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Make it compatible with the new UniversalIsomorphismTester.

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commit 7439b08f6d1ec4940c7c1ba7185ba7498c8939f7 1 parent 0a70c86
Yap Chun Wei yapchunwei authored egonw committed
11 src/main/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
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@@ -862,6 +862,7 @@ else if (getAtomTypeXCount(ac, atomi) == 2) {
}
}
+ UniversalIsomorphismTester universalIsomorphismTester = new UniversalIsomorphismTester();
if (checkAminoAcid>1){
// alpha amino acid
QueryAtomContainer aminoAcid =
@@ -885,8 +886,8 @@ else if (getAtomTypeXCount(ac, atomi) == 2) {
//AtomContainer aminoacid = sp.parseSmiles("NCC(=O)O");
try {
- if (UniversalIsomorphismTester.isSubgraph(ac, aminoAcid)) {
- List list = UniversalIsomorphismTester.getSubgraphAtomsMap(ac, aminoAcid);
+ if (universalIsomorphismTester.isSubgraph(ac, aminoAcid)) {
+ List list = universalIsomorphismTester.getSubgraphAtomsMap(ac, aminoAcid);
RMap map = null;
IAtom atom1=null;
for (int j = 0; j < list.size(); j++){
@@ -910,7 +911,7 @@ else if (getAtomTypeXCount(ac, atomi) == 2) {
IAtomContainer paba = createPaba(ac.getBuilder());
// p-amino sulphonic acid
try {
- if (UniversalIsomorphismTester.isSubgraph(ac, paba)) {
+ if (universalIsomorphismTester.isSubgraph(ac, paba)) {
xlogP -= 0.501;
//logger.debug("XLOGP: p-amino sulphonic acid -0.501");
}
@@ -922,7 +923,7 @@ else if (getAtomTypeXCount(ac, atomi) == 2) {
if (salicylFlag){
IAtomContainer salicilic = createSalicylicAcid(ac.getBuilder());
try {
- if (UniversalIsomorphismTester.isSubgraph(ac, salicilic)) {
+ if (universalIsomorphismTester.isSubgraph(ac, salicilic)) {
xlogP += 0.554;
//logger.debug("XLOGP: salicylic acid 0.554");
}
@@ -948,7 +949,7 @@ else if (getAtomTypeXCount(ac, atomi) == 2) {
orthopair.addBond(new OrderQueryBond(atom2,atom4,IBond.Order.SINGLE));
try {
- if (UniversalIsomorphismTester.isSubgraph(ac, orthopair)) {
+ if (universalIsomorphismTester.isSubgraph(ac, orthopair)) {
xlogP -= 0.268;
//logger.debug("XLOGP: Ortho oxygen pair -0.268");
}
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