_settings(new MMSettings);
+ harmonic_bond_settings->add_angles = false;
+ harmonic_bond_settings->add_dihedrals = false;
+ harmonic_bond_settings->add_impropers = false;
+ harmonic_bond_settings->add_nonbonded = false;
+ harmonic_bond_settings->add_cmaps = false;
+ harmonic_bond_settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+ harmonic_bond_settings->forcefield = forcefield;
+
+ MMSettingsPtr urey_bradley_angle_settings(new MMSettings);
+ urey_bradley_angle_settings->add_bonds = false;
+ urey_bradley_angle_settings->add_dihedrals = false;
+ urey_bradley_angle_settings->add_impropers = false;
+ urey_bradley_angle_settings->add_nonbonded = false;
+ urey_bradley_angle_settings->add_cmaps = false;
+ urey_bradley_angle_settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+ urey_bradley_angle_settings->forcefield = forcefield;
+
+ MMSettingsPtr periodic_dihedral_settings(new MMSettings);
+ periodic_dihedral_settings->add_bonds = false;
+ periodic_dihedral_settings->add_angles = false;
+ periodic_dihedral_settings->add_impropers = false;
+ periodic_dihedral_settings->add_nonbonded = false;
+ periodic_dihedral_settings->add_cmaps = false;
+ periodic_dihedral_settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+ periodic_dihedral_settings->forcefield = forcefield;
+
+ MMSettingsPtr harmonic_improper_settings(new MMSettings);
+ harmonic_improper_settings->add_bonds = false;
+ harmonic_improper_settings->add_angles = false;
+ harmonic_improper_settings->add_dihedrals = false;
+ harmonic_improper_settings->add_nonbonded = false;
+ harmonic_improper_settings->add_cmaps = false;
+ harmonic_improper_settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+ harmonic_improper_settings->forcefield = forcefield;
+
+ MMSettingsPtr cmap_settings(new MMSettings);
+ cmap_settings->add_bonds = false;
+ cmap_settings->add_angles = false;
+ cmap_settings->add_dihedrals = false;
+ cmap_settings->add_nonbonded = false;
+ cmap_settings->add_impropers = false;
+ cmap_settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+ cmap_settings->forcefield = forcefield;
+
+ MMSettingsPtr nonbonded_settings(new MMSettings);
+ nonbonded_settings->add_bonds = false;
+ nonbonded_settings->add_angles = false;
+ nonbonded_settings->add_dihedrals = false;
+ nonbonded_settings->add_cmaps = false;
+ nonbonded_settings->add_impropers = false;
+ nonbonded_settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+ nonbonded_settings->forcefield = forcefield;
+
+ Simulation sim_harmonic_bond(minimized_ent,harmonic_bond_settings);
+ Simulation sim_urey_bradley_angle(minimized_ent,urey_bradley_angle_settings);
+ Simulation sim_periodic_dihedral(minimized_ent,periodic_dihedral_settings);
+ Simulation sim_harmonic_improper(minimized_ent,harmonic_improper_settings);
+ Simulation sim_cmap(minimized_ent,cmap_settings);
+ Simulation sim_nonbonded(minimized_ent, nonbonded_settings);
+
+ Real e_harmonic_bond = sim_harmonic_bond.GetPotentialEnergy();
+ Real e_urey_bradley_angle = sim_urey_bradley_angle.GetPotentialEnergy();
+ Real e_periodic_dihedral = sim_periodic_dihedral.GetPotentialEnergy();
+ Real e_harmonic_improper = sim_harmonic_improper.GetPotentialEnergy();
+ Real e_cmap = sim_cmap.GetPotentialEnergy();
+ Real e_nonbonded = sim_nonbonded.GetPotentialEnergy();
+
+
+ //the energy values have been compared with the results from the
+ //CHARMM27 forcefield in gromacs
+
+ //differenecs in energy(kJ/mol):
+ //harmonic_bond: 0.00021344800001
+ //urey_bradley_angle: 0.00021319300003
+ //periodic_dihedral: 0.00018275799993
+ //harmonic_improper: 0.00001410630000
+ //cmap: 0.00192255100001
+ //nonbonded: 0.00204422999968
+
+ //You'll most likely get different results when repeating the comparison with gromacs
+ //this is because of the precision.
+ //Right now we have full real precision in the positions.
+ //When you write down the pdb, precision will be lowered to 3 digits.
+ //Another digit gets lost, when you create a gromacs topology...
+ //Gromacs writes down the positions using nm instead of A, but
+ //also has a precision of 3 digits.
