mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
857 lines
24 KiB
C++
857 lines
24 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2006 Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <fstream>
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#include <iostream>
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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 <sstream>
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#include <boost/shared_ptr.hpp>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
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#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h>
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#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
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#include <GraphMol/MolChemicalFeatures/FeatureParser.h>
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using namespace RDKit;
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void test1(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "AtomType parser testing." << std::endl;
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std::string inLine;
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std::map<std::string,std::string> atomTypeDefs;
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atomTypeDefs.clear();
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bool ok;
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inLine="AtomType donor [N,O]";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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TEST_ASSERT(atomTypeDefs.count("{donor}"));
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TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
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TEST_ASSERT(atomTypeDefs["{donor}"]=="$([N,O])");
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// check robustness to whitespace as we expand:
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inLine=" AtomType donor\t[S]";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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TEST_ASSERT(atomTypeDefs.count("{donor}"));
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TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
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TEST_ASSERT(atomTypeDefs["{donor}"]=="$([N,O,$([S])])");
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inLine="AtomType !donor [NH0]";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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TEST_ASSERT(atomTypeDefs.count("{donor}"));
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TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
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TEST_ASSERT(atomTypeDefs["{donor}"]=="$([!$([NH0]);N,O,$([S])])");
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inLine="AtomType unsaturatedDonor [$([{donor}]!-[*])]";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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TEST_ASSERT(atomTypeDefs.count("{donor}"));
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TEST_ASSERT(atomTypeDefs.count("{unsaturatedDonor}"));
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TEST_ASSERT(atomTypeDefs["{donor}"]=="$([!$([NH0]);N,O,$([S])])");
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TEST_ASSERT(atomTypeDefs["{unsaturatedDonor}"]=="$([$([$([!$([NH0]);N,O,$([S])])]!-[*])])");
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ok=false;
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try {
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inLine="";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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} catch (FeatureFileParseException &fpe) {
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ok=true;
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TEST_ASSERT(fpe.lineNo()==0);
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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ok=false;
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try {
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inLine="AtomTyped donor [N,O]";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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} catch (FeatureFileParseException &fpe) {
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ok=true;
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TEST_ASSERT(fpe.lineNo()==0);
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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ok=false;
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try {
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inLine="AtomType";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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} catch (FeatureFileParseException &fpe) {
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ok=true;
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TEST_ASSERT(fpe.lineNo()==0);
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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ok=false;
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try {
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inLine="AtomType donor";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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} catch (FeatureFileParseException &fpe) {
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ok=true;
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TEST_ASSERT(fpe.lineNo()==0);
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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ok=false;
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try {
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inLine="AtomType donor [N,O";
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Local::parseAtomType(inLine,atomTypeDefs,0);
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} catch (FeatureFileParseException &fpe) {
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ok=true;
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TEST_ASSERT(fpe.lineNo()==0);
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test2(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "FeatureDefinition parser testing." << std::endl;
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std::string inText,inLine;
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std::istringstream ss;
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MolChemicalFeatureDef *featDef;
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bool ok;
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std::map<std::string,std::string> atomTypeDefs;
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atomTypeDefs["{donor}"]="$([O,N])";
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inText=
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"DefineFeature HDonor1 [O,N]\n"
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" Family HDONOR\n"
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" Weights 1.0\n"
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"EndFeature\n";
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ss.clear();
