mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
95a92282d1
o rdkit gains a RDKit::common_properties namespace that contains common string value properties o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns true/false on success or failure. This is used to optimize access. o rdkit learns how to pass property keys by reference, not value. A new namespace has been added to RDKit, common_properties that contains the std::string values for commonly used properties. This helps to avoid typos in string values but also avoids a creation of std::strings from character values. All accessors (has/get/clear and getPropIfPresent) now pass the key by reference. Additionally, getPropIfPresent removes the double lookup of hasProp/getProp which can be a significant speedup in the smiles and smarts parsers (10-20%)
1012 lines
29 KiB
C++
1012 lines
29 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2011 Greg Landrum and 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 <RDGeneral/utils.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/MonomerInfo.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/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <GraphMol/Substruct/SubstructMatch.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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#include <boost/algorithm/string.hpp>
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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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void testQueries(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << "Testing query serialization." << std::endl;
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std::string smi,pickle,smi2;
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int tmpInt;
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ROMol *m1,*m2;
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MatchVectType matchV;
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// start simple : atom map numbers
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smi="C";
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m1= SmilesToMol(smi);
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TEST_ASSERT(m1);
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m1->getAtomWithIdx(0)->setProp(common_properties::molAtomMapNumber,1);
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MolPickler::pickleMol(*m1,pickle);
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delete m1;
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m1 = new ROMol();
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MolPickler::molFromPickle(pickle,*m1);
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TEST_ASSERT(m1->getNumAtoms()==1);
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TEST_ASSERT(m1->getAtomWithIdx(0)->hasProp(common_properties::molAtomMapNumber));
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m1->getAtomWithIdx(0)->getProp(common_properties::molAtomMapNumber,tmpInt);
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TEST_ASSERT(tmpInt==1);
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delete m1;
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// now a basic query:
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smi="C";
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m1= SmartsToMol(smi);
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TEST_ASSERT(m1);
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MolPickler::pickleMol(*m1,pickle);
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delete m1;
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m1 = new ROMol();
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MolPickler::molFromPickle(pickle,*m1);
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TEST_ASSERT(m1->getNumAtoms()==1);
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TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
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TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
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// query should be for aliphatic C:
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smi="C";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m2;
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smi="O";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m2;
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smi="c1ccccc1";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m1;
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// atom lists:
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smi="[C,N,O]";
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m1= SmartsToMol(smi);
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TEST_ASSERT(m1);
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MolPickler::pickleMol(*m1,pickle);
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delete m1;
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m1 = new ROMol();
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MolPickler::molFromPickle(pickle,*m1);
