From dbdf6721134eb282b4a14caabcbc9ed45fe10754 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 20 Sep 2017 15:16:20 +0200
Subject: [PATCH] SCHWED-1740: test multi-loop handling for
SidechainReconstructor
---
modelling/src/sidechain_reconstructor.hh | 6 +-
modelling/tests/data/1crn_sc_test.pdb | 275 ------------------
.../tests/test_sidechain_reconstructor.cc | 80 ++++-
3 files changed, 70 insertions(+), 291 deletions(-)
diff --git a/modelling/src/sidechain_reconstructor.hh b/modelling/src/sidechain_reconstructor.hh
index abe8be22..6c1a4ac0 100644
--- a/modelling/src/sidechain_reconstructor.hh
+++ b/modelling/src/sidechain_reconstructor.hh
@@ -41,7 +41,7 @@ class SidechainReconstructor {
public:
SidechainReconstructor(bool keep_sidechains = true,
- bool build_disulfids = true,
+ bool build_disulfids = true,
bool optimize_subrotamers = false,
Real remodel_cutoff = 20,
Real rigid_frame_cutoff = 0,
@@ -63,8 +63,8 @@ public:
Reconstruct(uint start_resnum, uint num_residues, uint chain_idx = 0) const;
SidechainReconstructionDataPtr
- Reconstruct(const std::vector<uint>& start_resnums,
- const std::vector<uint>& num_residues,
+ Reconstruct(const std::vector<uint>& start_resnums,
+ const std::vector<uint>& num_residues,
const std::vector<uint>& chain_indices) const;
// options as in SidechainEnvListener (only used if no listener there yet!)
diff --git a/modelling/tests/data/1crn_sc_test.pdb b/modelling/tests/data/1crn_sc_test.pdb
index e05c7c36..fd1c58c1 100644
--- a/modelling/tests/data/1crn_sc_test.pdb
+++ b/modelling/tests/data/1crn_sc_test.pdb
@@ -1,275 +1,3 @@
-HEADER PLANT PROTEIN 30-APR-81 1CRN
-TITLE WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION.
-TITLE 2 PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF CRAMBIN
-COMPND MOL_ID: 1;
-COMPND 2 MOLECULE: CRAMBIN;
-COMPND 3 CHAIN: A;
-COMPND 4 ENGINEERED: YES
-SOURCE MOL_ID: 1;
-SOURCE 2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA;
-SOURCE 3 ORGANISM_TAXID: 3721;
-SOURCE 4 STRAIN: SUBSP. ABYSSINICA
-KEYWDS PLANT SEED PROTEIN, PLANT PROTEIN
-EXPDTA X-RAY DIFFRACTION
-AUTHOR W.A.HENDRICKSON,M.M.TEETER
-REVDAT 7 11-JUL-12 1CRN 1 SCALE1 VERSN HEADER
-REVDAT 6 24-FEB-09 1CRN 1 VERSN
-REVDAT 5 16-APR-87 1CRN 1 HEADER
-REVDAT 4 04-MAR-85 1CRN 1 REMARK
-REVDAT 3 30-SEP-83 1CRN 1 REVDAT
-REVDAT 2 03-DEC-81 1CRN 1 SHEET
-REVDAT 1 28-JUL-81 1CRN 0
-JRNL AUTH M.M.TEETER
-JRNL TITL WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC
-JRNL TITL 2 RESOLUTION: PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF
-JRNL TITL 3 CRAMBIN.
-JRNL REF PROC.NATL.ACAD.SCI.USA V. 81 6014 1984
-JRNL REFN ISSN 0027-8424
-JRNL PMID 16593516
-JRNL DOI 10.1073/PNAS.81.19.6014
-REMARK 1
-REMARK 1 REFERENCE 1
-REMARK 1 AUTH W.A.HENDRICKSON,M.M.TEETER
-REMARK 1 TITL STRUCTURE OF THE HYDROPHOBIC PROTEIN CRAMBIN DETERMINED
-REMARK 1 TITL 2 DIRECTLY FROM THE ANOMALOUS SCATTERING OF SULPHUR
-REMARK 1 REF NATURE V. 290 107 1981
-REMARK 1 REFN ISSN 0028-0836
-REMARK 1 REFERENCE 2
-REMARK 1 AUTH M.M.TEETER,W.A.HENDRICKSON
-REMARK 1 TITL HIGHLY ORDERED CRYSTALS OF THE PLANT SEED PROTEIN CRAMBIN
-REMARK 1 REF J.MOL.BIOL. V. 127 219 1979
-REMARK 1 REFN ISSN 0022-2836
-REMARK 2
-REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
-REMARK 3
-REMARK 3 REFINEMENT.
