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// $Id$
//
// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <boost/python.hpp>
#include <GraphMol/GraphMol.h>
#include <RDBoost/Wrap.h>
#include <ForceField/ForceField.h>
#include <ForceField/Wrap/PyForceField.h>
#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/MMFF/Builder.h>
namespace python = boost::python;
namespace RDKit {
int UFFOptimizeMolecule(ROMol &mol, int maxIters=200,
double vdwThresh=10.0, int confId=-1,
bool ignoreInterfragInteractions=true ){
ForceFields::ForceField *ff=UFF::constructForceField(mol,vdwThresh, confId,
ignoreInterfragInteractions);
ff->initialize();
int res=ff->minimize(maxIters);
delete ff;
return res;
}
ForceFields::PyForceField *UFFGetMoleculeForceField(ROMol &mol,
double vdwThresh=10.0,
int confId=-1,
bool ignoreInterfragInteractions=true ){
ForceFields::ForceField *ff=UFF::constructForceField(mol,vdwThresh, confId,
ignoreInterfragInteractions);
ForceFields::PyForceField *res=new ForceFields::PyForceField(ff);
res->initialize();
return res;
}
bool UFFHasAllMoleculeParams(const ROMol &mol){
UFF::AtomicParamVect types;
bool foundAll;
boost::tie(types,foundAll)=UFF::getAtomTypes(mol);
return foundAll;
}
int MMFFOptimizeMolecule(ROMol &mol, std::string mmffVariant = "MMFF94",
int maxIters = 200, double nonBondedThresh = 100.0, int confId = -1,
bool ignoreInterfragInteractions = true)
{
int res = -1;
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
if (mmffMolProperties.isValid()) {
ForceFields::ForceField *ff = MMFF::constructForceField(mol,
&mmffMolProperties, nonBondedThresh, confId, ignoreInterfragInteractions);
ff->initialize();
res = ff->minimize(maxIters);
delete ff;
}
return res;
}
unsigned int SanitizeMMFFMol(ROMol &mol)
{
return MMFF::sanitizeMMFFMol((RWMol &)mol);
};
ForceFields::PyMMFFMolProperties *GetMMFFMolProperties
(ROMol &mol, std::string mmffVariant = "MMFF94",
unsigned int mmffVerbosity = MMFF::MMFF_VERBOSITY_NONE)
{
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(mol, mmffVariant, mmffVerbosity);
ForceFields::PyMMFFMolProperties *pyMP = NULL;
if (mmffMolProperties && mmffMolProperties->isValid()) {
pyMP = new ForceFields::PyMMFFMolProperties(mmffMolProperties);
}
return pyMP;
}
ForceFields::PyForceField *MMFFGetMoleculeForceField(ROMol &mol,
ForceFields::PyMMFFMolProperties *pyMMFFMolProperties,
double nonBondedThresh = 100.0, int confId = -1,
bool ignoreInterfragInteractions = true)
{
ForceFields::PyForceField *pyFF = NULL;
boost::python::list res;
if (pyMMFFMolProperties) {
MMFF::MMFFMolProperties *mmffMolProperties =
&(*(pyMMFFMolProperties->mmffMolProperties));
ForceFields::ForceField *ff = MMFF::constructForceField(mol,
mmffMolProperties, nonBondedThresh,
confId, ignoreInterfragInteractions);
pyFF = new ForceFields::PyForceField(ff);
if (pyFF) {
pyFF->initialize();
}
}
return pyFF;
}
bool MMFFHasAllMoleculeParams(ROMol &mol)
{
MMFF::MMFFMolProperties mmffMolProperties(mol);
return mmffMolProperties.isValid();
}
}
BOOST_PYTHON_MODULE(rdForceFieldHelpers) {
python::scope().attr("__doc__") =
"Module containing functions to handle UFF force field"
;
std::string docString = "uses UFF to optimize a molecule's structure\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- maxIters : the maximum number of iterations (defaults to 200)\n\
- vdwThresh : used to exclude long-range van der Waals interactions\n\
(defaults to 10.0)\n\
- confId : indicates which conformer to optimize\n\
- ignoreInterfragInteractions : if true, nonbonded terms between\n\
fragments will not be added to the forcefield.\n\
\n\
RETURNS: 0 if the optimization converged, 1 if more iterations are required.\n\
\n";
python::def("UFFOptimizeMolecule", RDKit::UFFOptimizeMolecule,
(python::arg("self"),python::arg("maxIters")=200,
python::arg("vdwThresh")=10.0,python::arg("confId")=-1,
python::arg("ignoreInterfragInteractions")=true),
