pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-05 22:04:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
329bf48b77c5918ba76719776523917df336334e
rdkit/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp
Greg Landrum 699588fe0f Fixes #252
2014-04-25 07:21:10 +02:00

896 lines
26 KiB
C++
Raw Blame History

// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <fstream>
#include <iostream>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/StreamOps.h>
#include <sstream>
#include <boost/shared_ptr.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
#include <GraphMol/MolChemicalFeatures/FeatureParser.h>
using namespace RDKit;
void test1(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "AtomType parser testing." << std::endl;
std::string inLine;
std::map<std::string,std::string> atomTypeDefs;
atomTypeDefs.clear();
bool ok;
inLine="AtomType donor [N,O]";
Local::parseAtomType(inLine,atomTypeDefs,0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"]=="$([N,O])");
// check robustness to whitespace as we expand:
inLine=" AtomType donor\t[S]";
Local::parseAtomType(inLine,atomTypeDefs,0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"]=="$([N,O,$([S])])");
inLine="AtomType !donor [NH0]";
Local::parseAtomType(inLine,atomTypeDefs,0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"]=="$([!$([NH0]);N,O,$([S])])");
inLine="AtomType unsaturatedDonor [$([{donor}]!-[*])]";
Local::parseAtomType(inLine,atomTypeDefs,0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"]=="$([!$([NH0]);N,O,$([S])])");
TEST_ASSERT(atomTypeDefs["{unsaturatedDonor}"]=="$([$([$([!$([NH0]);N,O,$([S])])]!-[*])])");
ok=false;
try {
inLine="";
Local::parseAtomType(inLine,atomTypeDefs,0);
} catch (FeatureFileParseException &fpe) {
ok=true;
TEST_ASSERT(fpe.lineNo()==0);
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
ok=false;
try {
inLine="AtomTyped donor [N,O]";
Local::parseAtomType(inLine,atomTypeDefs,0);
} catch (FeatureFileParseException &fpe) {
ok=true;
TEST_ASSERT(fpe.lineNo()==0);
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
ok=false;
try {
inLine="AtomType";
Local::parseAtomType(inLine,atomTypeDefs,0);
} catch (FeatureFileParseException &fpe) {
ok=true;
TEST_ASSERT(fpe.lineNo()==0);
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
ok=false;
try {
inLine="AtomType donor";
Local::parseAtomType(inLine,atomTypeDefs,0);
} catch (FeatureFileParseException &fpe) {
ok=true;
TEST_ASSERT(fpe.lineNo()==0);
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
ok=false;
try {
inLine="AtomType donor [N,O";
Local::parseAtomType(inLine,atomTypeDefs,0);
} catch (FeatureFileParseException &fpe) {
ok=true;
TEST_ASSERT(fpe.lineNo()==0);
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test2(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureDefinition parser testing." << std::endl;
std::string inText,inLine;
std::istringstream ss;
MolChemicalFeatureDef *featDef;
bool ok;
std::map<std::string,std::string> atomTypeDefs;
atomTypeDefs["{donor}"]="$([O,N])";
inText=
"DefineFeature HDonor1 [O,N]\n"
" Family HDONOR\n"
" Weights 1.0\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
unsigned int tmpLine=2;
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonor1");
TEST_ASSERT(featDef->getSmarts()=="[O,N]");
TEST_ASSERT(featDef->getNumWeights()==1);
TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
delete featDef;
inText=
"DefineFeature HDonor1 [{donor}]\n"
" Family HDONOR\n"
" Weights 2.0\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonor1");
TEST_ASSERT(featDef->getSmarts()=="[$([O,N])]");
TEST_ASSERT(featDef->getNumWeights()==1);
TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
delete featDef;
inText=
"DefineFeature HDonorPair [{donor}][{donor}]\n"
" Family HDONOR\n"
" Weights 1.0,1\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonorPair");
TEST_ASSERT(featDef->getSmarts()=="[$([O,N])][$([O,N])]");
TEST_ASSERT(featDef->getNumWeights()==2);
TEST_ASSERT(feq(*featDef->beginWeights(),0.5));
TEST_ASSERT(feq(*++(featDef->beginWeights()),0.5));
delete featDef;
ok=false;
inText=
"DefineFeature HDonor1 [{donor}]\n"
" Family HDONOR\n"
" Weights 1.0\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
try{
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
} catch (FeatureFileParseException &){
ok=true;
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
ok=false;
inText=
"DefineFeature HDonor1 [{donor}]\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
try{
