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088256bfb13d14f998f6325669c2cfbabc498308
rdkit/Code/ForceField/Wrap/ForceField.cpp
Paolo Tosco 088256bfb1 - fixed a typo in the Python docs
2016-05-11 23:45:37 +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 <RDBoost/python.h>
#include <RDBoost/Wrap.h>
#include <RDGeneral/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;
}
python::tuple PyForceField::minimizeTrajectory(unsigned int snapshotFreq, int maxIts, double forceTol, double energyTol) {
PRECONDITION(this->field, "no force field");
RDKit::SnapshotVect snapshotVect;
int resInt = this->field->minimize(snapshotFreq, &snapshotVect,
maxIts, forceTol, energyTol);
python::list l;
for (RDKit::SnapshotVect::const_iterator it = snapshotVect.begin(); it != snapshotVect.end(); ++it)
l.append(new RDKit::Snapshot(*it));
return python::make_tuple(resInt, l);
}
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("MinimizeTrajectory", &PyForceField::minimizeTrajectory,
(python::arg("snapshotFreq"), python::arg("maxIts") = 200,
python::arg("forceTol") = 1e-4, python::arg("energyTol") = 1e-6),
"Runs some minimization iterations, recording the minimization "
"trajectory every snapshotFreq steps.\n\n"
"Returns a (int, []) tuple; the int is 0 if the minimization succeeded, "
"while the list contains Snapshot objects.")
.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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