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// $Id$
//
// 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
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <Geometry/point.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/BadFileException.h>
#include "ConformerParser.h"
#include <fstream>
namespace RDKit {
namespace ConformerParser {
INT_VECT addConformersFromList(ROMol &mol,
const std::vector<std::vector<double>> &coords,
int numConf) {
unsigned int numAtomsPerConf = mol.getNumAtoms();
unsigned int numCoordPerConf = 3 * numAtomsPerConf;
PRECONDITION(numConf <= int(coords.size()),
"numConf greater than number of conformations");
if (numConf < 0) {
numConf = coords.size();
}
// loop over the conformers
INT_VECT confIds;
for (int i = 0; i < numConf; ++i) {
if (coords[i].size() != numCoordPerConf) {
throw ValueErrorException("Wrong number of coordinates");
}
RDKit::Conformer *conf = new RDKit::Conformer(numAtomsPerConf);
// loop over atoms
for (unsigned int atom = 0; atom < numAtomsPerConf; ++atom) {
// RDGeom::Point3D p(coords[i][3*atom], coords[i][3*atom+1],
// coords[i][3*atom+2]);
(*conf).setAtomPos(
atom, RDGeom::Point3D(coords[i][3 * atom], coords[i][3 * atom + 1],
coords[i][3 * atom + 2]));
}
int confId = mol.addConformer(conf, true);
confIds.push_back(confId);
}
return confIds;
}
void readAmberTrajectory(const std::string &fName,
std::vector<std::vector<double>> &coords,
unsigned int numAtoms) {
std::ifstream inStream(fName.c_str());
if (!inStream || (inStream.bad())) {
std::ostringstream errout;
errout << "Bad input file " << fName;
throw BadFileException(errout.str());
}
std::string tempStr;
// title
std::getline(inStream, tempStr);
// read coordinates
std::vector<double> tmpCoords;
while (true) {
double c;
if (!(inStream >> c)) {
if (!inStream.eof()) {
throw ValueErrorException("Error while reading file");
}
break;
}
tmpCoords.push_back(c);
}
// convert to conformers
unsigned int numCoordsPerConf = 3 * numAtoms;
if (tmpCoords.size() % numCoordsPerConf != 0) {
throw ValueErrorException("Wrong number of coordinates");
}
unsigned int numConfs = tmpCoords.size() / numCoordsPerConf;
unsigned int c = 0;
for (unsigned int i = 0; i < numConfs; ++i) {
std::vector<double> coordConf(numCoordsPerConf);
for (unsigned int atom = 0; atom < numCoordsPerConf; ++atom, ++c) {
coordConf[atom] = tmpCoords[c];
}
coords.push_back(coordConf);
}
}
} // end namespace ConformerParser
} // end namespace RDKit
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