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
} catch (FeatureFileParseException &){
ok=true;
}
CHECK_INVARIANT(ok,"expected parse failure did not happen");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test3(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test pulling feat defs from a string." << std::endl;
//std::string pathName=getenv("RDBASE");
//pathName += "/Code/GraphMol/MolChemicalFeatures/test_data/smallsample.feats";
std::string inText,inLine;
std::istringstream ss;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
inText=
"AtomType donor [N,O]\n"
"AtomType !donor [H0]\n"
"DefineFeature HDonor1 [{donor}]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n";
res=parseFeatureData(inText,featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size()==1);
TEST_ASSERT((*featureDefs.begin())->getSmarts()=="[$([!$([H0]);N,O])]");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test4(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureDef functionality testing." << std::endl;
ROMol *testMol;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText=
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
res=parseFeatureData(inText,featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size()==2);
featDefIt=featureDefs.begin();
featDef=*featDefIt;
TEST_ASSERT(featDef->getSmarts()=="[N,O;!H0]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms()==1);
TEST_ASSERT(featDef->getNumWeights()==1);
featDef=*(++featureDefs.begin());
TEST_ASSERT(featDef->getSmarts()=="[N,O]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms()==1);
TEST_ASSERT(featDef->getNumWeights()==1);
testMol=SmilesToMol("COCN");
TEST_ASSERT(testMol);
featDef=*featureDefs.begin();
TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
TEST_ASSERT(mv.size()==1);
TEST_ASSERT(mv[0].first==0);
TEST_ASSERT(mv[0].second==3);
featDef=*(++featureDefs.begin());
TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
TEST_ASSERT(mv.size()==1);
TEST_ASSERT(mv[0].first==0);
TEST_ASSERT(mv[0].second==1||mv[0].second==3);
delete testMol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test5(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureFactory testing." << std::endl;
ROMol *testMol;
MatchVectType mv;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText=
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HBondAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
testMol=SmilesToMol("COCN");
TEST_ASSERT(testMol);
featDef=*factory->beginFeatureDefs();
TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
BOOST_LOG(rdErrorLog) << "1" << std::endl;
TEST_ASSERT(mv.size()==1);
TEST_ASSERT(mv[0].first==0);
TEST_ASSERT(mv[0].second==3);
featDef=*(++factory->beginFeatureDefs());
TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
BOOST_LOG(rdErrorLog) << "2" << std::endl;
TEST_ASSERT(mv.size()==1);
TEST_ASSERT(mv[0].first==0);
TEST_ASSERT(mv[0].second==1||mv[0].second==3);
// Test using the factory to find features:
featSPtrs = factory->getFeaturesForMol(*testMol);
BOOST_LOG(rdErrorLog) << "3" << std::endl;
TEST_ASSERT(featSPtrs.size()==3);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="HBondDonor");
TEST_ASSERT(featSPtr->getType()=="HDonor1");
featSPtr=*(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
featSPtr=*(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
// Test limiting stuff with includeOnly
featSPtrs = factory->getFeaturesForMol(*testMol,"HBondAcceptor");
BOOST_LOG(rdErrorLog) << "4" << std::endl;
TEST_ASSERT(featSPtrs.size()==2);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
featSPtr=*(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
featSPtrs = factory->getFeaturesForMol(*testMol,"HBondDonor");
BOOST_LOG(rdErrorLog) << "5" << std::endl;
TEST_ASSERT(featSPtrs.size()==1);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="HBondDonor");
TEST_ASSERT(featSPtr->getType()=="HDonor1");
featSPtrs = factory->getFeaturesForMol(*testMol,"NotPresent");
BOOST_LOG(rdErrorLog) << "6" << std::endl;
TEST_ASSERT(featSPtrs.size()==0);
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test6(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Feature Location testing." << std::endl;
ROMol *testMol;
Conformer *conf;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText=
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature Carboxyl1 C(=O)[O;H1,-]\n"
" Family ZnBinder\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
testMol=SmilesToMol("C(=O)O");
TEST_ASSERT(testMol);
conf = new Conformer(3);
