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273 lines
9.2 KiB
C++
Executable File
273 lines
9.2 KiB
C++
Executable File
// $Id: testMol2ToMol.cpp 1457 2009-04-03 09:05:17Z landrgr1 $
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//
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// Copyright (c) 2008, 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
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// written 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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// created by Nik Stiefl May 2008
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//
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include "FileParsers.h"
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <RDGeneral/FileParseException.h>
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#include <RDGeneral/BadFileException.h>
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#include <string>
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using namespace RDKit;
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void testGeneral(std::string rdbase){
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BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "-- testing general mol2 file parsing --" << std::endl;
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BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
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{
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bool ok=false;
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/nonExistFile.mol2";
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try{
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RWMol *m = Mol2FileToMol(fName);
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delete m;
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} catch(const BadFileException &e){
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ok=true;
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}
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TEST_ASSERT(ok);
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/pyrazole_pyridine.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms()==5);
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// this was sf.net issue 2727976:
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TEST_ASSERT(m->getNumConformers()==1);
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TEST_ASSERT(m->getConformer().is3D());
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TEST_ASSERT(feq(m->getConformer().getAtomPos(0).x,1.5019));
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TEST_ASSERT(feq(m->getConformer().getAtomPos(0).y,1.0435));
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TEST_ASSERT(feq(m->getConformer().getAtomPos(0).z,0.0000));
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/benzene.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms()==6);
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delete m;
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}
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{
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bool ok=false;
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/mol_noatoms.mol2";
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try {
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RWMol *m = Mol2FileToMol(fName);
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delete m;
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} catch(const FileParseException &e){
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ok=true;
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}
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TEST_ASSERT(ok);
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}
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{
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bool ok=false;
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/mol_nomol.mol2";
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try {
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RWMol *m = Mol2FileToMol(fName);
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delete m;
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} catch(const FileParseException &e){
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ok=true;
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}
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TEST_ASSERT(ok);
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/lonePairMol.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms()==5 && m->getNumBonds()==4);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/symmetricGuanidine.mol2";
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RWMol *m = Mol2FileToMol(fName,false);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==1);
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TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/highlySymmetricGuanidine.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(4)->getFormalCharge()==1);
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TEST_ASSERT(m->getAtomWithIdx(12)->getFormalCharge()==1);
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TEST_ASSERT(m->getAtomWithIdx(20)->getFormalCharge()==1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
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TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==-1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
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TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==-1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/fusedRing.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge()==0);
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TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge()==0);
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TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==0);
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TEST_ASSERT(m->getAtomWithIdx(13)->getFormalCharge()==0);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/pyridiniumPhenyl.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge()==1);
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TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge()==0);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/sulfonAmide.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==0);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineRWH.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge()==1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineEC.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(3)->getFormalCharge()==1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidine.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateCharged.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateUncharged.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==0);
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delete m;
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}
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateUnchargedRing.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getAtomWithIdx(2)->getFormalCharge()==0);
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delete m;
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}
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#if 0
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{
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Sulfonate.mol2";
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RWMol *m = Mol2FileToMol(fName);
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TEST_ASSERT(m);
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BOOST_LOG(rdInfoLog) <<MolToSmiles(*m)<<std::endl;
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delete m;
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}
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#endif
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BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "-- DONE general mol2 file parsing --" << std::endl;
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BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
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}
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void testAromaticChargedFail(std::string rdbase){
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BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "-- testing subst arom groups in mol2 --" << std::endl;
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BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
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//this one checks on substituted aromatic groups that need to be charged, e.g. c1ccccn1C which
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//should convert to c1cccc[n+]1C
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{
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//this one is supposed to have a sanitisation error!
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//have to fix that one next ...
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std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/badSubstPyridine.mol2";
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RWMol *m = Mol2FileToMol(fName);
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if(m){
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delete m;
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}
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}
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BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "-- DONE subst arom groups in mol2 --" << std::endl;
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BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
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}
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//FIX still missing chirality by 3D structure
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// still missing input std::string
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int main(int argc,char *argv[]){
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RDLog::InitLogs();
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std::string rdbase = getenv("RDBASE");
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testGeneral(rdbase);
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testAromaticChargedFail(rdbase);
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return 0;
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}
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