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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 java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.BufferedReader;
import java.util.Arrays;
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 testMatchingDepictions() {
ROMol template = RWMol.MolFromSmiles("c1nccc2n1ccc2");
template.compute2DCoords();
ROMol m = RWMol.MolFromSmiles("c1cccc2ncn3cccc3c21");
ROMol patt = RWMol.MolFromSmarts("*1****2*1***2");
Match_Vect mv = m.generateDepictionMatching2DStructure(template,-1,patt);
assertTrue(mv.size() == 9);
int[] expected = new int[]{ 6, 5, 4, 12, 11, 7, 8, 9, 10 };
for (int i = 0; i < mv.size(); ++i) {
assertTrue(mv.get(i).getFirst() == i);
assertTrue(mv.get(i).getSecond() == expected[i]);
}
// System.out.print(template.MolToMolBlock());
// System.out.print(m.MolToMolBlock());
assertEquals(template.MolToMolBlock(), RDKFuncs.MolToMolBlock(template));
Conformer c1 = template.getConformer();
Conformer c2 = m.getConformer();
assertEquals(c1.getAtomPos(0).getX(), c2.getAtomPos(6).getX(), defaultDoubleTol);
assertEquals(c1.getAtomPos(0).getY(), c2.getAtomPos(6).getY(), defaultDoubleTol);
assertEquals(c1.getAtomPos(0).getZ(), c2.getAtomPos(6).getZ(), 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 testNormalizeStraightenDepiction() {
ROMol noradrenalineMJ = RWMol.MolFromMolBlock("\n" +
" MJ201100 \n" +
"\n" +
" 12 12 0 0 1 0 0 0 0 0999 V2000\n" +
" 2.2687 1.0716 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.4437 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.0312 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.4437 -0.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 0.2062 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -0.2062 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.0312 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.4437 -1.0716 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.4437 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -2.2687 0.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.0312 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -0.2062 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1 2 1 0 0 0 0\n" +
" 3 2 1 0 0 0 0\n" +
" 3 4 1 6 0 0 0\n" +
" 3 5 1 0 0 0 0\n" +
" 5 6 2 0 0 0 0\n" +
" 6 7 1 0 0 0 0\n" +
" 7 8 1 0 0 0 0\n" +
" 7 9 2 0 0 0 0\n" +
" 9 10 1 0 0 0 0\n" +
" 9 11 1 0 0 0 0\n" +
" 11 12 2 0 0 0 0\n" +
" 5 12 1 0 0 0 0\n" +
"M END");
{
ROMol noradrenalineMJCopy = new RWMol(noradrenalineMJ);
Conformer conformer0 = noradrenalineMJCopy.getConformer(0);
Conformer conformer1 = new Conformer(conformer0);
noradrenalineMJCopy.addConformer(conformer1, true);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) < 1.e-5);
double scalingFactor = noradrenalineMJCopy.normalizeDepiction(1);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) > 1.e-5);
assertEquals(scalingFactor, 1.875, 1.e-3);
Conformer conformer2 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer2, true);
Point3D bond10_11Conf0 = conformer0.getAtomPos(11).minus(conformer0.getAtomPos(10));
assertEquals(bond10_11Conf0.getX(), 0.825, 1.e-3);
assertEquals(bond10_11Conf0.getY(), 0.0, 1.e-3);