testMol->addConformer(conf);
conf->setAtomPos(0,RDGeom::Point3D(0,0,0.0));
conf->setAtomPos(1,RDGeom::Point3D(1.2,0,0.0));
conf->setAtomPos(2,RDGeom::Point3D(0,1.5,0.0));
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size()==2);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="HBondDonor");
TEST_ASSERT(featSPtr->getType()=="HDonor1");
TEST_ASSERT(feq(featSPtr->getPos().x,0.0));
TEST_ASSERT(feq(featSPtr->getPos().y,1.5));
TEST_ASSERT(feq(featSPtr->getPos().z,0.0));
featSPtr=*(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily()=="ZnBinder");
TEST_ASSERT(featSPtr->getType()=="Carboxyl1");
TEST_ASSERT(feq(featSPtr->getPos().x,0.4));
TEST_ASSERT(feq(featSPtr->getPos().y,0.5));
TEST_ASSERT(feq(featSPtr->getPos().z,0.0));
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test7(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test building a FeatureFactory from a file" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/MolChemicalFeatures/test_data/featDef.txt";
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
std::ifstream inStream(fName.c_str());
TEST_ASSERT(inStream.is_open());
std::istream &instrm = static_cast<std::istream &>(inStream);
factory = buildFeatureFactory(instrm);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
featDefIt=factory->beginFeatureDefs();
featDef=*featDefIt;
TEST_ASSERT(featDef->getFamily()=="HBondDonor");
featDefIt++;
featDef=*featDefIt;
TEST_ASSERT(featDefIt!=factory->endFeatureDefs());
TEST_ASSERT(featDef->getFamily()=="HBondAcceptor");
featDefIt++;
TEST_ASSERT(featDefIt==factory->endFeatureDefs());
delete(factory);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue224(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue 224." << std::endl;
std::string inText,inLine;
std::istringstream ss;
MolChemicalFeatureDef *featDef;
std::map<std::string,std::string> atomTypeDefs;
atomTypeDefs["{donor}"]="$([O,N])";
inText=
"\n"
"DefineFeature HDonor1 [O,N]\n"
" Family HDONOR\n"
" Weights 1.0\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
unsigned int tmpLine=2;
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonor1");
TEST_ASSERT(featDef->getSmarts()=="[O,N]");
TEST_ASSERT(featDef->getNumWeights()==1);
TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
delete featDef;
inText=
"\n"
"# comment, ignore me\n"
"DefineFeature HDonor1 [O,N]\n"
" \n"
" Family HDONOR\n"
" \n"
"# comment, ignore me\n"
" Weights 1.0\n"
"# comment, ignore me\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonor1");
TEST_ASSERT(featDef->getSmarts()=="[O,N]");
TEST_ASSERT(featDef->getNumWeights()==1);
TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
delete featDef;
// repeat those tests using some continuation lines
// (Issue 346):
inText=
"\n"
"# comment, ignore me\n"
"DefineFeature HDonor1 \\\n"
" [O,N]\n"
" Family HDONOR\n"
" \n"
"# comment, ignore me\n"
" Weights 1.0\n"
"# comment, ignore me\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonor1");
TEST_ASSERT(featDef->getSmarts()=="[O,N]");
TEST_ASSERT(featDef->getNumWeights()==1);
TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
delete featDef;
inText=
"\n"
"# comment, ignore me\n"
"DefineFeature HDonor1 \\\n"
"# comment, ignore me\n"
" [O,N]\n"
" Family \\\n"
"\tHDONOR\n"
"# comment, ignore me\n"
" Weights \\\n"
"1.0\n"
"# comment, ignore me\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily()=="HDONOR");
TEST_ASSERT(featDef->getType()=="HDonor1");
TEST_ASSERT(featDef->getSmarts()=="[O,N]");
TEST_ASSERT(featDef->getNumWeights()==1);
TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
delete featDef;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue225(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue 225." << std::endl;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText=
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
res=parseFeatureData(inText,featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size()==2);
featDefIt=featureDefs.begin();
featDef=*featDefIt;
TEST_ASSERT(featDef->getSmarts()=="[N,O;!H0]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms()==1);
TEST_ASSERT(featDef->getNumWeights()==1);
featDef=*(++featureDefs.begin());
TEST_ASSERT(featDef->getSmarts()=="[N,O]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms()==1);
TEST_ASSERT(featDef->getNumWeights()==1);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue346(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test Issue346" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName = rdbase + "/Code/GraphMol/MolChemicalFeatures/test_data/featDef2.txt";