+
+ BOOST_CHECK_CLOSE(e_harmonic_bond, 150.238, Real(1e-3));
+ BOOST_CHECK_CLOSE(e_urey_bradley_angle, 499.690, Real(1e-3));
+ BOOST_CHECK_CLOSE(e_periodic_dihedral, 879.744, Real(1e-3));
+ BOOST_CHECK_CLOSE(e_harmonic_improper, 15.7698, Real(1e-3));
+ BOOST_CHECK_CLOSE(e_cmap, -303.904, Real(1e-3));
+ BOOST_CHECK_CLOSE(e_nonbonded, -3626.539, Real(1e-3));
+}
+
+
+
+BOOST_AUTO_TEST_SUITE_END();
\ No newline at end of file
diff --git a/modules/mol/mm/tests/test_topology.cc b/modules/mol/mm/tests/test_topology.cc
new file mode 100644
index 0000000000000000000000000000000000000000..52744ed6cdb261fac98c91a3fc5b0c1f28b64079
--- /dev/null
+++ b/modules/mol/mm/tests/test_topology.cc
@@ -0,0 +1,627 @@
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/mm/mm_settings.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/conop/heuristic.hh>
+#include <ost/message.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_topology_basics){
+
+ String pdb_name = "1CRN.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ //check initialisation without settings
+ std::vector<Real> zero_real(0);
+ std::vector<Real> lot_of_reals(test_ent.GetAtomCount());
+
+ BOOST_CHECK_THROW(Topology(test_ent,zero_real),ost::Error);
+
+ TopologyPtr top(new Topology(test_ent,lot_of_reals));
+
+ uint ui1(0), ui2(0), ui3(0), ui4(0), ui5(0);
+ int i1(0), i5(0);
+ Real r1(0.0), r2(0.0), r3(0.0), r4(0.0);
+ geom::Vec3 zero_vec(0.0,0.0,0.0);
+ geom::Vec3 test_vec(0.0,1.0,2.0);
+
+ //check wether errors geth thrown, when atom indices are too big
+ BOOST_CHECK_THROW(top->AddHarmonicBond(700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicBond(0,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicAngle(700,1,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicAngle(1,700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicAngle(1,1,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddUreyBradleyAngle(700,1,1,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddUreyBradleyAngle(1,700,1,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddUreyBradleyAngle(1,1,700,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(700,1,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(1,700,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(1,1,700,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(1,1,1,700,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(700,1,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(1,700,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(1,1,700,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(1,1,1,700,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(700,1,1,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(1,700,1,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(1,1,700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(1,1,1,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(700,1,1,1,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,700,1,1,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,700,1,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,1,700,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,1,1,700,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,1,1,1,0,lot_of_reals),ost::Error); //additionally checks error, when dimension and cmap are inconsistent
+ BOOST_CHECK_THROW(top->AddLJPair(1,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddLJPair(700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(1,700),ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(700,1),ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(1,700,r1),ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(700,1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicPositionRestraint(700,zero_vec,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicDistanceRestraint(700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicDistanceRestraint(1,700,r1,r2),ost::Error);
+
+ //check whether errors get thrown when single atom parameters are inconsistent with number of atoms in topology
+ BOOST_CHECK_THROW(top->SetSigmas(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetEpsilons(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetGBSARadii(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetOBCScalings(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetMasses(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetCharges(zero_real),ost::Error);
+
+ //Single atom parameters are not allowed to be modified, without being set initially
+ BOOST_CHECK_THROW(top->SetSigma(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetEpsilon(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetGBSARadius(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetOBCScaling(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetCharge(1,r1),ost::Error);
+
+ //Let's set the single atom parameters initially
+ top->SetSigmas(lot_of_reals);
+ top->SetEpsilons(lot_of_reals);
+ top->SetGBSARadii(lot_of_reals);
+ top->SetOBCScalings(lot_of_reals);
+ top->SetCharges(lot_of_reals);
+
+ //do the index checks for them
+ BOOST_CHECK_THROW(top->SetSigma(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetEpsilon(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetGBSARadius(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetOBCScaling(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetMass(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetCharge(1000,1.0),ost::Error);
+
+ //similar stupid checks for SetParameter functions
+ BOOST_CHECK_THROW(top->SetHarmonicBondParameters(700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicAngleParameters(3000,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetUreyBradleyAngleParameters(3000,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->SetPeriodicDihedralParameters(3000,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetPeriodicImproperParameters(3000,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicImproperParameters(3000,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetCMapParameters(3000,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetLJPairParameters(3000,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetDistanceConstraintParameters(3000,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicPositionRestraintParameters(3000,zero_vec,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicDistanceRestraintParameters(3000,r1,r2),ost::Error);
