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# $Id$
#
# Copyright (C) 2004, 2005 Rational Discovery LLC
# All Rights Reserved
#
import os
import sys
import tempfile
import Chem
from Chem import TemplateAlign
from Chem.Draw.MolDrawing import MolDrawing
from mod_python import apache
from sping.SVG.pidSVG import SVGCanvas as Canvas
from utils import cactvs
def gif(req, smiles, width=100, height=100, highlight='[]', frame=0, dblSize=0, **kwargs):
req.content_type = 'image/gif'
width = int(width)
height = int(height)
frame = int(frame)
dblSize = int(dblSize)
# FIX: unsafe:
highlight = eval(highlight)
imgD = ''
if smiles:
fName = tempfile.NamedTemporaryFile(suffix='.gif', delete=False).name
cactvs.SmilesToGif(smiles, fName, (width, height), dblSize=dblSize, frame=frame)
if os.path.exists(fName):
imgD = open(fName, 'rb').read()
try:
os.unlink(fName)
except OSError:
pass
return imgD
def svg(req, smiles, width=100, height=100, highlight='[]', frame=0, template='', numbers=0,
**kwargs):
req.content_type = 'image/svg+xml'
width = int(width)
height = int(height)
frame = int(frame)
# FIX: unsafe:
highlight = eval(highlight)
imgD = ''
mol = None
if smiles:
mol = Chem.MolFromSmiles(smiles)
if mol:
if kwargs.get('kekulize', True):
Chem.Kekulize(mol)
if template and highlight:
try:
patt = Chem.MolFromSmiles(template)
Chem.Compute2DCoords(patt)
TemplateAlign.AlignMolToTemplate2D(mol, patt, highlight)
except Exception:
Chem.Compute2DCoords(mol)
else:
Chem.Compute2DCoords(mol)
canvas = Canvas(size=(width, height))
drawer = MolDrawing(canvas=canvas)
if numbers and numbers != '0':
drawer.includeAtomNumbers = True
drawer.atomNumberOffset = 1
drawer.noCarbonSymbols = 1
drawer.AddMol(mol, highlightAtoms=highlight)
svg = canvas._txt + '</svg>'
else:
svg = ''
return svg
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