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210a8635bf16eb99652fc33f4c701fcafa69e0a4
rdkit/Code/ForceField/Wrap/ForceField.cpp
Greg Landrum 210a8635bf add units to force field docs
2015-01-29 14:05:16 +01:00

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// $Id$
//
// Copyright (C) 2004-2006 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 <RDBoost/Wrap.h>
#include <RDBoost/Exceptions.h>
#include <GraphMol/GraphMol.h>
#include <ForceField/ForceField.h>
#include <ForceField/UFF/DistanceConstraint.h>
#include <ForceField/UFF/AngleConstraint.h>
#include <ForceField/UFF/TorsionConstraint.h>
#include <ForceField/UFF/PositionConstraint.h>
#include <ForceField/MMFF/DistanceConstraint.h>
#include <ForceField/MMFF/AngleConstraint.h>
#include <ForceField/MMFF/TorsionConstraint.h>
#include <ForceField/MMFF/PositionConstraint.h>
#include "PyForceField.h"
using namespace ForceFields;
namespace python = boost::python;
void ForceFieldAddDistanceConstraint(PyForceField *self,unsigned int idx1,unsigned int idx2,
double minLen,double maxLen,double forceConstant){
UFF::DistanceConstraintContrib *constraint;
constraint = new UFF::DistanceConstraintContrib(self->field.get(),idx1,idx2,minLen,maxLen,
forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void ForceFieldAddFixedPoint(PyForceField *self, unsigned int idx) {
self->field->fixedPoints().push_back(idx);
}
void UFFAddDistanceConstraint(PyForceField *self, unsigned int idx1, unsigned int idx2,
bool relative, double minLen, double maxLen, double forceConstant) {
UFF::DistanceConstraintContrib *constraint =
new UFF::DistanceConstraintContrib(self->field.get(),
idx1, idx2, relative, minLen, maxLen, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void UFFAddAngleConstraint(PyForceField *self, unsigned int idx1, unsigned int idx2,
unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg,
double forceConstant) {
UFF::AngleConstraintContrib *constraint =
new UFF::AngleConstraintContrib(self->field.get(),
idx1, idx2, idx3, relative, minAngleDeg, maxAngleDeg, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void UFFAddTorsionConstraint(PyForceField *self, unsigned int idx1, unsigned int idx2,
unsigned int idx3, unsigned int idx4, bool relative, double minDihedralDeg,
double maxDihedralDeg, double forceConstant) {
UFF::TorsionConstraintContrib *constraint =
new UFF::TorsionConstraintContrib(self->field.get(),
idx1, idx2, idx3, idx4, relative, minDihedralDeg, maxDihedralDeg, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void UFFAddPositionConstraint(PyForceField *self, unsigned int idx,
double maxDispl, double forceConstant) {
UFF::PositionConstraintContrib *constraint =
new UFF::PositionConstraintContrib(self->field.get(),
idx, maxDispl, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void MMFFAddDistanceConstraint(PyForceField *self, unsigned int idx1, unsigned int idx2,
bool relative, double minLen, double maxLen, double forceConstant) {
MMFF::DistanceConstraintContrib *constraint =
new MMFF::DistanceConstraintContrib(self->field.get(),
idx1, idx2, relative, minLen, maxLen, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void MMFFAddAngleConstraint(PyForceField *self, unsigned int idx1, unsigned int idx2,
unsigned int idx3, bool relative, double minAngleDeg, double maxAngleDeg,
double forceConstant) {
MMFF::AngleConstraintContrib *constraint =
new MMFF::AngleConstraintContrib(self->field.get(),