+
+ BOOST_CHECK_THROW(top->GetHarmonicBondParameters(700,ui1,ui2,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicAngleParameters(3000,ui1,ui2,ui3,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetUreyBradleyAngleParameters(3000,ui1,ui2,ui3,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->GetPeriodicDihedralParameters(3000,ui1,ui2,ui3,ui4,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetPeriodicImproperParameters(3000,ui1,ui2,ui3,ui4,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicImproperParameters(3000,ui1,ui2,ui3,ui4,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetCMapParameters(3000,ui1,ui2,ui3,ui4,ui5,i1,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->GetLJPairParameters(3000,ui1,ui2,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetDistanceConstraintParameters(3000,ui1,ui2,r1),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicPositionRestraintParameters(3000,ui1,zero_vec,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicDistanceRestraintParameters(3000,ui1,ui2,r1,r2),ost::Error);
+
+ //let's add some interactions to the topology
+ for(int i = 0; i < 10; ++i){
+ top->AddHarmonicBond(0,1,r1,r2);
+ top->AddHarmonicAngle(0,1,2,r1,r2);
+ top->AddUreyBradleyAngle(0,1,2,r1,r2,r3,r4);
+ top->AddPeriodicDihedral(0,1,2,3,i1,r1,r2);
+ top->AddPeriodicImproper(0,1,2,3,i1,r1,r2);
+ top->AddHarmonicImproper(0,1,2,3,r1,r2);
+ top->AddCMap(0,1,2,3,4,i1,zero_real);
+ top->AddHarmonicPositionRestraint(0,zero_vec,r1,r2,r3,r4);
+ top->AddHarmonicDistanceRestraint(0,1,r1,r2);
+ }
+
+ //following interactions are unique for a pair of atoms
+ top->AddLJPair(0,1,r1,r2);
+ top->AddDistanceConstraint(0,1,r1);
+ top->AddExclusion(0,1);
+
+ //errors should be thrown, when previously added interactions are added again
+ BOOST_CHECK_THROW(top->AddLJPair(0,1,r1,r2), ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(0,1,r1), ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(0,1), ost::Error);
+ BOOST_CHECK_THROW(top->AddLJPair(1,0,r1,r2), ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(1,0,r1), ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(1,0), ost::Error);
+
+ //check set and get parameter stuff, but also the GetIndices functionality
+ std::vector<uint> ind1,ind2;
+ top->SetHarmonicBondParameters(0,0.5,15.0);
+ top->GetHarmonicBondParameters(0,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 0.5 && r2 == 15.0);
+ ind1 = top->GetHarmonicBondIndices(0,1);
+ ind2 = top->GetHarmonicBondIndices(1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicBondIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicBondIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicBondIndices(2).size() == 0);
+
+
+ top->SetHarmonicAngleParameters(0,1.0,10.0);
+ top->GetHarmonicAngleParameters(0,ui1,ui2,ui3,r1,r2);
+ BOOST_CHECK(r1 == 1.0 && r2 == 10.0);
+ ind1 = top->GetHarmonicAngleIndices(0,1,2);
+ ind2 = top->GetHarmonicAngleIndices(2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(2).size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(3).size() == 0);
+
+ top->SetUreyBradleyAngleParameters(0,0.5,0.5,0.5,0.5);
+ top->GetUreyBradleyAngleParameters(0,ui1,ui2,ui3,r1,r2,r3,r4);
+ BOOST_CHECK( r1 == 0.5 && r2 == 0.5 && r3 == 0.5 && r3 == 0.5 );
+ ind1 = top->GetUreyBradleyAngleIndices(0,1,2);
+ ind2 = top->GetUreyBradleyAngleIndices(2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(0).size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(1).size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(2).size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(3).size() == 0);
+
+
+ top->SetPeriodicDihedralParameters(0,2,5.0,0.5);
+ top->GetPeriodicDihedralParameters(0,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK( i5 == 0 && r1 == 5.0 && r2 == 0.5 );
+ ind1 = top->GetPeriodicDihedralIndices(0,1,2,3);
+ ind2 = top->GetPeriodicDihedralIndices(3,2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(0).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(1).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(2).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(3).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(4).size() == 0);
+
+ top->SetPeriodicImproperParameters(6,2,2.0,1.0);
+ top->GetPeriodicImproperParameters(6,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK( i5 == 0 && r1 == 2.0 && r2 == 1.0 );
+ ind1 = top->GetPeriodicImproperIndices(0,1,2,3);
+ ind2 = top->GetPeriodicImproperIndices(3,2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(0).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(1).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(2).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(3).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(4).size() == 0);
+
+ top->SetHarmonicImproperParameters(0,4.0,4.0);
+ top->GetHarmonicImproperParameters(0,ui1,ui2,ui3,ui4,r1,r2);
+ BOOST_CHECK(r1 == 4.0 && r2 == 4.0);
+ ind1 = top->GetHarmonicImproperIndices(0,1,2,3);
+ ind2 = top->GetHarmonicImproperIndices(3,2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(2).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(3).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(4).size() == 0);
+
+ std::vector<Real> one_real(1);
+ one_real[0] = 42;
+ top->SetCMapParameters(0,1,one_real);
+ std::vector<Real> temp_real;
+ top->GetCMapParameters(0,ui1,ui2,ui3,ui4,ui5,i1,temp_real);
+ BOOST_CHECK( ui1 == 0 && temp_real.size() == 1 && temp_real[0] == 42);
+ ind1 = top->GetCMapIndices(0,1,2,3,4);
+ ind2 = top->GetCMapIndices(4,3,2,1,0);
+ BOOST_CHECK(ind1.size() == 10);
+ BOOST_CHECK(ind2.size() == 0); //cmaps are sensitive for the ordering!!
