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// $Id$
//
// Copyright (C) 2005-2006 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 <RDGeneral/export.h>
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <ForceField/MMFF/Params.h>
#include <GraphMol/Trajectory/Snapshot.h>
#include <boost/python/tuple.hpp>
#include <boost/shared_ptr.hpp>
#include <vector>
#include <algorithm>
#include <Geometry/point.h>
namespace python = boost::python;
namespace ForceFields {
class PyForceField {
public:
PyForceField(ForceField *f) : field(f){};
~PyForceField() {
// std::cerr << " *** destroy PyForce field " << std::endl;
field.reset();
// std::cerr << " *** reset DONE" << std::endl;
extraPoints.clear();
// std::cerr << " *** destroy PyForce field DONE" << std::endl;
}
int addExtraPoint(double x, double y, double z, bool fixed = true) {
RDGeom::Point3D *pt = new RDGeom::Point3D(x, y, z);
PRECONDITION(this->field, "no force field");
this->extraPoints.push_back(boost::shared_ptr<RDGeom::Point3D>(pt));
unsigned int ptIdx = this->extraPoints.size() - 1;
RDGeom::Point3D *ptr = this->extraPoints[ptIdx].get();
this->field->positions().push_back(ptr);
int idx = this->field->positions().size();
if (fixed) {
this->field->fixedPoints().push_back(idx - 1);
}
return idx;
}
double calcEnergyWithPos(const python::object &pos = python::object());
double calcEnergy() {
return calcEnergyWithPos();
}
PyObject *calcGradWithPos(const python::object &pos = python::object());
PyObject *positions();
int minimize(int maxIts, double forceTol, double energyTol) {
PRECONDITION(this->field, "no force field");
return this->field->minimize(maxIts, forceTol, energyTol);
}
boost::python::tuple minimizeTrajectory(unsigned int snapshotFreq, int maxIts, double forceTol, double energyTol);
void initialize() {
PRECONDITION(this->field, "no force field");
this->field->initialize();
}
unsigned int dimension() {
PRECONDITION(this->field, "no force field");
return this->field->dimension();
}
unsigned int numPoints() {
PRECONDITION(this->field, "no force field");
return this->field->numPoints();
}
// private:
std::vector<boost::shared_ptr<RDGeom::Point3D> > extraPoints;
boost::shared_ptr<ForceField> field;
};
class PyMMFFMolProperties {
public:
PyMMFFMolProperties(RDKit::MMFF::MMFFMolProperties *mp)
: mmffMolProperties(mp){};
~PyMMFFMolProperties(){};
unsigned int getMMFFAtomType(unsigned int idx) {
return (unsigned int)(mmffMolProperties->getMMFFAtomType(idx));
};
double getMMFFFormalCharge(unsigned int idx) {
return mmffMolProperties->getMMFFFormalCharge(idx);
};
double getMMFFPartialCharge(unsigned int idx) {
return mmffMolProperties->getMMFFPartialCharge(idx);
};
PyObject *getMMFFBondStretchParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2);
PyObject *getMMFFAngleBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3);
PyObject *getMMFFStretchBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3);
PyObject *getMMFFTorsionParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4);
PyObject *getMMFFOopBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4);
PyObject *getMMFFVdWParams(const unsigned int idx1, const unsigned int idx2);
void setMMFFDielectricModel(boost::uint8_t dielModel) {
mmffMolProperties->setMMFFDielectricModel(dielModel);
};
void setMMFFDielectricConstant(double dielConst) {
mmffMolProperties->setMMFFDielectricConstant(dielConst);
};
void setMMFFBondTerm(bool state) {
mmffMolProperties->setMMFFBondTerm(state);
};
void setMMFFAngleTerm(const bool state) {
mmffMolProperties->setMMFFAngleTerm(state);
};
void setMMFFStretchBendTerm(const bool state) {
mmffMolProperties->setMMFFStretchBendTerm(state);
};
void setMMFFOopTerm(const bool state) {
mmffMolProperties->setMMFFOopTerm(state);
};
void setMMFFTorsionTerm(const bool state) {
mmffMolProperties->setMMFFTorsionTerm(state);
};
void setMMFFVdWTerm(const bool state) {
mmffMolProperties->setMMFFVdWTerm(state);
};
void setMMFFEleTerm(const bool state) {
mmffMolProperties->setMMFFEleTerm(state);
};
void setMMFFVariant(const std::string &mmffVariant) {
mmffMolProperties->setMMFFVariant(mmffVariant);
};
void setMMFFVerbosity(unsigned int verbosity) {
mmffMolProperties->setMMFFVerbosity(verbosity);
};
boost::shared_ptr<RDKit::MMFF::MMFFMolProperties> mmffMolProperties;
};
PyObject *getUFFBondStretchParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2);
PyObject *getUFFAngleBendParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3);
PyObject *getUFFTorsionParams(const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2, const unsigned int idx3,
const unsigned int idx4);
PyObject *getUFFInversionParams(const RDKit::ROMol &mol,
const unsigned int idx1,
const unsigned int idx2,
const unsigned int idx3,
const unsigned int idx4);
PyObject *getUFFVdWParams(const RDKit::ROMol &mol, const unsigned int idx1,
const unsigned int idx2);
}
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