Error on MolSearch #2 - ChemAxon Forum Archive

User dfeb81947d

12-09-2005 14:04:29

Dear Support,

I'm using Jchem3.0.14 and I have almost the same error as describe here:

http://www.chemaxon.com/forum/ftopic745.html

This is my code to compare two Molecule object: mol1 and mol2

Code:

search = new MolSearch();

search.setSubgraphSearch(false);

search.setExactBondMatching(true);

search.setExactChargeMatching(true);

search.setExactIsotopeMatching(false);

search.setExactQueryAtomMatching(true);

search.setExactStereoMatching(true);

search.setExactRadicalMatching(true);

search.setQueryAbsoluteStereo(false);

search.setStereoSearch(true);

search.setHCountMatching(SearchConstants.HCOUNT_MATCHING_AUTO);

search.setQuery(mol1);

search.setTarget(mol2);

try {

return search.isMatching();

}

for some structure I've got the following exception:

Quote:

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.sss.search.StructureSearch.compareAtomQueryProperties(StructureSearch.java:2671)

at chemaxon.sss.search.StructureSearch.compareAtoms(StructureSearch.java:2852)

at chemaxon.sss.search.StructureSearch.initMaps(StructureSearch.java:2374)

at chemaxon.sss.search.StructureSearch.findFirst(StructureSearch.java:4166)

at chemaxon.sss.search.StructureSearch.isMatching(StructureSearch.java:4539)

at chemaxon.sss.search.MolSearch.isMatching(MolSearch.java:666)

Some molecule that are involved in that exception contains tritium atoms as:

Quote:

mol1

IS csfc04240521072D 0 0.00000 0.00000182482

17 17 0 0 0 0 0 0 0 0999 V2000

4.1742 0.5794 0.0000 T 2 0 0 0 0 0 0 0 0 0 0 0

4.7111 0.2694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.5772 0.7694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.4432 0.2694 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

5.5772 1.7694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.7111 2.2694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

6.4432 2.2694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

4.7111 -0.7306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.9021 -1.3184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.2111 -2.2694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

5.2111 -2.2694 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

5.5201 -1.3184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.4712 -1.0093 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

2.9511 -1.0093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.2601 -0.0583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

2.0000 -0.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

2.6420 -1.9604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

2 3 1 0 0 0 0

3 4 1 0 0 0 0

3 5 1 0 0 0 0

5 6 1 0 0 0 0

5 7 2 0 0 0 0

2 8 1 0 0 0 0

8 9 2 0 0 0 0

9 10 1 0 0 0 0

10 11 1 0 0 0 0

11 12 1 0 0 0 0

8 12 1 0 0 0 0

12 13 2 0 0 0 0

9 14 1 0 0 0 0

14 15 1 0 0 0 0

14 16 1 0 0 0 0

14 17 1 0 0 0 0

M ISO 1 1 3

M END

Are the molecules contains error according to JChem?

Best Regards

Jacques

ChemAxon a3d59b832c

13-09-2005 07:40:41

Dear Jacques,

The molecules seem OK, this is a bug in the searching. It will be fixed in version 3.1.2. Thank you for reporting this.

Best regards,

Szabolcs

User dfeb81947d

13-09-2005 12:38:09

Thanks, Szabolcs

ChemAxon a3d59b832c

05-11-2005 15:36:47

JChem 3.1.2 is out and this contains the above mentioned fix.

Best regards,

Szabolcs

User dfeb81947d

14-11-2005 11:01:17

Thank you very much.