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// $Id$
//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include "FragCatGenerator.h"
#include "FragCatalogEntry.h"
#include "FragCatParams.h"
#include "FragCatalogUtils.h"
#include "FragFPGenerator.h"
#include <cstdlib>
#include <iostream>
#include <fstream>
#include <GraphMol/Subgraphs/SubgraphUtils.h>
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <RDGeneral/types.h>
#include <RDGeneral/FileParseException.h>
#include <DataStructs/BitVects.h>
using namespace RDKit;
void testMols(std::vector<std::unique_ptr<ROMol>> &mols, FragFPGenerator &fpGen,
FragCatalog &fcat) {
int nDone = 0;
for (auto &&mi : mols) {
ExplicitBitVect *fp = fpGen.getFPForMol(*mi, fcat);
switch (nDone) {
case 0:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[2]);
break;
case 1:
TEST_ASSERT(fp->getNumOnBits() == 2);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[3]);
break;
case 2:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[4]);
TEST_ASSERT((*fp)[5]);
break;
case 3:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[6]);
TEST_ASSERT((*fp)[7]);
break;
case 4:
TEST_ASSERT(fp->getNumOnBits() == 2);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[8]);
break;
case 5:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[6]);
TEST_ASSERT((*fp)[9]);
break;
case 6:
TEST_ASSERT(fp->getNumOnBits() == 5);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[2]);
TEST_ASSERT((*fp)[3]);
TEST_ASSERT((*fp)[10]);
break;
}
delete fp;
nDone += 1;
}
}
void test1() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi";
std::string fgrpFile =
rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt";
SmilesMolSupplier suppl(fname, " ", 0, 1, false);
auto *fparams = new FragCatParams(1, 6, fgrpFile, 1.0e-8);
TEST_ASSERT(fparams->getNumFuncGroups() == 15);
FragCatalog fcat(fparams);
FragCatGenerator catGen;
std::vector<std::unique_ptr<ROMol>> mols;
unsigned int nDone = 0;
ROMol *m = suppl.next();
while (m) {
mols.push_back(std::unique_ptr<ROMol>(m));
nDone += 1;
catGen.addFragsFromMol(*m, &fcat);
try {
m = suppl.next();
} catch (FileParseException &) {
m = nullptr;
}
}
TEST_ASSERT(mols.size() == 16);
TEST_ASSERT(nDone == 16);
int nents = fcat.getNumEntries();
std::cerr << " " << nents << std::endl;
TEST_ASSERT(nents == 21);
FragFPGenerator fpGen;
BOOST_LOG(rdInfoLog) << "----- Test 1" << std::endl;
testMols(mols, fpGen, fcat);
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
//----------------------------------------------------------
// SERIALIZATION TESTS
//----------------------------------------------------------
// make sure we can pickle and unpickle parameter objects:
FragCatParams newParams;
std::string pickle = fparams->Serialize();
newParams.initFromString(pickle);
TEST_ASSERT(newParams.getLowerFragLength() == fparams->getLowerFragLength());
TEST_ASSERT(newParams.getUpperFragLength() == fparams->getUpperFragLength());
TEST_ASSERT(newParams.getTolerance() == fparams->getTolerance());
TEST_ASSERT(newParams.getNumFuncGroups() == fparams->getNumFuncGroups());
// make sure we can pickle and unpickle catalog entries:
const FragCatalogEntry *fpEntry = fcat.getEntryWithIdx(0);
auto *fpEntry2 = new FragCatalogEntry();
fpEntry2->initFromString(fpEntry->Serialize());
TEST_ASSERT(fpEntry->getDescription() == fpEntry2->getDescription());
TEST_ASSERT(fpEntry->getOrder() == fpEntry2->getOrder());
TEST_ASSERT(fpEntry->getBitId() == fpEntry2->getBitId());
TEST_ASSERT(fpEntry2->match(fpEntry, 1e-8));
TEST_ASSERT(fpEntry->match(fpEntry2, 1e-8));
delete fpEntry2;
// test catalogs' initFromString:
FragCatalog fcat2;
fcat2.initFromString(fcat.Serialize());
TEST_ASSERT(fcat2.getNumEntries() == fcat.getNumEntries());
BOOST_LOG(rdInfoLog) << "----- Test 2" << std::endl;
testMols(mols, fpGen, fcat2);
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
// and the pickle ctor:
FragCatalog *fcat3 = new FragCatalog(fcat.Serialize());
