mirror of
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a6354d1501
Set svg as the default xmlns, so no prefix is needed for every svg tag. Also remove all code in python wrappers that stripped these prefixes.
228 lines
8.2 KiB
Java
228 lines
8.2 KiB
Java
/*
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* $Id: Chemv2Tests.java 131 2011-01-20 22:01:29Z ebakke $
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*
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* Copyright (c) 2010, 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
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* 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 org.junit.Test;
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public class Chemv2Tests extends GraphMolTest {
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/* Pickling tests skipped for the time being */
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@Test
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public void testBasicStuff() {
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ROMol m = RWMol.MolFromSmiles("COC(=O)O");
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Atom a1 = m.getAtomWithIdx(1);
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assertEquals( 8,a1.getAtomicNum() );
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assertEquals( 6,m.getAtomWithIdx(2).getAtomicNum() );
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Bond b1 = m.getBondWithIdx(1);
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assertEquals( Bond.BondType.SINGLE,b1.getBondType() );
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assertEquals( Bond.BondType.DOUBLE,m.getBondWithIdx(2).getBondType() );
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assertEquals( Bond.BondType.SINGLE,m.getBondBetweenAtoms(0, 1).getBondType() );
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}
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@Test
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public void testEditingPersisting() {
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RWMol m = RWMol.MolFromSmiles("COC(=C)O");
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Atom a1 = m.getAtomWithIdx(3);
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assertEquals("bad atom order",6, a1.getAtomicNum());
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a1.setAtomicNum(7);
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assertEquals("bad atom order",7, a1.getAtomicNum());
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assertEquals("atom order not stored",7, m.getAtomWithIdx(3).getAtomicNum());
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}
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@Test
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public void testSMARTSBasics () {
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ROMol m = RWMol.MolFromSmiles("COC(=O)O");
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ROMol p = RWMol.MolFromSmarts("CO");
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assertTrue(m.hasSubstructMatch(p));
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ROMol p2 = RWMol.MolFromSmarts("CS");
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assertFalse(m.hasSubstructMatch(p2));
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assertEquals( 2,p.getNumAtoms() );
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assertEquals( 1,p.getNumBonds() );
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assertTrue(m.hasSubstructMatch(p));
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Match_Vect_Vect matches = m.getSubstructMatches(p);
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assertEquals( 3,matches.size() );
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Match_Vect match = matches.get(0);
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assertEquals("bad match length", 2, match.size() );
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matches = m.getSubstructMatches(p, false);
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assertEquals( 3,matches.size() );
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match = matches.get(0);
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assertEquals("bad match length", 2, match.size() );
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p = RWMol.MolFromSmarts("COC");
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assertTrue(m.hasSubstructMatch(p));
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assertEquals( 3,p.getNumAtoms() );
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assertEquals( 2,p.getNumBonds() );
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assertTrue(m.hasSubstructMatch(p));
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matches = m.getSubstructMatches(p);
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assertEquals( 1,matches.size() );
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matches = m.getSubstructMatches(p, false);
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assertEquals( 2,matches.size() );
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}
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@Test
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public void testDataGetSetSuccess() {
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ROMol m = RWMol.MolFromSmiles("CCOC");
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m.setProp("foo", "3");
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String v = m.getProp("foo");
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assertEquals("3",v);
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}
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@Test(expected=KeyErrorException.class)
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public void testDataGetSetFailure() {
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ROMol m = RWMol.MolFromSmiles("CCOC");
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m.getProp("monkey");
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}
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@Test
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public void testIssue399() {
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ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
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m.compute2DCoords();
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Conformer c = m.getConformer();
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m.WedgeMolBonds(c);
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assertEquals( Bond.BondDir.BEGINDASH,m.getBondWithIdx(0).getBondDir() );
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assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(1).getBondDir() );
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assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(2).getBondDir() );
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assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(3).getBondDir() );
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}
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@Test
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public void test2DWithSetAtomLocs() {
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ROMol m = RWMol.MolFromSmiles("C[C@H]1CO1");
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Atom a0 = m.getAtomWithIdx(0);
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Int_Point2D_Map coords = new Int_Point2D_Map();
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coords.set((int) a0.getIdx(), new Point2D(1.0, 1.5));