-REMARK 3 PROGRAM : PROLSQ
-REMARK 3 AUTHORS : KONNERT,HENDRICKSON
-REMARK 3
-REMARK 3 DATA USED IN REFINEMENT.
-REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
-REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL
-REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
-REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
-REMARK 3 NUMBER OF REFLECTIONS : NULL
-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) : NULL
-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 : 327
-REMARK 3 NUCLEIC ACID ATOMS : 0
-REMARK 3 HETEROGEN ATOMS : 0
-REMARK 3 SOLVENT ATOMS : 0
-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) : NULL
-REMARK 3
-REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
-REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
-REMARK 3 BOND LENGTH (A) : NULL ; NULL
-REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
-REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
-REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
-REMARK 3
-REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
-REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
-REMARK 3
-REMARK 3 NON-BONDED CONTACT RESTRAINTS.
-REMARK 3 SINGLE TORSION (A) : NULL ; NULL
-REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
-REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
-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) : NULL ; NULL
-REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
-REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
-REMARK 3
-REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
-REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
-REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
-REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
-REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
-REMARK 3
-REMARK 3 OTHER REFINEMENT REMARKS: NULL
-REMARK 4
-REMARK 4 1CRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
-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 : NULL
-REMARK 200 TEMPERATURE (KELVIN) : NULL
-REMARK 200 PH : NULL
-REMARK 200 NUMBER OF CRYSTALS USED : NULL
-REMARK 200
-REMARK 200 SYNCHROTRON (Y/N) : NULL
-REMARK 200 RADIATION SOURCE : NULL
-REMARK 200 BEAMLINE : NULL
-REMARK 200 X-RAY GENERATOR MODEL : NULL
-REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
-REMARK 200 WAVELENGTH OR RANGE (A) : NULL
-REMARK 200 MONOCHROMATOR : NULL
-REMARK 200 OPTICS : NULL
-REMARK 200
-REMARK 200 DETECTOR TYPE : NULL
-REMARK 200 DETECTOR MANUFACTURER : NULL
-REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
-REMARK 200 DATA SCALING SOFTWARE : NULL
-REMARK 200
-REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
-REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
-REMARK 200 RESOLUTION RANGE LOW (A) : NULL
-REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
-REMARK 200
-REMARK 200 OVERALL.
-REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
-REMARK 200 DATA REDUNDANCY : NULL
-REMARK 200 R MERGE (I) : NULL
-REMARK 200 R SYM (I) : NULL
-REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
-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: NULL
-REMARK 200 SOFTWARE USED: NULL
-REMARK 200 STARTING MODEL: NULL
-REMARK 200
-REMARK 200 REMARK: NULL
-REMARK 280
-REMARK 280 CRYSTAL
-REMARK 280 SOLVENT CONTENT, VS (%): 32.16
-REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81
-REMARK 280
-REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
-REMARK 290
-REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
-REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
-REMARK 290
-REMARK 290 SYMOP SYMMETRY
-REMARK 290 NNNMMM OPERATOR
-REMARK 290 1555 X,Y,Z
-REMARK 290 2555 -X,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 0.00000
-REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 9.32500
-REMARK 290 SMTRY3 2 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 400
-REMARK 400 COMPOUND
-REMARK 400 THE SECONDARY STRUCTURE SPECIFICATIONS ARE THOSE DEFINED
-REMARK 400 IN REFERENCE 1 ABOVE AND DEPEND ON PARTICULAR DEFINITIONS
-REMARK 400 THAT MAY AFFECT THE DETERMINATION OF END POINTS. PLEASE
-REMARK 400 CONSULT THE PRIMARY REFERENCE AND EXAMINE STRUCTURAL
-REMARK 400 DETAILS SUCH AS HYDROGEN BONDING AND CONFORMATION ANGLES
-REMARK 400 WHEN MAKING USE OF THE SPECIFICATIONS.
