mirror of
https://github.com/rdkit/rdkit.git
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257 lines
7.4 KiB
C++
Executable File
257 lines
7.4 KiB
C++
Executable File
// $Id$
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//
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// Copyright (C) 2003-2006 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 <RDGeneral/RDLog.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include "FragCatGenerator.h"
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#include "FragCatalogEntry.h"
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#include "FragCatParams.h"
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#include "FragCatalogUtils.h"
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#include "FragFPGenerator.h"
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#include <stdlib.h>
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#include <iostream>
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#include <fstream>
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#include <GraphMol/Subgraphs/SubgraphUtils.h>
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#include <GraphMol/Subgraphs/Subgraphs.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <RDGeneral/types.h>
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#include <RDGeneral/FileParseException.h>
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#include <DataStructs/BitVects.h>
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using namespace RDKit;
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void testMols(std::vector<ROMol *> &mols,FragFPGenerator &fpGen,FragCatalog &fcat){
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std::vector<ROMol *>::iterator mi;
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int nDone=0;
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for (mi = mols.begin(); mi != mols.end(); mi++) {
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ExplicitBitVect *fp = fpGen.getFPForMol(*(*mi), fcat);
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switch(nDone){
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case 0:
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TEST_ASSERT(fp->GetNumOnBits()==3);
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TEST_ASSERT((*fp)[0]);
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TEST_ASSERT((*fp)[1]);
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TEST_ASSERT((*fp)[2]);
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break;
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case 1:
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TEST_ASSERT(fp->GetNumOnBits()==2);
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TEST_ASSERT((*fp)[1]);
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TEST_ASSERT((*fp)[3]);
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break;
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case 2:
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TEST_ASSERT(fp->GetNumOnBits()==3);
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TEST_ASSERT((*fp)[1]);
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TEST_ASSERT((*fp)[4]);
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TEST_ASSERT((*fp)[5]);
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break;
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case 3:
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TEST_ASSERT(fp->GetNumOnBits()==3);
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TEST_ASSERT((*fp)[1]);
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TEST_ASSERT((*fp)[6]);
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TEST_ASSERT((*fp)[7]);
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break;
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case 4:
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TEST_ASSERT(fp->GetNumOnBits()==2);
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TEST_ASSERT((*fp)[0]);
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TEST_ASSERT((*fp)[8]);
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break;
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case 5:
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TEST_ASSERT(fp->GetNumOnBits()==3);
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TEST_ASSERT((*fp)[0]);
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TEST_ASSERT((*fp)[6]);
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TEST_ASSERT((*fp)[9]);
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break;
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case 6:
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TEST_ASSERT(fp->GetNumOnBits()==5);
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TEST_ASSERT((*fp)[0]);
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TEST_ASSERT((*fp)[1]);
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TEST_ASSERT((*fp)[2]);
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TEST_ASSERT((*fp)[3]);
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TEST_ASSERT((*fp)[10]);
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break;
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}
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nDone += 1;
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}
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}
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void test1(){
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi";
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std::string fgrpFile = rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt";
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SmilesMolSupplier suppl(fname," ",0,1,false);
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FragCatParams *fparams = new FragCatParams(1, 6, fgrpFile, 1.0e-8);
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TEST_ASSERT(fparams->getNumFuncGroups()==15);
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FragCatalog fcat(fparams);
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FragCatGenerator catGen;
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std::vector<ROMol *> mols;
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unsigned int nDone=0;
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ROMol *m = suppl.next();
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while (m) {
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mols.push_back(m);
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nDone+=1;
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catGen.addFragsFromMol(*m, &fcat);
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try{
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m = suppl.next();
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} catch( FileParseException &) {
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m = NULL;
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}
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}
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TEST_ASSERT(mols.size()==16);
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TEST_ASSERT(nDone==16);
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int nents = fcat.getNumEntries();
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TEST_ASSERT(nents==21);
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FragFPGenerator fpGen;
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BOOST_LOG(rdInfoLog) << "----- Test 1" << std::endl;
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testMols(mols,fpGen,fcat);
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BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
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//----------------------------------------------------------
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// SERIALIZATION TESTS
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//----------------------------------------------------------
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// make sure we can pickle and unpickle parameter objects:
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FragCatParams newParams;
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std::string pickle=fparams->Serialize();
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newParams.initFromString(pickle);
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TEST_ASSERT(newParams.getLowerFragLength()==fparams->getLowerFragLength());
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TEST_ASSERT(newParams.getUpperFragLength()==fparams->getUpperFragLength());
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TEST_ASSERT(newParams.getTolerance()==fparams->getTolerance());
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TEST_ASSERT(newParams.getNumFuncGroups()==fparams->getNumFuncGroups());
