pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-04 21:54:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
6fa65fbc688065dd990860f476af9f82bc5f9dd5
rdkit/Code/Demos/SWIG/java_example/WrapperTests.java
Greg Landrum 6fa65fbc68 move the _VSA descriptors into C++
2011-03-21 05:02:12 +00:00

385 lines
12 KiB
Java
Raw Blame History

// $Id$
// Copyright (C) 2008-2010 Greg Landrum
//
// @@ All Rights Reserved @@
//package org.RDKit;
import org.junit.*;
import static org.junit.Assert.*;
import org.RDKit.*;
public class WrapperTests {
private ROMol mol1;
@Before public void setUp() {
String smiles="c1ccccc1";
mol1 = RDKFuncs.MolFromSmiles(smiles);
}
@Test public void testBasics() {
assertTrue(mol1.getNumAtoms()==6);
assertTrue(mol1.getNumBonds()==6);
}
@Test public void testAtoms() {
assertTrue(mol1.getAtomWithIdx(0).getAtomicNum()==6);
assertFalse(mol1.hasAtomBookmark(1));
mol1.setAtomBookmark(mol1.getAtomWithIdx(0),1);
assertTrue(mol1.hasAtomBookmark(1));
}
@Test public void testBonds() {
assertTrue(mol1.getBondWithIdx(0).getBondType()==Bond.BondType.AROMATIC);
}
@Test public void testSmilesWrite() {
String smi=RDKFuncs.MolToSmiles(mol1);
assertEquals(smi,"c1ccccc1",smi);
}
@Test public void testReactionBasics() {
ChemicalReaction rxn;
rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
assertTrue(rxn.getNumReactantTemplates()==2);
assertTrue(rxn.getNumProductTemplates()==1);
ROMol r1,r2;
r1=RDKFuncs.MolFromSmiles("CC(=O)O");
r2=RDKFuncs.MolFromSmiles("ClCN");
assertTrue(r1.getNumAtoms()==4);
assertTrue(r2.getNumAtoms()==3);
ROMol_Vect rs= new ROMol_Vect(2);
rs.set(0,r1);
rs.set(1,r2);
ROMol_Vect_Vect ps;
ps=rxn.runReactants(rs);
assertFalse(ps.isEmpty());
assertTrue(ps.size()==1);
assertFalse(ps.get(0).isEmpty());
assertTrue(ps.get(0).size()==1);
assertTrue(r1.getNumAtoms()==4);
assertTrue(r2.getNumAtoms()==3);
assertTrue(ps.get(0).get(0).getNumAtoms()==6);
}
@Test public void testSubstruct1() {
ROMol p;
Match_Vect mv;
p = RDKFuncs.MolFromSmarts("c");
assertTrue(mol1.hasSubstructMatch(p));
mv=mol1.getSubstructMatch(p);
assertTrue(mv.size()==1);
assertTrue(mv.get(0).getFirst()==0);
assertTrue(mv.get(0).getSecond()==0);
}
@Test public void testSubstruct2() {
ROMol p;
Match_Vect mv;
p = RDKFuncs.MolFromSmarts("C");
assertFalse(mol1.hasSubstructMatch(p));
mv=mol1.getSubstructMatch(p);
assertTrue(mv.size()==0);
}
@Test public void testSubstruct3() {
ROMol p;
Match_Vect mv;
ROMol m2;
m2 = RDKFuncs.MolFromSmiles("NC(=O)CC");
p = RDKFuncs.MolFromSmarts("CN");
mv=m2.getSubstructMatch(p);
assertTrue(mv.size()==2);
assertTrue(mv.get(0).getFirst()==0);
assertTrue(mv.get(0).getSecond()==1);
assertTrue(mv.get(1).getFirst()==1);
assertTrue(mv.get(1).getSecond()==0);
}
@Test public void testSubstruct4() {
ROMol p;
Match_Vect_Vect mvv;
ROMol m2;
m2 = RDKFuncs.MolFromSmiles("NC(=O)CC");
