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https://github.com/rdkit/rdkit.git
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4f2ec84e7b
* update .gitignore * foundation for 3D descriptors move PBF into core * cleanup work * a bit more cleanup * move the principal moments calc to MolTransforms * cleanup * cleanups * add caching of the principal moments and values * do not include the 3D descriptors in MolDescriptors.h * the properties are computed * add PMI descriptors and tests * add tests for NPR descriptors * return 0 when the largest PMI is zero * PMI edge case tests * NPR edge case tests * PBF edge case tests * PBF edge case tests * more edge cases * add a few more 3d descriptors * add defns to docs * tests for the new descriptors * add versions to new descriptors * add 3d descriptors to python wrapper * add eigen support to the travis build * try to get non-windows builds working * remove computeCovarianceMatrix() from java wrapper * make pmi property names "private"
121 lines
3.3 KiB
C++
121 lines
3.3 KiB
C++
//
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// Copyright (C) 2012-2016 Greg Landrum
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// @@ All Rights Reserved @@
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//
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <RDGeneral/RDLog.h>
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#include <vector>
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#include <algorithm>
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#include <fstream>
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#include <GraphMol/Descriptors/PBF.h>
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void test1(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " Basic PBF tests." << std::endl;
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std::string pathName = getenv("RDBASE");
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std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";
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RDKit::SDMolSupplier reader(sdfName,true,false);
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std::string fName = pathName+"/Code/GraphMol/Descriptors/test_data/PBF_egfr.out";
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std::ifstream instrm(fName.c_str());
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int nDone=0;
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while(!reader.atEnd()){
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RDKit::ROMol *m=reader.next();
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TEST_ASSERT(m);
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std::string nm;
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m->getProp("_Name",nm);
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double dpbf=RDKit::Descriptors::PBF(*m);
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std::string inm;
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double ref;
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instrm>>inm;
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instrm>>ref;
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TEST_ASSERT(inm==nm);
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if(fabs(ref-dpbf)>.001){
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std::cerr<<"value mismatch: "<<inm<<" "<<ref<<" "<<dpbf<<std::endl;
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}
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TEST_ASSERT(fabs(ref-dpbf)<0.001);
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delete m;
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++nDone;
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}
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void testPBFEdges(){
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " PBF edge cases." << std::endl;
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/linear.mol";
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RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double dpbf=RDKit::Descriptors::PBF(*m);
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TEST_ASSERT(dpbf<=1e-4);
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delete m;
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}
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/linear_2atom.mol";
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RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double dpbf=RDKit::Descriptors::PBF(*m);
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TEST_ASSERT(dpbf<=1e-4);
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delete m;
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}
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/planar.mol";
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RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double dpbf=RDKit::Descriptors::PBF(*m);
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TEST_ASSERT(dpbf<=1e-4);
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delete m;
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}
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName = pathName+"/Code/GraphMol/Descriptors/test_data/planar_3atom.mol";
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RDKit::ROMol *m=RDKit::MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double dpbf=RDKit::Descriptors::PBF(*m);
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TEST_ASSERT(dpbf<=1e-4);
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delete m;
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}
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{
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RDKit::RWMol m;
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m.addAtom(new RDKit::Atom(6));
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m.addAtom(new RDKit::Atom(6));
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m.addAtom(new RDKit::Atom(6));
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m.addAtom(new RDKit::Atom(6));
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m.addAtom(new RDKit::Atom(6));
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m.addAtom(new RDKit::Atom(6));
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m.addConformer(new RDKit::Conformer(m.getNumAtoms()));
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double dpbf=RDKit::Descriptors::PBF(m);
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TEST_ASSERT(dpbf<=1e-4);
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}
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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int
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main(int argc, char *argv[])
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{
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RDLog::InitLogs();
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test1();
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testPBFEdges();
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}
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