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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