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// $Id$
//
// Copyright (C) 2004-2008 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.
//
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>
#include "rdchem.h"
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <Geometry/point.h>
#include <GraphMol/Conformer.h>
#include <RDBoost/PySequenceHolder.h>
//#include "seqs.hpp"
namespace python = boost::python;
namespace RDKit {
RDGeom::Point3D GetAtomPos(const Conformer *conf, unsigned int aid) {
RDGeom::Point3D res = conf->getAtomPos(aid);
return res;
}
void SetAtomPos(Conformer *conf, unsigned int aid, python::object loc) {
// const std::vector<double> &loc) {
int dim = python::extract<int>(loc.attr("__len__")());
CHECK_INVARIANT(dim == 3, "");
PySequenceHolder<double> pdata(loc);
RDGeom::Point3D pt(pdata[0], pdata[1], pdata[2]);
conf->setAtomPos(aid, pt);
}
std::string confClassDoc =
"The class to store 2D or 3D conformation of a molecule\n";
struct conformer_wrapper {
static void wrap() {
python::class_<Conformer, CONFORMER_SPTR>("Conformer", confClassDoc.c_str(),
python::init<>())
.def(python::init<unsigned int>(
"Constructor with the number of atoms specified"))
.def(python::init<const Conformer &>())
.def("GetNumAtoms", &Conformer::getNumAtoms,
"Get the number of atoms in the conformer\n")
.def("GetOwningMol", &Conformer::getOwningMol,
"Get the owning molecule\n",
python::return_value_policy<python::reference_existing_object>())
.def("GetId", &Conformer::getId, "Get the ID of the conformer")
.def("SetId", &Conformer::setId, "Set the ID of the conformer\n")
.def("GetAtomPosition", GetAtomPos, "Get the posistion of an atom\n")
.def("SetAtomPosition", SetAtomPos,
"Set the position of the specified atom\n")
.def("SetAtomPosition", (void (Conformer::*)(unsigned int, const RDGeom::Point3D&)) &
Conformer::setAtomPos,
"Set the position of the specified atom\n")
.def("Set3D", &Conformer::set3D, "Set the 3D flag of the conformer\n")
.def("Is3D", &Conformer::is3D,
"returns the 3D flag of the conformer\n");
};
};
}
void wrap_conformer() { RDKit::conformer_wrapper::wrap(); }
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