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76ed536c87
* Remove out_1 and out_2, only need for directed graphs. * Variable renaming, no other changes. * Fix a couple things that were forgotten during the rename * Only one of these counts is updated now. * Add ifdef to enable/disable VF2Pruning * Add degree bound check, could be pushed down to the generic VertexCheck predicate. * The stack knows at each point what was added, by passing these into the Backtrack call the clone allocation can be removed. * Indent and rename added_node1 to node1. * Now the clone is removed we can add a member function to handle the recursion cleanly. * Also make for MatchAll a member function. * Set lim=0 to mean infinity. * VF2Plus optimisation, when candidate is in the terminal set select from a mapped neighbours adjacency list. * Optimisation hint. * Use a struct for the Pair removing the need for double pointer and heap alloc/delete of the iterators. * disable pruning by default (it's a bit quicker to not do this) * update expected test results The updated VF2 code can return symmetric results in a different order than we were getting previously. The results are still correct, but they change some of the downstream things that don't do symmetrization * update expected java results
125 lines
3.9 KiB
C++
125 lines
3.9 KiB
C++
// $Id$
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//
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// Copyright (C) 2005-2006 Rational Discovery LLC
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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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#include <RDGeneral/test.h>
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#include <Geometry/UniformGrid3D.h>
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#include "ShapeEncoder.h"
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#include "ShapeUtils.h"
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#include <GraphMol/RDKitBase.h>
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//#include <GraphMol/DistGeomHelpers/Embedder.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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//#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
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//#include <ForceField/ForceField.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <Geometry/GridUtils.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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using namespace RDKit;
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void test1Encode() {
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RDGeom::UniformGrid3D grd(30.0, 16.0, 10.0);
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std::string rdbase = getenv("RDBASE");
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std::string fname1 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
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ROMol *m = MolFileToMol(fname1);
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MolTransforms::canonicalizeMol(*m);
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MolShapes::EncodeShape(*m, grd, 0);
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delete m;
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// RDGeom::writeGridToFile(grd, "junk.grd");
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// MolToMolFile(m, "junk.mol", 0);
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CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 7405, "");
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}
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void test2Compare() {
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RDGeom::UniformGrid3D grd(30.0, 16.0, 10.0);
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std::string rdbase = getenv("RDBASE");
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std::string fname1 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
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ROMol *m = MolFileToMol(fname1);
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MolTransforms::canonicalizeMol(*m);
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ROMol *mdup = MolFileToMol(fname1);
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MolTransforms::canonicalizeMol(*mdup);
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double dist = MolShapes::tanimotoDistance(*m, *mdup);
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CHECK_INVARIANT(dist == 0.0, "");
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dist = MolShapes::tverskyIndex(*m, *mdup, 1.0, 1.0);
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CHECK_INVARIANT(dist == 1.0, "");
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delete m;
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delete mdup;
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m = MolFileToMol(fname1);
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std::string fname2 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol";
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ROMol *m2 = MolFileToMol(fname2);
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double rmsd = MolAlign::alignMol(*m, *m2);
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CHECK_INVARIANT(rmsd >= 0.0, "");
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dist = MolShapes::tanimotoDistance(*m, *m2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.31, 0.01), "");
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dist = MolShapes::tverskyIndex(*m, *m2, 1.0, 1.0);
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CHECK_INVARIANT(RDKit::feq(dist, 0.68, 0.01), "");
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delete m2;
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m2 = MolFileToMol(fname2);
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MatchVectType atomMap;
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atomMap.push_back(std::pair<int, int>(18, 27));
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atomMap.push_back(std::pair<int, int>(13, 23));
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atomMap.push_back(std::pair<int, int>(21, 14));
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atomMap.push_back(std::pair<int, int>(24, 7));
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atomMap.push_back(std::pair<int, int>(9, 19));
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atomMap.push_back(std::pair<int, int>(16, 30));
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rmsd = MolAlign::alignMol(*m2, *m, 0, 0, &atomMap);
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dist = MolShapes::tanimotoDistance(*m, *m2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.3593), "");
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delete m;
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delete m2;
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}
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void test3Methane() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/methane.mol";
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ROMol *m = MolFileToMol(fname);
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RDGeom::Point3D dims, offSet;
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MolShapes::computeConfDimsAndOffset(m->getConformer(), dims, offSet, nullptr,
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3.0);
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std::cout << dims << " " << offSet << "\n";
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RDGeom::UniformGrid3D grd(6.5, 6.5, 6.5);
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// dims.x, dims.y, dims.z, 0.5, DiscreteValueVect::TWOBITVALUE, &offSet);
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MolShapes::EncodeShape(*m, grd, 0);
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RDGeom::writeGridToFile(grd, "methane.grd");
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delete m;
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}
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int main() {
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#if 1
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std::cout << "***********************************************************\n";
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std::cout << "Testing ShapeHelpers\n";
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test1Encode \n\n";
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test1Encode();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test2Compare \n\n";
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test2Compare();
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std::cout << "***********************************************************\n";
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#endif
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// test3Methane();
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return 0;
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}
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