mirror of
https://github.com/rdkit/rdkit.git
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10fbd483bb
* Add parameter to skip proximity bonding during PDB reading * Test proximityBonding flag * Remove multivalent Hs and bonds to metals in PDB * Add tests for multivalent Hs and metal unbinding * Remove covalent bonds to waters * Test unbinding of HOHs * Refactor funxtions * Rename flag for cosistency * Include flavor in double bond perception * Add metalorganic test (APW ligand) * Validate input foe IsBlacklistedPair and minor changes.
464 lines
14 KiB
Plaintext
464 lines
14 KiB
Plaintext
//
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// Copyright (C) 2016 Greg Landrum
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//
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// @@ All Rights Reserved @@
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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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#ifdef _MSC_VER
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// disable warnings about getenv in visual C++
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#define _CRT_SECURE_NO_WARNINGS
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#endif
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#include <iostream>
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#include <fstream>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/algorithm/string.hpp>
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#include <boost/algorithm/string/trim.hpp>
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#include <boost/lexical_cast.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/utils.h>
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#include <RDGeneral/StreamOps.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/Descriptors/MolDescriptors3D.h>
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using namespace RDKit;
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using namespace RDKit::Descriptors;
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bool compare(const std::string &inm, double ref, double val,
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double tol = 1e-3) {
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if (fabs(ref - val) >= tol) {
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std::cerr << "value mismatch: " << inm << " " << ref << " " << val
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<< std::endl;
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}
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return fabs(ref - val) < tol;
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}
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bool frac_compare(const std::string &inm, double ref, double val,
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double frac = .01) {
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if (fabs(ref - val) / ref >= frac) {
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std::cerr << "value mismatch: " << inm << " " << ref << " " << val
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<< std::endl;
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}
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return fabs(ref - val) / ref < frac;
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}
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void testPMI1() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " Basic PMI tests." << std::endl;
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std::string pathName = getenv("RDBASE");
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std::string sdfName =
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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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/PMI_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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RDKit::ROMol mcpy(*m);
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std::string nm;
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m->getProp("_Name", nm);
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std::string inm;
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instrm >> inm;
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TEST_ASSERT(inm == nm);
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double val;
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double pmi1_m, pmi2_m, pmi3_m, pmi1_nom, pmi2_nom, pmi3_nom;
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instrm >> pmi1_m;
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instrm >> pmi2_m;
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instrm >> pmi3_m;
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instrm >> pmi1_nom;
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instrm >> pmi2_nom;
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instrm >> pmi3_nom;
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val = RDKit::Descriptors::PMI1(*m);
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TEST_ASSERT(frac_compare(inm, pmi1_m, val));
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val = RDKit::Descriptors::PMI2(*m);
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TEST_ASSERT(frac_compare(inm, pmi2_m, val));
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val = RDKit::Descriptors::PMI3(*m);
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TEST_ASSERT(frac_compare(inm, pmi3_m, val));
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val = RDKit::Descriptors::PMI1(*m, -1, false);
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TEST_ASSERT(frac_compare(inm, pmi1_nom, val));
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val = RDKit::Descriptors::PMI2(*m, -1, false);
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TEST_ASSERT(frac_compare(inm, pmi2_nom, val));
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val = RDKit::Descriptors::PMI3(*m, -1, false);
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TEST_ASSERT(frac_compare(inm, pmi3_nom, val));
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// now try doing it in the reverse order to make sure caching doesn't
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// screw up.
