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Commit df9e4aa3 authored by Bienchen's avatar Bienchen
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Merge branch 'mm' into develop

parents 7c55ff7d 851d6e1a
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.gitignore
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− 0
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...@@ -72,3 +72,4 @@ build.ninja ...@@ -72,3 +72,4 @@ build.ninja
modules/gui/src/dngr.qrc.depends modules/gui/src/dngr.qrc.depends
/compile_commands.json /compile_commands.json
/modules/bindings/tests/formatdb.log /modules/bindings/tests/formatdb.log
/modules/mol/mm/src/settings.hh
CMakeLists.txt
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− 4
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...@@ -51,6 +51,7 @@ option(COMPILE_TESTS "whether unit tests should be compiled by default" OFF) ...@@ -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(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(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(HIDDEN_VISIBILITY "on gcc, use -fvisibility=hidden" OFF)
option(ENABLE_MM "whether openmm support is added" OFF)
if (CXX) if (CXX)
set(CMAKE_CXX_COMPILER ${CXX}) set(CMAKE_CXX_COMPILER ${CXX})
...@@ -140,6 +141,12 @@ if (PROFILE) ...@@ -140,6 +141,12 @@ if (PROFILE)
else() else()
set(_PROFILE OFF) set(_PROFILE OFF)
endif() endif()
if(ENABLE_MM)
set(_OPENMM ON)
else()
set(_OPENMM OFF)
endif()
if (UBUNTU_LAYOUT) if (UBUNTU_LAYOUT)
set(_UBUNTU_LAYOUT ON) set(_UBUNTU_LAYOUT ON)
...@@ -147,8 +154,6 @@ else() ...@@ -147,8 +154,6 @@ else()
set(_UBUNTU_LAYOUT OFF) set(_UBUNTU_LAYOUT OFF)
endif() endif()
add_definitions(-DEIGEN2_SUPPORT)
if (COMPOUND_LIB) if (COMPOUND_LIB)
set(_COMP_LIB "${COMPOUND_LIB}") set(_COMP_LIB "${COMPOUND_LIB}")
if (NOT IS_ABSOLUTE "${COMPOUND_LIB}") if (NOT IS_ABSOLUTE "${COMPOUND_LIB}")
...@@ -227,13 +232,20 @@ else() ...@@ -227,13 +232,20 @@ else()
set (PNG_LIBRARY "") set (PNG_LIBRARY "")
endif() endif()
find_package(Eigen 2.0.0 REQUIRED) find_package(Eigen 3.2.0 REQUIRED)
find_package(Python 2.4 REQUIRED) find_package(Python 2.4 REQUIRED)
if(USE_NUMPY) if(USE_NUMPY)
find_package(Numpy REQUIRED) find_package(Numpy REQUIRED)
endif() endif()
if(ENABLE_MM)
find_package(OpenMM REQUIRED)
set(_OPENMM_PLUGINS "${OPEN_MM_PLUGIN_DIR}")
else(ENABLE_MM)
set(_OPENMM_PLUGINS "NONE")
endif(ENABLE_MM)
if (ENABLE_IMG) if (ENABLE_IMG)
find_package(FFTW REQUIRED) find_package(FFTW REQUIRED)
find_package(TIFF REQUIRED) find_package(TIFF REQUIRED)
...@@ -287,9 +299,10 @@ endif() ...@@ -287,9 +299,10 @@ endif()
# basic environment # basic environment
include_directories(${Boost_INCLUDE_DIRS} include_directories(${Boost_INCLUDE_DIRS}
${FFTW_INCLUDE_DIRS} ${FFTW_INCLUDE_DIRS}
${EIGEN2_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS}
${TIFF_INCLUDE_DIR} ${TIFF_INCLUDE_DIR}
${PNG_INCLUDE_DIRS} ${PNG_INCLUDE_DIRS}
${OPEN_MM_INCLUDE_DIRS}
) )
if(USE_NUMPY) if(USE_NUMPY)
include_directories(${PYTHON_NUMPY_INCLUDE_DIR}) include_directories(${PYTHON_NUMPY_INCLUDE_DIR})
...@@ -344,6 +357,8 @@ message(STATUS ...@@ -344,6 +357,8 @@ message(STATUS
" Shader support (-DUSE_SHADER) : ${_SHADER}\n" " Shader support (-DUSE_SHADER) : ${_SHADER}\n"
" Numpy support (-DUSE_NUMPY) : ${_NUMPY}\n" " Numpy support (-DUSE_NUMPY) : ${_NUMPY}\n"
" SpaceNav Device support (-DENABLE_SPNAV) : ${_SPNAV}\n" " SpaceNav Device support (-DENABLE_SPNAV) : ${_SPNAV}\n"
" OpenMM support (-DENABLE_MM) : ${_OPENMM}\n"
" OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : ${_OPENMM_PLUGINS}\n"
" Optimize (-DOPTIMIZE) : ${_OPT}\n" " Optimize (-DOPTIMIZE) : ${_OPT}\n"
" Profiling support (-DPROFILE) : ${_PROFILE}\n" " Profiling support (-DPROFILE) : ${_PROFILE}\n"
" Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n" " Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
......
