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c1f3e68afb400a955645b8f233d2b2913aaa5c43
rdkit/Code/GraphMol/Descriptors/test.cpp
Greg Landrum c1f3e68afb this is just a test
2008-12-08 06:34:45 +00:00

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// $Id$
//
// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include <iostream>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/Descriptors/Crippen.h>
#include <GraphMol/Descriptors/AtomPairs.h>
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
using namespace RDKit;
using namespace RDKit::Descriptors;
void test1(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Crippen parameter acquisition." << std::endl;
CrippenParamCollection *params=CrippenParamCollection::getParams();
TEST_ASSERT(params);
CrippenParams p=*(params->begin());
TEST_ASSERT(p.label=="C1");
TEST_ASSERT(p.smarts=="[CH4]");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test2(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Crippen calculation." << std::endl;
ROMol *mol;
double logp,mr;
mol = SmilesToMol("C");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,0.6361));
TEST_ASSERT(feq(mr,6.7310));
// check that caching works:
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,0.6361));
TEST_ASSERT(feq(mr,6.7310));
CalcCrippenDescriptors(*mol,logp,mr,true,true);
TEST_ASSERT(feq(logp,0.6361));
TEST_ASSERT(feq(mr,6.7310));
// check that things work when we don't add Hs:
CalcCrippenDescriptors(*mol,logp,mr,false,true);
TEST_ASSERT(feq(logp,0.1441));
TEST_ASSERT(feq(mr,2.503));
delete mol;
mol = SmilesToMol("C=C");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr,true);
TEST_ASSERT(feq(logp,0.8022));
TEST_ASSERT(feq(mr,11.2540));
delete mol;
mol = SmilesToMol("C#C");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,0.2494));
TEST_ASSERT(feq(mr,9.8900));
delete mol;
mol = SmilesToMol("CO");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,-0.3915));
TEST_ASSERT(feq(mr,8.1428));
delete mol;
mol = SmilesToMol("C=O");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,-0.1849));
TEST_ASSERT(feq(mr,7.121));
delete mol;
mol = SmilesToMol("C#[O+]");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,0.0059));
TEST_ASSERT(feq(mr,5.6315));
delete mol;
mol = SmilesToMol("C(C)(C)C");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,1.6623));
TEST_ASSERT(feq(mr,20.512));
delete mol;
mol = SmilesToMol("C(C)(C)(C)O");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,logp,mr);
TEST_ASSERT(feq(logp,0.7772));
TEST_ASSERT(feq(mr,21.9718));
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue262(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Issue262: problems with Crippen calculation from pickles." << std::endl;
ROMol *mol,*mol2;
RWMol *mol3;
std::string pkl;
double rlogp,rmr,logp,mr;
mol = SmilesToMol("c1ncccc1");
TEST_ASSERT(mol);
CalcCrippenDescriptors(*mol,rlogp,rmr);
MolPickler::pickleMol(*mol,pkl);
mol2=new ROMol(pkl);
TEST_ASSERT(mol2);
CalcCrippenDescriptors(*mol2,logp,mr);
TEST_ASSERT(feq(logp,rlogp));
TEST_ASSERT(feq(mr,rmr));
mol3=new RWMol();
TEST_ASSERT(mol3);
MolPickler::molFromPickle(pkl,mol3);
CalcCrippenDescriptors(*mol3,logp,mr);
TEST_ASSERT(feq(logp,rlogp));
TEST_ASSERT(feq(mr,rmr));
delete mol;
delete mol2;
delete mol3;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test3(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test AMW calculation." << std::endl;
ROMol *mol,*mol2;
double amw;
mol = SmilesToMol("C");
TEST_ASSERT(mol);
amw = CalcAMW(*mol);
TEST_ASSERT(feq(amw,16.043,.001));
amw = CalcAMW(*mol,true);
TEST_ASSERT(feq(amw,12.011,.001));
mol2 = MolOps::addHs(*mol);
amw = CalcAMW(*mol2);
TEST_ASSERT(feq(amw,16.043,.001));
amw = CalcAMW(*mol2,true);
TEST_ASSERT(feq(amw,12.011,.001));
delete mol;
delete mol2;
mol = SmilesToMol("[CH4]");
TEST_ASSERT(mol);
amw = CalcAMW(*mol);
TEST_ASSERT(feq(amw,16.043,.001));
amw = CalcAMW(*mol,true);
TEST_ASSERT(feq(amw,12.011,.001));
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testAtomCodes(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Atom Codes." << std::endl;
ROMol *mol;
boost::uint32_t tgt;
mol = SmilesToMol("C=C");
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0))==AtomPairs::getAtomCode(mol->getAtomWithIdx(1)));
tgt = 1 | (1 | 1<<AtomPairs::numPiBits)<<AtomPairs::numBranchBits;
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0))==tgt);
tgt = 1<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0),1)==tgt);
delete mol;
mol = SmilesToMol("C#CO");
tgt = 1 | 2<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0))==tgt);
tgt = 2 | 2<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(1))==tgt);
tgt = 1 | 0<<AtomPairs::numBranchBits | 3<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(2))==tgt);
delete mol;
mol = SmilesToMol("CC(O)C(O)(O)C");
tgt = 1 | 0<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(1),2)==tgt);
tgt = 2 | 0<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(3),2)==tgt);
delete mol;
mol = SmilesToMol("C=CC(=O)O");
tgt = 0 | 0<<AtomPairs::numBranchBits | 3<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(4),1)==tgt);
tgt = 3 | 1<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(2))==tgt);
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testAtomPairs(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Atom Pairs." << std::endl;