Point3D bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 1.513, 1.e-3);
assertEquals(bond10_11Conf1.getY(), -0.321, 1.e-3);
noradrenalineMJCopy.straightenDepiction(1);
bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 1.340, 1.e-3);
assertEquals(bond10_11Conf1.getY(), -0.773, 1.e-3);
Point3D bond4_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(4));
assertEquals(bond4_11Conf1.getX(), 0.0, 1.e-3);
assertEquals(bond4_11Conf1.getY(), 1.547, 1.e-3);
noradrenalineMJCopy.straightenDepiction(2, true);
Point3D bond10_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(10));
assertEquals(bond10_11Conf2.getX(), 1.547, 1.e-3);
assertEquals(bond10_11Conf2.getY(), 0.0, 1.e-3);
Point3D bond4_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(4));
assertEquals(bond4_11Conf2.getX(), -0.773, 1.e-3);
assertEquals(bond4_11Conf2.getY(), 1.339, 1.e-3);
noradrenalineMJCopy.delete();
conformer1.delete();
conformer2.delete();
}
{
ROMol noradrenalineMJCopy = new RWMol(noradrenalineMJ);
Conformer conformer0 = noradrenalineMJCopy.getConformer(0);
Conformer conformer1 = new Conformer(conformer0);
noradrenalineMJCopy.addConformer(conformer1, true);
double scalingFactor = noradrenalineMJCopy.normalizeDepiction(1, -1);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) > 1.e-5);
assertEquals(scalingFactor, 1.875, 1.e-3);
Conformer conformer2 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer2, true);
Point3D bond10_11Conf0 = conformer0.getAtomPos(11).minus(conformer0.getAtomPos(10));
assertEquals(bond10_11Conf0.getX(), 0.825, 1.e-3);
assertEquals(bond10_11Conf0.getY(), 0.0, 1.e-3);
Point3D bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 0.321, 1.e-3);
assertEquals(bond10_11Conf1.getY(), 1.513, 1.e-3);
noradrenalineMJCopy.straightenDepiction(1);
bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 0.0, 1.e-3);
assertEquals(bond10_11Conf1.getY(), 1.547, 1.e-3);
noradrenalineMJCopy.straightenDepiction(2, true);
Point3D bond10_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(10));
assertEquals(bond10_11Conf2.getX(), bond10_11Conf1.getX(), 1.e-3);
assertEquals(bond10_11Conf2.getY(), bond10_11Conf1.getY(), 1.e-3);
noradrenalineMJCopy.delete();
conformer1.delete();
conformer2.delete();
}
{
ROMol noradrenalineMJCopy = new RWMol(noradrenalineMJ);
Conformer conformer0 = noradrenalineMJCopy.getConformer(0);
Conformer conformer1 = new Conformer(conformer0);
noradrenalineMJCopy.addConformer(conformer1, true);
double scalingFactor = noradrenalineMJCopy.normalizeDepiction(1, 0, 3.0);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 0) < 1.e-5);
assertTrue(noradrenalineMJ.calcRMS(noradrenalineMJCopy, 0, 1) > 1.e-5);
assertEquals(scalingFactor, 3.0, 1.e-3);
Conformer conformer2 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer2, true);
Conformer conformer3 = new Conformer(conformer1);
noradrenalineMJCopy.addConformer(conformer3, true);
Point3D bond10_11Conf0 = conformer0.getAtomPos(11).minus(conformer0.getAtomPos(10));
assertEquals(bond10_11Conf0.getX(), 0.825, 1.e-3);
assertEquals(bond10_11Conf0.getY(), 0.0, 1.e-3);
Point3D bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 2.475, 1.e-3);
