Hi,
Today I checked out the lastest version from the svn. I took only the
trunk and built this and ran a python script I used with a previous
version to depict a molecule. However, I received the following error:
AttributeError: type object 'MolDrawing' has no attribute 'registerCanvas'
I did the following in the python script much like the people at cinfony
do to depict with aggdraw:
import os, sys, copy
from rdkit.Chem import rdDepictor
from rdkit import Geometry
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Draw import MolDrawing
from rdkit.Chem.AvailDescriptors import descDict
import rdkit.DataStructs
import rdkit.Chem.MACCSkeys
import rdkit.Chem.AtomPairs.Pairs
import rdkit.Chem.AtomPairs.Torsions
# PIL and Tkinter
try:
import Tkinter as tk
import Image as PIL
import ImageTk as PILtk
except:
PILtk = None
# Aggdraw
try:
import aggdraw
except ImportError:
aggdraw = None
def draw(Mol, show=True, filename=None, update=False, usecoords=False,
width=300, height=300, background='white', atoms='color'):
"""Create a 2D depiction of the molecule. This method was taken
from cinfony.
Optional parameters:
show -- display on screen (default is True)
filename -- write to file (default is None)
update -- update the coordinates of the atoms to those
determined by the structure diagram generator
(default is False)
usecoords -- don't calculate 2D coordinates, just use
the current coordinates (default is False)
Aggdraw is used for 2D depiction. Tkinter and
Python Imaging Library are required for image display.
Python code found at: /usr/local/RDKit_2010_12_1/rdkit
"""
if usecoords:
confId = 0
else:
if update:
AllChem.Compute2DCoords(Mol)
confId = 0
else:
confId = Mol.GetNumConformers()
AllChem.Compute2DCoords(Mol, clearConfs = False)
if show or filename:
if not aggdraw:
errormessage = ("Aggdraw not found, but is required for 2D"
"structure depiction. "
"See installation instructions for more "
"information.")
raise ImportError, errormessage
Chem.Kekulize(Mol)
MolDrawing.registerCanvas('agg')
import pdb;pdb.set_trace()
img = PIL.new("RGBA",(width,height),background)
canvas = aggdraw.Draw(img)
canvas.setantialias(True)
drawer = MolDrawing.MolDrawing(canvas)
MolDrawing.elemDict
if atoms == 'color' and background == 'white' :
print 'Color on white'
MolDrawing.elemDict[6] = (0,0,0)
elif atoms == 'color' and background == 'black':
print 'Color on black'
MolDrawing.elemDict[6] = (1,1,1)
elif atoms == 'white' and background == 'black':
print 'White on black'
MolDrawing.elemDict = {
16: (0,0,0),
17: (0,0,0),
35: (0,0,0),
6: (1,1,1),
0: (0,0,0),
7: (0,0,0),
8: (0,0,0),
9: (0,0,0),
15: (0,0,0)
}
elif atoms == 'black' and background == 'white':
print 'Black on white'
MolDrawing.elemDict = {
16: (0,0,0),
17: (0,0,0),
35: (0,0,0),
6: (0,0,0),
0: (0,0,0),
7: (0,0,0),
8: (0,0,0),
9: (0,0,0),
15: (0,0,0)
}
drawer.wedgeDashedBonds = True
drawer.bondLineWidth = 2.5
drawer.AddMol(Mol, confId = confId)
canvas.flush()
if filename: # Note: overwrite is allowed
img.save(filename)
if show:
if not tk:
errormessage = ("Tkinter or Python Imaging "
"Library not found, but is required for
image "
"display. See installation instructions
for "
"more information.")
raise ImportError, errormessage
root = tk.Tk()
root.title((hasattr(Mol, "title") and Mol.title)
or Mol.__str__().rstrip())
frame = tk.Frame(root, colormap="new",
visual='truecolor').pack()
imagedata = PILtk.PhotoImage(img)
label = tk.Label(frame, image=imagedata).pack()
quitbutton = tk.Button(root, text="Close",
command=root.destroy).pack(fill=tk.X)
root.mainloop()
Chem.SanitizeMol(Mol)
Sorry for all the code, but I think much of it is relevant so I pasted
it here.
Is the registerCanvas method removed from newer version? If so how can
I modify my Draw function so that it will work with the newest version
from svn?
Thank you for any help.
Don
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