p = RDKFuncs.MolFromSmarts("CN");
mvv=m2.getSubstructMatches(p);
assertTrue(mvv.size()==1);
assertTrue(mvv.get(0).size()==2);
assertTrue(mvv.get(0).get(0).getFirst()==0);
assertTrue(mvv.get(0).get(0).getSecond()==1);
assertTrue(mvv.get(0).get(1).getFirst()==1);
assertTrue(mvv.get(0).get(1).getSecond()==0);
}
@Test public void testSubstruct5() {
ROMol p;
Match_Vect_Vect mvv;
ROMol m2;
m2 = RDKFuncs.MolFromSmiles("NC(=O)NCC");
p = RDKFuncs.MolFromSmarts("[$(C=O)]N");
mvv=m2.getSubstructMatches(p);
assertTrue(mvv.size()==2);
assertTrue(mvv.get(0).size()==2);
assertTrue(mvv.get(0).get(0).getFirst()==0);
assertTrue(mvv.get(0).get(0).getSecond()==1);
assertTrue(mvv.get(0).get(1).getFirst()==1);
assertTrue(mvv.get(0).get(1).getSecond()==0);
assertTrue(mvv.get(1).size()==2);
assertTrue(mvv.get(1).get(0).getFirst()==0);
assertTrue(mvv.get(1).get(0).getSecond()==1);
assertTrue(mvv.get(1).get(1).getFirst()==1);
assertTrue(mvv.get(1).get(1).getSecond()==3);
}
@Test public void testFingerprints1() {
ROMol m1,m2;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
ExplicitBitVect fp1,fp2;
fp1=RDKFuncs.RDKFingerprintMol(m1);
fp2=RDKFuncs.RDKFingerprintMol(m1);
assertTrue(RDKFuncs.TanimotoSimilarityEBV(fp1,fp2)==1.0);
fp2=RDKFuncs.RDKFingerprintMol(m2);
assertTrue(RDKFuncs.TanimotoSimilarityEBV(fp1,fp2)<1.0);
assertTrue(RDKFuncs.TanimotoSimilarityEBV(fp1,fp2)>0.0);
}
@Test public void testFingerprints2() {
ROMol m1,m2;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
SparseIntVectu32 fp1,fp2;
fp1=RDKFuncs.getMorganFingerprint(m1,2);
fp2=RDKFuncs.getMorganFingerprint(m1,2);
assertTrue(RDKFuncs.DiceSimilaritySIVu32(fp1,fp2)==1.0);
fp2=RDKFuncs.getMorganFingerprint(m2,2);
assertTrue(RDKFuncs.DiceSimilaritySIVu32(fp1,fp2)<1.0);
assertTrue(RDKFuncs.DiceSimilaritySIVu32(fp1,fp2)>0.0);
UInt_Pair_Vect v1=fp1.getNonzero();
assertTrue(v1.size()>0);
UInt_Pair_Vect v2=fp2.getNonzero();
assertTrue(v2.size()>0);
assertTrue(v2.size()>v1.size());
}
@Test public void testFingerprints3() {
ROMol m1,m2;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
SparseIntVecti32 fp1,fp2;
fp1=RDKFuncs.getAtomPairFingerprint(m1,2,6);
fp2=RDKFuncs.getAtomPairFingerprint(m1,2,6);
assertTrue(RDKFuncs.DiceSimilaritySIVi32(fp1,fp2)==1.0);
fp2=RDKFuncs.getAtomPairFingerprint(m2,2,6);
assertEquals(RDKFuncs.DiceSimilaritySIVi32(fp1,fp2),0.66667,.0001);
}
@Test public void testFingerprints4() {
ROMol m1,m2;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
SparseIntVecti64 fp1,fp2;
fp1=RDKFuncs.getTopologicalTorsionFingerprint(m1);
fp2=RDKFuncs.getTopologicalTorsionFingerprint(m1);
assertTrue(RDKFuncs.DiceSimilaritySIVi64(fp1,fp2)==1.0);
fp2=RDKFuncs.getTopologicalTorsionFingerprint(m2);
assertEquals(RDKFuncs.DiceSimilaritySIVi64(fp1,fp2),0.3333,.0001);
}
@Test public void testErrorHandling() {
ROMol m1;