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ss.str(inText);
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inLine = RDKit::getLine(ss);
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unsigned int tmpLine=2;
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featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
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TEST_ASSERT(featDef);
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TEST_ASSERT(featDef->getFamily()=="HDONOR");
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TEST_ASSERT(featDef->getType()=="HDonor1");
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TEST_ASSERT(featDef->getSmarts()=="[O,N]");
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TEST_ASSERT(featDef->getNumWeights()==1);
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TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
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delete featDef;
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inText=
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"DefineFeature HDonor1 [{donor}]\n"
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" Family HDONOR\n"
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" Weights 2.0\n"
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"EndFeature\n";
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ss.clear();
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ss.str(inText);
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inLine = RDKit::getLine(ss);
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featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
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TEST_ASSERT(featDef);
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TEST_ASSERT(featDef->getFamily()=="HDONOR");
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TEST_ASSERT(featDef->getType()=="HDonor1");
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TEST_ASSERT(featDef->getSmarts()=="[$([O,N])]");
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TEST_ASSERT(featDef->getNumWeights()==1);
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TEST_ASSERT(feq(*featDef->beginWeights(),1.0));
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delete featDef;
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inText=
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"DefineFeature HDonorPair [{donor}][{donor}]\n"
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" Family HDONOR\n"
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" Weights 1.0,1\n"
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"EndFeature\n";
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ss.clear();
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ss.str(inText);
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inLine = RDKit::getLine(ss);
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featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
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TEST_ASSERT(featDef);
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TEST_ASSERT(featDef->getFamily()=="HDONOR");
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TEST_ASSERT(featDef->getType()=="HDonorPair");
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TEST_ASSERT(featDef->getSmarts()=="[$([O,N])][$([O,N])]");
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TEST_ASSERT(featDef->getNumWeights()==2);
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TEST_ASSERT(feq(*featDef->beginWeights(),0.5));
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TEST_ASSERT(feq(*++(featDef->beginWeights()),0.5));
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delete featDef;
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ok=false;
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inText=
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"DefineFeature HDonor1 [{donor}]\n"
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" Family HDONOR\n"
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" Weights 1.0\n";
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ss.clear();
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ss.str(inText);
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inLine = RDKit::getLine(ss);
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try{
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featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
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} catch (FeatureFileParseException &){
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ok=true;
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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ok=false;
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inText=
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"DefineFeature HDonor1 [{donor}]\n"
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"EndFeature\n";
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ss.clear();
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ss.str(inText);
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inLine = RDKit::getLine(ss);
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try{
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featDef = Local::parseFeatureDef(ss,inLine,tmpLine,atomTypeDefs);
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} catch (FeatureFileParseException &){
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ok=true;
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}
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CHECK_INVARIANT(ok,"expected parse failure did not happen");
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test3(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test pulling feat defs from a string." << std::endl;
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//std::string pathName=getenv("RDBASE");
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//pathName += "/Code/GraphMol/MolChemicalFeatures/test_data/smallsample.feats";
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std::string inText,inLine;
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std::istringstream ss;
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int res;
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MolChemicalFeatureDef::CollectionType featureDefs;
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inText=
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"AtomType donor [N,O]\n"
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"AtomType !donor [H0]\n"
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"DefineFeature HDonor1 [{donor}]\n"
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" Family HBondDonor\n"
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" Weights 1.0\n"
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"EndFeature\n";
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res=parseFeatureData(inText,featureDefs);
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TEST_ASSERT(!res);
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TEST_ASSERT(featureDefs.size()==1);
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TEST_ASSERT((*featureDefs.begin())->getSmarts()=="[$([!$([H0]);N,O])]");