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val = RDKit::Descriptors::PMI1(mcpy, -1, false);
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TEST_ASSERT(frac_compare(inm, pmi1_nom, val));
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val = RDKit::Descriptors::PMI2(mcpy, -1, false);
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TEST_ASSERT(frac_compare(inm, pmi2_nom, val));
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val = RDKit::Descriptors::PMI3(mcpy, -1, false);
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TEST_ASSERT(frac_compare(inm, pmi3_nom, val));
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val = RDKit::Descriptors::PMI1(mcpy);
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TEST_ASSERT(frac_compare(inm, pmi1_m, val));
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val = RDKit::Descriptors::PMI2(mcpy);
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TEST_ASSERT(frac_compare(inm, pmi2_m, val));
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val = RDKit::Descriptors::PMI3(mcpy);
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TEST_ASSERT(frac_compare(inm, pmi3_m, val));
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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 testPMIEdges() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " PMI edge cases." << std::endl;
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName =
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pathName + "/Code/GraphMol/Descriptors/test_data/linear.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::PMI1(*m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::PMI2(*m);
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TEST_ASSERT(fabs(val) >= 10);
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val = RDKit::Descriptors::PMI3(*m);
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TEST_ASSERT(val >= 10);
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TEST_ASSERT(RDKit::Descriptors::PMI3(*m) - RDKit::Descriptors::PMI2(*m) <
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1e-2);
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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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/linear_2atom.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::PMI1(*m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::PMI2(*m);
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TEST_ASSERT(fabs(val) >= 1);
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val = RDKit::Descriptors::PMI3(*m);
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TEST_ASSERT(val >= 1);
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TEST_ASSERT(RDKit::Descriptors::PMI3(*m) - RDKit::Descriptors::PMI2(*m) <
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1e-2);
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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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/planar.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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TEST_ASSERT(RDKit::Descriptors::PMI2(*m) - RDKit::Descriptors::PMI1(*m) <
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1e-2);
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TEST_ASSERT(RDKit::Descriptors::PMI3(*m) - RDKit::Descriptors::PMI1(*m) >
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10);
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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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/planar_3atom.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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TEST_ASSERT(RDKit::Descriptors::PMI2(*m) - RDKit::Descriptors::PMI1(*m) <
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1e-2);
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TEST_ASSERT(RDKit::Descriptors::PMI3(*m) - RDKit::Descriptors::PMI1(*m) >
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1);
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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 val = RDKit::Descriptors::PMI1(m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::PMI2(m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::PMI3(m);
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TEST_ASSERT(fabs(val) < 1e-4);
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}
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void testNPR1() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " Basic NPR tests." << std::endl;
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std::string pathName = getenv("RDBASE");
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std::string sdfName =
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pathName + "/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";
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RDKit::SDMolSupplier reader(sdfName, true, false);
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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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RDKit::ROMol mcpy(*m);
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std::string nm;
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m->getProp("_Name", nm);
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double val;
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double pmi1_m, pmi2_m, pmi3_m, pmi1_nom, pmi2_nom, pmi3_nom;
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pmi1_m = RDKit::Descriptors::PMI1(*m);
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pmi2_m = RDKit::Descriptors::PMI2(*m);
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pmi3_m = RDKit::Descriptors::PMI3(*m);
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pmi1_nom = RDKit::Descriptors::PMI1(*m, -1, false);
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pmi2_nom = RDKit::Descriptors::PMI2(*m, -1, false);
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pmi3_nom = RDKit::Descriptors::PMI3(*m, -1, false);
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val = RDKit::Descriptors::NPR1(*m);
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compare(nm, pmi1_m / pmi3_m, val);
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val = RDKit::Descriptors::NPR2(*m);
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compare(nm, pmi2_m / pmi3_m, val);
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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 testNPREdges() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " NPR edge cases." << std::endl;
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName =
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pathName + "/Code/GraphMol/Descriptors/test_data/linear.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::NPR1(*m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::NPR2(*m);
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TEST_ASSERT(fabs(val - 1) < 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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/linear_2atom.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::NPR1(*m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::NPR2(*m);
