Pharmacophore fingerprint

Hello, I need to obtain a binary pharmacophore fingerprint but when I precise the option -2 in generatemd, I obtain an empty file...


How can I obtain this binary pharmacophore fingerprint?


Thank You!!!

Theres an additional problem with generatemd, because scalar descriptors


like logP, logD and topological polar surface area (TPSA) can be listed,


but logP and logD are not calculated. Also binary descriptors for BCUT and


PF just generating empty lines (with -2 option)








Z:\>generatemd -k -L





GenerateMD - Molecular Descriptor Generator 3.2, (C) 2002-2006 ChemAxon Ltd.


Built in descriptor types:


Chemical Fingerprint (CF)


Pharmacophore Fingerprint (PF)


BCUT descriptors (BCUT)


Hydrogen bond Donor/Acceptor count (HDon/HAcc)


octanol-water distribution coefficient (LogD)


octanol-water partition coefficient (LogP)


Topological Polar Surface Area (TPSA)


Mass of molcule (Mass)


number of Heavy atoms (Heavy)





Tobias

Guys, you are right, the binary option does not work with those descriptors that are not binary.


So we cn say that it's a feature :-), however, printing the empty lines is inconsistent, so that's a bug.


If you need binary output for those descriptors that are not binary, please let us know and we will implement it. However, we this should be limited to decimal descriptors as binary representation of floating point descriptors is meaningless, I reckon.





LogD and LogP work for me quite nicely. Mind the capital L...





Regards,


Miklos

Ok, It will be a good thing for me to obtain this binary pharmacophore fingerprints and also for the other descriptors when it is possible.


Thank You very much


PS:When will we obtain it?

Hi Miklos,

mvargyas wrote:

Guys, you are right, the binary option does not work with those descriptors that are not binary. So we cn say that it's a feature :-), however, printing the empty lines is inconsistent, so that's a bug. If you need binary output for those descriptors that are not binary, please let us know and we will implement it. However, we this should be limited to decimal descriptors as binary representation of floating point descriptors is meaningless, I reckon. Regards, Miklos

GenerateMD says BCUT descriptor(s) and the Handbook of molecular Descriptors and VCCLAB list 64 of them, like *highest eigenvalue n. 5 of Burden matrix / weighted by atomic masses


*lowest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities so how can I generate the others?





Tobias

Hi Tobias,





there is a bug in the BCUT generator, see this post http://www.chemaxon.com/forum/viewpost9155.html#9155





The example config files (bcut-charge.xml, bcut-hbond.xml, bcut-polarizability.xml, bcut.xml)


in examples/config (under your JChem installation directory) can also be useful in finding out how to obtain all types of BCUT descriptors.





HTH


Miklos