bracketed expansion of chemical abbreviations

[Gabe]

Hi everyone,

I'm new to Indigo (and chemi-informatics in general) so forgive me if
this is a simple question. I'm using indigo-depict to convert SDF and
MOL files to images (PNGs). When the MOL files contain chemical
abbreviations like "NO2" or "CH2CH3", indigo-depict correctly expands
them to show the entire structure, however it also puts brackets
around the expanded group, and shows the abbreviation that was
expanded next to it. Here's an example:

http://i.imgur.com/QI9fL.jpg

is it possible to control this behavior? It would be nice, for
example, to be able to turn-off the brackets with a command-line
switch.

Thanks very much for your help,

Gabe

[Mikhail Kozhevnikov]

Hello Gabe,

These structures are represented by S-groups in MOL/SDF files -- in this case, so-called Superatom S-groups. Indigo-depict generally renders whatever it is given, but one can get rid of the S-groups using the Indigo API prior to rendering. That should only take several lines of code in C, Java or Python. Would that work for you?

Cheers, 

Mikhail

[Gabe]

Thanks very much Mikhail,

Since your reply, I've gotten a little python script up-and-running that does the rending for me, instead of using indigo-depict.  However, I'm not sure how to change the S-group behavior... could you give me a little more info?  The only rendering option I can find that mentions superatoms is render-superatom-mode, but when I try to change this to 'collapse' it crashes with this error:

indigo.IndigoException: 'red-black tree: insert(): key already present'

which I'm afraid I don't understand.  I apologize if this is a trivial problem -- I don't know much python (and zero C++/java)... thanks very much in advance for your patience and for any tips you can give me.

Best,

Gabe

PS - here's my little script:

#!/usr/bin/python

import sys

import indigo_renderer

from indigo import *

indigo = Indigo()

renderer = indigo_renderer.IndigoRenderer(indigo)

mol1 = indigo.loadMoleculeFromFile(sys.argv[1])

print "\tmol weight: " + str(mol1.molecularWeight())

print "\trendering PNG..."

indigo.setOption("render-output-format","png")

#indigo.setOption("render-superatom-mode", "collapse")  #<-- causes crash 

indigo.setOption("render-margins",50,50)

mol1.layout()

renderer.renderToFile(mol1, sys.argv[1] + ".png")

On Monday, April 16, 2012 3:44:53 AM UTC-5, Mikhail Kozhevnikov wrote:

Hello Gabe,

These structures are represented by S-groups in MOL/SDF files -- in this case, so-called Superatom S-groups. Indigo-depict generally renders whatever it is given, but one can get rid of the S-groups using the Indigo API prior to rendering. That should only take several lines of code in C, Java or Python. Would that work for you?

Cheers, 

Mikhail

[Mikhail Kozhevnikov]

Try running this before rendering: 

for g in [g for g in mol1.iterateSuperatoms()]:

g.remove()

And thanks for reporting the crash! It looks like a bug, we'll fix it shortly.

Cheers,

Mikhail