+ BOOST_CHECK(top->GetCMapIndices(0).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(1).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(2).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(3).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(4).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(5).size() == 0);
+
+ top->SetLJPairParameters(0,3.5,4.5);
+ top->GetLJPairParameters(0,ui1,ui2,r1,r2);
+ BOOST_CHECK( r1 == 3.5 && r2 == 4.5 );
+ i1 = top->GetLJPairIndex(0,1);
+ i5 = top->GetLJPairIndex(1,0);
+ BOOST_CHECK(i1 == i5 && i1 != -1);
+ BOOST_CHECK(top->GetLJPairIndices(0).size() == 1);
+ BOOST_CHECK(top->GetLJPairIndices(1).size() == 1);
+ BOOST_CHECK(top->GetLJPairIndices(2).size() == 0);
+
+ top->SetDistanceConstraintParameters(0,42.0);
+ top->GetDistanceConstraintParameters(0,ui1,ui2,r1);
+ BOOST_CHECK( r1 == 42.0 );
+ i1 = top->GetDistanceConstraintIndex(0,1);
+ i5 = top->GetDistanceConstraintIndex(1,0);
+ BOOST_CHECK(i1 == i5 && i1 != -1);
+
+ top->SetHarmonicPositionRestraintParameters(0,test_vec,3.0);
+ top->GetHarmonicPositionRestraintParameters(0,ui1,zero_vec,r1,r2,r3,r4);
+ BOOST_CHECK(zero_vec == test_vec);
+ BOOST_CHECK(r1 == 3.0);
+ BOOST_CHECK(r2 == 1.0); //should be the same for r3 and r4
+ //no reverse checking necessary
+ BOOST_CHECK(top->GetHarmonicPositionRestraintIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicPositionRestraintIndices(1).size() == 0);
+
+ top->SetHarmonicDistanceRestraintParameters(0,2.0,2.0);
+ top->GetHarmonicDistanceRestraintParameters(0,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 2.0 && r2 == 2.0);
+ ind1 = top->GetHarmonicDistanceRestraintIndices(0,1);
+ ind2 = top->GetHarmonicDistanceRestraintIndices(1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicDistanceRestraintIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicDistanceRestraintIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicDistanceRestraintIndices(2).size() == 0);
+
+ ost::mol::EntityHandle top_test_ent = top->GetEntity();
+ ost::mol::AtomHandleList atom_list = top_test_ent.GetAtomList();
+ top->AddPositionConstraint(atom_list[0]);
+ BOOST_CHECK(top->GetNumPositionConstraints() == 1);
+ top->ResetPositionConstraints();
+ BOOST_CHECK(top->GetNumPositionConstraints() == 0);
+}
+
+BOOST_AUTO_TEST_CASE(test_topology_index_getters){
+
+ String pdb_name = "1CRN.pdb";
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ //check initialisation without settings
+ std::vector<Real> fake_masses(test_ent.GetAtomCount());
+ TopologyPtr top(new Topology(test_ent,fake_masses));
+ test_ent = top->GetEntity(); //we do a copy in the constructor of the topology
+
+ ost::mol::AtomHandleList atom_list = test_ent.GetAtomList();
+ ost::mol::ResidueHandleList res_list = test_ent.GetResidueList();
+
+ for(uint i = 0; i < atom_list.size(); ++i){
+ BOOST_CHECK(top->GetAtomIndex(atom_list[i]) == i);
+ }
+ for(uint i = 0; i < res_list.size(); ++i){
+ BOOST_CHECK(top->GetResidueIndex(res_list[i]) == i);
+ }
+
+ ost::mol::AtomHandle test_atom_one = res_list[10].FindAtom("CA");
+ ost::mol::AtomHandle test_atom_two = res_list[9].FindAtom("CA");
+ ost::mol::AtomHandle test_atom_three = res_list[11].FindAtom("CA");
+
+ uint index_one = top->GetAtomIndex(test_atom_one);
+ uint index_two = top->GetAtomIndex(test_atom_two);
+ uint index_three = top->GetAtomIndex(test_atom_three);
+
+ BOOST_CHECK(top->GetAtomIndex(10,"CA") == index_one);
+ BOOST_CHECK(top->GetAtomIndex(10,"-CA") == index_two);
+ BOOST_CHECK(top->GetAtomIndex(10,"+CA") == index_three);
+}
+
+BOOST_AUTO_TEST_CASE(test_topology_merge){
+
+ String pdb_name = "1CRN.pdb";
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ForcefieldPtr ff = Forcefield::Load("CHARMM27.dat");