build_configs/buildconfig_bc2
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set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "") set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/lib/libfftw3f.so" CACHE PATH "") set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a" CACHE PATH "")
set(Boost_COMPILER "-gcc41" CACHE PATH "") set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10" CACHE PATH "")
set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "") set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "") set(BOOST_ROOT "/import/bc2/apps/Boost/1.53.0-goolf-1.4.10-Python-2.7.5" CACHE PATH "")
set(BOOST_ROOT "/import/bc2/soft/app/boost/current/Linux" CACHE PATH "") set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "") set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
set (CMAKE_BUILD_TYPE "Release" CACHE PATH "") set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
build_configs/buildconfig_bc2_static
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set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "") set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/lib/libfftw3f.a" CACHE PATH "") set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a" CACHE PATH "")
set(DL_LIBRARIES "/usr/lib64/libdl.a" CACHE PATH "") set(DL_LIBRARIES "/usr/lib64/libdl.a" CACHE PATH "")
set(PTHREAD_LIBRARIES "/usr/lib64/libpthread.a" CACHE PATH "") set(PTHREAD_LIBRARIES "/usr/lib64/libpthread.a" CACHE PATH "")
set(ZLIB_LIBRARY "/usr/lib64/libz.a" CACHE PATH "") set(ZLIB_LIBRARY "/scicore/soft/apps/zlib/1.2.8-goolf-1.4.10/lib/libz.a" CACHE PATH "")
set(Boost_COMPILER "-gcc41" CACHE PATH "") set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10" CACHE PATH "")
set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "") set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "") set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "") set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
set (CMAKE_BUILD_TYPE "Release" CACHE PATH "") set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
build_configs/darwin_homebrew.txt
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set(PNG_INCLUDE_DIR "/usr/X11/include" CACHE PATH "include path for system libpng") set(PNG_INCLUDE_DIR "/usr/X11/include" CACHE PATH "include path for system libpng")
set(EIGEN2_INCLUDE_DIR "/usr/local/include/eigen3" CACHE PATH "Eigen3-compatible include path") set(EIGEN3_INCLUDE_DIR "/usr/local/include/eigen3" CACHE PATH "Eigen3-compatible include path")
build_configs/win32
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...@@ -10,7 +10,7 @@ set(PNG_LIBRARY "${USER_DIR}/lib/libpng13.lib" CACHE PATH "includes for libpng") ...@@ -10,7 +10,7 @@ set(PNG_LIBRARY "${USER_DIR}/lib/libpng13.lib" CACHE PATH "includes for libpng")
set(ZLIB_INCLUDE_DIR "${USER_DIR}/include/" CACHE PATH "zlib includes") set(ZLIB_INCLUDE_DIR "${USER_DIR}/include/" CACHE PATH "zlib includes")
set(TIFF_INCLUDE_DIR "${USER_DIR}/include/" CACHE PATH "tiff includes") set(TIFF_INCLUDE_DIR "${USER_DIR}/include/" CACHE PATH "tiff includes")
set(TIFF_LIBRARY "${USER_DIR}/lib/libtiff_i.lib/" CACHE PATH "tiff includes") set(TIFF_LIBRARY "${USER_DIR}/lib/libtiff_i.lib/" CACHE PATH "tiff includes")
set(EIGEN2_INCLUDE_DIR "${USER_DIR}/include/eigen2" CACHE PATH "gsl includes") set(EIGEN3_INCLUDE_DIR "${USER_DIR}/include/Eigen" CACHE PATH "gsl includes")
set(USE_DOUBLE_PRECISION "OFF" CACHE PATH "double precision") set(USE_DOUBLE_PRECISION "OFF" CACHE PATH "double precision")
set(FFTW_LIBRARIES "${USER_DIR}/lib/libfftw3f-3.lib" CACHE PATH "fftw libs") set(FFTW_LIBRARIES "${USER_DIR}/lib/libfftw3f-3.lib" CACHE PATH "fftw libs")
#set(FFTW_LIBRARIES "${USER_DIR}/lib/libfftw3-3.lib" CACHE PATH "fftw libs") #set(FFTW_LIBRARIES "${USER_DIR}/lib/libfftw3-3.lib" CACHE PATH "fftw libs")
......