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RDKFuncs.setPreferCoordGen(false);
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long confIdx = m.compute2DCoords(coords);
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Conformer c = m.getConformer((int) confIdx);
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assertEquals(1.0, c.getAtomPos(a0.getIdx()).getX(), defaultDoubleTol);
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assertEquals(1.5, c.getAtomPos(a0.getIdx()).getY(), defaultDoubleTol);
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}
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@Test
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public void testGenerateSVG() {
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ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
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m.compute2DCoords();
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Conformer c = m.getConformer();
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m.WedgeMolBonds(c);
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String svg=m.ToSVG(8,50);
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assertTrue(svg.indexOf("<svg")>-1);
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assertTrue(svg.indexOf("</svg>")>-1);
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}
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@Test
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public void testMolDraw2DSVG() {
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ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1");
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m.compute2DCoords();
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Conformer c = m.getConformer();
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m.WedgeMolBonds(c);
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MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
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drawer.drawMolecule(m);
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drawer.finishDrawing();
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String svg = drawer.getDrawingText();
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assertTrue(svg.indexOf("<svg") > -1);
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assertTrue(svg.indexOf("</svg>") > -1);
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}
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@Test
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public void testMolDraw2DSVGSingleAtomMol() {
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ROMol m = RWMol.MolFromSmiles("C");
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m.compute2DCoords();
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Conformer c = m.getConformer();
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m.WedgeMolBonds(c);
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MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
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drawer.drawMolecule(m);
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drawer.finishDrawing();
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String svg = drawer.getDrawingText();
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assertTrue(svg.indexOf("<svg") > -1);
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assertTrue(svg.indexOf("</svg>") > -1);
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}
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@Test
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public void testPrepareMolForDrawing() {
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RWMol m = RWMol.MolFromSmiles("c1ccccc1");
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RDKFuncs.prepareMolForDrawing(m);
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assertEquals(m.getNumConformers(), 1);
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assertTrue(m.getBondBetweenAtoms(0, 1).getBondType() !=
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Bond.BondType.AROMATIC);
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assertTrue(m.getBondBetweenAtoms(0, 1).getIsAromatic());
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MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
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drawer.drawMolecule(m);
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drawer.finishDrawing();
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String svg = drawer.getDrawingText();
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assertTrue(svg.indexOf("<svg") > -1);
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assertTrue(svg.indexOf("</svg>") > -1);
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}
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@Test
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public void testMolDraw2DHighlight() {
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RWMol m = RWMol.MolFromSmiles("CCCCCOC");
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RDKFuncs.prepareMolForDrawing(m);
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Int_Vect hats = new Int_Vect();
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hats.add(0);
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hats.add(1);
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hats.add(2);
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Int_Vect hbs = new Int_Vect();
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hbs.add(0);
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hbs.add(1);
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hbs.add(2);
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ColourPalette atCs = new ColourPalette();
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atCs.set(0, new DrawColour(1, 1, 0));
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atCs.set(1, new DrawColour(1, 0, 1));
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atCs.set(2, new DrawColour(0, 1, 1));
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ColourPalette bCs = new ColourPalette();
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MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
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drawer.drawMolecule(m, "THE_LEGEND", hats, hbs, atCs, bCs);
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drawer.finishDrawing();
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String svg = drawer.getDrawingText();
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// System.out.print(svg);
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assertTrue(svg.indexOf("<svg") > -1);
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assertTrue(svg.indexOf("</svg>") > -1);
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assertTrue(svg.indexOf("THE_LEGEND") > -1);
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assertTrue(svg.indexOf("fill:#FFFF00;") > -1);
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assertTrue(svg.indexOf("fill:#FF00FF;") > -1);
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assertTrue(svg.indexOf("fill:#00FFFF;") > -1);
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// default line color:
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assertTrue(svg.indexOf("stroke:#FF7F7F;") > -1);
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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.Chemv2Tests");
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}
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}
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