CCL:W:Substructure matching

25-04-2005 06:00:56

A question on CCL:





Hi All,





I am searching for some software that will help me to identify the atoms within a molecule that match a query substructure. For example I wish to find which atoms belong to an imidazole ring. The aim is to extract the matching substructure while keeping the original atomic coordinates.





I know that several substructure matching routines exist, and some are even freely available but I haven't found any that return the identity of the matching atoms. Some return the whole molecule or a tally of how many times the substructure is present. They obviously "know" which atoms match but I am having difficulty identifying them. Similarly matching strings in SMILES doesn't return the initial atom ids.





I would be very grateful for any routines that do this, or that can be modified for this purpose,





Many Thanks,

ChemAxon a3d59b832c

25-04-2005 06:02:14

Hi,





You can do this easily in Java using the MolSearch class of the


JChem API. See documentation including example:





http://www.jchem.com/doc/api/chemaxon/sss/search/MolSearch.html





We also have a command-line program called jcsearch:





$ jcsearch --allHits -q 'c1cncn1' 'C1CCC(CC1)c2c[nH]cn2'


Query has 1 match:


Match 1:[ 7, 8, 9, 10, 11 ]


C1CCC(CC1)c2c[nH]cn2





$ jcsearch --allHits --orderSensitive -q 'c1cncn1' 'C1CCC(CC1)c2c[nH]cn2'


Query has 2 matches:


Match 1:[ 7, 8, 9, 10, 11 ]


Match 2:[ 8, 7, 11, 10, 9 ]


C1CCC(CC1)c2c[nH]cn2





http://www.jchem.com/doc/user/Jcsearch.html





JChem is free for academia, see:


http://www.chemaxon.hu/forum/ftopic193.html





All the best,


Szabolcs