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TEST_ASSERT(fabs(val - 1) < 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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/planar.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::NPR1(*m);
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TEST_ASSERT(fabs(val - 0.5) < 1e-4);
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val = RDKit::Descriptors::NPR2(*m);
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TEST_ASSERT(fabs(val - 0.5) < 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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/planar_3atom.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::NPR1(*m);
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TEST_ASSERT(fabs(val - 0.5) < 1e-4);
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val = RDKit::Descriptors::NPR2(*m);
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TEST_ASSERT(fabs(val - 0.5) < 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 val = RDKit::Descriptors::NPR1(m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::NPR2(m);
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TEST_ASSERT(fabs(val) < 1e-4);
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}
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BOOST_LOG(rdErrorLog) << " done" << std::endl;
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}
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void test3DEdges() {
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BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdErrorLog) << " 3D descriptor edge cases." << std::endl;
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{
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std::string pathName = getenv("RDBASE");
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std::string sdfName =
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pathName + "/Code/GraphMol/Descriptors/test_data/linear.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::radiusOfGyration(*m);
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TEST_ASSERT(fabs(val - 0.922) < 1e-2);
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val = RDKit::Descriptors::inertialShapeFactor(*m);
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::eccentricity(*m);
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TEST_ASSERT(fabs(1.0 - val) < 1e-4);
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val = RDKit::Descriptors::asphericity(*m);
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TEST_ASSERT(fabs(0.5 - val) < 1e-4);
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val = RDKit::Descriptors::spherocityIndex(*m);
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TEST_ASSERT(fabs(val) < 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 =
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pathName + "/Code/GraphMol/Descriptors/test_data/planar.mol";
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RDKit::ROMol *m = MolFileToMol(sdfName);
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TEST_ASSERT(m);
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double val;
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val = RDKit::Descriptors::radiusOfGyration(*m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) > 1e-2);
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val = RDKit::Descriptors::inertialShapeFactor(*m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::eccentricity(*m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(1.0 - val) < 1e-4);
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val = RDKit::Descriptors::asphericity(*m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(0.5 - val) < 1e-4);
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val = RDKit::Descriptors::spherocityIndex(*m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) < 1e-4);
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delete m;
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}
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{ // octahedron
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RDKit::RWMol m;
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m.addAtom(new RDKit::Atom(1));
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m.addAtom(new RDKit::Atom(1));
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m.addAtom(new RDKit::Atom(1));
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m.addAtom(new RDKit::Atom(1));
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m.addAtom(new RDKit::Atom(1));
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m.addAtom(new RDKit::Atom(1));
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m.addConformer(new RDKit::Conformer(m.getNumAtoms()));
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m.getConformer().setAtomPos(0, RDGeom::Point3D(1, 0, 0));
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m.getConformer().setAtomPos(1, RDGeom::Point3D(-1, 0, 0));
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m.getConformer().setAtomPos(2, RDGeom::Point3D(0, 1, 0));
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m.getConformer().setAtomPos(3, RDGeom::Point3D(0, -1, 0));
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m.getConformer().setAtomPos(4, RDGeom::Point3D(0, 0, 1));
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m.getConformer().setAtomPos(5, RDGeom::Point3D(0, 0, -1));
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double val;
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val = RDKit::Descriptors::radiusOfGyration(m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) > 0.1);
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val = RDKit::Descriptors::inertialShapeFactor(m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) > 1);
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val = RDKit::Descriptors::eccentricity(m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::asphericity(m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(val) < 1e-4);
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val = RDKit::Descriptors::spherocityIndex(m);
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std::cerr << val << std::endl;
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TEST_ASSERT(fabs(1. - val) < 1e-4);
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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));
|
|
m.addConformer(new RDKit::Conformer(m.getNumAtoms()));
|
|
double val;
|
|
val = RDKit::Descriptors::radiusOfGyration(m);
|
|
TEST_ASSERT(fabs(val) < 1e-4);
|
|
val = RDKit::Descriptors::inertialShapeFactor(m);
|
|
TEST_ASSERT(fabs(val) < 1e-4);
|
|
val = RDKit::Descriptors::eccentricity(m);
|
|
TEST_ASSERT(fabs(val) < 1e-4);
|
|
val = RDKit::Descriptors::asphericity(m);
|
|
TEST_ASSERT(fabs(val) < 1e-4);
|
|
val = RDKit::Descriptors::spherocityIndex(m);
|
|
TEST_ASSERT(fabs(val) < 1e-4);
|
|
}
|
|
|
|
BOOST_LOG(rdErrorLog) << " done" << std::endl;
|
|
}
|
|
|
|
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
|
|
//
|
|
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
|
|
int main() {
|
|
RDLog::InitLogs();
|
|
testPMIEdges();
|
|
testNPREdges();
|
|
testPMI1();
|
|
test3DEdges();
|
|
testNPR1();
|
|
}
|