binary pharmacophore fingerprints

Dear all,

I thing that I have been searched everywhere any answer about me problem in this forum. One upon a time someone have asked about it but the problem did not solved, so I have to ask one more again. It is possible to generate binary form of pharmacophore fingerprints?? If yes, what is the simples way to do that.

I will be appreciate for any information on that.

 

Best regards for all

 

Rafal

Hi Rafal,

I'm afraid that's not directly possible. Since PF is not a binary fingerprint, this options is not supported.

Do you use the batch command generatemd, or you access fingerprint generation via the API from your java code? In either case you need some extra work to get the required binary output.

Regards,

Miklos

Hello,

Thank you very much Miklos for your reply. Actually I used command line version of generatemd to obtain this kind of fingerprints. I have planed to write some extra codes to covert pharmacophore fingerprints to fixed-positioned bit strings. But firstly I wanted to know that someone did it before me. 

So my idea was to fix positions for all individual pharmacophore faetures. Distances for given faeture will be normalized.

 

Do you thing that this is make any sence ??

Or maybe there is another, simplier way to convert it ??

 

Best regards

 

Rafal

Hi Rafal,

O.k. so you are ready to do some coding, great. Just to satisfy my curiosity, what purpose do you need the binary representation for?

I'm not sure I understand the concept of normalised distances, I can imagine normalisation with respect to absolute frequencies. I mean, over represented properties, like hydrophobic and aromatic generate high peaks in the histogram, suppressing specific features like hydrogen bond donors and acceptors.

Regards,

Miklos

 

This question is still on fly and unsolved .... I am in the same truck and wondering how can I generate a binary code ?

Hi,

If you are happy to do some programming to process the output of generatemd, then the best is to use -D option in the commandline, this generates a decimal output. Please note, that these decimal values are fixed point real numbers with 2 decimal digits. If your fingerprint is not a fuzzy fingerprint, then decimal digits are all 0 (but they are still printed invariably).

I'm sure you can find some code examples on the internet which reads in an integer number as decimal string (you'll need to read floating point that you can truncate to integer...) and then print it as a decimal string. Is this what you need?

 

Miklos