assertEquals(bond10_11Conf1.getY(), 0.0, 1.e-3);
noradrenalineMJCopy.straightenDepiction(1);
bond10_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(10));
assertEquals(bond10_11Conf1.getX(), 2.143, 1.e-3);
assertEquals(bond10_11Conf1.getY(), -1.237, 1.e-3);
Point3D bond4_11Conf1 = conformer1.getAtomPos(11).minus(conformer1.getAtomPos(4));
assertEquals(bond4_11Conf1.getX(), 0.0, 1.e-3);
assertEquals(bond4_11Conf1.getY(), 2.475, 1.e-3);
noradrenalineMJCopy.straightenDepiction(2, true);
Point3D bond10_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(10));
Point3D bond10_11Conf3 = conformer3.getAtomPos(11).minus(conformer3.getAtomPos(10));
assertEquals(bond10_11Conf2.getX(), bond10_11Conf3.getX(), 1.e-3);
assertEquals(bond10_11Conf2.getY(), bond10_11Conf3.getY(), 1.e-3);
Point3D bond4_11Conf2 = conformer2.getAtomPos(11).minus(conformer2.getAtomPos(4));
Point3D bond4_11Conf3 = conformer3.getAtomPos(11).minus(conformer3.getAtomPos(4));
assertEquals(bond4_11Conf2.getX(), bond4_11Conf3.getX(), 1.e-3);
assertEquals(bond4_11Conf2.getY(), bond4_11Conf3.getY(), 1.e-3);
noradrenalineMJCopy.delete();
conformer1.delete();
conformer2.delete();
conformer3.delete();
}
}
@Test
public void testGetBestRMS() {
String rdpath = System.getenv("RDBASE");
if (rdpath == null)
org.junit.Assert.fail("No definition for RDBASE");
File base = new File(rdpath);
File testFile = new File(base, "Code" + File.separator + "GraphMol"
+ File.separator + "MolAlign" + File.separator + "test_data"
+ File.separator + "probe_mol.sdf");
String fName = testFile.getAbsolutePath();
SDMolSupplier supplier = new SDMolSupplier(fName, true, false);
supplier.next();
ROMol prb = supplier.next();
ROMol ref = supplier.next();
ROMol prbCopy1 = new ROMol(prb);
ROMol prbCopy2 = new ROMol(prb);
ROMol prbCopy3 = new ROMol(prb);
Transform3D bestTrans = new Transform3D();
Match_Vect bestMatch = new Match_Vect();
// alignMol() would return this for the rms: 2.50561
// But the best rms is: 2.43449
double rmsdInPlace = prbCopy1.calcRMS(ref);
assertEquals(rmsdInPlace, 2.6026, 1.e-3);
double rmsd = prb.getBestRMS(ref);
assertEquals(rmsd, 2.43449, 1.e-3);
double rmsdCopy = prbCopy1.getBestAlignmentTransform(ref, bestTrans, bestMatch);
assertEquals(rmsd, rmsdCopy, 1.e-3);
assertEquals(bestMatch.size(), ref.getNumAtoms());
SmilesParserParams params = new SmilesParserParams();
params.setRemoveHs(false);
RWMol scaffold = RWMol.MolFromSmiles("N1C([H])([H])C([H])([H])C([H])([H])[N+]([H])([H])C([H])([H])C1([H])[H]", params);
Match_Vect scaffoldMatch = ref.getSubstructMatch(scaffold);
assertFalse(scaffoldMatch.isEmpty());
int nAtoms = (int)ref.getNumAtoms();
boolean[] scaffoldIndices = new boolean[nAtoms];
Arrays.fill(scaffoldIndices, false);
for (int i = 0; i < scaffoldMatch.size(); ++i) {
int pairSecond = scaffoldMatch.get(i).getSecond();
scaffoldIndices[pairSecond] = true;
}
Match_Vect_Vect matches = ref.getSubstructMatches(prb, false);
Match_Vect_Vect matchesPruned = new Match_Vect_Vect(matches.size());
for (int i = 0; i < matches.size(); ++i) {
Match_Vect match = matches.get(i);
Match_Vect matchPruned = new Match_Vect();
