rdkit/Code/GraphMol/Descriptors/testPBF.cpp

//
//  Copyright (C) 2012-2016 Greg Landrum
//   @@ 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 <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <fstream>

#include <GraphMol/Descriptors/PBF.h>

void test1(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Basic PBF tests." << std::endl;

  std::string pathName = getenv("RDBASE");
  std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";
  RDKit::SDMolSupplier reader(sdfName,true,false);
  std::string fName = pathName+"/Code/GraphMol/Descriptors/test_data/PBF_egfr.out";
  std::ifstream instrm(fName.c_str());
  int nDone=0;
  while(!reader.atEnd()){
    RDKit::ROMol *m=reader.next();
    TEST_ASSERT(m);
    std::string nm;
    m->getProp("_Name",nm);
    double dpbf=RDKit::Descriptors::PBF(*m);

    std::string inm;
    double ref;
    instrm>>inm;
    instrm>>ref;
    TEST_ASSERT(inm==nm);
    if(fabs(ref-dpbf)>.001){
      std::cerr<<"value mismatch: "<<inm<<" "<<ref<<" "<<dpbf<<std::endl;
    }
    TEST_ASSERT(fabs(ref-dpbf)<0.001);
    delete m;
    ++nDone;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testPBFEdges(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    PBF edge cases." << std::endl;

  {
    std::string pathName = getenv("RDBASE");
    std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/linear.mol";

    RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
    TEST_ASSERT(m);
    double dpbf=RDKit::Descriptors::PBF(*m);
    TEST_ASSERT(dpbf<=1e-4);
    delete m;
  }
  {
    std::string pathName = getenv("RDBASE");
    std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/linear_2atom.mol";

    RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
    TEST_ASSERT(m);
    double dpbf=RDKit::Descriptors::PBF(*m);
    TEST_ASSERT(dpbf<=1e-4);
    delete m;
  }
  {
    std::string pathName = getenv("RDBASE");
    std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/planar.mol";

    RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
    TEST_ASSERT(m);
    double dpbf=RDKit::Descriptors::PBF(*m);
    TEST_ASSERT(dpbf<=1e-4);
    delete m;
  }
  {
    std::string pathName = getenv("RDBASE");
    std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/planar_3atom.mol";

    RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
    TEST_ASSERT(m);
    double dpbf=RDKit::Descriptors::PBF(*m);
    TEST_ASSERT(dpbf<=1e-4);
    delete m;
  }
  {
    RDKit::RWMol m;
	bool updateLabel = true;
    bool takeOwnership = true;
    m.addAtom(new RDKit::Atom(6), updateLabel, takeOwnership);
    m.addAtom(new RDKit::Atom(6), updateLabel, takeOwnership);
    m.addAtom(new RDKit::Atom(6), updateLabel, takeOwnership);
    m.addAtom(new RDKit::Atom(6), updateLabel, takeOwnership);
    m.addAtom(new RDKit::Atom(6), updateLabel, takeOwnership);
    m.addAtom(new RDKit::Atom(6), updateLabel, takeOwnership);
    m.addConformer(new RDKit::Conformer(m.getNumAtoms()));
    double dpbf=RDKit::Descriptors::PBF(m);
    TEST_ASSERT(dpbf<=1e-4);
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

int main() {
  RDLog::InitLogs();
  test1();
  testPBFEdges();
}