+ MMSettingsPtr settings = MMSettingsPtr(new MMSettings);
+ settings->add_gbsa = true;
+ settings->forcefield = ff;
+
+ ost::mol::EntityHandle new_ent = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(1,1,1))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(2,2,2))
+ .Atom("B",geom::Vec3(3,3,3))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(4,4,4))
+ .Atom("B",geom::Vec3(5,5,5));
+
+ //check whether error gets thrown when chain with same name is already present
+ std::vector<Real> real_vec(6);
+ TopologyPtr merge_top_one(new Topology(new_ent,real_vec));
+ merge_top_one->SetCharges(real_vec);
+ merge_top_one->SetOBCScalings(real_vec);
+ merge_top_one->SetGBSARadii(real_vec);
+ merge_top_one->SetSigmas(real_vec);
+ merge_top_one->SetEpsilons(real_vec);
+ merge_top_one->SetFudgeQQ(1.0);
+ merge_top_one->SetFudgeLJ(1.0);
+ TopologyPtr top_one = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_one->Merge(merge_top_one),ost::Error);
+ ost::mol::XCSEditor ed = new_ent.EditXCS();
+ ed.RenameChain(new_ent.GetChainList()[0],"B");
+ TopologyPtr merge_top_one_two(new Topology(new_ent,real_vec)); // I know...
+ merge_top_one_two->SetCharges(real_vec);
+ merge_top_one_two->SetOBCScalings(real_vec);
+ merge_top_one_two->SetGBSARadii(real_vec);
+ merge_top_one_two->SetSigmas(real_vec);
+ merge_top_one_two->SetEpsilons(real_vec);
+ merge_top_one_two->SetFudgeQQ(1.0);
+ merge_top_one_two->SetFudgeLJ(1.0);
+ BOOST_CHECK_NO_THROW(top_one->Merge(merge_top_one_two));
+
+
+ //check whether error gets thrown, when fudge parameters are inconsistent
+ TopologyPtr merge_top_two(new Topology(new_ent,real_vec));
+ merge_top_two->SetCharges(real_vec);
+ merge_top_two->SetOBCScalings(real_vec);
+ merge_top_two->SetGBSARadii(real_vec);
+ merge_top_two->SetSigmas(real_vec);
+ merge_top_two->SetEpsilons(real_vec);
+ merge_top_two->SetFudgeQQ(42.0);
+ merge_top_two->SetFudgeLJ(42.0);
+ TopologyPtr top_two = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_two->Merge(merge_top_two),ost::Error);
+ merge_top_two->SetFudgeQQ(1.0);
+ merge_top_two->SetFudgeLJ(1.0);
+ BOOST_CHECK_NO_THROW(top_two->Merge(merge_top_two));
+
+
+ //check whether error gets thrown when charges are not set
+ TopologyPtr merge_top_three(new Topology(new_ent,real_vec));
+ merge_top_three->SetOBCScalings(real_vec);
+ merge_top_three->SetGBSARadii(real_vec);
+ merge_top_three->SetSigmas(real_vec);
+ merge_top_three->SetEpsilons(real_vec);
+ merge_top_three->SetFudgeQQ(1.0);
+ merge_top_three->SetFudgeLJ(1.0);
+ TopologyPtr top_three = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_three->Merge(merge_top_three),ost::Error);
+ TopologyPtr top_three_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_three->SetCharges(real_vec);
+ BOOST_CHECK_NO_THROW(top_three_two->Merge(merge_top_three));
+
+ //check whether error gets thrown when obc scaling factors are not set
+ TopologyPtr merge_top_four(new Topology(new_ent,real_vec));
+ merge_top_four->SetCharges(real_vec);
+ merge_top_four->SetGBSARadii(real_vec);
+ merge_top_four->SetSigmas(real_vec);
+ merge_top_four->SetEpsilons(real_vec);
+ merge_top_four->SetFudgeQQ(1.0);
+ merge_top_four->SetFudgeLJ(1.0);
+ TopologyPtr top_four = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_four->Merge(merge_top_four),ost::Error);
+ TopologyPtr top_four_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_four->SetOBCScalings(real_vec);
+ BOOST_CHECK_NO_THROW(top_four_two->Merge(merge_top_four));
+
+ //check whether error gets thrown when gbsa radii are not set
+ TopologyPtr merge_top_five(new Topology(new_ent,real_vec));
+ merge_top_five->SetCharges(real_vec);
