problems with generatemd ward and libmcs

User c5d952d4f4

11-12-2006 08:21:51

Dir support scientist,

I am trying to cluster a set of molecule based on CF fingerprints and I have run into several problems.

This is urgent to me and I will appreciate your help.

1. molecule names are not preserved in the generatemd output file. instead, I get serial numbers. Is it possible to keep molecule names as identifiers?

I am using the following command:

generatemd c file.sdf -k CF -D -g -v -o fingerprints.txt

2. when I try to run ward clustering, I am required to specify the -f and -m options. How do I know the values when running the above generatemd command?

3. I tried running libmcs with or w/o the -w option. In either case a GUI was started, some calculation was documented in the terminal but no results were shown in the GUI and no files were written. Is this GUI operational?

Thanks and best regards,

Ori Kalid

ChemAxon efa1591b5a

12-12-2006 10:16:42

Dear Ori Kalid,

1. The use of natural identifiers optionally present in the input SDFile is possible only if those IDs are integer numbers. Names, or other strings cannot be used yet. This feature has already been asked by other users so it will be implemented in a future vesion of JChem.

2. -m should be 0, as you do not use so called external data (only the fingerprint data). The value for -f is 1024 by default (the generatemd command line you quote uses the default settings).

3. The user documentation for LibMCS is outdated, I regret to admit this discrepancy. We will update it very soon and make it available on the LibMCS demo pages at

Briefly: command line options were supported by the old version and they have not been incorporated in the new one. This will be done later. The GUI, however, is fully functional, actually, this is what we are heavily developing right now (beside the clustering algorithms).

The results of clusteing can be saved in files from the GUI, check the File menu.

Hope this helps. It is worth visiting the above referred LibMCS demo page as it is updated more frequently than JChem is released. New features are easy to try, bug fixes are available.