LibraryMCS -m (resolved)

LibraryMCS - Maximum Common Structure Search for a Set of Structures 3.0.11, (C) 2004-2005 ChemAxon Ltd.





The command line option:


-m, --minMCS <size> minimum required size of any MCS found





Doesn't appear to be working. I'm trying to force the minimum required size of any MCS found to a more meaningful fragment size. It always seems to give very simple fragments (i.e. a chain of 5 atoms) at the top level even if I specify a "-m 10" option. I've tried tweaking other options from their defaults as they are probably dependent.





Wait! In the middle of my post, I found the important dependent option: - c. I had to increase the maximum number of clusters on top level to accommodate the flatter cluster that results with larger fragment sizes.





Thanks,





- Mark

Dear Mark,





apparently there was a silly bug in the MCS implementation that caused the -m be ignored (min MCS size was reset to default before the search began). It is fixed now and -m works fine.


It will be available in the next JChem minor release within few weeks. Send me an email in case you need it sooner.





Thanks for the bug report.





Regards,


Miklos

What is the file format to input SMILES into LibMcs?

One SMILES string per each line. That simple.


Good luck and get back to the forum for further assistance.





Regards,


Miklos