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rdkit/Code/GraphMol/FileParsers/testMol2ToMol.cpp
Greg Landrum 82129c3e13 fix and test Issue3399798
2011-08-30 09:13:07 +00:00

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// $Id: testMol2ToMol.cpp 1457 2009-04-03 09:05:17Z landrgr1 $
//
// Copyright (c) 2008, 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.
//
// created by Nik Stiefl May 2008
//
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include "FileParsers.h"
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <string>
using namespace RDKit;
void testGeneral(std::string rdbase){
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- testing general mol2 file parsing --" << std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
{
bool ok=false;
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/nonExistFile.mol2";
try{
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch(const BadFileException &e){
ok=true;
}
TEST_ASSERT(ok);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/pyrazole_pyridine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
// this was sf.net issue 2727976:
TEST_ASSERT(m->getNumConformers()==1);
TEST_ASSERT(m->getConformer().is3D());
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).x,1.5019));
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).y,1.0435));
TEST_ASSERT(feq(m->getConformer().getAtomPos(0).z,0.0000));
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/benzene.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==6);
delete m;
}
{
bool ok=false;
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/mol_noatoms.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch(const FileParseException &e){
ok=true;
}
TEST_ASSERT(ok);
}
{
bool ok=false;
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/mol_nomol.mol2";
try {
RWMol *m = Mol2FileToMol(fName);
delete m;
} catch(const FileParseException &e){
ok=true;
}
TEST_ASSERT(ok);
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/lonePairMol.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5 && m->getNumBonds()==4);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/symmetricGuanidine.mol2";
RWMol *m = Mol2FileToMol(fName,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/highlySymmetricGuanidine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(4)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(12)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(20)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==-1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Noxide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==-1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/fusedRing.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge()==0);
TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge()==0);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==0);
TEST_ASSERT(m->getAtomWithIdx(13)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/pyridiniumPhenyl.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(5)->getFormalCharge()==1);
TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/sulfonAmide.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineRWH.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(6)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidineEC.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(3)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/chargedAmidine.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(9)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateCharged.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==1);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateUncharged.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(8)->getFormalCharge()==0);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/dbtranslateUnchargedRing.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(2)->getFormalCharge()==0);
delete m;
}
#if 0
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Sulfonate.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
BOOST_LOG(rdInfoLog) <<MolToSmiles(*m)<<std::endl;
delete m;
}
#endif
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE general mol2 file parsing --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
void testAromaticChargedFail(std::string rdbase){
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- testing subst arom groups in mol2 --" << std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
//this one checks on substituted aromatic groups that need to be charged, e.g. c1ccccn1C which
//should convert to c1cccc[n+]1C
{
//this one is supposed to have a sanitisation error!
//have to fix that one next ...
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/badSubstPyridine.mol2";
RWMol *m = Mol2FileToMol(fName);
if(m){
delete m;
}
}
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE subst arom groups in mol2 --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
void testIssue3399798(std::string rdbase){
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- testing issue 3399798 --" << std::endl;
BOOST_LOG(rdInfoLog) << "---------------------------------------" << std::endl;
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3399798.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
}
{
std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3399798.2.mol2";
RWMol *m = Mol2FileToMol(fName);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
}
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "-- DONE --" << std::endl;
BOOST_LOG(rdInfoLog) << "------------------------------------" << std::endl;
}
//FIX still missing chirality by 3D structure
// still missing input std::string
int main(int argc,char *argv[]){
RDLog::InitLogs();
std::string rdbase = getenv("RDBASE");
testGeneral(rdbase);
testAromaticChargedFail(rdbase);
testIssue3399798(rdbase);
return 0;
}
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