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rdkit/Code/GraphMol/Descriptors/test.cpp

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// $Id$
//
// Copyright (C) 2004-2011 Greg Landrum and 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 <iostream>
#include <fstream>
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/lexical_cast.hpp>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/StreamOps.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 <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;
mol = SmilesToMol("C[2H]");
TEST_ASSERT(mol);
amw = calcAMW(*mol);
TEST_ASSERT(feq(amw,17.0,.1));
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test3a(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Exact MW calculation." << std::endl;
ROMol *mol,*mol2;
double mw;
mol = SmilesToMol("C");
TEST_ASSERT(mol);
mw = calcExactMW(*mol);
TEST_ASSERT(feq(mw,16.031,.001));
mw = calcExactMW(*mol,true);
TEST_ASSERT(feq(mw,12.000,.001));
mol2 = MolOps::addHs(*mol);
mw = calcExactMW(*mol2);
TEST_ASSERT(feq(mw,16.031,.001));
mw = calcExactMW(*mol2,true);
TEST_ASSERT(feq(mw,12.000,.001));
delete mol;
delete mol2;
mol = SmilesToMol("[CH4]");
TEST_ASSERT(mol);
mw = calcExactMW(*mol);
TEST_ASSERT(feq(mw,16.031,.001));
mw = calcExactMW(*mol,true);
TEST_ASSERT(feq(mw,12.000,.001));
delete mol;
mol = SmilesToMol("C[2H]");
TEST_ASSERT(mol);
mw = calcExactMW(*mol);
TEST_ASSERT(feq(mw,17.023,.001));
mw = calcExactMW(*mol,true);
TEST_ASSERT(feq(mw,12.000,.001));
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;
}
void testTPSA(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test TPSA descriptors." << std::endl;
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.tpsa.csv";
std::ifstream inf(fName.c_str());
TEST_ASSERT(inf && !inf.bad());
while(!inf.eof()){
std::string inl=getLine(inf);
boost::trim(inl);
if(inl.size()==0 || inl[0]=='#') continue;
std::vector<std::string> tokens;
boost::split(tokens,inl,boost::is_any_of(","));
if(tokens.size()!=2) continue;
std::string smiles=tokens[0];
double oTPSA=boost::lexical_cast<double>(tokens[1]);
RWMol *mol = SmilesToMol(smiles);
TEST_ASSERT(mol);
double nTPSA = calcTPSA(*mol);
if(!feq(nTPSA,oTPSA,.0001)){
std::cerr<<" TPSA ERR: "<<smiles<<" "<<oTPSA<<" "<<nTPSA<<std::endl;
std::vector<double> contribs(mol->getNumAtoms());
getTPSAAtomContribs(*mol,contribs);
for(unsigned int i=0;i<mol->getNumAtoms();++i){
std::cerr<<"\t"<<i<<"\t"<<contribs[i]<<std::endl;
}
}
TEST_ASSERT(feq(nTPSA,oTPSA,.0001));
// make sure that adding Hs doesn't affect the value
// (this was issue 1969745)
ROMol *mol2 = MolOps::addHs(*mol);
double hTPSA=calcTPSA(*mol2);
TEST_ASSERT(feq(nTPSA,hTPSA,.0001));
delete mol2;
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testLipinski1(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Lipinski parameters." << std::endl;
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
SDMolSupplier suppl(fName);
int idx=-1;
while(!suppl.atEnd()){
ROMol *mol=0;
++idx;
try{
mol=suppl.next();
} catch(...){
continue;
}
if(!mol) continue;
unsigned int oVal,nVal;
std::string foo;
mol->getProp("NUM_HACCEPTORS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcNumHBA(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
mol->getProp("NUM_HDONORS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcNumHBD(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
mol->getProp("NUM_LIPINSKIHDONORS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcLipinskiHBD(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
mol->getProp("NUM_LIPINSKIHACCEPTORS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcLipinskiHBA(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
mol->getProp("NUM_RINGS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcNumRings(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
mol->getProp("NUM_HETEROATOMS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcNumHeteroatoms(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
mol->getProp("NUM_ROTATABLEBONDS",foo);
oVal=boost::lexical_cast<unsigned int>(foo);
nVal = calcNumRotatableBonds(*mol);
if(oVal!=nVal){
std::cerr<<" failed: "<<idx<<" "<<oVal<<" "<<nVal<<std::endl;
}
TEST_ASSERT(oVal==nVal);
