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https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
2afb4fbac4
* fix leak in testConformerParser * fix leaks in testMultithreadedMolSupplier * fix leak in catch_graphmol * pass build type to YAEHMOP * cleanup fragments in CoordGen minimizeOnly * fix leaking ConjElectrons stack in res mol supplier * avoid double delete * do not delete 'this'; clean ce not added to map * delete mol if Multithreaded SD readMolProps throws * fix typo * fix typo in comment
121 lines
4.3 KiB
C++
121 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 <iostream>
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#include <fstream>
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#include <memory>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/utils.h>
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#include <RDGeneral/StreamOps.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include "ConformerParser.h"
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#include <DataStructs/BitVects.h>
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#include <DataStructs/BitOps.h>
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using namespace RDKit;
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using namespace RDKit::ConformerParser;
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void test1() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " Test ConformerParser." << std::endl;
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std::unique_ptr<ROMol> mol{SmilesToMol("CCC")};
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std::vector<std::vector<double>> coords;
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad.trx";
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bool ok = false;
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try {
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readAmberTrajectory(fName, coords, mol->getNumAtoms());
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} catch (ValueErrorException &e) {
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ok = true;
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}
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TEST_ASSERT(ok);
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fName = rdbase + "/Code/GraphMol/test_data/water_coords_bad2.trx";
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ok = false;
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try {
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readAmberTrajectory(fName, coords, mol->getNumAtoms());
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} catch (ValueErrorException &e) {
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// std::cout << e.what() << std::endl;
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ok = true;
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}
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TEST_ASSERT(ok);
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fName = rdbase + "/Code/GraphMol/test_data/water_coords.trx";
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readAmberTrajectory(fName, coords, mol->getNumAtoms());
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TEST_ASSERT(coords.size() == 1);
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TEST_ASSERT(coords[0].size() == 9);
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INT_VECT res = addConformersFromList(*mol, coords);
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TEST_ASSERT((*mol).getNumConformers() == 1);
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TEST_ASSERT((*mol).getConformer().getNumAtoms() == 3);
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TEST_ASSERT((*mol).getConformer(0).getAtomPos(0).x == 0.1941767);
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coords.push_back(coords[0]);
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mol->clearConformers();
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res = addConformersFromList(*mol, coords);
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TEST_ASSERT(mol->getNumConformers() == 2);
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mol->clearConformers();
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res = addConformersFromList(*mol, coords, 1);
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TEST_ASSERT(mol->getNumConformers() == 1);
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coords.resize(0);
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mol->clearConformers();
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fName = rdbase + "/Code/GraphMol/test_data/water_coords2.trx";
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readAmberTrajectory(fName, coords, mol->getNumAtoms());
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TEST_ASSERT(coords.size() == 2);
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TEST_ASSERT(coords[1].size() == 9);
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res = addConformersFromList(*mol, coords);
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TEST_ASSERT((*mol).getNumConformers() == 2);
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
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//
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//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
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int main() {
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RDLog::InitLogs();
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#if 1
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test1();
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#endif
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}
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