[Open Babel] OB segfault
Hi all,
for this I'm using D-Alanine from PubChem:
https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=71080
inchi string is copy-pasted from the page, the SDF is from "download 2D
SDF" button.
Enjoy:
> $ python
> Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
import sys
sys.path.append( "/share/linux/openbabel-2.3.2/lib" )
import pybel
import openbabel
mol = pybel.readstring( "inchi",
"InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1" )
mol.removeh()
svg = mol.write( format = "svg", opt = { "b" : "none" } )
> Segmentation fault (core dumped)
> $ python
> Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
import sys
sys.path.append( "/share/linux/openbabel-2.3.2/lib" )
import pybel
import openbabel
mol = pybel.readfile( "sdf",
"/share/dmaziuk/projects/metabolomics/71080.sdf" ).next()
mol.removeh()
svg = mol.write( format = "svg", opt = { "b" : "none" } )
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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[Open Babel] SVG draws unwanted extra hydrogens
Hi there,
I'm using the Python interface to OpenBabel to create 2D representations of my
molecules. I'm having a great time except when it decides to draw extra
hydrogens. I'm quite sure these hydrogens are not supposed to be drawn. In
the attached image, the "CH" on carbon monoxide is not numbered; I think this
means it's not explicitly represented in the OBMol object, but the SVG writer
decides to draw it anyway. In the SVG file, the text comes out as "CH" in a
single element.
I've tried almost all combinations of add/delete, implicit/explicit hydrogens
in the input and output options. If I set {"C":True} in write(), it won't draw
the "CH" on carbon monoxide - in fact it doesn't draw any atoms to the right of
the triple bond, but I do want it to draw "C". I could just edit the .svg file
manually, but that's probably not the best solution.
Generally speaking, all I want is for OpenBabel to draw exactly the same atoms
that I gave it! :)
In [1]: import pybel
In [2]: mol = pybel.readfile('can', 'can.txt', opt={"h":True})
In [3]: mol.next().write("svg", "can.svg", opt={"a":True,"P":600,"i":True},
overwrite=True)
Thanks,
- Lee-Ping
[OH][CH]=O.C#[O].[CH2]=O.[NH2][NH2]
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Re: [Open Babel] SVG draws unwanted extra hydrogens
Sorry for the extra email; I'm attaching the original .xyz file that I am
trying to represent in the 2D image.
- Original Message -
From: "Lee-Ping Wang"
To: openbabel-discuss@lists.sourceforge.net
Sent: Thursday, September 25, 2014 8:34:41 PM
Subject: SVG draws unwanted extra hydrogens
Hi there,
I'm using the Python interface to OpenBabel to create 2D representations of my
molecules. I'm having a great time except when it decides to draw extra
hydrogens. I'm quite sure these hydrogens are not supposed to be drawn. In
the attached image, the "CH" on carbon monoxide is not numbered; I think this
means it's not explicitly represented in the OBMol object, but the SVG writer
decides to draw it anyway. In the SVG file, the text comes out as "CH" in a
single element.
I've tried almost all combinations of add/delete, implicit/explicit hydrogens
in the input and output options. If I set {"C":True} in write(), it won't draw
the "CH" on carbon monoxide - in fact it doesn't draw any atoms to the right of
the triple bond, but I do want it to draw "C". I could just edit the .svg file
manually, but that's probably not the best solution.
Generally speaking, all I want is for OpenBabel to draw exactly the same atoms
that I gave it! :)
In [1]: import pybel
In [2]: mol = pybel.readfile('can', 'can.txt', opt={"h":True})
In [3]: mol.next().write("svg", "can.svg", opt={"a":True,"P":600,"i":True},
overwrite=True)
Thanks,
- Lee-Ping
coords.xyz
Description: Xmol XYZ data
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