+ merge_top_five->SetOBCScalings(real_vec);
+ merge_top_five->SetSigmas(real_vec);
+ merge_top_five->SetEpsilons(real_vec);
+ merge_top_five->SetFudgeQQ(1.0);
+ merge_top_five->SetFudgeLJ(1.0);
+ TopologyPtr top_five = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_five->Merge(merge_top_five),ost::Error);
+ TopologyPtr top_five_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_five->SetGBSARadii(real_vec);
+ BOOST_CHECK_NO_THROW(top_five_two->Merge(merge_top_five));
+
+ //check whether error gets thrown when sigmas are not set
+ TopologyPtr merge_top_six(new Topology(new_ent,real_vec));
+ merge_top_six->SetCharges(real_vec);
+ merge_top_six->SetOBCScalings(real_vec);
+ merge_top_six->SetGBSARadii(real_vec);
+ merge_top_six->SetEpsilons(real_vec);
+ merge_top_six->SetFudgeQQ(1.0);
+ merge_top_six->SetFudgeLJ(1.0);
+ TopologyPtr top_six = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_six->Merge(merge_top_six),ost::Error);
+ TopologyPtr top_six_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_six->SetSigmas(real_vec);
+ BOOST_CHECK_NO_THROW(top_six_two->Merge(merge_top_six));
+
+ //check whether error gets thrown when epsilons are not set
+ TopologyPtr merge_top_seven(new Topology(new_ent,real_vec));
+ merge_top_seven->SetCharges(real_vec);
+ merge_top_seven->SetOBCScalings(real_vec);
+ merge_top_seven->SetGBSARadii(real_vec);
+ merge_top_seven->SetSigmas(real_vec);
+ merge_top_seven->SetFudgeQQ(1.0);
+ merge_top_seven->SetFudgeLJ(1.0);
+ TopologyPtr top_seven = TopologyCreator::Create(test_ent,settings);
+ BOOST_CHECK_THROW(top_seven->Merge(merge_top_seven),ost::Error);
+ TopologyPtr top_seven_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_seven->SetEpsilons(real_vec);
+ BOOST_CHECK_NO_THROW(top_seven_two->Merge(merge_top_seven));
+
+ TopologyPtr merge_top_eight(new Topology(new_ent,real_vec));
+ merge_top_eight->SetCharges(real_vec);
+ merge_top_eight->SetOBCScalings(real_vec);
+ merge_top_eight->SetGBSARadii(real_vec);
+ merge_top_eight->SetSigmas(real_vec);
+ merge_top_eight->SetFudgeQQ(1.0);
+ merge_top_eight->SetFudgeLJ(1.0);
+ merge_top_eight->SetEpsilons(real_vec);
+
+ //let's add every possible interaction
+
+ merge_top_eight->AddHarmonicBond(0,1,42.0,42000.0);
+ merge_top_eight->AddHarmonicAngle(0,1,2,24.0,24000.0);
+ merge_top_eight->AddUreyBradleyAngle(1,2,3,1.0,2.0,3.0,4.0);
+ merge_top_eight->AddPeriodicDihedral(0,1,2,3,10,2.0,42.0);
+ merge_top_eight->AddPeriodicImproper(1,2,3,4,3,5.0,10.0);
+ merge_top_eight->AddHarmonicImproper(0,1,2,3,8.0,12.0);
+ std::vector<Real> cmap;
+ cmap.push_back(0.0);
+ cmap.push_back(1.0);
+ cmap.push_back(2.0);
+ cmap.push_back(3.0);
+ merge_top_eight->AddCMap(0,1,2,3,4,2,cmap);
+ merge_top_eight->AddLJPair(3,4,1.0,2.0);
+ merge_top_eight->AddDistanceConstraint(2,3,10.0);
+ merge_top_eight->AddExclusion(3,4);
+ merge_top_eight->AddPositionConstraint(2);
+ geom::Vec3 pos(1.0,2.0,3.0);
+ merge_top_eight->AddHarmonicPositionRestraint(2,pos,10.0,5.0,6.0,7.0);
+ merge_top_eight->AddHarmonicDistanceRestraint(1,2,10.0,1000.0);
+
+ TopologyPtr top_eight = TopologyCreator::Create(test_ent,settings);\
+
+ uint num_harmonic_bonds = top_eight->GetNumHarmonicBonds();
+ uint num_harmonic_angles = top_eight->GetNumHarmonicAngles();
+ uint num_urey_bradley_angles = top_eight->GetNumUreyBradleyAngles();
+ uint num_periodic_dihedrals = top_eight->GetNumPeriodicDihedrals();
+ uint num_periodic_impropers = top_eight->GetNumPeriodicImpropers();
+ uint num_harmonic_impropers = top_eight->GetNumHarmonicImpropers();
+ uint num_cmaps = top_eight->GetNumCMaps();
+ uint num_lj_pairs = top_eight->GetNumLJPairs();
+ uint num_distance_constraints = top_eight->GetNumDistanceConstraints();
