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/*
* $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("<svg")>-1);
assertTrue(svg.indexOf("</svg>")>-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("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -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("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -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("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -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("<svg") > -1);
assertTrue(svg.indexOf("</svg>") > -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");
}
}
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