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#!/usr/bin/env python |
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import sys |
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import os |
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import glob |
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import pybel |
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# don't need to reimport openbabel |
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ob = pybel.ob |
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# count the matches for each pattern and the total # of mol matching pattterns |
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patterns = [ "[a][a]!@;-[CX3](=[CX3])!@-[a][a]", |
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"[a][a]!@;-[NX3H1]!@;-[CX3](=S)[!#1]", |
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"[a][c]!@;-[CX4H0]([CX3,N])!@;-[c][a]", |
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"[a][c]!@;-[CX4H1]([N,O,H])!@;-[c][a]", |
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"[a][c]!@;-[CH2]!@;-[n][a]", |
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"[a][c]!@;-[CX4H2]!@;-[OX2][C]", |
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"[a][c]!@;-[CX4H1]!@;-[OX2][!#1]", |
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"[c][c]!@;-[CX4]!@;-[c][c]", |
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"[cH0][c]!@;-[CX4H2]!@;-[a][a]", |
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"[cH0][c]([cH0])!@;-[NX3]!@;-[a][a]", |
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"[cH1][c]([cH1])!@;-[NX3]([CX4])!@;-[a][a]", |
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"[!#1][c]!@;-[SX2]!@;-[c][aH1,aH0]", |
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"[!#1][NX3H0]!@;-[C](=O)!@;-[O][CH0]", |
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"[CX3,CX4][CX4H2]!@;-[C](=O)!@;-[O]~[C]", |
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"[N,O,NH1,OH1][CX4]!@;-[C](=O)!@;-[O]~[C]", |
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"[C,c][NH]!@;-[C](=S)!@;-[NH][C,c]", |
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"[aH1][c]([aH1])!@;-[$(S(=O)=O)]!@;-[NX3H0][*]", |
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"[O]=[C]!@;-[O]!@;-[CX4H0][!#1]", |
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"[O]=[C]!@;-[NX3H0](A)!@;-[a][cH0]" ] |
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smarts = [] |
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for pattern in patterns: |
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smart = pybel.Smarts(pattern) |
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smarts.append(smart) |
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molecules = 0 |
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matches = [0]*len(smarts) |
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mol_matching = 0 |
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# repeat through all the files on the command-line |
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# we can change this to use the glob module as well |
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# e.g., find all the files in a set of folders |
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print('filename', 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19, 'didmatch', sep=',' ) |
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for argument in sorted(glob.iglob("*.sdf")): |
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filename, extension = os.path.splitext(argument) |
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# read all the molecules from the supplied file |
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# (i.e. might be more than one molecule in a file) |
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for mol in pybel.readfile(extension[1:], argument): |
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molecules += 1 |
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this_one_matched = False |
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this_match = [0]*len(smarts) |
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for i in range(len(smarts)): |
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count = smarts[i].findall(mol) |
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if len(count) > 0: |
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this_one_matched = True |
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this_match[i] = len(count) |
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# total matches across the data set |
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matches[i] += len(count) |
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if this_one_matched: |
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mol_matching += 1 |
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# print the dihedral angle |
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print(mol.title, *this_match, this_one_matched, sep=',') |
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print('total', *matches, mol_matching, molecules, sep=',') |