+ uint num_exclusions = top_eight->GetNumExclusions();
+ uint num_position_constraints = top_eight->GetNumPositionConstraints();
+ uint num_harmonic_position_restraints = top_eight->GetNumHarmonicPositionRestraints();
+ uint num_harmonic_distance_restraints = top_eight->GetNumHarmonicDistanceRestraints();
+
+ top_eight->Merge(merge_top_eight);
+
+ BOOST_CHECK(top_eight->GetNumHarmonicBonds() == num_harmonic_bonds+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicAngles() == num_harmonic_angles+1);
+ BOOST_CHECK(top_eight->GetNumUreyBradleyAngles() == num_urey_bradley_angles+1);
+ BOOST_CHECK(top_eight->GetNumPeriodicDihedrals() == num_periodic_dihedrals+1);
+ BOOST_CHECK(top_eight->GetNumPeriodicImpropers() == num_periodic_impropers+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicImpropers() == num_harmonic_impropers+1);
+ BOOST_CHECK(top_eight->GetNumCMaps() == num_cmaps+1);
+ BOOST_CHECK(top_eight->GetNumLJPairs() == num_lj_pairs+1);
+ BOOST_CHECK(top_eight->GetNumDistanceConstraints() == num_distance_constraints+1);
+ BOOST_CHECK(top_eight->GetNumExclusions() == num_exclusions+1);
+ BOOST_CHECK(top_eight->GetNumPositionConstraints() == num_position_constraints+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicPositionRestraints() == num_harmonic_position_restraints+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicDistanceRestraints() == num_harmonic_distance_restraints+1);
+
+
+ //check wether the new indices are right...
+ ost::mol::EntityHandle top_ent = top_eight->GetEntity();
+ ost::mol::ChainHandle top_chain = top_ent.FindChain("B");
+ ost::mol::ResidueHandleList res_list = top_chain.GetResidueList();
+ ost::mol::AtomHandleList atom_list = top_chain.GetAtomList();
+ uint res_index_one = top_eight->GetResidueIndex(res_list[0]);
+ uint res_index_two = top_eight->GetResidueIndex(res_list[1]);
+ uint res_index_three = top_eight->GetResidueIndex(res_list[2]);
+ uint atom_index_zero = top_eight->GetAtomIndex(res_index_one,"A");
+ uint atom_index_one = top_eight->GetAtomIndex(res_index_one,"B");
+ uint atom_index_two = top_eight->GetAtomIndex(res_index_two,"A");
+ uint atom_index_three = top_eight->GetAtomIndex(res_index_two,"B");
+ uint atom_index_four = top_eight->GetAtomIndex(res_index_three,"A");
+ uint atom_index_five = top_eight->GetAtomIndex(res_index_three,"B");
+
+ BOOST_CHECK(atom_index_zero == top_eight->GetAtomIndex(atom_list[0]));
+ BOOST_CHECK(atom_index_one == top_eight->GetAtomIndex(atom_list[1]));
+ BOOST_CHECK(atom_index_two == top_eight->GetAtomIndex(atom_list[2]));
+ BOOST_CHECK(atom_index_three == top_eight->GetAtomIndex(atom_list[3]));
+ BOOST_CHECK(atom_index_four == top_eight->GetAtomIndex(atom_list[4]));
+ BOOST_CHECK(atom_index_five == top_eight->GetAtomIndex(atom_list[5]));
+
+ //check whether the unique interactions are properly mapped
+ BOOST_CHECK_THROW(top_eight->AddExclusion(atom_index_three,atom_index_four),ost::Error);
+ BOOST_CHECK_THROW(top_eight->AddDistanceConstraint(atom_index_two,atom_index_three,10.0),ost::Error);
+ BOOST_CHECK_THROW(top_eight->AddLJPair(atom_index_three,atom_index_four,1.0,2.0),ost::Error);
+
+ //check whether the interactions are properly added (we do not check the correct parametrization at this point)
+
+ std::vector<uint> harmonic_bond_indices = top_eight->GetHarmonicBondIndices(atom_index_zero,atom_index_one);
+ std::vector<uint> harmonic_angle_indices = top_eight->GetHarmonicAngleIndices(atom_index_zero,atom_index_one,atom_index_two);
+ std::vector<uint> urey_bradley_angle_indices = top_eight->GetUreyBradleyAngleIndices(atom_index_one,atom_index_two,atom_index_three);
