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87 lines
3.3 KiB
C++
87 lines
3.3 KiB
C++
// $Id$
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//
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// Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include <boost/python.hpp>
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#include <GraphMol/GraphMol.h>
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#include <RDBoost/Wrap.h>
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#include "../ConformerParser.h"
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namespace python = boost::python;
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namespace RDKit {
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INT_VECT AddConformersFromAmberTrajectory(ROMol &mol, std::string fName,
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int numConfs, bool clearConfs) {
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if (clearConfs) {
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mol.clearConformers();
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}
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std::vector<std::vector<double>> coords;
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ConformerParser::readAmberTrajectory(fName, coords, mol.getNumAtoms());
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INT_VECT res = ConformerParser::addConformersFromList(mol, coords, numConfs);
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if (numConfs < 0) {
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numConfs = coords.size();
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}
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return res;
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}
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} // namespace RDKit
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BOOST_PYTHON_MODULE(rdConformerParser) {
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python::scope().attr("__doc__") =
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"Module containing functions to read conformations of a molecule from MD trajectories";
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// import_array();
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std::string docString =
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"Read conformations of a molecule from \n\
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an Amber trajectory\n\n\
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\n\
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ARGUMENTS:\n\n\
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- mol : the molecule of interest\n\
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- traj : the filename of the trajectory \n\
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- numConfs : number of conformations to read \n\
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The default (-1) reads all. \n\
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- clearConfs : clear all existing conformations on the molecule\n\
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The default is true. \n\
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\n\
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RETURNS:\n\n\
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IDs of the new conformations added to the molecule \n\
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\n";
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python::def("AddConformersFromAmberTrajectory",
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RDKit::AddConformersFromAmberTrajectory,
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(python::arg("mol"), python::arg("traj"),
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python::arg("numConfs") = -1, python::arg("clearConfs") = true),
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docString.c_str());
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}
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