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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 <iostream>
#include <fstream>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/StreamOps.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include "ConformerParser.h"
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
using namespace RDKit;
using namespace RDKit::ConformerParser;
void test1(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test ConformerParser." << std::endl;
ROMol *mol = SmilesToMol("CCC");
std::vector<std::vector<double> > coords;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Contrib/ConformerParser/test_data/water_coords_bad.trx";
bool ok = false;
try {
readAmberTrajectory(fName, coords, mol->getNumAtoms());
} catch (ValueErrorException &e) {
ok = true;
}
TEST_ASSERT(ok);
fName = rdbase + "/Contrib/ConformerParser/test_data/water_coords_bad2.trx";
ok = false;
try {
readAmberTrajectory(fName, coords, mol->getNumAtoms());
} catch (ValueErrorException &e) {
//std::cout << e.message() << std::endl;
ok = true;
}
TEST_ASSERT(ok);
fName = rdbase + "/Contrib/ConformerParser/test_data/water_coords.trx";
readAmberTrajectory(fName, coords, mol->getNumAtoms());
TEST_ASSERT(coords.size() == 1);
TEST_ASSERT(coords[0].size() == 9);
INT_VECT res = addConformersFromList(*mol, coords);
TEST_ASSERT((*mol).getNumConformers() == 1);
TEST_ASSERT((*mol).getConformer().getNumAtoms() == 3);
TEST_ASSERT((*mol).getConformer(0).getAtomPos(0).x == 0.1941767);
coords.push_back(coords[0]);
mol->clearConformers();
res = addConformersFromList(*mol, coords);
TEST_ASSERT(mol->getNumConformers() == 2);
mol->clearConformers();
res = addConformersFromList(*mol, coords, 1);
TEST_ASSERT(mol->getNumConformers() == 1);
coords.resize(0);
mol->clearConformers();
fName = rdbase + "/Contrib/ConformerParser/test_data/water_coords2.trx";
readAmberTrajectory(fName, coords, mol->getNumAtoms());
TEST_ASSERT(coords.size() == 2);
TEST_ASSERT(coords[1].size() == 9);
res = addConformersFromList(*mol, coords);
TEST_ASSERT((*mol).getNumConformers() == 2);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(){
RDLog::InitLogs();
#if 1
test1();
#endif
}
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