m1 = RDKFuncs.MolFromSmiles("C1CC");
assertTrue(m1==null);
m1 = RDKFuncs.MolFromSmiles("c1cc1");
assertTrue(m1==null);
System.err.println("ok!");
ChemicalReaction rxn=RDKFuncs.ReactionFromSmarts("OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
assertTrue(rxn==null);
}
@Test public void testPickling() {
Int_Vect pkl=RDKFuncs.MolToBinary(mol1);
ROMol m1 = RDKFuncs.MolFromBinary(pkl);
assertTrue(m1.getNumAtoms()==6);
assertTrue(m1.getNumBonds()==6);
}
@Test public void testReactionPickling() {
ChemicalReaction rxn;
rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
assertTrue(rxn.getNumReactantTemplates()==2);
assertTrue(rxn.getNumProductTemplates()==1);
Int_Vect pkl=RDKFuncs.RxnToBinary(rxn);
ChemicalReaction rxn2=RDKFuncs.RxnFromBinary(pkl);
assertTrue(rxn2.getNumReactantTemplates()==2);
assertTrue(rxn2.getNumProductTemplates()==1);
}
@Test public void testReactionToSmarts() {
ChemicalReaction rxn;
rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
assertTrue(rxn.getNumReactantTemplates()==2);
assertTrue(rxn.getNumProductTemplates()==1);
String sma=RDKFuncs.ReactionToSmarts(rxn);
ChemicalReaction rxn2;
rxn2=RDKFuncs.ReactionFromSmarts(sma);
assertTrue(rxn2.getNumReactantTemplates()==2);
assertTrue(rxn2.getNumProductTemplates()==1);
}
@Test public void testSupplier() {
SDMolSupplier suppl=new SDMolSupplier("./test_data/NCI_aids_few.sdf");
int i=0;
while(! suppl.atEnd()){
ROMol m1 = suppl.next();
if(m1==null) continue;
assertTrue(m1.hasProp("NSC"));
assertFalse(m1.hasProp("monkey"));
if(i==0){
assertEquals(m1.getProp("_Name"),"128");
assertEquals(m1.getProp("CAS_RN"),"5395-10-8");
}
String smi1=RDKFuncs.MolToSmiles(m1);
String txt=suppl.getItemText(i);
i++;
ROMol m2 = RDKFuncs.MolFromMolBlock(txt);
assertFalse(m2==null);
String smi2=RDKFuncs.MolToSmiles(m2);
assertEquals(smi1,smi2);
}
}
@Test public void testDescriptors1() {
ROMol m1,m2,m3;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
m3 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1CC(=O)O");
long tmp;
tmp=RDKFuncs.calcNumHBA(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcNumHBA(m2);
assertEquals(tmp,1);
tmp=RDKFuncs.calcNumHBA(m3);
assertEquals(tmp,1);
tmp=RDKFuncs.calcNumHBD(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcNumHBD(m2);
assertEquals(tmp,0);
tmp=RDKFuncs.calcNumHBD(m3);
assertEquals(tmp,1);
tmp=RDKFuncs.calcLipinskiHBA(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcLipinskiHBA(m2);
assertEquals(tmp,1);
tmp=RDKFuncs.calcLipinskiHBA(m3);
assertEquals(tmp,2);
tmp=RDKFuncs.calcLipinskiHBD(m1);
assertEquals(tmp,0);
tmp=RDKFuncs.calcLipinskiHBD(m2);
assertEquals(tmp,0);
tmp=RDKFuncs.calcLipinskiHBD(m3);
assertEquals(tmp,1);
}
@Test public void testDescriptors2() {
ROMol m1,m2;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
double tmp;
tmp=RDKFuncs.calcMolLogP(m1);
assertEquals(tmp,1.687,0.001);
