On 09/02/2017 11:05 PM, Konrad Koehler wrote:
> Hi everyone,
>
> As a followup to my previous post, in reading the Stiefl paper (Chem.
> Inf. Model. 2006, 46, 208-220) closer, I see my question about
> converting ErG numpy array into a bit vector was a little naive. It
> turns out that ErG array contains floating point numbers, not integers.
> One could bin these numbers and then convert into a count vector, but
> this seems like a lot of work.
There are better things than histograms out there, this one for example:
@article{Wand1994,
title = {Fast {Computation} of {Multivariate} {Kernel} {Estimators}},
volume = {3},
issn = {1061-8600},
url =
{http://amstat.tandfonline.com/doi/abs/10.1080/10618600.1994.10474656},
doi = {10.1080/10618600.1994.10474656},
number = {4},
journal = {Journal of Computational and Graphical Statistics},
author = {Wand, M. P.},
month = dec,
year = {1994},
pages = {433--445}
"Linear binning" they call it.
> If anyone is interested, I was able create and store ErG fingerprints of
> a large database (one million compounds), and then do a ErG fingerprint
> similarity search in several minutes without using PostgreSQL (see
> example scripts below). Binary fingerprint searches are much faster,
> but the method below is fast enough for my purposes.
>
> Cheers,
>
> Konrad
>
> Using the following post as a guide:
>
> https://iwatobipen.wordpress.com/2016/01/16/ergfingerprint-in-rdkit/
>
> The first script below will create ErG Fingerprints for a smiles file
> and the second script will sort the smiles file based on the ErG
> Taniomoto coefficient to a query molecule.
>
> ===== CreateErGFingerprints.py =====
>
> import gzip, cPickle
> from rdkit import Chem
> from rdkit.Chem import AllChem, rdReducedGraphs
>
> mols =
> Chem.SmilesMolSupplier("MolSupplier.smi",titleLine=False,smilesColumn =
> 0,nameColumn = 1,delimiter = " \t")
> ergfps = [rdReducedGraphs.GetErGFingerprint(mol) for mol in mols]
> fp=gzip.open('MolSupplier_ergfps.pkl.gz','wb')
> cPickle.dump(ergfps,fp)
> fp.close()
>
> ===== ErGFingerprintSimilaritySearch.py =====
>
> import gzip, cPickle
> from rdkit import Chem
> from rdkit.Chem import AllChem, rdReducedGraphs
> import numpy as np
> import os, re, sys
> import fileinput
>
> # ErG FP is not bit vect.
> def calc_ergtc( fp1, fp2 ):
> denominator = np.sum( np.dot(fp1,fp1) ) + np.sum( np.dot(fp2,fp2) )
> - np.sum( np.dot(fp1,fp2 ))
> numerator = np.sum( np.dot(fp1,fp2) )
> return numerator / denominator
>
> for line in fileinput.input():
> (query_smiles, query_name) = line.strip().split("\t")
>
> query_mol = Chem.MolFromSmiles(query_smiles)
> query_ergfp = rdReducedGraphs.GetErGFingerprint(query_mol)
>
> fp_file = "MolSupplier_ergfps.pkl.gz"
>
> mols =
> Chem.SmilesMolSupplier("MolSupplier.smi",titleLine=False,smilesColumn =
> 0,nameColumn = 1,delimiter = " \t")
>
> fp=gzip.open(fp_file,'rb')
> ergfps=cPickle.load(fp)
> fp.close()
>
> results = []
> f = open("MolSupplier.smi",'r')
> for index, line in enumerate(f.readlines()):
> (smiles, name) = line.strip().split("\t")
> ergtc = calc_ergtc(query_ergfp, ergfps[index])
> results.append([smiles, name, ergtc])
> sorted_results = sorted(results, key = lambda x: x[2], reverse=True)
>
> print '%s\t%s\t%.4f' % (query_smiles, query_name, 1.0)
> for result in sorted_results:
> (smiles, name, ergtc) = result
> print '%s\t%s\t%.4f' % (smiles, name, ergtc)
>
>> On 1 Sep 2017, at 09:36, Konrad Koehler <konrad.koeh...@icloud.com
>> <mailto:konrad.koeh...@icloud.com>> wrote:
>>
>> Hi,
>>
>> I am trying to add ErG fingerprints to PostgreSQL using the following
>> post as a guide:
>>
>> https://github.com/greglandrum/rdkit_blog/blob/master/notebooks/Custom%20fingerprint%20in%20PostgreSQL.ipynb
>>
>> My installation is as follows:
>>
>> Debian 3.16.43-2
>> rdkit 2016.03.4 np111py27_1 rdkit
>> rdkit-postgresql 2016.03.4 py27_1 rdkit
>>
>> In the example linked above, I had to replace the following line with
>> the next line (presumably because I am running python 2.7 instead of 3.x):
>> m = Chem.Mol(pkl.tobytes())
>> m = Chem.Mol(str(pkl))
>>
>> I then run into the following two problems:
>>
>> *
>> *
>> *First problem*: Null characters. When I run the example script
>> (using the Sheridan bit vector fingerprints), I generate the following
>> error message:
>>
>> /curs.executemany('insert into fps values
>> (%s,bfp_from_binary_text(%s))',[(x,DataStructs.BitVectToBinaryText(y))
>> for x,y in fps])/
>> /ValueError: A string literal cannot contain NUL (0x00) characters./
>>
>> I am not sure what I should do here. I could strip the null characters
>> from the binary text, but are the null characters supposed to be
>> there? Should I use the bytea data type on PostgreSQL side?
>>
>> *
>> *
>> *Second problem*: convert numpy array into bit vector
>>
>> The linked example creates a fingerprint as a bit vector:
>> fp =
>> Sheridan.GetBTFingerprint(m,fpfn=rdMolDescriptors.GetHashedTopologicalTorsionFingerprintAsBitVect)
>>
>> whereas rdReducedGraphs.GetErGFingerprint method produces a numpy array:
>> fp = rdReducedGraphs.GetErGFingerprint(m)
>>
>> Is there anyway of converting this numpy array into a bit vector?
>>
>>
>> Any suggestions would be greatly appreciated. Thanks,
>>
>> Konrad
>>
>
>
>
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