TEST_ASSERT(fcat3->getNumEntries() == fcat.getNumEntries());
BOOST_LOG(rdInfoLog) << "----- Test 3" << std::endl;
testMols(mols, fpGen, *fcat3);
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
//----------------------------------------------------------
// test issue 115
//----------------------------------------------------------
BOOST_LOG(rdInfoLog) << "----- Test Issue 115" << std::endl;
delete fparams;
fparams = new FragCatParams(3, 3, fgrpFile, 1.0e-8);
TEST_ASSERT(fparams->getNumFuncGroups() == 15);
delete fcat3;
fcat3 = new FragCatalog(fparams);
suppl.reset();
nDone = 0;
while (!suppl.atEnd()) {
nDone++;
ROMol *m = suppl.next();
catGen.addFragsFromMol(*m, fcat3);
delete m;
}
TEST_ASSERT(nDone == suppl.length());
TEST_ASSERT(fcat3->getNumEntries() == 21);
TEST_ASSERT(fcat3->getFPLength() == 10);
for (unsigned int i = 0; i < fcat3->getFPLength(); i++) {
TEST_ASSERT(fcat3->getEntryWithBitId(i)->getOrder() == 3);
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
//----------------------------------------------------------
// test issue 117
//----------------------------------------------------------
BOOST_LOG(rdInfoLog) << "----- Test Issue 117" << std::endl;
delete fparams;
fparams = new FragCatParams(1, 2, fgrpFile, 1.0e-8);
delete fcat3;
fcat3 = new FragCatalog(fparams);
ROMol *tmpMol = SmilesToMol("OC(N)CO");
TEST_ASSERT(tmpMol);
catGen.addFragsFromMol(*tmpMol, fcat3);
TEST_ASSERT(fcat3->getNumEntries() == 1);
// std::cout << fcat3->getEntryWithBitId(0)->getDescription() << std::endl;
TEST_ASSERT(fcat3->getEntryWithBitId(0)->getDescription() ==
"C(<-O>)<-N>C<-O>");
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
delete tmpMol;
delete fparams;
delete fcat3;
}
void testIssue294() {
BOOST_LOG(rdInfoLog) << "---- Test Issue294\n Watch memory usage."
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FragCatalog/test_data/mols.smi";
std::string fgrpFile =
rdbase + "/Code/GraphMol/FragCatalog/test_data/funcGroups.txt";
SmilesMolSupplier suppl(fname, " ", 0, 1, false);
auto *fparams = new FragCatParams(1, 6, fgrpFile, 1.0e-8);
FragCatalog fcat(fparams);
FragCatGenerator catGen;
std::vector<std::unique_ptr<ROMol>> mols;
ROMol *m = suppl.next();
while (m) {
mols.push_back(std::unique_ptr<ROMol>(m));
catGen.addFragsFromMol(*m, &fcat);
try {
m = suppl.next();
} catch (FileParseException &) {
m = nullptr;
}
}
int nents = fcat.getNumEntries();
TEST_ASSERT(nents == 21);
FragFPGenerator fpGen;
for (unsigned int i = 0; i < 200; i++) {
for (auto &&mi : mols) {
ExplicitBitVect *fp = fpGen.getFPForMol(*mi, fcat);
delete fp;
}
}
delete fparams;
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
}
void testWhiteSpaceInSmarts() {
BOOST_LOG(rdInfoLog) << "----- Test Whitespace in SMARTS Fragment string."
<< std::endl;
std::vector<std::string> data(
{" ", // whitespace only
" \n", // whitespace plus new line
" // initial space plus comment\nfluorine\t[F]\n"});
std::vector<size_t> reference_sizes({0, 0, 1});
auto reference = reference_sizes.cbegin();
for (const auto &smarts : data) {
std::istringstream input(smarts);
auto groups = readFuncGroups(input);
TEST_ASSERT(groups.size() == *reference);
++reference;
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
}
void testFragmentWithoutSmarts() {
BOOST_LOG(rdInfoLog) << "----- Test Fragment string without SMARTS."
<< std::endl;
std::vector<std::string> data(
{"// Name SMARTS\nnonsense\n",
"// Name SMARTS\nnonsense no new line",
"// Name SMARTS\nnonsense with tab\t\n"});
for (const auto &smarts : data) {
bool ok = false;
std::istringstream input(smarts);
RDKit::MOL_SPTR_VECT groups;
try {
groups = readFuncGroups(input);
} catch (const Invar::Invariant &) {
ok = true;
}
TEST_ASSERT(ok);
TEST_ASSERT(groups.empty());
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
}
int main() {
RDLog::InitLogs();
test1();
testIssue294();
testWhiteSpaceInSmarts();
testFragmentWithoutSmarts();
return 0;
}
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