Greg Landrum schrieb:
> Dear Thomas,
>
> On Thu, Apr 29, 2010 at 4:05 PM, Thomas Heller wrote:
>>
>> I get errors when trying to depict this smiles string: OC(=O)[C@@H]1CCCN1
>>
>> It is from the wikipedia entry for Proline:
>> http://en.wikipedia.org/wiki/Proline
>>
>> As it turns out rdkit is passing 'nan' as coordinates to all the drawing
>> functions ;-(
>
> Can you please provide a bit of code that demonstrates the problem?
>
> The following works fine for me:
> [16]>>> from rdkit import Chem
> [17]>>> from rdkit.Chem import Draw
> [18]>>> m = Chem.MolFromSmiles('OC(=O)[C@@H]1CCCN1')
> [19]>>> Draw.MolToImageFile(m,'proline.png')
Greg, does 'proline.png' contain a valid image in your case?
Attached is a script that demonstrates the problem. It uses a custom Canvas
class that prints the calls to stdout - my real code uses a canvas
that directly draws into a windows device context.
Running the script with Python2.6 (on Windows) and RDKit_Q12010_1 I get this
output:
c:\code>\python26\python test.py
drawline (nan, nan, nan, nan) {'color': Color(1.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
stringBox ('HO', Font(10,0,0,0,'helvetica')) {}
drawRect (nan, nan, nan, nan) {'edgeColor': Color(-1.00,-1.00,-1.00),
'edgeWidth': 0, 'fillColor': Color(1.00,1.00,1.00)}
drawString HO (nan, nan) Font(10,0,0,0,'helvetica') Color(1.00,0.00,0.00)
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(1.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(1.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1}
stringBox ('O', Font(10,0,0,0,'helvetica')) {}
drawRect (nan, nan, nan, nan) {'edgeColor': Color(-1.00,-1.00,-1.00),
'edgeWidth': 0, 'fillColor': Color(1.00,1.00,1.00)}
drawString O (nan, nan) Font(10,0,0,0,'helvetica') Color(1.00,0.00,0.00)
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,1.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,0.00), 'width': 1,
'dash': None}
drawline (nan, nan, nan, nan) {'color': Color(0.00,0.00,1.00), 'width': 1,
'dash': None}
stringBox ('HN', Font(10,0,0,0,'helvetica')) {}
drawRect (nan, nan, nan, nan) {'edgeColor': Color(-1.00,-1.00,-1.00),
'edgeWidth': 0, 'fillColor': Color(1.00,1.00,1.00)}
drawString HN (nan, nan) Font(10,0,0,0,'helvetica') Color(0.00,0.00,1.00)
c:\code>
Other examples work fine:
c:\code>\python26\python test.py CN
drawline (77.5, 100.0, 100.0, 100.0) {'color': Color(0.00,0.00,0.00), 'width':
1, 'dash': None}
drawline (100.0, 100.0, 122.5, 100.0) {'color': Color(0.00,0.00,1.00), 'width':
1, 'dash': None}
stringBox ('NH2', Font(12,0,0,0,'helvetica')) {}
drawRect (120.5, 102.0, 124.5, 98.0) {'edgeColor': Color(-1.00,-1.00,-1.00),
'edgeWidth': 0, 'fillColor': Color(1.00,1.00,1.00)}
drawString NH2 (120.5, 102.0) Font(12,0,0,0,'helvetica') Color(0.00,0.00,1.00)
c:\code>
Here is the test script:
import sys
from rdkit.Chem import AllChem
def draw(canvas, mol, size=(300,300), kekulize=True, wedgeBonds=True,
highlightAtoms=["N"]):
if not mol:
raise ValueError,'Null molecule provided'
from rdkit.Chem.Draw import MolDrawing
drawer = MolDrawing.MolDrawing(canvas)
if kekulize:
from rdkit import Chem
mol = Chem.Mol(mol.ToBinary())
Chem.Kekulize(mol)
if not mol.GetNumConformers():
from rdkit.Chem import AllChem
AllChem.Compute2DCoords(mol)
drawer.wedgeDashedBonds=wedgeBonds
drawer.AddMol(mol,highlightAtoms=highlightAtoms)
class Canvas(object):
size = (200, 200)
def drawLine(self, *args, **kw):
print "drawline", args, kw
def stringBox(self, *args, **kw):
print "stringBox", args, kw
return (5, 5)
def drawRect(self, *args, **kw):
print "drawRect", args, kw
def drawString(self, text, x, y, font, color):
print "drawString", text, (x, y), font, color
if len(sys.argv) > 1:
smiles = sys.argv[1]
else:
smiles = "OC(=O)[C@@H]1CCCN1"
mol = AllChem.MolFromSmiles(smiles)
draw(Canvas(), mol, size=(200, 200))
--
Thanks,
Thomas
--
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