-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 10 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
-REMARK 500 TYR A 29 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES
-REMARK 500
-REMARK 500 REMARK: NULL
-DBREF 1CRN A 1 46 UNP P01542 CRAM_CRAAB 1 46
-SEQRES 1 A 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE
-SEQRES 2 A 46 ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS
-SEQRES 3 A 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR
-SEQRES 4 A 46 CYS PRO GLY ASP TYR ALA ASN
-HELIX 1 H1 ILE A 7 PRO A 19 13/10 CONFORMATION RES 17,19 13
-HELIX 2 H2 GLU A 23 THR A 30 1DISTORTED 3/10 AT RES 30 8
-SHEET 1 S1 2 THR A 1 CYS A 4 0
-SHEET 2 S1 2 CYS A 32 ILE A 35 -1
-SSBOND 1 CYS A 3 CYS A 40 1555 1555 2.00
-SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.04
-SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.05
-CRYST1 40.960 18.650 22.520 90.00 90.77 90.00 P 1 21 1 2
-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 0.024414 0.000000 0.000328 0.00000
-SCALE2 0.000000 0.053619 0.000000 0.00000
-SCALE3 0.000000 0.000000 0.044409 0.00000
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
@@ -282,14 +10,11 @@ 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
diff --git a/modelling/tests/test_sidechain_reconstructor.cc b/modelling/tests/test_sidechain_reconstructor.cc
index 4f0f2e01..e6f9a9a2 100644
--- a/modelling/tests/test_sidechain_reconstructor.cc
+++ b/modelling/tests/test_sidechain_reconstructor.cc
@@ -42,13 +42,14 @@ SidechainReconstructorPtr GetScRec(const ost::mol::EntityHandle& test_ent) {
return sc_rec;
}
-void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
- uint start_resnum, uint loop_length, uint num_residues) {
- // reconstruct
- SidechainReconstructionDataPtr sc_data;
- sc_data = sc_rec->Reconstruct(start_resnum, loop_length);
+// assume: single chain and res_idx = resnum-1
+void CheckRecData(SidechainReconstructionDataPtr sc_data,
+ const std::vector<uint>& start_resnums,
+ const std::vector<uint>& loop_lengths,
+ uint num_residues) {
// check all_pos size
BOOST_CHECK_EQUAL(sc_data->all_pos->GetNumResidues(), num_residues);
+
// check env_pos consistency
const uint num_rec_residues = sc_data->env_pos->res_indices.size();
BOOST_CHECK_EQUAL(sc_data->env_pos->all_pos->GetNumResidues(),
@@ -60,16 +61,32 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
BOOST_CHECK_EQUAL(sc_data->env_pos->all_pos->GetAA(i),
sc_data->all_pos->GetAA(res_idx));
}
- // check loop
- BOOST_CHECK_EQUAL(sc_data->loop_start_indices.size(), 1u);
- BOOST_CHECK_EQUAL(sc_data->loop_lengths.size(), 1u);
- BOOST_CHECK_EQUAL(sc_data->loop_lengths[0], loop_length);
- for (uint i = 0; i < loop_length; ++i) {
+
+ // generate expected data for loops -> set to be ok with flips
+ const uint num_loops = start_resnums.size();
+ std::set<uint> exp_loop_lengths(loop_lengths.begin(), loop_lengths.end());
+ std::set<uint> exp_res_indices;
+ for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
+ for (uint idx = 0; idx < loop_lengths[i_loop]; ++idx) {
+ exp_res_indices.insert(start_resnums[i_loop] + idx - 1);
+ }
+ }
+ // check loops
+ BOOST_CHECK_EQUAL(sc_data->loop_start_indices.size(), num_loops);
+ BOOST_CHECK_EQUAL(sc_data->loop_lengths.size(), num_loops);
+ std::set<uint> sc_loop_lengths(sc_data->loop_lengths.begin(),
+ sc_data->loop_lengths.end());
+ BOOST_CHECK(sc_loop_lengths == exp_loop_lengths);
+ std::set<uint> sc_res_indices;