+ std::vector<uint> periodic_dihedral_indices = top_eight->GetPeriodicDihedralIndices(atom_index_zero,atom_index_one,atom_index_two,atom_index_three);
+ std::vector<uint> periodic_improper_indices = top_eight->GetPeriodicImproperIndices(atom_index_one,atom_index_two,atom_index_three,atom_index_four);
+ std::vector<uint> harmonic_improper_indices = top_eight->GetHarmonicImproperIndices(atom_index_zero,atom_index_one,atom_index_two,atom_index_three);
+ std::vector<uint> cmap_indices = top_eight->GetCMapIndices(atom_index_zero,atom_index_one,atom_index_two,atom_index_three,atom_index_four);
+ int lj_pair_index = top_eight->GetLJPairIndex(atom_index_three,atom_index_four);
+ int distance_constraint_index = top_eight->GetDistanceConstraintIndex(atom_index_two,atom_index_three);
+ std::vector<uint> harmonic_distance_restraint_indices = top_eight->GetHarmonicDistanceRestraintIndices(atom_index_one,atom_index_two);
+ std::vector<uint> harmonic_position_restraint_indices = top_eight->GetHarmonicPositionRestraintIndices(atom_index_two);
+
+ BOOST_CHECK(harmonic_bond_indices.size() == 1);
+ BOOST_CHECK(harmonic_angle_indices.size() == 1);
+ BOOST_CHECK(urey_bradley_angle_indices.size() == 1);
+ BOOST_CHECK(periodic_dihedral_indices.size() == 1);
+ BOOST_CHECK(periodic_improper_indices.size() == 1);
+ BOOST_CHECK(harmonic_improper_indices.size() == 1);
+ BOOST_CHECK(cmap_indices.size() == 1);
+ BOOST_CHECK(harmonic_distance_restraint_indices.size() == 1);
+ BOOST_CHECK(harmonic_position_restraint_indices.size() == 1);
+ BOOST_CHECK(lj_pair_index != -1);
+ BOOST_CHECK(distance_constraint_index != -1);
+
+
+ //let's finally check the parameters
+
+ uint ui0,ui1,ui2,ui3,ui4;
+ int i0;
+ Real r0,r1,r2,r3;
+ geom::Vec3 v0;
+
+ top_eight->GetHarmonicBondParameters(harmonic_bond_indices[0],ui0,ui1,r0,r1);
+ BOOST_CHECK(r0 = 42.0 && r1 == 42000.0);
+
+ top_eight->GetHarmonicAngleParameters(harmonic_angle_indices[0],ui0,ui1,ui2,r0,r1);
+ BOOST_CHECK(r0 == 24.0 && r1 == 24000.0);
+
+ top_eight->GetUreyBradleyAngleParameters(urey_bradley_angle_indices[0],ui0,ui1,ui2,r0,r1,r2,r3);
+ BOOST_CHECK(r0 == 1.0 && r1 == 2.0 && r2 == 3.0 && r3 == 4.0);
+
+ top_eight->GetPeriodicDihedralParameters(periodic_dihedral_indices[0],ui0,ui1,ui2,ui3,i0,r0,r1);
+ BOOST_CHECK(i0 == 10 && r0 == 2.0 && r1 == 42.0);
+
+ top_eight->GetPeriodicImproperParameters(periodic_improper_indices[0],ui0,ui1,ui2,ui3,i0,r0,r1);
+ BOOST_CHECK(i0 == 3 && r0 == 5.0 && r1 == 10.0);
+
+ top_eight->GetHarmonicImproperParameters(harmonic_improper_indices[0],ui0,ui1,ui2,ui3,r0,r1);
+ BOOST_CHECK(r0 == 8.0 && r1 == 12.0);
+
+ top_eight->GetCMapParameters(cmap_indices[0],ui0,ui1,ui2,ui3,ui4,i0,real_vec);
+ BOOST_CHECK(real_vec == cmap && i0 == 2);
+
+ top_eight->GetLJPairParameters(lj_pair_index,ui0,ui1,r0,r1);
+ BOOST_CHECK(r0 == 1.0 && r1 == 2.0);
+
+ top_eight->GetDistanceConstraintParameters(distance_constraint_index,ui0,ui1,r0);
+ BOOST_CHECK(r0 == 10.0);
+
+ top_eight->GetHarmonicPositionRestraintParameters(harmonic_position_restraint_indices[0],ui0,v0,r0,r1,r2,r3);
+ BOOST_CHECK(v0 == pos && r0 == 10.0 && r1 == 5.0 && r2 == 6.0 && r3 == 7.0);
+
+ top_eight->GetHarmonicDistanceRestraintParameters(harmonic_distance_restraint_indices[0],ui0,ui1,r0,r1);
+ BOOST_CHECK(r0 == 10.0 && r1 == 1000.0);
+
+}
+
+
+BOOST_AUTO_TEST_SUITE_END();
\ No newline at end of file
diff --git a/modules/mol/mm/tests/tests.cc b/modules/mol/mm/tests/tests.cc
new file mode 100644
index 0000000000000000000000000000000000000000..8fb5bbd47707615b1702765ff363cf8525716942
--- /dev/null
+++ b/modules/mol/mm/tests/tests.cc
@@ -0,0 +1,24 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE ost_mol_base
+#define BOOST_AUTO_TEST_MAIN
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+