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test4(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "FeatureDef functionality testing." << std::endl;
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ROMol *testMol;
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MatchVectType mv;
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std::string inText;
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int res;
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MolChemicalFeatureDef::CollectionType featureDefs;
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MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
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MolChemicalFeatureDef::CollectionType::value_type featDef;
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inText=
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"DefineFeature HDonor1 [N,O;!H0]\n"
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" Family HBondDonor\n"
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" Weights 1.0\n"
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"EndFeature\n"
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"DefineFeature HAcceptor1 [N,O]\n"
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" Family HAcceptor\n"
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" Weights 1.0\n"
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"EndFeature\n";
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res=parseFeatureData(inText,featureDefs);
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TEST_ASSERT(!res);
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TEST_ASSERT(featureDefs.size()==2);
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featDefIt=featureDefs.begin();
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featDef=*featDefIt;
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TEST_ASSERT(featDef->getSmarts()=="[N,O;!H0]");
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TEST_ASSERT(featDef->getPattern());
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TEST_ASSERT(featDef->getPattern()->getNumAtoms()==1);
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TEST_ASSERT(featDef->getNumWeights()==1);
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featDef=*(++featureDefs.begin());
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TEST_ASSERT(featDef->getSmarts()=="[N,O]");
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TEST_ASSERT(featDef->getPattern());
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TEST_ASSERT(featDef->getPattern()->getNumAtoms()==1);
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TEST_ASSERT(featDef->getNumWeights()==1);
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testMol=SmilesToMol("COCN");
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TEST_ASSERT(testMol);
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featDef=*featureDefs.begin();
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TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
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TEST_ASSERT(mv.size()==1);
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TEST_ASSERT(mv[0].first==0);
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TEST_ASSERT(mv[0].second==3);
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featDef=*(++featureDefs.begin());
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TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
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TEST_ASSERT(mv.size()==1);
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TEST_ASSERT(mv[0].first==0);
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TEST_ASSERT(mv[0].second==1||mv[0].second==3);
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delete testMol;
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test5(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "FeatureFactory testing." << std::endl;
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ROMol *testMol;
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MatchVectType mv;
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std::string inText;
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FeatSPtrList featSPtrs;
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boost::shared_ptr<MolChemicalFeature> featSPtr;
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MolChemicalFeatureFactory *factory;
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MolChemicalFeatureDef::CollectionType::value_type featDef;
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inText=
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"DefineFeature HDonor1 [N,O;!H0]\n"
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" Family HBondDonor\n"
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" Weights 1.0\n"
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"EndFeature\n"
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"DefineFeature HAcceptor1 [N,O]\n"
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" Family HBondAcceptor\n"
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" Weights 1.0\n"
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"EndFeature\n";
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factory = buildFeatureFactory(inText);
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TEST_ASSERT(factory);
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TEST_ASSERT(factory->getNumFeatureDefs()==2);
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testMol=SmilesToMol("COCN");
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TEST_ASSERT(testMol);
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featDef=*factory->beginFeatureDefs();
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TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
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BOOST_LOG(rdErrorLog) << "1" << std::endl;
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TEST_ASSERT(mv.size()==1);
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TEST_ASSERT(mv[0].first==0);
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TEST_ASSERT(mv[0].second==3);
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featDef=*(++factory->beginFeatureDefs());
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TEST_ASSERT(SubstructMatch(*testMol,*featDef->getPattern(),mv));
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BOOST_LOG(rdErrorLog) << "2" << std::endl;
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TEST_ASSERT(mv.size()==1);
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TEST_ASSERT(mv[0].first==0);
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TEST_ASSERT(mv[0].second==1||mv[0].second==3);
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// Test using the factory to find features:
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featSPtrs = factory->getFeaturesForMol(*testMol);
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BOOST_LOG(rdErrorLog) << "3" << std::endl;
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TEST_ASSERT(featSPtrs.size()==3);
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featSPtr=*featSPtrs.begin();
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TEST_ASSERT(featSPtr->getFamily()=="HBondDonor");