for (int j = 0; j < match.size(); ++j) {
int pairSecond = match.get(j).getSecond();
if (scaffoldIndices[pairSecond]) {
matchPruned.add(match.get(j));
}
}
matchesPruned.set(i, matchPruned);
matchPruned.delete();
}
rmsdInPlace = prbCopy2.calcRMS(ref, -1, -1, matchesPruned);
assertEquals(rmsdInPlace, 2.5672, 1.e-3);
rmsd = prb.getBestRMS(ref, -1, -1, matchesPruned);
assertEquals(rmsd, 1.14329, 1.e-3);
rmsdCopy = prbCopy2.getBestAlignmentTransform(ref, bestTrans, bestMatch, -1, -1, matchesPruned);
assertEquals(rmsd, rmsdCopy, 1.e-3);
assertEquals(bestMatch.size(), scaffoldMatch.size());
DoubleVector weights = new DoubleVector(nAtoms, 1.0);
for (int i = 0; i < nAtoms; ++i) {
if (scaffoldIndices[i]) {
weights.setVal(i, 100.0);
}
}
rmsdInPlace = prbCopy3.calcRMS(ref, -1, -1, matches, 1000, true, weights);
assertEquals(rmsdInPlace, 17.7959, 1.e-3);
rmsd = prb.getBestRMS(ref, -1, -1, matches, 1000, true, weights);
assertEquals(rmsd, 10.9681, 1.e-3);
rmsdCopy = prbCopy3.getBestAlignmentTransform(ref, bestTrans, bestMatch, -1, -1, matches, 1000, true, weights);
assertEquals(rmsd, rmsdCopy, 1.e-3);
assertEquals(bestMatch.size(), ref.getNumAtoms());
supplier.delete();
prbCopy1.delete();
prbCopy2.delete();
prbCopy3.delete();
params.delete();
matchesPruned.delete();
weights.delete();
}
@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("fill:#FFFF00;") > -1);
assertTrue(svg.indexOf("fill:#FF00FF;") > -1);
assertTrue(svg.indexOf("fill:#00FFFF;") > -1);
// default line color:
assertTrue(svg.indexOf("stroke:#FF7F7F;") == -1);
assertTrue(svg.indexOf("stroke:#FFFF00;") > -1);
assertTrue(svg.indexOf("stroke:#FF00FF;") > -1);
}
@Test
public void testMolDraw2DContours() {
// really just a test to make sure this can be called
RWMol m = RWMol.MolFromSmiles("CCCCCOC");
RDKFuncs.prepareMolForDrawing(m);
Point2D_Vect cents = new Point2D_Vect();
Double_Vect weights = new Double_Vect();
Double_Vect widths = new Double_Vect();
for(int i=0;i<m.getNumAtoms();++i){
cents.add(new Point2D(m.getConformer().getAtomPos(i)));
weights.add(1.0);
widths.add(0.4);
}
MolDraw2DSVG drawer = new MolDraw2DSVG(300, 300);
drawer.clearDrawing();
RDKFuncs.ContourAndDrawGaussians(drawer,cents,weights,widths,10);
drawer.drawOptions().setClearBackground(false);
drawer.drawMolecule(m);
drawer.finishDrawing();
String svg = drawer.getDrawingText();
System.out.print(svg);
}
@Test
public void testStrictParsingAndLogging() {
RDKFuncs.InitLogs();
String badMolBlock = "\n" +
" MJ201100 \n" +
"\n" +
" 3 2 0 0 0 0 0 0 0 0999 V2000\n" +
" -0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1.0717 0.6187 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1 2 1 0 0 0 0\n" +
" 2 3 3 0 0 0 0\n" +
"M STY 1 1 SUP\n" +
"M SAL 1 2 2 3\n" +
"M SMT 1 CN\n" +
"M SBL 1 1 1\n" +
"M SAP 1 1 2\n" +
"M END\n";
boolean exceptionThrown = false;
boolean molIsValid = false;
ROMol mol = null;
try {
mol = RWMol.MolFromMolBlock(badMolBlock);
} catch(Exception e) {
exceptionThrown = true;
} finally {
if (mol != null) {
molIsValid = true;
mol.delete();
}
}
assertTrue(exceptionThrown);
assertFalse(molIsValid);
exceptionThrown = false;
BufferedReader reader = null;
