// $Id$
//
//  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;
}

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)")
*/