mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
338 lines
9.8 KiB
C++
338 lines
9.8 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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//
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <RDGeneral/RDLog.h>
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#include <stdlib.h>
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#include <ctime>
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#include <iostream>
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#include <fstream>
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using namespace RDKit;
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void test1(bool doLong=0){
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std::string fName = getenv("RDBASE");
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fName += "/Code/GraphMol/test_data/canonSmiles.smi";
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing String Pickle Roundtrips." << std::endl;
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SmilesMolSupplier suppl(fName,"\t",0,1,false);
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int count = 0;
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while(!suppl.atEnd()){
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ROMol *m = suppl.next();
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TEST_ASSERT(m);
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std::string pickle;
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MolPickler::pickleMol(*m,pickle);
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TEST_ASSERT(pickle.size());
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ROMol m2;
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MolPickler::molFromPickle(pickle,m2);
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std::string smi1=MolToSmiles(*m);
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//BOOST_LOG(rdInfoLog) << smi << " " << smi1 << std::endl;
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std::string smi2=MolToSmiles(m2);
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if(smi1!=smi2){
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BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1 << "\n != \n " << smi2 << std::endl;
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}
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TEST_ASSERT(smi1==smi2);
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delete m;
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count++;
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if(!doLong && count >= 100) break;
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}
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void _createPickleFile(){
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std::string smiName = getenv("RDBASE");
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smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
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std::string pklName = getenv("RDBASE");
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#ifdef OLD_PICKLE
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pklName += "/Code/GraphMol/test_data/canonSmiles.v1.pkl";
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#else
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pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
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#endif
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "creating pickle file." << std::endl;
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SmilesMolSupplier suppl(smiName,"\t",0,1,false);
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std::ofstream outStream(pklName.c_str(),std::ios_base::binary);
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int count = 0;
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while(!suppl.atEnd()){
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ROMol *m = suppl.next();
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TEST_ASSERT(m);
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std::string pickle;
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MolPickler::pickleMol(*m,outStream);
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delete m;
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count++;
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}
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void test2(bool doLong=0){
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std::string smiName = getenv("RDBASE");
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smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
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std::string pklName = getenv("RDBASE");
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pklName += "/Code/GraphMol/test_data/canonSmiles.v1.pkl";
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing reading existing pickle file (v1)." << std::endl;
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SmilesMolSupplier suppl(smiName,"\t",0,1,false);
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std::ifstream inStream(pklName.c_str(),std::ios_base::binary);
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int count = 0;
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while(!suppl.atEnd()){
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ROMol *m1 = suppl.next();
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TEST_ASSERT(m1);
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ROMol m2;
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MolPickler::molFromPickle(inStream,m2);
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std::string smi1=MolToSmiles(*m1);
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std::string smi2=MolToSmiles(m2);
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if(smi1!=smi2){
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BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1 << "\n != \n " << smi2 << std::endl;
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}
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TEST_ASSERT(smi1==smi2);
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delete m1;
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count++;
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if(!doLong && count >= 100) break;
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}
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void test3(bool doLong=0){
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std::string smiName = getenv("RDBASE");
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smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
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std::string pklName = getenv("RDBASE");
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pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing reading existing pickle file (v2)." << std::endl;
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SmilesMolSupplier suppl(smiName,"\t",0,1,false);
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std::ifstream inStream(pklName.c_str(),std::ios_base::binary);
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int count = 0;
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while(!suppl.atEnd()){
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ROMol *m1 = suppl.next();
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TEST_ASSERT(m1);
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ROMol m2;
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MolPickler::molFromPickle(inStream,m2);
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std::string smi1=MolToSmiles(*m1,1);
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std::string smi2=MolToSmiles(m2,1);
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if(smi1!=smi2){
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BOOST_LOG(rdInfoLog) << "Line: " << count << "\n " << smi1 << "\n != \n " << smi2 << std::endl;
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}
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TEST_ASSERT(smi1==smi2);
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delete m1;
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count++;
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if(!doLong && count >= 100) break;
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}
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void timeTest(bool doLong=0){
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time_t t1,t2;
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std::string smiName = getenv("RDBASE");
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smiName += "/Code/GraphMol/test_data/canonSmiles.smi";
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std::string pklName = getenv("RDBASE");
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pklName += "/Code/GraphMol/test_data/canonSmiles.v2.pkl";
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Timing reads." << std::endl;
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t1 = std::time(0);
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SmilesMolSupplier suppl(smiName,"\t",0,1,false);
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int count = 0;
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while(!suppl.atEnd()){
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ROMol *m1 = suppl.next();
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TEST_ASSERT(m1);
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count++;
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if(!doLong && count >= 100) break;
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delete m1;
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}
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t2 = std::time(0);
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BOOST_LOG(rdInfoLog) << " Smiles time: " << std::difftime(t2,t1) << std::endl;;
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std::ifstream inStream(pklName.c_str(),std::ios_base::binary);
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t1 = std::time(0);
