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5b70cdbdc12c19eee9ddb20f2a0ef60be1fb098d
rdkit/Code/ForceField/Wrap/ForceField.cpp
ptosco 5b70cdbdc1 - added relative DistanceConstraints (i.e., +/- with respect 
to the current value) (C++/Python)
- added absolute/relative AngleConstraints (C++/Python)
- added absolute/relative TorsionConstraints (C++/Python)
- added PositionConstraints (C++/Python)
- exposed fixedPoints from Python
- added relevant C++/Python tests
- removed a number of redundant "this->" in member functions
- moved some getGrad() code into Utils::calcAngleBendGrad and
  Utils::calcTorsionGrad to avoid repeating the same code
  for constraints
2013-12-02 19:58:29 +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 <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 <boost/shared_ptr.hpp>
#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;
}
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 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("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)")
;
}
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