try {
String filename = "java_warning_log.txt";
RDKFuncs.getRdWarningLog().SetTee(filename);
mol = RWMol.MolFromMolBlock(badMolBlock, true, true, false);
reader = new BufferedReader(new FileReader(filename));
String line = reader.readLine();
assertTrue(line != null);
assertTrue(line.contains("SGroup SAP line too short"));
} catch(Exception e) {
exceptionThrown = true;
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {}
}
if (mol != null) {
molIsValid = true;
mol.delete();
}
}
assertFalse(exceptionThrown);
assertTrue(molIsValid);
}
@Test
public void testMostSubstitutedCoreMatch() {
RWMol core = RWMol.MolFromSmarts("[*:1]c1cc([*:2])ccc1[*:3]");
RWMol orthoMeta = RWMol.MolFromSmiles("c1ccc(-c2ccc(-c3ccccc3)c(-c3ccccc3)c2)cc1");
RWMol ortho = RWMol.MolFromSmiles("c1ccc(-c2ccccc2-c2ccccc2)cc1");
RWMol meta = RWMol.MolFromSmiles("c1ccc(-c2cccc(-c3ccccc3)c2)cc1");
RWMol biphenyl = RWMol.MolFromSmiles("c1ccccc1-c1ccccc1");
RWMol phenyl = RWMol.MolFromSmiles("c1ccccc1");
class NumHsMatchingDummies {
public int get(RWMol mol, RWMol core, Match_Vect match) {
int count = 0;
for (int i = 0; i < match.size(); ++i) {
Int_Pair pair = match.get(i);
if (core.getAtomWithIdx(pair.getFirst()).getAtomicNum() == 0 &&
mol.getAtomWithIdx(pair.getSecond()).getAtomicNum() == 1) {
++count;
}
}
return count;
}
};
NumHsMatchingDummies numHsMatchingDummies = new NumHsMatchingDummies();
RWMol_Vect mols = new RWMol_Vect(5);
mols.set(0, orthoMeta);
mols.set(1, ortho);
mols.set(2, meta);
mols.set(3, biphenyl);
mols.set(4, phenyl);
int[] expected = new int[]{ 0, 1, 1, 2, 3 };
assertTrue(mols.size() == expected.length);
for (int i = 0; i < expected.length; ++i) {
RWMol mol = mols.get(i);
int res = expected[i];
RDKFuncs.addHs(mol);
Match_Vect_Vect matches = mol.getSubstructMatches(core);
Match_Vect bestMatch = mol.getMostSubstitutedCoreMatch(core, matches);
assertTrue(numHsMatchingDummies.get(mol, core, bestMatch) == res);
int[] ctrlCounts = new int[(int)matches.size()];
for (int j = 0; j < ctrlCounts.length; ++j) {
ctrlCounts[j] = numHsMatchingDummies.get(mol, core, matches.get(j));
}
Arrays.sort(ctrlCounts);
int[] sortedCounts = new int[ctrlCounts.length];
Match_Vect_Vect sortedMatches = mol.sortMatchesByDegreeOfCoreSubstitution(core, matches);
for (int j = 0; j < sortedMatches.size(); ++j) {
sortedCounts[j] = numHsMatchingDummies.get(mol, core, sortedMatches.get(j));
}
assertTrue(Arrays.equals(ctrlCounts, sortedCounts));
matches.delete();
sortedMatches.delete();
}
Match_Vect_Vect emptyMatches = new Match_Vect_Vect();
boolean raised = false;
try {
orthoMeta.getMostSubstitutedCoreMatch(core, emptyMatches);
} catch (Exception e) {
raised = true;
}
assertTrue(raised);
raised = false;
try {
orthoMeta.sortMatchesByDegreeOfCoreSubstitution(core, emptyMatches);
} catch (Exception e) {
raised = true;
}
assertTrue(raised);
emptyMatches.delete();
mols.delete();
core.delete();
orthoMeta.delete();
ortho.delete();
meta.delete();
biphenyl.delete();
phenyl.delete();
}
@Test
public void testStereoChemFunctions() {
boolean useLegacyStereo = RDKFuncs.getUseLegacyStereoPerception();
boolean allowNonTetrahedralChirality = RDKFuncs.getAllowNontetrahedralChirality();