idx1, idx2, idx3, relative, minAngleDeg, maxAngleDeg, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void MMFFAddTorsionConstraint(PyForceField *self, unsigned int idx1, unsigned int idx2,
unsigned int idx3, unsigned int idx4, bool relative, double minDihedralDeg,
double maxDihedralDeg, double forceConstant) {
MMFF::TorsionConstraintContrib *constraint =
new MMFF::TorsionConstraintContrib(self->field.get(),
idx1, idx2, idx3, idx4, relative, minDihedralDeg, maxDihedralDeg, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
void MMFFAddPositionConstraint(PyForceField *self, unsigned int idx,
double maxDispl, double forceConstant) {
MMFF::PositionConstraintContrib *constraint =
new MMFF::PositionConstraintContrib(self->field.get(),
idx, maxDispl, forceConstant);
self->field->contribs().push_back(ForceFields::ContribPtr(constraint));
}
PyObject *ForceFieldGetExtraPointLoc(PyForceField *self,unsigned int idx){
if(idx >= self->extraPoints.size()){
throw IndexErrorException(idx);
}
PyObject *res = PyTuple_New(3);
PyTuple_SetItem(res,0,PyFloat_FromDouble(self->extraPoints[idx]->x));
PyTuple_SetItem(res,1,PyFloat_FromDouble(self->extraPoints[idx]->y));
PyTuple_SetItem(res,2,PyFloat_FromDouble(self->extraPoints[idx]->z));
return res;
}
PyObject *PyMMFFMolProperties::getMMFFBondStretchParams
(const RDKit::ROMol &mol, const unsigned int idx1, const unsigned int idx2) {
PyObject *res = NULL;
unsigned int bondType;
ForceFields::MMFF::MMFFBond mmffBondStretchParams;
if (mmffMolProperties->getMMFFBondStretchParams(mol,
idx1, idx2, bondType, mmffBondStretchParams)) {
res = PyTuple_New(3);
PyTuple_SetItem(res, 0, PyInt_FromLong(bondType));
PyTuple_SetItem(res, 1, PyFloat_FromDouble(mmffBondStretchParams.kb));
PyTuple_SetItem(res, 2, PyFloat_FromDouble(mmffBondStretchParams.r0));
}
return res;
};
PyObject *PyMMFFMolProperties::getMMFFAngleBendParams
(const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3) {
PyObject *res = NULL;
unsigned int angleType;
ForceFields::MMFF::MMFFAngle mmffAngleBendParams;
if (mmffMolProperties->getMMFFAngleBendParams(mol,
idx1, idx2, idx3, angleType, mmffAngleBendParams)) {
res = PyTuple_New(3);
PyTuple_SetItem(res, 0, PyInt_FromLong(angleType));
PyTuple_SetItem(res, 1, PyFloat_FromDouble(mmffAngleBendParams.ka));
PyTuple_SetItem(res, 2, PyFloat_FromDouble(mmffAngleBendParams.theta0));
}
return res;
};
PyObject *PyMMFFMolProperties::getMMFFStretchBendParams
(const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3) {
PyObject *res = NULL;
unsigned int stretchBendType;
ForceFields::MMFF::MMFFStbn mmffStretchBendParams;
ForceFields::MMFF::MMFFBond mmffBondStretchParams[2];
ForceFields::MMFF::MMFFAngle mmffAngleBendParams;
if (mmffMolProperties->getMMFFStretchBendParams(mol,
idx1, idx2, idx3, stretchBendType, mmffStretchBendParams,
mmffBondStretchParams, mmffAngleBendParams)) {
res = PyTuple_New(3);
PyTuple_SetItem(res, 0, PyInt_FromLong(stretchBendType));
PyTuple_SetItem(res, 1, PyFloat_FromDouble(mmffStretchBendParams.kbaIJK));
PyTuple_SetItem(res, 2, PyFloat_FromDouble(mmffStretchBendParams.kbaKJI));
}
return res;
};
PyObject *PyMMFFMolProperties::getMMFFTorsionParams
(const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3,
const unsigned int idx4) {
PyObject *res = NULL;
unsigned int torType;
ForceFields::MMFF::MMFFTor mmffTorsionParams;
if (mmffMolProperties->getMMFFTorsionParams(mol,
idx1, idx2, idx3, idx4, torType, mmffTorsionParams)) {
