rdkit/Code/GraphMol/Descriptors/test.cpp

// $Id$
//
//  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 <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 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();
  testLabute();
#endif
}