/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp is in rdkit-data 201603.5-2.
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//
// Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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//
#include <boost/python.hpp>
#include <GraphMol/GraphMol.h>
#include <RDBoost/Wrap.h>
#include "../ConformerParser.h"
namespace python = boost::python;
namespace RDKit {
INT_VECT AddConformersFromAmberTrajectory(ROMol &mol, std::string fName, int numConfs,
bool clearConfs) {
if (clearConfs) {
mol.clearConformers();
}
std::vector<std::vector<double> > coords;
ConformerParser::readAmberTrajectory(fName, coords, mol.getNumAtoms());
INT_VECT res = ConformerParser::addConformersFromList(mol, coords, numConfs);
if (numConfs < 0) {
numConfs = coords.size();
}
return res;
}
}
BOOST_PYTHON_MODULE(rdConformerParser) {
python::scope().attr("__doc__") =
"Module containing functions to read conformations of a molecule from MD trajectories"
;
//import_array();
std::string docString = "Read conformations of a molecule from \n\
an Amber trajectory\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- traj : the filename of the trajectory \n\
- numConfs : number of conformations to read \n\
The default (-1) reads all. \n\
- clearConfs : clear all existing conformations on the molecule\n\
The default is true. \n\
\n\
RETURNS:\n\n\
IDs of the new conformations added to the molecule \n\
\n";
python::def("AddConformersFromAmberTrajectory", RDKit::AddConformersFromAmberTrajectory,
(python::arg("mol"), python::arg("traj"),
python::arg("numConfs")=-1, python::arg("clearConfs")=true),
docString.c_str());
}
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