res = PyTuple_New(4);
PyTuple_SetItem(res, 0, PyInt_FromLong(torType));
PyTuple_SetItem(res, 1, PyFloat_FromDouble(mmffTorsionParams.V1));
PyTuple_SetItem(res, 2, PyFloat_FromDouble(mmffTorsionParams.V2));
PyTuple_SetItem(res, 3, PyFloat_FromDouble(mmffTorsionParams.V3));
}
return res;
};
PyObject *PyMMFFMolProperties::getMMFFOopBendParams
(const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3,
const unsigned int idx4) {
PyObject *res = NULL;
ForceFields::MMFF::MMFFOop mmffOopBendParams;
if (mmffMolProperties->getMMFFOopBendParams(mol,
idx1, idx2, idx3, idx4, mmffOopBendParams)) {
res = PyFloat_FromDouble(mmffOopBendParams.koop);
}
return res;
};
PyObject *PyMMFFMolProperties::getMMFFVdWParams
(const unsigned int idx1, const unsigned int idx2) {
PyObject *res = NULL;
ForceFields::MMFF::MMFFVdWRijstarEps mmffVdWParams;
if (mmffMolProperties->getMMFFVdWParams(idx1, idx2, mmffVdWParams)) {
res = PyTuple_New(4);
PyTuple_SetItem(res, 0, PyFloat_FromDouble(mmffVdWParams.R_ij_starUnscaled));
PyTuple_SetItem(res, 1, PyFloat_FromDouble(mmffVdWParams.epsilonUnscaled));
PyTuple_SetItem(res, 2, PyFloat_FromDouble(mmffVdWParams.R_ij_star));
PyTuple_SetItem(res, 3, PyFloat_FromDouble(mmffVdWParams.epsilon));
}
return res;
};
BOOST_PYTHON_MODULE(rdForceField) {
python::scope().attr("__doc__") =
"Exposes the ForceField class"
;
std::string docString;
python::class_<PyForceField>("ForceField","A force field",python::no_init)
.def("CalcEnergy",(double (PyForceField::*)() const)&PyForceField::calcEnergy,
"Returns the energy (in kcal/mol) of the current arrangement")
.def("Minimize",&PyForceField::minimize,(python::arg("maxIts")=200,
python::arg("forceTol")=1e-4,
python::arg("energyTol")=1e-6),
"Runs some minimization iterations.\n\n Returns 0 if the minimization succeeded.")
.def("AddDistanceConstraint",ForceFieldAddDistanceConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),
python::arg("minLen"),python::arg("maxLen"),
python::arg("forceConstant")),
"Adds a distance constraint to the UFF force field "
"(deprecated, use UFFAddDistanceConstraint instead).")
.def("AddFixedPoint",ForceFieldAddFixedPoint,
(python::arg("self"),python::arg("idx")),
"Adds a fixed point to the force field.")
.def("UFFAddDistanceConstraint",UFFAddDistanceConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),
python::arg("relative"),python::arg("minLen"),python::arg("maxLen"),
python::arg("forceConstant")),
"Adds a distance constraint to the UFF force field; if relative == True, "
"then minLen and maxLen are intended as relative to the current distance.")
.def("UFFAddAngleConstraint",UFFAddAngleConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),python::arg("idx3"),
python::arg("relative"),python::arg("minAngleDeg"),python::arg("maxAngleDeg"),
python::arg("forceConstant")),
"Adds an angle constraint to the UFF force field; if relative == True, "
"then minAngleDeg and maxAngleDeg are intended as relative to the current angle.")
.def("UFFAddTorsionConstraint",UFFAddTorsionConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),python::arg("idx3"),
python::arg("idx4"),python::arg("relative"),python::arg("minDihedralDeg"),
python::arg("maxDihedralDeg"),python::arg("forceConstant")),
"Adds a dihedral angle constraint to the UFF force field; if relative == True, "
"then minDihedralDeg and maxDihedralDeg are intended as relative to the current "
"dihedral angle.")