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TEST_ASSERT(featSPtr->getType()=="HDonor1");
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featSPtr=*(++featSPtrs.begin());
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TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
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TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
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featSPtr=*(++featSPtrs.begin());
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TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
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TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
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// Test limiting stuff with includeOnly
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featSPtrs = factory->getFeaturesForMol(*testMol,"HBondAcceptor");
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BOOST_LOG(rdErrorLog) << "4" << std::endl;
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TEST_ASSERT(featSPtrs.size()==2);
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featSPtr=*featSPtrs.begin();
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TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
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TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
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featSPtr=*(++featSPtrs.begin());
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TEST_ASSERT(featSPtr->getFamily()=="HBondAcceptor");
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TEST_ASSERT(featSPtr->getType()=="HAcceptor1");
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featSPtrs = factory->getFeaturesForMol(*testMol,"HBondDonor");
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BOOST_LOG(rdErrorLog) << "5" << std::endl;
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TEST_ASSERT(featSPtrs.size()==1);
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featSPtr=*featSPtrs.begin();
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TEST_ASSERT(featSPtr->getFamily()=="HBondDonor");
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TEST_ASSERT(featSPtr->getType()=="HDonor1");
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featSPtrs = factory->getFeaturesForMol(*testMol,"NotPresent");
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BOOST_LOG(rdErrorLog) << "6" << std::endl;
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TEST_ASSERT(featSPtrs.size()==0);
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delete testMol;
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delete factory;
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test6(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Feature Location testing." << std::endl;
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ROMol *testMol;
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Conformer *conf;
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std::string inText;
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FeatSPtrList featSPtrs;
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boost::shared_ptr<MolChemicalFeature> featSPtr;
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MolChemicalFeatureFactory *factory;
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MolChemicalFeatureDef::CollectionType::value_type featDef;
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inText=
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"DefineFeature HDonor1 [N,O;!H0]\n"
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" Family HBondDonor\n"
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" Weights 1.0\n"
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"EndFeature\n"
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"DefineFeature Carboxyl1 C(=O)[O;H1,-]\n"
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" Family ZnBinder\n"
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" Weights 1.0,1.0,1.0\n"
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"EndFeature\n";
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factory = buildFeatureFactory(inText);
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TEST_ASSERT(factory);
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TEST_ASSERT(factory->getNumFeatureDefs()==2);
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testMol=SmilesToMol("C(=O)O");
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TEST_ASSERT(testMol);
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conf = new Conformer(3);
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testMol->addConformer(conf);
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conf->setAtomPos(0,RDGeom::Point3D(0,0,0.0));
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conf->setAtomPos(1,RDGeom::Point3D(1.2,0,0.0));
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conf->setAtomPos(2,RDGeom::Point3D(0,1.5,0.0));
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featSPtrs = factory->getFeaturesForMol(*testMol);
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TEST_ASSERT(featSPtrs.size()==2);
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featSPtr=*featSPtrs.begin();
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TEST_ASSERT(featSPtr->getFamily()=="HBondDonor");
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TEST_ASSERT(featSPtr->getType()=="HDonor1");
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TEST_ASSERT(feq(featSPtr->getPos().x,0.0));
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TEST_ASSERT(feq(featSPtr->getPos().y,1.5));
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TEST_ASSERT(feq(featSPtr->getPos().z,0.0));
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featSPtr=*(++featSPtrs.begin());
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TEST_ASSERT(featSPtr->getFamily()=="ZnBinder");
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TEST_ASSERT(featSPtr->getType()=="Carboxyl1");
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TEST_ASSERT(feq(featSPtr->getPos().x,0.4));
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TEST_ASSERT(feq(featSPtr->getPos().y,0.5));
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TEST_ASSERT(feq(featSPtr->getPos().z,0.0));
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delete testMol;
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delete factory;
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test7(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Test building a FeatureFactory from a file" << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/MolChemicalFeatures/test_data/featDef.txt";
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|
|
|
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;
|
|
|
|
|
|
}
|
|
|
|
|
|
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
|
|
//
|
|
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
|
|
int main(){
|
|
RDLog::InitLogs();
|
|
#if 1
|
|
test1();
|
|
test2();
|
|
test3();
|
|
test4();
|
|
test5();
|
|
test6();
|
|
test7();
|
|
testIssue224();
|
|
testIssue225();
|
|
testIssue346();
|
|
testIssue347();
|
|
testIssue348();
|
|
#endif
|
|
testNestedAtomTypes();
|
|
}
|