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TEST_ASSERT(m1->getNumAtoms()==1);
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TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
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TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomOr");
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smi="C";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m2;
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smi="O";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m2;
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smi="N";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m2;
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smi="F";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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delete m2;
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smi="c1nocc1";
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m2= SmilesToMol(smi);
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TEST_ASSERT(m2);
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TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
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TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(1)));
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TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(2)));
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delete m1;
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// more complex atom queries:
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smi="[C&D2,N&D1]";
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m1= SmartsToMol(smi);
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TEST_ASSERT(m1);
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|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomOr");
|
|
smi="C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="CC";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="C(C)C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="C(C)(C)C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="N";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="NC";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="N(C)C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
|
|
// basic recursive queries:
|
|
smi="[$([#6])]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="RecursiveStructure");
|
|
smi="C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="N";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="c1ccccc1";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m1;
|
|
|
|
smi="[R2]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomInNRings");
|
|
smi="C1CCC1";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
delete m2;
|
|
smi="C12(CCC2)CCC1";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(0)));
|
|
TEST_ASSERT(!m1->getAtomWithIdx(0)->Match(m2->getAtomWithIdx(1)));
|
|
delete m2;
|
|
|
|
// basic bond queries:
|
|
smi="[#6][#6]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==2);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m1->getBondWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getBondWithIdx(0)->getQuery()->getDescription()=="BondOr");
|
|
smi="CC";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="C=C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="CN";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="c1ccccc1";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
|
|
smi="[#6]-[#6]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==2);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(1)->hasQuery());
|
|
TEST_ASSERT(m1->getBondWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getBondWithIdx(0)->getQuery()->getDescription()=="BondOrder");
|
|
smi="CC";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="C=C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="CN";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="c1ccccc1";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
|
|
smi="C=C";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==2);
|
|
smi=MolToSmarts(*m1);
|
|
TEST_ASSERT(smi=="C=C");
|
|
|
|
smi="C=[$(C=O)]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==2);
|
|
smi=MolToSmarts(*m1);
|
|
BOOST_LOG(rdErrorLog)<<smi<<std::endl;
|
|
TEST_ASSERT(smi=="C=[$(C=O)]");
|
|
|
|
smi="S(=O)(=O)-[C;H2]([F,Br,I,Cl])";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
smi=MolToSmarts(*m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
smi2=MolToSmarts(*m1);
|
|
BOOST_LOG(rdErrorLog)<<smi<<" "<<smi2<<std::endl;
|
|
TEST_ASSERT(smi==smi2);
|
|
|
|
// more complex recursive queries:
|
|
smi="[$(C)]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="RecursiveStructure");
|
|
smi="C";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="N";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="c1ccccc1";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m1;
|
|
|
|
// more complex recursive queries:
|
|
smi="[$(C=O);$(C-N)]";
|
|
m1= SmartsToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
delete m1;
|
|
