several maximal common substructures

User 604930abc9

13-10-2005 16:41:11


I try to use mcs.bat module from trial JCHEM and found that in cases when two compared molecules have several maximal substructures only one is shown. Is it a feature or bug?

Also, how you decide this problem of possible multiple maximal common substructures in LibMCS clusterisation? Get to work the first founded one?

Example of two molecules that have 18 equivalent multiple maximal common substructures is enclosed.

ChemAxon efa1591b5a

14-10-2005 14:52:58


both, feature and bug! ;-)

The MCS application does not support multiple mcs hits, so this is a feature.

I'll remove this feature :) and will add another one that allows user to retrieve multiple MCS hits.

The API provides two methods, findFirst() and findNext() for programmatic access to multiple mcs result. However, findNext() fails in case of your input molecules. I will fix this bug. It'll be available in the next JChem release.

Many thanks for the bug& missing feature report!



User 604930abc9

20-02-2006 17:29:28

Hi Miklos,

I tried to use MCS API and found that findNext() does not work on above-mentioned example:


if (maxcss.findFirst()) {

int[] hit = maxcss.getResult();

boolean zzz = maxcss.findNext();

System.out.println(zzz); //output - false


check please, you wanted to fix it last time :)

ChemAxon efa1591b5a

20-02-2006 17:37:49

Hi Vladimir,

indeed... I am currently working on a new implementation of MCS/MCES. I will announce here when the new algorithm is available.

Thanks for your patience.