WARD kelley method problem

User 7d9f893e3a

23-11-2007 10:06:52


i need to calculate with the KELLY method the cluster number with ward.

i had generated the PF fingerprint with the command

generatemd c files.sdf -k PF -c pharma-frag.xml -D -o fingerprint.txt -v

when ward runs with the command

ward -f 1024 -g -K KELLY.txt < fingerprint.txt> neighborLs.txt

the output is

Error: For input string: "0.00"

i don't know how solve the problem.

Best Regards


ChemAxon efa1591b5a

23-11-2007 11:41:07

The rub is with -f 1024 in

ward -f 1024 -g -K KELLY.txt < fingerprint.txt> neighborLs.txt

which attempts to read binary fingerprint (CF) form the input file. -f 1024 tells to read 1024 bits. In your file you use pharmacophore fingerprint which is represented by 210 decimal numbers (in case if you use the default settings...), not 1024 bits.

Therefore ward should be invoked like that:

ward -f 0 -m 210 ....
and the rest remains the same.

This tells that there are 0 bits but 210 decimal numbers (i.e. the dimensionality of the chemical space is 210).

Hope this helps, regards,


User 7d9f893e3a

23-11-2007 13:17:14

Thank you very much

you have solve my problem.

Best Regards