+ for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
// all loop res. assumed to be contiguous
- const uint start_idx = sc_data->loop_start_indices[0];
- const uint res_idx = sc_data->env_pos->res_indices[start_idx + i];
- BOOST_CHECK(res_idx == start_resnum + i - 1);
+ const uint start_idx = sc_data->loop_start_indices[i_loop];
+ for (uint idx = 0; idx < sc_data->loop_lengths[i_loop]; ++idx) {
+ sc_res_indices.insert(sc_data->env_pos->res_indices[start_idx + idx]);
+ }
}
+ BOOST_CHECK(sc_res_indices == exp_res_indices);
+
// check N-ter / C-ter info
BOOST_CHECK_EQUAL(sc_data->env_pos->res_indices.size(),
sc_data->is_n_ter.size());
@@ -82,6 +99,7 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
BOOST_CHECK(is_nter == sc_data->is_n_ter[i]);
BOOST_CHECK(is_cter == sc_data->is_c_ter[i]);
}
+
// check rotamer_res_indices
for (uint i = 0; i < sc_data->rotamer_res_indices.size(); ++i) {
const uint i_res = sc_data->rotamer_res_indices[i];
@@ -89,6 +107,7 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
const uint res_idx = sc_data->env_pos->res_indices[i_res];
BOOST_CHECK(!(sc_data->all_pos->IsAllSet(res_idx)));
}
+
// check disulfid_bridges
for (uint i = 0; i < sc_data->disulfid_bridges.size(); ++i) {
const uint i_res1 = sc_data->disulfid_bridges[i].first;
@@ -102,6 +121,29 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
}
}
+void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
+ uint start_resnum, uint loop_length, uint num_residues) {
+ // reconstruct
+ SidechainReconstructionDataPtr sc_data;
+ sc_data = sc_rec->Reconstruct(start_resnum, loop_length);
+ // DEBUG-OUT
+ // std::cout << "SRN: " << start_resnum << ", LL: " << loop_length
+ // << ", NR: " << num_residues
+ // << ", RIS: " << sc_data->env_pos->res_indices.size()
+ // << ", RRIS: " << sc_data->rotamer_res_indices.size()
+ // << ", DBS: " << sc_data->disulfid_bridges.size() << "\n";
+ // turn into vector for check and to call other one
+ std::vector<uint> start_resnums(1, start_resnum);
+ std::vector<uint> loop_lengths(1, loop_length);
+ // check
+ CheckRecData(sc_data, start_resnums, loop_lengths, num_residues);
+ // call other one
+ std::vector<uint> chain_indices(1, 0);
+ sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
+ // check
+ CheckRecData(sc_data, start_resnums, loop_lengths, num_residues);
+}
+
void CheckEmptyLoop(const SidechainReconstructionDataPtr sc_data,
uint num_residues) {
// must all be valid and empty
@@ -145,11 +187,23 @@ BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops) {
std::vector<uint> chain_indices(1, 0);
sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
CheckEmptyLoop(sc_data, num_residues);
+
+ // try three loops (note: overlap resolution is tested with IdxHandler)
+ loop_lengths[0] = 3;
+ start_resnums.push_back(20);
+ start_resnums.push_back(30);
+ loop_lengths.push_back(2);
+ loop_lengths.push_back(1);
+ chain_indices.push_back(0);
+ chain_indices.push_back(0);
+ sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
+ CheckRecData(sc_data, start_resnums, loop_lengths, num_residues);
}
BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops_crn) {
// setup crn to test disulfid bridges
ost::mol::EntityHandle test_ent = LoadTestStructure("data/1crn_sc_test.pdb");
+ // -> sc missing for THR2 & CYS3, 3 disulfid bridges expected...
uint num_residues = test_ent.GetResidueCount();
SidechainReconstructorPtr sc_rec = GetScRec(test_ent);
--
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