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testVSADescriptors(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test VSA descriptors." << std::endl;
{
ROMol *mol;
std::vector<double> vals;
mol = SmilesToMol("CO");
vals = calcSlogP_VSA(*mol);
TEST_ASSERT(vals.size()==12);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 1:
TEST_ASSERT(feq(vals[i],12.216,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
mol = SmilesToMol("CCO");
vals = calcSlogP_VSA(*mol);
TEST_ASSERT(vals.size()==12);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 1:
TEST_ASSERT(feq(vals[i],11.713,.001));
break;
case 4:
TEST_ASSERT(feq(vals[i],6.924,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
mol = SmilesToMol("Fc1ccccc1");
vals = calcSlogP_VSA(*mol);
TEST_ASSERT(vals.size()==12);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 3:
TEST_ASSERT(feq(vals[i],5.817,.001));
break;
case 5:
TEST_ASSERT(feq(vals[i],30.332,.001));
break;
case 9:
TEST_ASSERT(feq(vals[i],4.390,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
}
{
ROMol *mol;
std::vector<double> vals;
mol = SmilesToMol("CO");
vals = calcSMR_VSA(*mol);
TEST_ASSERT(vals.size()==10);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 0:
TEST_ASSERT(feq(vals[i],5.106,.001));
break;
case 5:
TEST_ASSERT(feq(vals[i],7.110,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
mol = SmilesToMol("CCO");
vals = calcSMR_VSA(*mol);
TEST_ASSERT(vals.size()==10);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 0:
TEST_ASSERT(feq(vals[i],5.106,.001));
break;
case 4:
TEST_ASSERT(feq(vals[i],6.924,.001));
break;
case 5:
TEST_ASSERT(feq(vals[i],6.607,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
}
{
ROMol *mol;
std::vector<double> vals;
mol = SmilesToMol("CO");
vals = calcPEOE_VSA(*mol);
TEST_ASSERT(vals.size()==14);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 0:
TEST_ASSERT(feq(vals[i],5.106,.001));
break;
case 7:
TEST_ASSERT(feq(vals[i],7.110,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
mol = SmilesToMol("CCO");
vals = calcPEOE_VSA(*mol);
TEST_ASSERT(vals.size()==14);
for(unsigned int i=0;i<vals.size();++i){
switch(i){
case 0:
TEST_ASSERT(feq(vals[i],5.106,.001));
break;
case 6:
TEST_ASSERT(feq(vals[i],6.924,.001));
break;
case 7:
TEST_ASSERT(feq(vals[i],6.607,.001));
break;
default:
TEST_ASSERT(feq(vals[i],0,.001));
}
}
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMolFormula(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test molecular formula calculation." << std::endl;
ROMol *mol,*mol2;
std::string formula;
mol = SmilesToMol("C");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH4");
mol2 = MolOps::addHs(*mol);
formula = calcMolFormula(*mol2);
TEST_ASSERT(formula=="CH4");
delete mol;
delete mol2;
mol = SmilesToMol("[CH4]");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH4");
delete mol;
mol = SmilesToMol("CO");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH4O");
mol2 = MolOps::addHs(*mol);
formula = calcMolFormula(*mol2);
TEST_ASSERT(formula=="CH4O");
delete mol;
delete mol2;
mol = SmilesToMol("C(=O)N");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH3NO");
mol2 = MolOps::addHs(*mol);
formula = calcMolFormula(*mol2);
TEST_ASSERT(formula=="CH3NO");
delete mol;
delete mol2;
mol = SmilesToMol("C(=O)=O");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CO2");
delete mol;
mol = SmilesToMol("C(=O)[O-]");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CHO2-");
delete mol;
mol = SmilesToMol("C([O-])[O-]");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH2O2-2");
delete mol;
mol = SmilesToMol("C([NH3+])[O-]");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH5NO");
delete mol;
mol = SmilesToMol("C([NH3+])O");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH6NO+");
delete mol;
mol = SmilesToMol("C([NH3+])[NH3+]");
TEST_ASSERT(mol);
formula = calcMolFormula(*mol);
TEST_ASSERT(formula=="CH8N2+2");
delete mol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(){
RDLog::InitLogs();
#if 1
test1();
test2();
testIssue262();
test3();
test3a();
testLabute();
testTPSA();
testLipinski1();
testVSADescriptors();
testMolFormula();
#endif
}
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