cmake_support/FindEigen.cmake
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# - Try to find Eigen2 lib # - Try to find Eigen3 lib
# Once done this will define # Once done this will define
# #
# EIGEN2_FOUND - system has eigen lib # EIGEN3_FOUND - system has eigen lib
# EIGEN2_INCLUDE_DIRS - the eigen include directories # EIGEN3_INCLUDE_DIRS - the eigen include directories
find_path(EIGEN2_INCLUDE_DIR NAMES Eigen/Core find_path(EIGEN3_INCLUDE_DIR NAMES Eigen/Core
PATH_SUFFIXES eigen2
PATH_SUFFIXES eigen3 PATH_SUFFIXES eigen3
) )
set(EIGEN2_INCLUDE_DIRS ${EIGEN2_INCLUDE_DIR}) set(EIGEN3_INCLUDE_DIRS ${EIGEN3_INCLUDE_DIR})
include (FindPackageHandleStandardArgs) include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (EIGEN DEFAULT_MSG EIGEN2_INCLUDE_DIR) find_package_handle_standard_args (EIGEN DEFAULT_MSG EIGEN3_INCLUDE_DIR)
mark_as_advanced (EIGEN2_INCLUDE_DIR) mark_as_advanced (EIGEN3_INCLUDE_DIR)
......
cmake_support/FindOpenMM.cmake 0 → 100644
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# Try to find OpenMM
#
# Once done this will define
# - Find OpenMM
# Find the native OpenMM includes and library
#
# OPEN_MM_INCLUDE_DIR - OpenMM include dirs.
# OPEN_MM_LIBRARIES - List of libraries when using OpenMM.
# OPEN_MM_FOUND - True if OpenMM found.
# OPEN_MM_PLUGIN_DIR - Default for ressource plugins
if (OPEN_MM_INCLUDE_DIR)
set(OPEN_MM_FOUND TRUE)
else (OPEN_MM_INCLUDE_DIR)
find_path (OPEN_MM_INCLUDE_DIR OpenMM.h)
endif (OPEN_MM_INCLUDE_DIR)
if (OPEN_MM_LIBRARY)
set(OPEN_MM_FOUND TRUE)
else (OPEN_MM_LIBRARY)
find_library (OPEN_MM_LIBRARY NAMES OpenMM)
endif(OPEN_MM_LIBRARY)
set(OPEN_MM_LIBRARIES ${OPEN_MM_LIBRARY})
set(OPEN_MM_INCLUDE_DIRS ${OPEN_MM_INCLUDE_DIR})
# handle the QUIETLY and REQUIRED arguments and set OpenMM_FOUND to TRUE if
# all listed variables are TRUE
include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (OpenMM DEFAULT_MSG OPEN_MM_LIBRARY OPEN_MM_INCLUDE_DIR)
if (OPEN_MM_LIBRARY)
set(OPEN_MM_FOUND TRUE)
if (NOT OPEN_MM_PLUGIN_DIR)
set(OPEN_MM_PLUGIN_DIR "/usr/local/openmm/lib/plugins")
endif (NOT OPEN_MM_PLUGIN_DIR)
if (NOT EXISTS "${OPEN_MM_PLUGIN_DIR}")
message(FATAL_ERROR "OpenMM plugin directory does not exist: '${OPEN_MM_PLUGIN_DIR}'")
endif (NOT EXISTS "${OPEN_MM_PLUGIN_DIR}")
endif (OPEN_MM_LIBRARY)
mark_as_advanced (OPEN_MM_LIBRARY OPEN_MM_INCLUDE_DIR OPEN_MM_FOUND
OPEN_MM_PLUGIN_DIR)
examples/code_fragments/mm/1CRN.pdb 0 → 100644
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examples/code_fragments/mm/ethanol.pdb 0 → 100644
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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
examples/code_fragments/mm/ethanol_example.py 0 → 100644
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from ost.mol.mm import *
from PyQt4 import QtCore
"""
MM - Demo
!!!Requires OpenStructure to be compiled with MM-Support!!!
This demo should show the procedure of building a custom forcefield.
The script can directly be started from within DNG.