m1 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m1);
|
|
TEST_ASSERT(m1->getNumAtoms()==1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->hasQuery());
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
|
|
smi="NCO";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
smi="CNC(=O)";
|
|
m2= SmilesToMol(smi);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(SubstructMatch(*m2,*m1,matchV));
|
|
delete m2;
|
|
|
|
delete m1;
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
|
|
void testRadicals(){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing radical handling in pickles." << std::endl;
|
|
|
|
std::string smi="C[CH]C";
|
|
ROMol *m1 = SmilesToMol(smi);
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(1)->getNumRadicalElectrons()==1);
|
|
std::string pickle;
|
|
ROMol *m2;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
m2 = new ROMol();
|
|
MolPickler::molFromPickle(pickle,*m2);
|
|
TEST_ASSERT(m1->getNumAtoms()==m2->getNumAtoms());
|
|
TEST_ASSERT(m1->getNumBonds()==m2->getNumBonds());
|
|
TEST_ASSERT(m2->getAtomWithIdx(1)->getNumRadicalElectrons()==1);
|
|
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
|
|
}
|
|
|
|
|
|
void testIssue2788233(bool doLong=0){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 2788233." << std::endl;
|
|
|
|
{
|
|
std::string fName = getenv("RDBASE");
|
|
fName += "/Code/GraphMol/test_data/Issue2788233.mol";
|
|
|
|
RWMol *m=MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms()==2);
|
|
TEST_ASSERT(m->getNumBonds()==0);
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m,pickle);
|
|
RWMol *m2 = new RWMol();
|
|
MolPickler::molFromPickle(pickle,*m2);
|
|
TEST_ASSERT(m2->getNumAtoms()==2);
|
|
TEST_ASSERT(m2->getNumBonds()==0);
|
|
|
|
delete m;
|
|
delete m2;
|
|
}
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
void testIssue3202580(){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 3202580." << std::endl;
|
|
|
|
{
|
|
ROMol *m1 = SmilesToMol("C");
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getMass(),12.011,.001));
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol();
|
|
MolPickler::molFromPickle(pickle,*m2);
|
|
TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getMass(),12.011,.001));
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
{
|
|
ROMol *m1 = SmilesToMol("[12CH4]");
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getMass(),12.000,.001));
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol();
|
|
MolPickler::molFromPickle(pickle,*m2);
|
|
TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getMass(),12.000,.001));
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
{
|
|
ROMol *m1 = SmilesToMol("[13CH4]");
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getAtomWithIdx(0)->getIsotope()==13);
|
|
std::cerr<<" mass! "<<m1->getAtomWithIdx(0)->getMass()<<std::endl;
|
|
TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getMass(),13.003,.001));
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol();
|
|
MolPickler::molFromPickle(pickle,*m2);
|
|
TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getMass(),13.003,.001));
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
void testIssue3316407(){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 3316407." << std::endl;
|
|
|
|
{
|
|
std::string fName = getenv("RDBASE");
|
|
fName += "/Code/GraphMol/FileParsers/test_data/rgroups1.mol";
|
|
|
|
RWMol *m=MolFileToMol(fName);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms()==5);
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m,pickle);
|
|
RWMol *m2 = new RWMol();
|
|
MolPickler::molFromPickle(pickle,*m2);
|
|
TEST_ASSERT(m2->getNumAtoms()==5);
|
|
for(unsigned int i=0;i<m->getNumAtoms();++i){
|
|
TEST_ASSERT(m->getAtomWithIdx(i)->getExplicitValence()==m2->getAtomWithIdx(i)->getExplicitValence());
|
|
TEST_ASSERT(m->getAtomWithIdx(i)->getImplicitValence()==m2->getAtomWithIdx(i)->getImplicitValence());
|
|
}
|
|
// part of sf.net issue 285:
|
|
TEST_ASSERT(m2->getAtomWithIdx(3)->hasProp(common_properties::dummyLabel));
|
|
TEST_ASSERT(m2->getAtomWithIdx(4)->hasProp(common_properties::dummyLabel));
|
|
|
|
delete m;
|
|
delete m2;
|
|
}
|
|
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
void testIssue3496759(){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 3496759." << std::endl;
|
|
|
|
{
|
|
ROMol *m1 = SmartsToMol("c1ncncn1");
|
|
TEST_ASSERT(m1);
|
|
std::string smi1=MolToSmiles(*m1,1);
|
|
TEST_ASSERT(smi1=="c1ncncn1");
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol(pickle);
|
|
TEST_ASSERT(m2);
|
|
|
|
std::string smi2=MolToSmiles(*m2,1);
|
|
TEST_ASSERT(smi2=="c1ncncn1");
|
|
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
{
|
|
std::string fName = getenv("RDBASE");
|
|
fName += "/Data/SmartsLib/RLewis_smarts.txt";
|
|
std::ifstream inf(fName.c_str());
|
|
while(!inf.eof()){
|
|
std::string inl;
|
|
std::getline(inf,inl);
|
|
if(inl[0]=='#'||inl.size()<2) continue;
|
|
std::vector<std::string> tokens;
|
|
boost::split(tokens,inl,boost::is_any_of(" \t"));
|
|
//std::cerr<<"smarts: "<<tokens[0]<<std::endl;
