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"""Render a molecule in SMILES format using GraphViz.
based on a work by Brian Kelley. New BSD license
requires frowns: http://frowns.sf.net/
"""
import os, re
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
class Error(Exception): pass
def generate_dot(mol_list):
"""(mol) Assign x,y coordinates to the atoms of a molecule
using AT&T's graph layout algorithm. This technique is
very fast but doesn't look very good so use with
caution."""
ofile = StringIO()
print >> ofile, "graph TEST {"
d = {}
for mol in mol_list:
atoms = mol.atoms
bonds = mol.bonds
for atom in mol.atoms:
d["atom%d"%atom.handle] = atom
print >> ofile, '\tatom%s [\n\t label="%s"\n\t\n\t shape=none];' % (atom.handle, atom.symbol)
for bond in mol.bonds:
atom1, atom2 = bond.atoms
print >> ofile, "\tatom%s -- atom%s;"%(atom1.handle, atom2.handle)
print >> ofile, "}"
return ofile.getvalue()
if __name__ == '__main__':
from frowns import Smiles
# read in a molecule
smiles = ["c1ccccc1C=O",
"c1ccc2cc1cccc2",
"CCN",
"CCCC(=O)NNCC",
"CCC(CC)([CH](OC(N)=O)C1=CC=CC=C1)C2=CC=CC=C2",
"ON=C(CC1=CC=CC=C1)[CH](C#N)C2=CC=CC=C2",
"C1=CC=C(C=C1)C(N=C(C2=CC=CC=C2)C3=CC=CC=C3)C4=CC=CC=C4",
]
mol_list = []
for smile in smiles:
mol = Smiles.smilin(smile)
mol.name = smile
mol_list.append(mol)
f = open('frowns.dot', 'w')
f.write(generate_dot(mol_list))
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