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//
// 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());
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;
}
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();
}
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