/* * $Id: Chemv2Tests.java 131 2011-01-20 22:01:29Z ebakke $ * * Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc. * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are * met: * * * Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * * Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * * Neither the name of Novartis Institutes for BioMedical Research Inc. * nor the names of its contributors may be used to endorse or promote * products derived from this software without specific prior written * permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ package org.RDKit; import static org.junit.Assert.*; import org.junit.Test; public class Chemv2Tests extends GraphMolTest { /* Pickling tests skipped for the time being */ @Test public void testBasicStuff() { ROMol m = RWMol.MolFromSmiles("COC(=O)O"); Atom a1 = m.getAtomWithIdx(1); assertEquals( 8,a1.getAtomicNum() ); assertEquals( 6,m.getAtomWithIdx(2).getAtomicNum() ); Bond b1 = m.getBondWithIdx(1); assertEquals( Bond.BondType.SINGLE,b1.getBondType() ); assertEquals( Bond.BondType.DOUBLE,m.getBondWithIdx(2).getBondType() ); assertEquals( Bond.BondType.SINGLE,m.getBondBetweenAtoms(0, 1).getBondType() ); } @Test public void testEditingPersisting() { RWMol m = RWMol.MolFromSmiles("COC(=C)O"); Atom a1 = m.getAtomWithIdx(3); assertEquals("bad atom order",6, a1.getAtomicNum()); a1.setAtomicNum(7); assertEquals("bad atom order",7, a1.getAtomicNum()); assertEquals("atom order not stored",7, m.getAtomWithIdx(3).getAtomicNum()); } @Test public void testSMARTSBasics () { ROMol m = RWMol.MolFromSmiles("COC(=O)O"); ROMol p = RWMol.MolFromSmarts("CO"); assertTrue(m.hasSubstructMatch(p)); ROMol p2 = RWMol.MolFromSmarts("CS"); assertFalse(m.hasSubstructMatch(p2)); assertEquals( 2,p.getNumAtoms() ); assertEquals( 1,p.getNumBonds() ); assertTrue(m.hasSubstructMatch(p)); Match_Vect_Vect matches = m.getSubstructMatches(p); assertEquals( 3,matches.size() ); Match_Vect match = matches.get(0); assertEquals("bad match length", 2, match.size() ); matches = m.getSubstructMatches(p, false); assertEquals( 3,matches.size() ); match = matches.get(0); assertEquals("bad match length", 2, match.size() ); p = RWMol.MolFromSmarts("COC"); assertTrue(m.hasSubstructMatch(p)); assertEquals( 3,p.getNumAtoms() ); assertEquals( 2,p.getNumBonds() ); assertTrue(m.hasSubstructMatch(p)); matches = m.getSubstructMatches(p); assertEquals( 1,matches.size() ); matches = m.getSubstructMatches(p, false); assertEquals( 2,matches.size() ); } @Test public void testDataGetSetSuccess() { ROMol m = RWMol.MolFromSmiles("CCOC"); m.setProp("foo", "3"); String v = m.getProp("foo"); assertEquals("3",v); } @Test(expected=KeyErrorException.class) public void testDataGetSetFailure() { ROMol m = RWMol.MolFromSmiles("CCOC"); m.getProp("monkey"); } @Test public void testIssue399() { ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1"); m.compute2DCoords(); Conformer c = m.getConformer(); m.WedgeMolBonds(c); assertEquals( Bond.BondDir.BEGINDASH,m.getBondWithIdx(0).getBondDir() ); assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(1).getBondDir() ); assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(2).getBondDir() ); assertEquals( Bond.BondDir.NONE,m.getBondWithIdx(3).getBondDir() ); } @Test public void test2DWithSetAtomLocs() { ROMol m = RWMol.MolFromSmiles("C[C@H]1CO1"); Atom a0 = m.getAtomWithIdx(0); Int_Point2D_Map coords = new Int_Point2D_Map(); coords.set((int) a0.getIdx(), new Point2D(1.0, 1.5)); RDKFuncs.setPreferCoordGen(false); long confIdx = m.compute2DCoords(coords); Conformer c = m.getConformer((int) confIdx); assertEquals(1.0, c.getAtomPos(a0.getIdx()).getX(), defaultDoubleTol); assertEquals(1.5, c.getAtomPos(a0.getIdx()).getY(), defaultDoubleTol); } @Test public void testGenerateSVG() { ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1"); m.compute2DCoords(); Conformer c = m.getConformer(); m.WedgeMolBonds(c); String svg=m.ToSVG(8,50); assertTrue(svg.indexOf("-1); assertTrue(svg.indexOf("")>-1); } @Test public void testMolDraw2DSVG() { ROMol m = RWMol.MolFromSmiles("[C@H]1(C)CO1"); m.compute2DCoords(); Conformer c = m.getConformer(); m.WedgeMolBonds(c); MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300); drawer.drawMolecule(m); drawer.finishDrawing(); String svg = drawer.getDrawingText(); assertTrue(svg.indexOf(" -1); assertTrue(svg.indexOf("") > -1); } @Test public void testMolDraw2DSVGSingleAtomMol() { ROMol m = RWMol.MolFromSmiles("C"); m.compute2DCoords(); Conformer c = m.getConformer(); m.WedgeMolBonds(c); MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300); drawer.drawMolecule(m); drawer.finishDrawing(); String svg = drawer.getDrawingText(); assertTrue(svg.indexOf(" -1); assertTrue(svg.indexOf("") > -1); } @Test public void testPrepareMolForDrawing() { RWMol m = RWMol.MolFromSmiles("c1ccccc1"); RDKFuncs.prepareMolForDrawing(m); assertEquals(m.getNumConformers(), 1); assertTrue(m.getBondBetweenAtoms(0, 1).getBondType() != Bond.BondType.AROMATIC); assertTrue(m.getBondBetweenAtoms(0, 1).getIsAromatic()); MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300); drawer.drawMolecule(m); drawer.finishDrawing(); String svg = drawer.getDrawingText(); assertTrue(svg.indexOf(" -1); assertTrue(svg.indexOf("") > -1); } @Test public void testMolDraw2DHighlight() { RWMol m = RWMol.MolFromSmiles("CCCCCOC"); RDKFuncs.prepareMolForDrawing(m); Int_Vect hats = new Int_Vect(); hats.add(0); hats.add(1); hats.add(2); Int_Vect hbs = new Int_Vect(); hbs.add(0); hbs.add(1); hbs.add(2); ColourPalette atCs = new ColourPalette(); atCs.set(0, new DrawColour(1, 1, 0)); atCs.set(1, new DrawColour(1, 0, 1)); atCs.set(2, new DrawColour(0, 1, 1)); ColourPalette bCs = new ColourPalette(); MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300); drawer.drawMolecule(m, "THE_LEGEND", hats, hbs, atCs, bCs); drawer.finishDrawing(); String svg = drawer.getDrawingText(); // System.out.print(svg); assertTrue(svg.indexOf(" -1); assertTrue(svg.indexOf("") > -1); assertTrue(svg.indexOf("THE_LEGEND") > -1); assertTrue(svg.indexOf("fill:#FFFF00;") > -1); assertTrue(svg.indexOf("fill:#FF00FF;") > -1); assertTrue(svg.indexOf("fill:#00FFFF;") > -1); // default line color: assertTrue(svg.indexOf("stroke:#FF7F7F;") > -1); } public static void main(String args[]) { org.junit.runner.JUnitCore.main("org.RDKit.Chemv2Tests"); } }