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
std::ifstream inStream(fName.c_str());
TEST_ASSERT(inStream.is_open());
std::istream &instrm = static_cast<std::istream &>(inStream);
factory = buildFeatureFactory(instrm);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
featDefIt=factory->beginFeatureDefs();
featDef=*featDefIt;
TEST_ASSERT(featDef->getFamily()=="HBondDonor");
featDefIt++;
featDef=*featDefIt;
TEST_ASSERT(featDefIt!=factory->endFeatureDefs());
TEST_ASSERT(featDef->getFamily()=="HBondAcceptor");
featDefIt++;
TEST_ASSERT(featDefIt==factory->endFeatureDefs());
delete(factory);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue347(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test Issue347" << std::endl;
ROMol *testMol;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
std::string fdef;
fdef=
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
featDefIt=factory->beginFeatureDefs();
featDef=*featDefIt;
TEST_ASSERT(featDef->getFamily()=="LumpedHydrophobe");
featDefIt++;
featDef=*featDefIt;
TEST_ASSERT(featDef->getFamily()=="LumpedHydrophobe");
featDefIt++;
TEST_ASSERT(featDefIt==factory->endFeatureDefs());
testMol=SmilesToMol("CCC");
TEST_ASSERT(testMol);
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size()==1);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType()=="CTriplet");
// now reverse the order and we should get two matches:
fdef=
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n"
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
featDefIt=factory->beginFeatureDefs();
featDef=*featDefIt;
TEST_ASSERT(featDef->getFamily()=="LumpedHydrophobe");
featDefIt++;
featDef=*featDefIt;
TEST_ASSERT(featDef->getFamily()=="LumpedHydrophobe");
featDefIt++;
TEST_ASSERT(featDefIt==factory->endFeatureDefs());
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size()==3);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType()=="CPair");
featSPtr=*(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily()=="LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType()=="CPair");
featSPtr=*(++++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily()=="LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType()=="CTriplet");
delete(factory);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue348(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue 348." << std::endl;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText=
"DefineFeature CTriplet \\\n"
"[C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CTriplet [C[C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
bool ok;
try{
res=parseFeatureData(inText,featureDefs);
ok=false;
} catch (FeatureFileParseException &fpe){
ok=true;
TEST_ASSERT(fpe.lineNo()==6);
}
TEST_ASSERT(ok);
}
void testNestedAtomTypes(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Nested AtomType definitions." << std::endl;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText=
"AtomType Carbon_NonPolar [C;!$(C=[O,N,P,S]);!$(C#N)]\n"
"AtomType Hphobe [{Carbon_NonPolar},c]\n"
"AtomType RingHphobe [{Hphobe};R]\n"
"DefineFeature HP1 [{RingHphobe}]\n"
" Family Hydrophobe\n"
" Weights 1.0\n"
"EndFeature\n";
res=parseFeatureData(inText,featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size()==1);
std::cerr << (*featureDefs.begin())->getSmarts() << std::endl;
}
void testGithub252(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Github Issue #252: crash when calling getPos() with no conformer." << std::endl;
BOOST_LOG(rdErrorLog) << " expect a precondition failure message below" << std::endl;
ROMol *testMol;
MolChemicalFeatureFactory *factory;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
std::string fdef=
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs()==2);
testMol=SmilesToMol("CCC");
TEST_ASSERT(testMol);
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size()==1);
featSPtr=*featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily()=="LumpedHydrophobe");
bool ok=false;
try{
featSPtr->getPos();
} catch (const Invar::Invariant &i){
ok=true;
}
TEST_ASSERT(ok);
BOOST_LOG(rdErrorLog) << " Done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(){
RDLog::InitLogs();
#if 1
test1();
test2();
test3();
test4();
test5();
test6();
test7();
testIssue224();
testIssue225();
testIssue346();
testIssue347();
testIssue348();
#endif
testNestedAtomTypes();
testGithub252();
}
Reference in New Issue View Git Blame Copy Permalink