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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
78 lines
3.0 KiB
Java
78 lines
3.0 KiB
Java
/*
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* $Id$
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*
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* Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import java.io.File;
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import org.junit.Test;
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public class AlignTests extends GraphMolTest {
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@Test
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public void testO3ABasic () {
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String fname = new File(getRdBase(),
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"Code/GraphMol/MolAlign/test_data/ref_e2.sdf").getPath();
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SDMolSupplier sdsup = new SDMolSupplier(fname);
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ROMol m1 = sdsup.next();
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ROMol m2 = sdsup.next();
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Double_Pair res = m1.O3AAlignMol(m2);
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assertEquals(res.getFirst(),0.049,.001);
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assertEquals(res.getSecond(),119.98,.01);
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}
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@Test
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public void testgetAlignmentTransform(){
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//Test alignment with Transform base on GraphMol/MolAlign/testMolAlign.cpp#test1MolAlign()
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String fname0 = new File(getRdBase(),
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"Code/GraphMol/MolAlign/test_data/1oir.mol").getPath();
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String fname1 = new File(getRdBase(),
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"Code/GraphMol/MolAlign/test_data/1oir_conf.mol").getPath();
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ROMol m0 = RWMol.MolFromMolFile(fname0);
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ROMol m1 = RWMol.MolFromMolFile(fname1);
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Transform3D trans = new Transform3D();
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double res = m0.getAlignmentTransform(m1, trans);
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assertEquals(res, 1.0345, 0.001);
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m0.delete();
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m1.delete();
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.AlignTests");
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}
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}
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