.def("UFFAddPositionConstraint",UFFAddPositionConstraint,
(python::arg("self"),python::arg("idx"),python::arg("maxDispl"),
python::arg("forceConstant")),
"Adds a position constraint to the UFF force field.")
.def("MMFFAddDistanceConstraint",MMFFAddDistanceConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),
python::arg("relative"),python::arg("minLen"),python::arg("maxLen"),
python::arg("forceConstant")),
"Adds a distance constraint to the MMFF force field; if relative == True, "
"then minLen and maxLen are intended as relative to the current distance.")
.def("MMFFAddAngleConstraint",MMFFAddAngleConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),python::arg("idx3"),
python::arg("relative"),python::arg("minAngleDeg"),python::arg("maxAngleDeg"),
python::arg("forceConstant")),
"Adds an angle constraint to the MMFF force field; if relative == True, "
"then minAngleDeg and maxAngleDeg are intended as relative to the current angle.")
.def("MMFFAddTorsionConstraint",MMFFAddTorsionConstraint,
(python::arg("self"),python::arg("idx1"),python::arg("idx2"),python::arg("idx3"),
python::arg("idx4"),python::arg("relative"),python::arg("minDihedralDeg"),
python::arg("maxDihedralDeg"),python::arg("forceConstant")),
"Adds a dihedral angle constraint to the MMFF force field; if relative == True, "
"then minDihedralDeg and maxDihedralDeg are intended as relative to the current "
"dihedral angle.")
.def("MMFFAddPositionConstraint",MMFFAddPositionConstraint,
(python::arg("self"),python::arg("idx"),python::arg("maxDispl"),
python::arg("forceConstant")),
"Adds a position constraint to the MMFF force field.")
.def("Initialize",&PyForceField::initialize,
"initializes the force field (call this before minimizing)")
.def("AddExtraPoint",&PyForceField::addExtraPoint,
(python::arg("self"),python::arg("x"),python::arg("y"),python::arg("z"),
python::arg("fixed")=true),
"Adds an extra point, this can be useful for adding constraints.")
.def("GetExtraPointPos",ForceFieldGetExtraPointLoc,
(python::arg("self"),python::arg("idx")),
"returns the location of an extra point as a tuple")
;
python::class_<PyMMFFMolProperties>("MMFFMolProperties",
"MMFF molecular properties", python::no_init)
.def("GetMMFFAtomType", &PyMMFFMolProperties::getMMFFAtomType,
(python::arg("self"), python::arg("idx")),
"Retrieves MMFF atom type for atom with index idx")
.def("GetMMFFFormalCharge", &PyMMFFMolProperties::getMMFFFormalCharge,
(python::arg("self"), python::arg("idx")),
"Retrieves MMFF formal charge for atom with index idx")
.def("GetMMFFPartialCharge", &PyMMFFMolProperties::getMMFFPartialCharge,
(python::arg("self"), python::arg("idx")),
"Retrieves MMFF partial charge for atom with index idx")
.def("GetMMFFBondStretchParams", &PyMMFFMolProperties::getMMFFBondStretchParams,
(python::arg("self"), python::arg("mol"), python::arg("idx1"), python::arg("idx2")),
"Retrieves MMFF bond stretch parameters for atoms with indexes idx1, idx2 "
"as a (bondType, kb, r0) tuple, or None if no parameters could be found")
.def("GetMMFFAngleBendParams", &PyMMFFMolProperties::getMMFFAngleBendParams,
(python::arg("self"), python::arg("mol"), python::arg("idx1"),
python::arg("idx2"), python::arg("idx3")),
"Retrieves MMFF angle bend parameters for atoms with indexes idx1, idx2, idx3 "
"as a (angleType, ka, theta0) tuple, or None if no parameters could be found")
.def("GetMMFFStretchBendParams", &PyMMFFMolProperties::getMMFFStretchBendParams,
(python::arg("self"), python::arg("mol"), python::arg("idx1"),
