CCL:W:Substructure matching

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,

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