/usr/share/RDKit/Contrib/fraggle/fraggle.py is in rdkit-data 201403-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | # Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
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# Created by Jameed Hussain, May 2013
from rdkit import Chem
from rdkit.Chem.Fraggle import FraggleSim
if __name__ =='__main__':
import sys,re
if (len(sys.argv) >= 2):
print "Program to run the first part of Fraggle. Program splits the molecule\nready for the search\n"
print "USAGE: ./fraggle.py <file_of_smiles"
print "Format of smiles file: SMILES ID (space or comma separated)"
print "Output: whole mol smiles,ID,fraggle split smiles\n"
sys.exit(1)
#read the STDIN
for line in sys.stdin:
line = line.rstrip()
smi,id_ = re.split('\s|,',line)
#print smi,id_
mol = Chem.MolFromSmiles(smi)
if mol is None:
sys.stderr.write("Can't generate mol for: %s\n" % (smi) )
continue
out_fragments = FraggleSim.generate_fraggle_fragmentation(mol)
#print out the unique fragments
for x in out_fragments:
#cansmi
temp = Chem.MolFromSmiles(x)
print "%s,%s,%s" % (smi,id_,Chem.MolToSmiles(temp))
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