"""
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(Interaction(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 = Interaction(FuncType.HarmonicBond)
c_c_bond = Interaction(FuncType.HarmonicBond)
c_o_bond = Interaction(FuncType.HarmonicBond)
o_h_bond = Interaction(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 = Interaction(FuncType.UreyBradleyAngle)
h_c_c_angle = Interaction(FuncType.UreyBradleyAngle)
h_c_o_angle = Interaction(FuncType.UreyBradleyAngle)
c_c_o_angle = Interaction(FuncType.UreyBradleyAngle)
c_o_h_angle = Interaction(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 = Interaction(FuncType.PeriodicDihedral)
c_c_o_h_dihedral_one = Interaction(FuncType.PeriodicDihedral)
c_c_o_h_dihedral_two = Interaction(FuncType.PeriodicDihedral)
c_c_o_h_dihedral_three = Interaction(FuncType.PeriodicDihedral)
x_c_o_x_dihedral = Interaction(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 = Interaction(FuncType.LJ)
o_lj = Interaction(FuncType.LJ)
h_lj = Interaction(FuncType.LJ)
oh_lj = Interaction(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 = Settings()
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)
examples/code_fragments/mm/ethanol_example_using_topology.py 0 → 100644
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from ost.mol.mm import *
from PyQt4 import QtCore
from math import sqrt
from math import sin
"""
MM - Demo
!!!Requires OpenStructure to be compiled with MM-Support!!!
This demo should show the procedure building a topology from scratch and
setting up a simulation. As an additional piece of sugar, it demonstrates
the capabilities of altering force parameters as the simulation runs.
The script can directly be started from within DNG.
"""
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(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 = Settings()
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,ent,settings)
go = gfx.Entity("ethanol",sim.GetEntity())
go.SetRenderMode(gfx.CUSTOM)
scene.Add(go)
anim = Anim(sim,go,cc_bond_index)
anim.start(2)
examples/code_fragments/mm/gb_example.py 0 → 100644
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from ost.mol import mm
from PyQt4 import QtCore
"""
MM - Demo
!!!Requires OpenStructure to be compiled with MM-Support!!!
This demo should show the setup of a simple simulation using implicit solvent.
The script can directly be started from within DNG.
"""
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.Settings()
settings.integrator = mm.LangevinIntegrator(310,1,0.002)
settings.add_gbsa = True
settings.forcefield = mm.LoadCHARMMForcefield()
settings.platform = mm.Platform.CPU
settings.nonbonded_method = mm.NonbondedMethod.CutoffNonPeriodic
sim = mm.Simulation(prot,settings)
sim.ApplyLBFGS(tolerance = 1.0, max_iterations = 200)
sim.UpdatePositions()
ent = sim.GetEntity()
go = gfx.Entity("crambin",ent)
scene.Add(go)
anim = Anim(sim,ent,go)
anim.start(1)
examples/code_fragments/mm/gb_example_traj.dcd 0 → 100644
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examples/code_fragments/mm/gb_example_traj.pdb 0 → 100644
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examples/code_fragments/mm/gb_example_view_trajectory.py 0 → 100644
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from ost.gui import trajectory_viewer
"""
MM - Demo
!!!Requires OpenStructure to be compiled with MM-Support!!!
This demo demonstrates how to actually look at the trajectory created
in the gb_example_writing_trajectory.py script.
"""
t = io.LoadCHARMMTraj("gb_example_traj.pdb","gb_example_traj.dcd")
go = gfx.Entity("gb",t.GetEntity())
scene.Add(go)
w = trajectory_viewer.TrajWidget([t],[go])
w.show()
examples/code_fragments/mm/gb_example_writing_trajectory.py 0 → 100644
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from ost.mol.mm import *
"""
MM - Demo
!!!Requires OpenStructure to be compiled with MM-Support!!!
This demo should show the procedure of setting up a simulation and write
the results directly to disk.
"""
prot=io.LoadPDB('1CRN.pdb')
#set up the simulation
settings = Settings()
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
settings.cpu_properties["CpuThreads"] = "2"
sim = Simulation(prot,settings)
#minimize it
sim.ApplySD(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()
modules/bindings/doc/bindings.rst
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...@@ -15,6 +15,7 @@ So far, the binding module includes: ...@@ -15,6 +15,7 @@ So far, the binding module includes:
dssp dssp
blast blast
hhblits
msms msms
tmtools tmtools
clustalw clustalw
......
modules/bindings/doc/hhblits.rst 0 → 100644
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:mod:`~ost.bindings.hhblits` - Search related sequences in databases
================================================================================
.. module:: ost.bindings.hhblits
:synopsis: Search related sequences in databases
Introduction
--------------------------------------------------------------------------------
HHblits is a sequence search tool like BLAST, able to find more distant
homologs This is achieved by performing `profile-profile searches`. In BLAST, a
\query sequence is searched against a sequence database. That is a
`sequence-sequence search`. HHblits works on a profile database, usually that
one is provided, queried with a sequence profile. The latter one needs to be
calculated before the actual search. In very simple words, HHblits is using
per-sequence scoring functions to be more sensitive, in this particular case
Hidden Markov models. The software suite needed for HHblits can be found
`here <http://toolkit.tuebingen.mpg.de/hhblits>`_.