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// make sure we can pickle and unpickle catalog entries:
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const FragCatalogEntry *fpEntry=fcat.getEntryWithIdx(0);
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FragCatalogEntry *fpEntry2 = new FragCatalogEntry();
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fpEntry2->initFromString(fpEntry->Serialize());
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TEST_ASSERT(fpEntry->getDescription()==fpEntry2->getDescription());
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TEST_ASSERT(fpEntry->getOrder()==fpEntry2->getOrder());
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TEST_ASSERT(fpEntry->getBitId()==fpEntry2->getBitId());
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TEST_ASSERT(fpEntry2->match(fpEntry,1e-8));
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TEST_ASSERT(fpEntry->match(fpEntry2,1e-8));
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// test catalogs' initFromString:
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FragCatalog fcat2;
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fcat2.initFromString(fcat.Serialize());
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TEST_ASSERT(fcat2.getNumEntries()==fcat.getNumEntries());
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BOOST_LOG(rdInfoLog) << "----- Test 2" << std::endl;
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testMols(mols,fpGen,fcat2);
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BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
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// and the pickle ctor:
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FragCatalog *fcat3 = new FragCatalog(fcat.Serialize());
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TEST_ASSERT(fcat3->getNumEntries()==fcat.getNumEntries());
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BOOST_LOG(rdInfoLog) << "----- Test 3" << std::endl;
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testMols(mols,fpGen,*fcat3);
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BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
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//----------------------------------------------------------
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// test issue 115
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//----------------------------------------------------------
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BOOST_LOG(rdInfoLog) << "----- Test Issue 115" << std::endl;
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delete fparams;
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fparams = new FragCatParams(3, 3, fgrpFile, 1.0e-8);
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TEST_ASSERT(fparams->getNumFuncGroups()==15);
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delete fcat3;
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fcat3 = new FragCatalog(fparams);
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suppl.reset();
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nDone=0;
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while (!suppl.atEnd()){
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nDone++;
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ROMol *m = suppl.next();
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catGen.addFragsFromMol(*m, fcat3);
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delete m;
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}
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TEST_ASSERT(nDone==suppl.length());
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TEST_ASSERT(fcat3->getNumEntries()==21);
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TEST_ASSERT(fcat3->getFPLength()==10);
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for(unsigned int i=0;i<fcat3->getFPLength();i++){
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TEST_ASSERT(fcat3->getEntryWithBitId(i)->getOrder()==3);
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}
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BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
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//----------------------------------------------------------
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// test issue 117
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//----------------------------------------------------------
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BOOST_LOG(rdInfoLog) << "----- Test Issue 117" << std::endl;
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delete fparams;
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fparams = new FragCatParams(1, 2, fgrpFile, 1.0e-8);
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delete fcat3;
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fcat3 = new FragCatalog(fparams);
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ROMol *tmpMol=SmilesToMol("OC(N)CO");
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TEST_ASSERT(tmpMol);
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catGen.addFragsFromMol(*tmpMol, fcat3);
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TEST_ASSERT(fcat3->getNumEntries()==1);
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//std::cout << fcat3->getEntryWithBitId(0)->getDescription() << std::endl;
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TEST_ASSERT(fcat3->getEntryWithBitId(0)->getDescription()=="C<-O>C(<-O>)<-N>");
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BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
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delete tmpMol;
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}
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void testIssue294(){
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BOOST_LOG(rdInfoLog) << "---- Test Issue294\n Watch memory usage." << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi";
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std::string fgrpFile = rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt";
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SmilesMolSupplier suppl(fname," ",0,1,false);
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FragCatParams *fparams = new FragCatParams(1, 6, fgrpFile, 1.0e-8);
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FragCatalog fcat(fparams);
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FragCatGenerator catGen;
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std::vector<ROMol *> mols;
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ROMol *m = suppl.next();
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while (m) {
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mols.push_back(m);
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catGen.addFragsFromMol(*m, &fcat);
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try{
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m = suppl.next();
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} catch( FileParseException &) {
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m = NULL;
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}
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}
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int nents = fcat.getNumEntries();
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TEST_ASSERT(nents==21);
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FragFPGenerator fpGen;
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m = mols[0];
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for(unsigned int i=0;i<200;i++){
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for (std::vector<ROMol *>::const_iterator mi = mols.begin();
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mi != mols.end(); mi++) {
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ExplicitBitVect *fp = fpGen.getFPForMol(*(*mi), fcat);
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delete fp;
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}
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}
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BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
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}
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int main() {
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RDLog::InitLogs();
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test1();
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testIssue294();
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return 0;
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}
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