python::arg("idx2"), python::arg("idx3")),
"Retrieves MMFF stretch-bend parameters for atoms with indexes idx1, idx2, idx3 "
"as a (stretchBendType, kbaIJK, kbaKJI) tuple, or None if no parameters could be found")
.def("GetMMFFTorsionParams", &PyMMFFMolProperties::getMMFFTorsionParams,
(python::arg("self"), python::arg("mol"), python::arg("idx1"),
python::arg("idx2"), python::arg("idx3"), python::arg("idx4")),
"Retrieves MMFF torsion parameters for atoms with indexes idx1, idx2, idx3, idx4 "
"as a (torsionType, V1, V2, V3) tuple, or None if no parameters could be found")
.def("GetMMFFOopBendParams", &PyMMFFMolProperties::getMMFFOopBendParams,
(python::arg("self"), python::arg("mol"), python::arg("idx1"),
python::arg("idx2"), python::arg("idx3"), python::arg("idx4")),
"Retrieves MMFF out-of-plane bending force constant for atoms with indexes "
"idx1, idx2, idx3, idx4 as a koop float value")
.def("GetMMFFVdWParams", &PyMMFFMolProperties::getMMFFVdWParams,
(python::arg("self"), python::arg("idx1"), python::arg("idx2")),
"Retrieves MMFF van der Waals parameters for atoms with indexes "
"idx1, idx2 as a (R_ij_starUnscaled, epsilonUnscaled, R_ij_star, epsilon) tuple, "
"or None if no parameters could be found")
.def("SetMMFFDielectricModel", &PyMMFFMolProperties::setMMFFDielectricModel,
(python::arg("self"), python::arg("dielModel") = 1),
"Sets the DielModel MMFF property (1: constant; 2: distance-dependent; "
"defaults to constant)")
.def("SetMMFFDielectricConstant", &PyMMFFMolProperties::setMMFFDielectricConstant,
(python::arg("self"), python::arg("dielConst") = 1.0),
"Sets the DielConst MMFF property (defaults to 1.0)")
.def("SetMMFFBondTerm", &PyMMFFMolProperties::setMMFFBondTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the bond term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFAngleTerm", &PyMMFFMolProperties::setMMFFAngleTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the angle term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFStretchBendTerm", &PyMMFFMolProperties::setMMFFStretchBendTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the stretch-bend term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFOopTerm", &PyMMFFMolProperties::setMMFFOopTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the out-of-plane bend term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFTorsionTerm", &PyMMFFMolProperties::setMMFFTorsionTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the torsional term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFVdWTerm", &PyMMFFMolProperties::setMMFFVdWTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the Van der Waals term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFEleTerm", &PyMMFFMolProperties::setMMFFEleTerm,
(python::arg("self"), python::arg("state") = true),
"Sets the electrostatic term to be included in the MMFF equation (defaults to True)")
.def("SetMMFFVariant", &PyMMFFMolProperties::setMMFFVariant,
(python::arg("self"), python::arg("mmffVariant") = "MMFF94"),
"Sets the MMFF variant to be used (\"MMFF94\" or \"MMFF94s\"; defaults to \"MMFF94\")")
.def("SetMMFFVerbosity", &PyMMFFMolProperties::setMMFFVerbosity,
(python::arg("self"), python::arg("verbosity") = 0),
"Sets the MMFF verbosity (0: none; 1: low; 2: high; defaults to 0)")
;
}
/*
(python::arg("self"), python::arg("mol"), python::arg("idx1"), python::arg("idx2")),
"Retrieves MMFF bond stretch parameters for atoms with indexes idx1, idx2; "
"as a tuple (bondType, kb, r0)")
*/
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