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while(count>0){
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ROMol m2;
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MolPickler::molFromPickle(inStream,m2);
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count--;
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if(!doLong && count >= 100) break;
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}
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t2 = std::time(0);
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BOOST_LOG(rdInfoLog) << " Pickle time: " << std::difftime(t2,t1) << std::endl;;
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BOOST_LOG(rdErrorLog) << "\tdone" << 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) << "Testing combining molecules using pickles." << std::endl;
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ROMol *m1 = SmilesToMol("C1CC1");
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TEST_ASSERT(m1);
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ROMol *m2 = SmilesToMol("C1COC1");
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TEST_ASSERT(m2);
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ROMol m3;
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std::string pickle;
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MolPickler::pickleMol(*m1,pickle);
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MolPickler::molFromPickle(pickle,m3);
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MolPickler::pickleMol(*m2,pickle);
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MolPickler::molFromPickle(pickle,m3);
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m3.debugMol(std::cout);
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TEST_ASSERT(m3.getNumAtoms()==7);
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TEST_ASSERT(m3.getNumBonds()==7);
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TEST_ASSERT(m3.getRingInfo()->numRings()==2);
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TEST_ASSERT(m3.getRingInfo()->isAtomInRingOfSize(0,3));
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TEST_ASSERT(!m3.getRingInfo()->isAtomInRingOfSize(0,4));
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TEST_ASSERT(!m3.getRingInfo()->isAtomInRingOfSize(4,3));
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TEST_ASSERT(m3.getRingInfo()->isAtomInRingOfSize(4,4));
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TEST_ASSERT(m3.getRingInfo()->isBondInRingOfSize(0,3));
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TEST_ASSERT(!m3.getRingInfo()->isBondInRingOfSize(0,4));
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TEST_ASSERT(!m3.getRingInfo()->isBondInRingOfSize(4,3));
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TEST_ASSERT(m3.getRingInfo()->isBondInRingOfSize(4,4));
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void testIssue164(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing Issue164: Roundtrip Pickle Failure." << std::endl;
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std::string smi="NCCCCC(NC(C(C(C)C)NC(=O)C1CCCN1C(C(N)CCCNC(=N)N)=O)=O)C(NC(C(C)C)C(NC(Cc2ccc(O)cc2)C(=O)N6C(C(NC(CC(N)=O)C(NCC(NC(C)C(NC(CCC(O)=O)C(NC(CC(O)=O)C(NC(C(NC(CO)C(NC(C)C(NC(CCC(O)=O)C(NC(C)C(NC(Cc3ccccc3)C(=O)N5C(C(NC(CC(C)C)C(NC(C(NC(C(O)=O)Cc4ccccc4)=O)CCC(O)=O)=O)=O)CCC5)=O)=O)=O)=O)=O)CCC(O)=O)=O)=O)=O)=O)=O)=O)CCC6)=O)=O";
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ROMol *m1 = SmilesToMol(smi);
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TEST_ASSERT(m1);
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std::string pickle;
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ROMol m2;
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MolPickler::pickleMol(*m1,pickle);
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MolPickler::molFromPickle(pickle,m2);
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TEST_ASSERT(m1->getNumAtoms()==m2.getNumAtoms());
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// the issue had to do with number of atoms, so let's make an enormous
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// molecule and try again:
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RWMol *m3 = static_cast<RWMol *>(SmilesToMol(smi));
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m3->insertMol(*m1);
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m3->insertMol(*m1);
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MolOps::sanitizeMol(*m3);
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MolPickler::pickleMol(*m3,pickle);
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ROMol m4;
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MolPickler::molFromPickle(pickle,m4);
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TEST_ASSERT(m3->getNumAtoms()==m4.getNumAtoms());
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TEST_ASSERT(m3->getNumBonds()==m4.getNumBonds());
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void testIssue219(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing Issue219: Pickle Failure with Conformations." << std::endl;
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std::string smi="CC";
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ROMol *m1 = SmilesToMol(smi);
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TEST_ASSERT(m1);
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std::string pickle;
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ROMol *m2;
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MolPickler::pickleMol(*m1,pickle);
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m2 = new ROMol();
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MolPickler::molFromPickle(pickle,*m2);
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TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
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Conformer *conf = new Conformer(2);
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conf->setId(23);
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m1->addConformer(conf);
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MolPickler::pickleMol(*m1,pickle);
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delete m2;
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m2 = new ROMol();
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MolPickler::molFromPickle(pickle,*m2);
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TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
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TEST_ASSERT(m2->getConformer().getId()==23);
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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void testIssue220(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing Issue220: Pickle problems with bond stereochemistry." << std::endl;
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std::string smi="N/N=C/C";
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ROMol *m1 = SmilesToMol(smi);
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TEST_ASSERT(m1);
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TEST_ASSERT(m1->getBondWithIdx(1)->getStereo()!=Bond::STEREONONE);
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std::string pickle;
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ROMol *m2;
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MolPickler::pickleMol(*m1,pickle);
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m2 = new ROMol();
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MolPickler::molFromPickle(pickle,*m2);
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TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
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TEST_ASSERT(m1->getNumBonds()==m2->getNumBonds());
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TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()!=Bond::STEREONONE);
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for(unsigned int i=0;i<m1->getNumBonds();++i){
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TEST_ASSERT(m1->getBondWithIdx(i)->getStereo() ==
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m2->getBondWithIdx(i)->getStereo());
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TEST_ASSERT(m1->getBondWithIdx(i)->getStereoAtoms() ==
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m2->getBondWithIdx(i)->getStereoAtoms());
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}
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BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
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}
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int main(int argc, char *argv[]) {
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RDLog::InitLogs();
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bool doLong=false;
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if(argc>1) {
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if(!strncmp(argv[1],"-l",2)){
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doLong=true;
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}
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}
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//_createPickleFile();
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#if 1
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test1(doLong);
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//test2(doLong);
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test3(doLong);
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test4();
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testIssue164();
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#endif
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//timeTest(doLong);
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testIssue219();
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testIssue220();
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return 0;
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}
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