records, but that's not what
I want.
Yours sincerely,
Thomas Womack (Global Phasing)
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Plus, you'll get a cha
I'm using babel as part of a process for producing dictionaries for
crystallographic refinement software. The formats for such dictionaries refer
to atoms by their names, and so it's very slightly annoying that the output
from babel hydrogenation calls all the added hydrogens 'H'.
Is there a w
On 23 Jan 2012, at 12:29, Douglas Houston wrote:
> Hi all,
>
> I wonder if anyone can help me work out what's going on here. I'm trying to
> convert a PDB file of ADP (from structure 3ATV) to mol2 format and add
> hydrogens. The first step seems to work fine:
>
> babel -ipdb 3ATV_ADP.pdb -omol
The two attached PDB files differ in that one has a hydrogen on N17 and the
other doesn't.
But, with openbabel-2.3.1, I get the same InChI key
twomack@fs1:~/projects/grade-inchi-2% obabel 4PC.grade_PDB_ligand.pdb -oinchi
-xK
GPLPRFCWPJTQND-IVZWLZJFSA-
If I have a file glycerol.smi containing
HOCC(OH)COH
and issue
% obabel glycerol.smi -osmiles -xK
0 molecules converted
% obabel -V
Open Babel 2.3.1 -- Jan 25 2012 -- 15:40:47
then it doesn't produce an INCHI key.
If I remove the hydrogens from the SMILES string, it does.
I think there shou
On 5 May 2012, at 13:40, Ferenc Szalai wrote:
> Hi,
>
> I attached a structure in 2d mol file. If I try to generate 3d
> coordinates for this structure ether using obgen or the pybel
> interface I get result with invalid coordinates ('nan') and a lot of
> warning messages which are stats the some
The CSD has a fair number of structures with a big charged aromatic moiety and
a counter-ion, things like the attached TUDTES.mol2
Using SVN 4747, I'm not seeing charges when I convert to SMILES - I get
OCCn1c(=O)n(C)c2c(c1=O)n(C)cn2C.I
out of obprop, where I would expect
OCCn1c(=O)n(C)c2c(c1