Examples
--------------------------------------------------------------------------------
A typical search: Get an instance of the bindings, build the search profile out
of the query sequence, run the search and iterate results. Since
:class:`~HHblits` works with a :class:`~ost.seq.SequenceHandle` or a FastA
file, both ways are shown.
First query by sequence:
.. code-block:: python
from ost.bindings import hhblits
# get a SequenceHandle
query_seq = seq.CreateSequence('Query',
'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGS'+
'ELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGF'+
'PRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPS'+
'GRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYH'+
'QMTAPLIGYYYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
# set up the search environment
# $EBROOTHHMINSUITE points to the root of a HHsuite installation
hh = hhblits.HHblits(query_seq, os.getenv('EBROOTHHMINSUITE'))
# now create a search profile for the query sequence against the NR20 db
# provided on the HHblits web page, nr20_12Aug11 is just the prefix common to
# all db files, so `ls hhtools/nr20_12Aug11*` would list all of them
a3m_file = hh.BuildQueryMSA(nrdb='hhtools/nr20_12Aug11')
# search time! we just search against NR20 again, but every HHblits db is
# working here, e.g. one build from all the sequences in PDB
hit_file = hh.Search(a3m_file, 'hhtools/nr20_12Aug11')
# lets have a look at the resuls
with open(hit_file) as hit_fh:
header, hits = hhblits.ParseHHblitsOutput(hit_fh)
for hit in hits:
print hit.aln
Very similar going by file:
.. code-block:: python
from ost.bindings import hhblits
# set up the search environment
# $EBROOTHHMINSUITE points to the root of a HHsuite installation
hh = hhblits.HHblits('query.fas', os.getenv('EBROOTHHMINSUITE'))
# now create a search profile for the query sequence against the NR20 db
# provided on the HHblits web page, nr20_12Aug11 is just the prefix common to
# all db files, so `ls hhtools/nr20_12Aug11*` would list all of them
a3m_file = hh.BuildQueryMSA(nrdb='hhtools/nr20_12Aug11')
# search time! we just search against NR20 again, but every HHblits db is
# working here, e.g. one build from all the sequences in PDB
hit_file = hh.Search(a3m_file, 'hhtools/nr20_12Aug11')
# lets have a look at the resuls
with open(hit_file) as hit_fh:
header, hits = hhblits.ParseHHblitsOutput(hit_fh)
for hit in hits:
print hit.aln
The alignments produced by HHblits are sometimes slightly better than by BLAST,
so one may want to extract them:
.. code-block:: python
from ost.bindings import hhblits
# set up the search environment
# $EBROOTHHMINSUITE points to the root of a HHsuite installation
hh = hhblits.HHblits('query.fas', os.getenv('EBROOTHHMINSUITE'))
# now create a search profile for the query sequence against the NR20 db
# provided on the HHblits web page, nr20_12Aug11 is just the prefix common to
# all db files, so `ls hhtools/nr20_12Aug11*` would list all of them
a3m_file = hh.BuildQueryMSA(nrdb='hhtools/nr20_12Aug11')
# note that ParseA3M is not a class method but a module function
output = hhblits.ParseA3M(open(a3m_file))
print output['msa']
Binding API
--------------------------------------------------------------------------------
.. autoclass:: ost.bindings.hhblits.HHblits
:members:
.. autoclass:: ost.bindings.hhblits.HHblitsHit
.. autoclass:: ost.bindings.hhblits.HHblitsHeader
.. autofunction:: ost.bindings.hhblits.ParseHHblitsOutput
.. autofunction:: ost.bindings.hhblits.ParseA3M
.. autofunction:: ost.bindings.hhblits.ParseHeaderLine
.. autofunction:: ost.bindings.hhblits.ParseHHM
.. autofunction:: ost.bindings.hhblits.EstimateMemConsumption
.. LocalWords: HHblits homologs
modules/bindings/pymod/CMakeLists.txt
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...@@ -8,6 +8,7 @@ dssp.py ...@@ -8,6 +8,7 @@ dssp.py
clustalw.py clustalw.py
utils.py utils.py
naccess.py naccess.py
hhblits.py
blast.py blast.py
cadscore.py cadscore.py
kclust.py kclust.py
......
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