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118 lines
4.3 KiB
C++
118 lines
4.3 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 <Geometry/point.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <RDGeneral/BadFileException.h>
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#include "ConformerParser.h"
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#include <fstream>
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namespace RDKit {
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namespace ConformerParser {
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INT_VECT addConformersFromList(ROMol &mol,
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const std::vector<std::vector<double>> &coords,
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int numConf) {
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unsigned int numAtomsPerConf = mol.getNumAtoms();
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unsigned int numCoordPerConf = 3 * numAtomsPerConf;
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PRECONDITION(numConf <= int(coords.size()),
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"numConf greater than number of conformations");
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if (numConf < 0) {
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numConf = coords.size();
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}
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// loop over the conformers
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INT_VECT confIds;
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for (int i = 0; i < numConf; ++i) {
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if (coords[i].size() != numCoordPerConf) {
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throw ValueErrorException("Wrong number of coordinates");
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}
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RDKit::Conformer *conf = new RDKit::Conformer(numAtomsPerConf);
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// loop over atoms
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for (unsigned int atom = 0; atom < numAtomsPerConf; ++atom) {
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// RDGeom::Point3D p(coords[i][3*atom], coords[i][3*atom+1],
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// coords[i][3*atom+2]);
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(*conf).setAtomPos(
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atom, RDGeom::Point3D(coords[i][3 * atom], coords[i][3 * atom + 1],
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coords[i][3 * atom + 2]));
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}
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int confId = mol.addConformer(conf, true);
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confIds.push_back(confId);
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}
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return confIds;
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}
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void readAmberTrajectory(const std::string &fName,
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std::vector<std::vector<double>> &coords,
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unsigned int numAtoms) {
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std::ifstream inStream(fName.c_str());
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if (!inStream || (inStream.bad())) {
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std::ostringstream errout;
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errout << "Bad input file " << fName;
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throw BadFileException(errout.str());
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}
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std::string tempStr;
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// title
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std::getline(inStream, tempStr);
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// read coordinates
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std::vector<double> tmpCoords;
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while (true) {
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double c;
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if (!(inStream >> c)) {
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if (!inStream.eof()) {
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throw ValueErrorException("Error while reading file");
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}
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break;
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}
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tmpCoords.push_back(c);
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}
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// convert to conformers
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unsigned int numCoordsPerConf = 3 * numAtoms;
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if (tmpCoords.size() % numCoordsPerConf != 0) {
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throw ValueErrorException("Wrong number of coordinates");
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}
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unsigned int numConfs = tmpCoords.size() / numCoordsPerConf;
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unsigned int c = 0;
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for (unsigned int i = 0; i < numConfs; ++i) {
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std::vector<double> coordConf(numCoordsPerConf);
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for (unsigned int atom = 0; atom < numCoordsPerConf; ++atom, ++c) {
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coordConf[atom] = tmpCoords[c];
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}
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coords.push_back(coordConf);
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}
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}
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} // end namespace ConformerParser
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} // end namespace RDKit
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