ROMol *mol;
SparseIntVect<boost::int32_t> *fp;
boost::uint32_t tgt;
boost::uint32_t c1,c2,c3;
mol = SmilesToMol("CCCCC");
c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0));
c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1));
c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2));
tgt = 1 | (std::min(c1,c2) | std::max(c1,c2)<<AtomPairs::codeSize)<< AtomPairs::numPathBits;
TEST_ASSERT(AtomPairs::getAtomPairCode(c1,c2,1)==tgt);
TEST_ASSERT(AtomPairs::getAtomPairCode(c2,c1,1)==tgt);
tgt = 2 | (std::min(c1,c3) | std::max(c1,c3)<<AtomPairs::codeSize)<< AtomPairs::numPathBits;
TEST_ASSERT(AtomPairs::getAtomPairCode(c1,c3,2)==tgt);
TEST_ASSERT(AtomPairs::getAtomPairCode(c3,c1,2)==tgt);
delete mol;
mol = SmilesToMol("CCC");
fp=AtomPairs::getAtomPairFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal()==3);
TEST_ASSERT(fp->getNonzeroElements().size()==2);
c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0));
c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1));
c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2));
TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c2,1))==2);
TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c3,2))==1);
delete mol;
delete fp;
mol = SmilesToMol("CC=O.Cl");
fp=AtomPairs::getAtomPairFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal()==3);
TEST_ASSERT(fp->getNonzeroElements().size()==3);
c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0));
c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1));
c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2));
TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c2,1))==1);
TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c2,1))==1);
TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c2,c3,1))==1);
delete mol;
delete fp;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testHashedAtomPairs(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Hashed Atom Pairs." << std::endl;
{
ROMol *mol;
mol = SmilesToMol("c1ccccc1");
ExplicitBitVect *fp1;
fp1=AtomPairs::getHashedAtomPairFingerprint(*mol);
ExplicitBitVect *fp2;
fp2=AtomPairs::getHashedAtomPairFingerprint(*mol);
TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
TEST_ASSERT(*fp1==*fp2);
delete mol;
delete fp2;
mol = SmilesToMol("c1ccccn1");
fp2=AtomPairs::getHashedAtomPairFingerprint(*mol);
RANGE_CHECK(0.0,TanimotoSimilarity(*fp1,*fp2),1.0);
delete mol;
delete fp1;
delete fp2;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testTorsions(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Topological Torsions." << std::endl;
ROMol *mol;
SparseIntVect<boost::int64_t> *fp;
boost::uint64_t tgt;
boost::uint64_t c1,c2,c3,c4;
std::vector<boost::uint32_t> codes;
mol = SmilesToMol("CCCC");
c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0))-1;
c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1))-2;
c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2))-2;
c4=AtomPairs::getAtomCode(mol->getAtomWithIdx(3))-1;
tgt = c1 | (c2 | (c3 | c4<<AtomPairs::codeSize)<<AtomPairs::codeSize)<<AtomPairs::codeSize;
codes.clear();
codes.push_back(static_cast<unsigned int>(c1));
codes.push_back(static_cast<unsigned int>(c2));
codes.push_back(static_cast<unsigned int>(c3));
codes.push_back(static_cast<unsigned int>(c4));
TEST_ASSERT(AtomPairs::getTopologicalTorsionCode(codes)==tgt);
fp = AtomPairs::getTopologicalTorsionFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal()==1);
TEST_ASSERT(fp->getNonzeroElements().size()==1);
delete mol;
delete fp;
mol = SmilesToMol("CCCCO.Cl");
fp=AtomPairs::getTopologicalTorsionFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal()==2);
TEST_ASSERT(fp->getNonzeroElements().size()==2);
delete fp;
fp = AtomPairs::getTopologicalTorsionFingerprint(*mol,3);
TEST_ASSERT(fp->getTotalVal()==3);
TEST_ASSERT(fp->getNonzeroElements().size()==3);
delete mol;
delete fp;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testBulkTorsions(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Bulk Topological Torsions." << std::endl;
std::string fName= getenv("RDBASE");
fName += "/Projects/DbCLI/testData/pubchem.200.sdf";
SDMolSupplier suppl(fName);
while(!suppl.atEnd()){
ROMol *mol=suppl.next();
SparseIntVect<boost::int64_t> *fp;
fp = AtomPairs::getTopologicalTorsionFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal()>1);
delete mol;
delete fp;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testLabute(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Labute ASA descriptors." << std::endl;
ROMol *mol;
double asa;
mol = SmilesToMol("CO");
asa=calcLabuteASA(*mol);
TEST_ASSERT(feq(asa,13.5335,.0001));
asa=calcLabuteASA(*mol);
TEST_ASSERT(feq(asa,13.5335,.0001));
asa=calcLabuteASA(*mol,true,true);
TEST_ASSERT(feq(asa,13.5335,.0001));
delete mol;
mol = SmilesToMol("OC(=O)c1ccncc1C(=O)O");
asa=calcLabuteASA(*mol);
TEST_ASSERT(feq(asa,67.2924,.0001));
delete mol;
mol = SmilesToMol("C1CCC(c2cccnc2)NC1");
asa=calcLabuteASA(*mol);
TEST_ASSERT(feq(asa,73.0198,.0001));
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(){
RDLog::InitLogs();
#if 1
test1();
test2();
testIssue262();
test3();
testAtomCodes();
testAtomPairs();
testTorsions();
testBulkTorsions();
testLabute();
#endif
testHashedAtomPairs();
}
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