|
|
ROMol *m1 = SmartsToMol(tokens[0]);
|
|
TEST_ASSERT(m1);
|
|
std::string smi1=MolToSmiles(*m1,1);
|
|
std::string sma1=MolToSmarts(*m1);
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol(pickle);
|
|
TEST_ASSERT(m2);
|
|
|
|
std::string smi2=MolToSmiles(*m2,1);
|
|
std::string sma2=MolToSmarts(*m2);
|
|
|
|
//std::cerr<<"smi match: "<<smi1<<" "<<smi2<<std::endl;
|
|
TEST_ASSERT(smi1==smi2);
|
|
//std::cerr<<"sma match: "<<sma1<<" "<<sma2<<std::endl;
|
|
TEST_ASSERT(sma1==sma2);
|
|
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
}
|
|
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
void testIssue280(){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 280." << std::endl;
|
|
|
|
{
|
|
ROMol *m1 = SmilesToMol("CCC");
|
|
TEST_ASSERT(m1);
|
|
std::string v="1";
|
|
m1->getAtomWithIdx(0)->setProp(common_properties::molAtomMapNumber,v);
|
|
// ints still work
|
|
m1->getAtomWithIdx(1)->setProp(common_properties::molAtomMapNumber,2);
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol(pickle);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp(common_properties::molAtomMapNumber));
|
|
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp(common_properties::molAtomMapNumber));
|
|
int iv;
|
|
m2->getAtomWithIdx(0)->getProp(common_properties::molAtomMapNumber,iv);
|
|
TEST_ASSERT(iv==1);
|
|
m2->getAtomWithIdx(1)->getProp(common_properties::molAtomMapNumber,iv);
|
|
TEST_ASSERT(iv==2);
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
{ // but bogus values are not propagated:
|
|
ROMol *m1 = SmilesToMol("CC");
|
|
TEST_ASSERT(m1);
|
|
std::string v="foo";
|
|
m1->getAtomWithIdx(0)->setProp(common_properties::molAtomMapNumber,v);
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol(pickle);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(!m2->getAtomWithIdx(0)->hasProp(common_properties::molAtomMapNumber));
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
void testIssue285(){
|
|
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdErrorLog) << "Testing sf.net issue 285." << std::endl;
|
|
|
|
{
|
|
ROMol *m1 = SmilesToMol("*C");
|
|
TEST_ASSERT(m1);
|
|
std::string v="R";
|
|
m1->getAtomWithIdx(0)->setProp(common_properties::dummyLabel,v);
|
|
|
|
std::string pickle;
|
|
MolPickler::pickleMol(*m1,pickle);
|
|
RWMol *m2 = new RWMol(pickle);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp(common_properties::dummyLabel));
|
|
m2->getAtomWithIdx(0)->getProp(common_properties::dummyLabel,v);
|
|
TEST_ASSERT(v=="R");
|
|
delete m1;
|
|
delete m2;
|
|
}
|
|
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
|
|
void testAtomResidues()
|
|
{
|
|
BOOST_LOG(rdInfoLog) << "-----------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Testing residue information handling on atoms" << std::endl;
|
|
{
|
|
RWMol *m=new RWMol();
|
|
|
|
m->addAtom(new Atom(6));
|
|
m->addAtom(new Atom(6));
|
|
m->addBond(0,1,Bond::SINGLE);
|
|
m->addAtom(new Atom(6));
|
|
m->addBond(1,2,Bond::SINGLE);
|
|
m->addAtom(new Atom(6));
|
|
m->addBond(2,3,Bond::SINGLE);
|
|
|
|
m->getAtomWithIdx(0)->setMonomerInfo(new AtomMonomerInfo(AtomMonomerInfo::OTHER,"m1"));
|
|
m->getAtomWithIdx(1)->setMonomerInfo(new AtomPDBResidueInfo("Ca",3));
|
|
MolOps::sanitizeMol(*m);
|
|
|
|
std::string pkl;
|
|
MolPickler::pickleMol(*m,pkl);
|
|
delete m;
|
|
RWMol *m2 = new RWMol(pkl);
|
|
TEST_ASSERT(m2);
|
|
TEST_ASSERT((m2->getAtomWithIdx(0)->getMonomerInfo()));
|
|
TEST_ASSERT(m2->getAtomWithIdx(0)->getMonomerInfo()->getName()=="m1");
|
|
TEST_ASSERT((m2->getAtomWithIdx(1)->getMonomerInfo()));
|
|
TEST_ASSERT(m2->getAtomWithIdx(1)->getMonomerInfo()->getName()=="Ca");
|
|
TEST_ASSERT(static_cast<const AtomPDBResidueInfo *>(m2->getAtomWithIdx(1)->getMonomerInfo())->getSerialNumber()==3);
|
|
TEST_ASSERT(!(m2->getAtomWithIdx(2)->getMonomerInfo()));
|
|
TEST_ASSERT(!(m2->getAtomWithIdx(3)->getMonomerInfo()));
|
|
}
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
void testGithub149()
|
|
{
|
|
BOOST_LOG(rdInfoLog) << "-----------------------\n";
|
|
BOOST_LOG(rdInfoLog) << "Testing Github issue 149: cannot pickle unsanitized molecules" << std::endl;
|
|
{
|
|
ROMol *m = SmilesToMol("CCO",0,0);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms()==3);
|
|
|
|
std::string pkl;
|
|
MolPickler::pickleMol(*m,pkl);
|
|
delete m;
|
|
m = new RWMol(pkl);
|
|
TEST_ASSERT(m);
|
|
TEST_ASSERT(m->getNumAtoms()==3);
|
|
delete m;
|
|
}
|
|
BOOST_LOG(rdErrorLog) << "\tdone" << std::endl;
|
|
}
|
|
|
|
|
|
int main(int argc, char *argv[]) {
|
|
RDLog::InitLogs();
|
|
bool doLong=false;
|
|
if(argc>1) {
|
|
if(!strncmp(argv[1],"-l",2)){
|
|
doLong=true;
|
|
}
|
|
}
|
|
|
|
//_createPickleFile();
|
|
#if 1
|
|
test1(doLong);
|
|
//test2(doLong);
|
|
test3(doLong);
|
|
test4();
|
|
testIssue164();
|
|
testIssue219();
|
|
testIssue220();
|
|
//timeTest(doLong);
|
|
testQueries();
|
|
testRadicals();
|
|
#endif
|
|
testIssue2788233();
|
|
testIssue3202580();
|
|
testIssue3316407();
|
|
testIssue3496759();
|
|
testIssue280();
|
|
testIssue285();
|
|
testAtomResidues();
|
|
testGithub149();
|
|
|
|
}
|
|
|
|
|