I'm trying to convert chemical structures to ECFP data.
Buy, I have a problem about folding step.
I understand all of the process about generating ECFP data though D. Rogers and M. Hahn's paper (J. Chem. Inf. Model., Vol. 50, No. 5, 2010)
I used a pinky module in python for computing the ECFP of each molecules.
(https://github.com/ubccr/pinky/blob/master/pinky/fingerprints/ecfp.py)
the output of this function is as follow
{6456320269923861509: 1,
-3040533427843102467: 2,
-7329542376511023568: 1,
-5821485132112031149: 1,
-643847807504931861: 1,
3054809300354049582: 1,
-3679727481768249355: 1,
-2240115528993944325: 1,
5159885938473603439: 1,
1268207003089618622: 1,
267156486644197995: 1,
6401915128722912935: 1,
-8944122298402911035: 1,
-7116035920000285502: 1}
I know what it is and what it means.
but i don't know how to convert this data to binary data form.
In this website(https://docs.chemaxon.com/display/docs/extended-connectivity-fingerprint-ecfp.md), above identifiers are converted to a fixed-length bit string (folding process)
How to convert above atomic identifiers to the fixed-length bit string?
Hi, Hyunwoo Yook .
According to the documentation of Chemaxon (https://docs.chemaxon.com/display/docs/chemical-hashed-fingerprint.md), the hashing function (the process of the conversion of atomic identifiers to the fixed-length bit string) is a proprietary module.
" Using a proprietary hashing method, a given number of bits in the bit string are set for each pattern. "
Thus, you cannot reveal this algorithm using free sources. However, you are free to use other common techniques in order to perform the "folding" operation. For instance, you can use a well-known CRC-32 algorithm (i.e., you can use a python zlib module). As you can read here: https://depth-first.com/articles/2019/01/11/extended-connectivity-fingerprints/ ("Hash function" section), you are allowed to choose any hashing function. However, it is advisable to find a balance between data size and data loss after the hashing.
visit the following link below:
Article A probabilistic molecular fingerprint for big data settings
Article Hashing Algorithms and Data Structures for Rapid Searches of...
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