docString.c_str());
docString = "returns a UFF force field for a molecule\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- vdwThresh : used to exclude long-range van der Waals interactions\n\
(defaults to 10.0)\n\
- confId : indicates which conformer to optimize\n\
- ignoreInterfragInteractions : if true, nonbonded terms between\n\
fragments will not be added to the forcefield.\n\
\n";
python::def("UFFGetMoleculeForceField", RDKit::UFFGetMoleculeForceField,
(python::arg("mol"),python::arg("vdwThresh")=10.0,python::arg("confId")=-1,
python::arg("ignoreInterfragInteractions")=true),
python::return_value_policy<python::manage_new_object>(),
docString.c_str());
docString = "checks if UFF parameters are available for all of a molecule's atoms\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest.\n\
\n";
python::def("UFFHasAllMoleculeParams", RDKit::UFFHasAllMoleculeParams,
(python::arg("mol")),
docString.c_str());
python::scope().attr("__doc__") =
"Module containing functions to handle MMFF force field"
;
docString = "uses MMFF to optimize a molecule's structure\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- mmffVariant : \"MMFF94\" or \"MMFF94s\"\n\
- maxIters : the maximum number of iterations (defaults to 200)\n\
- nonBondedThresh : used to exclude long-range non-bonded\n\
interactions (defaults to 100.0)\n\
- confId : indicates which conformer to optimize\n\
- ignoreInterfragInteractions : if true, nonbonded terms between\n\
fragments will not be added to the forcefield\n\
\n\
RETURNS: 0 if the optimization converged, -1 if the forcefield could\n\
not be set up, 1 if more iterations are required.\n\
\n";
python::def("MMFFOptimizeMolecule", RDKit::MMFFOptimizeMolecule,
(python::arg("mol"), python::arg("mmffVariant") = "MMFF94",
python::arg("maxIters") = 200,
python::arg("nonBondedThresh") = 100.0,
python::arg("confId") = -1,
python::arg("ignoreInterfragInteractions") = true),
docString.c_str());
docString = "sanitizes a molecule according to MMFF requirements.\n\n\
- mol : the molecule of interest.\n\
\n";
python::def("MMFFSanitizeMolecule", RDKit::SanitizeMMFFMol,
(python::arg("mol")),
docString.c_str());
docString = "returns a PyMMFFMolProperties object for a\n\
molecule, which is required by MMFFGetMoleculeForceField()\n\
and can be used to get/set MMFF properties\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- mmffVariant : \"MMFF94\" or \"MMFF94s\"\n\
(defaults to \"MMFF94\")\n\
- mmffVerbosity : 0: none; 1: low; 2: high (defaults to 0).\n\
\n";
python::def("MMFFGetMoleculeProperties", RDKit::GetMMFFMolProperties,
(python::arg("mol"), python::arg("mmffVariant") = "MMFF94",
python::arg("mmffVerbosity") = 0),
python::return_value_policy<python::manage_new_object>(),
docString.c_str());
docString = "returns a MMFF force field for a molecule\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- pyMMFFMolProperties : PyMMFFMolProperties object as returned\n\
by MMFFGetMoleculeProperties()\n\
- nonBondedThresh : used to exclude long-range non-bonded\n\
interactions (defaults to 100.0)\n\
- confId : indicates which conformer to optimize\n\
- ignoreInterfragInteractions : if true, nonbonded terms between\n\
fragments will not be added to the forcefield\n\
\n";
python::def("MMFFGetMoleculeForceField", RDKit::MMFFGetMoleculeForceField,
(python::arg("mol"),
python::arg("pyMMFFMolProperties"),
python::arg("nonBondedThresh") = 100.0,
python::arg("confId") = -1,
python::arg("ignoreInterfragInteractions") = true),
python::return_value_policy<python::manage_new_object>(),
docString.c_str());
docString = "checks if MMFF parameters are available for all of a molecule's atoms\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
\n";
python::def("MMFFHasAllMoleculeParams", RDKit::MMFFHasAllMoleculeParams,
(python::arg("mol")),
docString.c_str());
}
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