try {
RWMol m = RWMol.MolFromSmiles("CC(O)Cl |(-3.9163,5.4767,;-3.9163,3.9367,;-2.5826,3.1667,;-5.25,3.1667,),wU:1.0|");
assertTrue(m != null);
assertEquals(m.getBondWithIdx(0).getProp("_MolFileBondCfg"), "1");
assertEquals(m.getAtomWithIdx(1).getChiralTag(), Atom.ChiralType.CHI_TETRAHEDRAL_CW);
m.delete();
m = RWMol.MolFromSmiles("CC(O)Cl |(-3.9163,5.4767,;-3.9163,3.9367,;-2.5826,3.1667,;-5.25,3.1667,),wD:1.0|");
assertTrue(m != null);
assertEquals(m.getBondWithIdx(0).getProp("_MolFileBondCfg"), "3");
assertEquals(m.getAtomWithIdx(1).getChiralTag(), Atom.ChiralType.CHI_TETRAHEDRAL_CCW);
m.invertMolBlockWedgingInfo();
assertEquals(m.getBondWithIdx(0).getProp("_MolFileBondCfg"), "1");
m.reapplyMolBlockWedging();
RDKFuncs.assignChiralTypesFromBondDirs(m);
assertEquals(m.getAtomWithIdx(1).getChiralTag(), Atom.ChiralType.CHI_TETRAHEDRAL_CW);
m.invertMolBlockWedgingInfo();
assertEquals(m.getBondWithIdx(0).getProp("_MolFileBondCfg"), "3");
m.reapplyMolBlockWedging();
RDKFuncs.assignChiralTypesFromBondDirs(m);
assertEquals(m.getAtomWithIdx(1).getChiralTag(), Atom.ChiralType.CHI_TETRAHEDRAL_CCW);
m.clearMolBlockWedgingInfo();
m.getAtomWithIdx(1).setChiralTag(Atom.ChiralType.CHI_UNSPECIFIED);
assertFalse(m.getBondWithIdx(0).hasProp("_MolFileBondCfg"));
m.reapplyMolBlockWedging();
RDKFuncs.assignChiralTypesFromBondDirs(m);
assertEquals(m.getAtomWithIdx(1).getChiralTag(), Atom.ChiralType.CHI_UNSPECIFIED);
m.delete();
RDKFuncs.setUseLegacyStereoPerception(true);
m = RWMol.MolFromSmiles("O[C@@]1(C)C/C(/C1)=C(/C)\\CC");
assertTrue(m != null);
assertEquals(m.MolToSmiles(), "CCC(C)=C1CC(C)(O)C1");
m.delete();
RDKFuncs.setUseLegacyStereoPerception(false);
m = RWMol.MolFromSmiles("O[C@@]1(C)C/C(/C1)=C(/C)\\CC");
assertTrue(m != null);
assertEquals(m.MolToSmiles(), "CC/C(C)=C1\\C[C@](C)(O)C1");
m.delete();
RDKFuncs.setUseLegacyStereoPerception(useLegacyStereo);
String ctab = "\n" +
" Mrv2108 09132105183D \n" +
"\n" +
" 5 4 0 0 0 0 999 V2000\n" +
" -1.2500 1.4518 0.0000 Pt 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.2500 2.2768 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -0.4250 1.4518 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -2.0750 1.4518 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" -1.2500 0.6268 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n" +
" 1 2 1 0 0 0 0\n" +
" 1 3 1 0 0 0 0\n" +
" 1 4 1 0 0 0 0\n" +
" 1 5 1 0 0 0 0\n" +
"M END\n";
RDKFuncs.setAllowNontetrahedralChirality(true);
m = RWMol.MolFromMolBlock(ctab);
assertTrue(m != null);
assertEquals(m.MolToSmiles(), "[F][Pt@SP3]([F])([Cl])[Cl]");
m.delete();
RDKFuncs.setAllowNontetrahedralChirality(false);
m = RWMol.MolFromMolBlock(ctab);
assertTrue(m != null);
assertEquals(m.MolToSmiles(), "[F][Pt]([F])([Cl])[Cl]");
m.delete();
RDKFuncs.setAllowNontetrahedralChirality(allowNonTetrahedralChirality);
} finally {
RDKFuncs.setUseLegacyStereoPerception(useLegacyStereo);
RDKFuncs.setAllowNontetrahedralChirality(allowNonTetrahedralChirality);
}
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.Chemv2Tests");
}
}
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