tmp=RDKFuncs.calcMolLogP(m2);
assertEquals(tmp,1.082,0.001);
tmp=RDKFuncs.calcMolMR(m1);
assertEquals(tmp,26.442,0.001);
tmp=RDKFuncs.calcMolMR(m2);
assertEquals(tmp,24.237,0.001);
}
@Test public void testDescriptors3() {
ROMol m1,m2,m3;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1");
m2 = RDKFuncs.MolFromSmiles("C1=CC=CC=N1");
m3 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1CC(=O)O");
double tmp;
tmp=RDKFuncs.calcTPSA(m1);
assertEquals(tmp,0,0.01);
tmp=RDKFuncs.calcTPSA(m2);
assertEquals(tmp,12.89,0.01);
tmp=RDKFuncs.calcTPSA(m3);
assertEquals(tmp,37.30,0.01);
}
@Test public void testVSADescriptors() {
ROMol m1,m2,m3;
m1 = RDKFuncs.MolFromSmiles("CO");
m2 = RDKFuncs.MolFromSmiles("CCO");
Double_Vect v;
v = RDKFuncs.calcSlogP_VSA(m1);
assertEquals(v.get(0),0.0,0.001);
assertEquals(v.get(1),12.216,0.001);
v = RDKFuncs.calcSlogP_VSA(m2);
assertEquals(v.get(0),0.0,0.001);
assertEquals(v.get(1),11.713,0.001);
assertEquals(v.get(4),6.924,0.001);
v = RDKFuncs.calcSMR_VSA(m1);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(1),0.0,0.001);
assertEquals(v.get(5),7.110,0.001);
v = RDKFuncs.calcSMR_VSA(m2);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(4),6.924,0.001);
assertEquals(v.get(5),6.607,0.001);
v = RDKFuncs.calcPEOE_VSA(m1);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(7),7.110,0.001);
assertEquals(v.get(5),0.000,0.001);
v = RDKFuncs.calcPEOE_VSA(m2);
assertEquals(v.get(0),5.106,0.001);
assertEquals(v.get(6),6.924,0.001);
assertEquals(v.get(7),6.607,0.001);
}
/*@Test*/ public void testMemory2() {
ChemicalReaction rxn;
rxn=RDKFuncs.ReactionFromSmarts("[OH][C:1]=[O:2].[N!H0:3]>>[N:3][C:1]=[O:2]");
assertTrue(rxn.getNumReactantTemplates()==2);
assertTrue(rxn.getNumProductTemplates()==1);
ROMol r1,r2;
r1=RDKFuncs.MolFromSmiles("CC(=O)O");
r2=RDKFuncs.MolFromSmiles("ClCN");
assertTrue(r1.getNumAtoms()==4);
assertTrue(r2.getNumAtoms()==3);
for(int i=0;i<1000000;i++){
ROMol_Vect rs= new ROMol_Vect(2);
rs.set(0,r1);
rs.set(1,r2);
ROMol_Vect_Vect ps;
ps=rxn.runReactants(rs);
if((i%1000)==0){
System.err.println("done: "+i);
}
ps.delete();
}
}
/*@Test*/ public void testMemory3() {
ROMol m1;
m1 = RDKFuncs.MolFromSmiles("C1=CC=CC=C1C2CCC(C(=O)OCCC)CC2");
for(int i=0;i<1000000;i++){
/*SparseIntVecti64 fp1;
fp1=RDKFuncs.getTopologicalTorsionFingerprint(m1);*/
SparseIntVectu32 fp1;
fp1=RDKFuncs.getMorganFingerprint(m1,2);
if((i%1000)==0){
System.err.println("done: "+i);
}
fp1.delete();
}
}
static {
try {
System.loadLibrary("RDKFuncs");
} catch (UnsatisfiedLinkError e) {
System.err.println("Native code library failed to load. Make sure that libRDKFuncs.so is somewhere in your LD_LIBRARY_PATH.\n" + e);
System.exit(1);
}
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("WrapperTests");
}
}
Reference in New Issue View Git Blame Copy Permalink