Hi Greg,
Thanks for that.
Why do I ask? Because the sdf files [1] distributed by the wwPDB, such
as this one:
http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf
from this page:
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CQ8
are upper-cased. I didn't know whether that was right or not (and, as
you imply, RDKit will not parse it). I'll get in touch with them and
see if they can get it changed.
Paul.
[1] I thought that they were molfiles when I wrote the mail - and I
suppose the same thinking applies.
On 18/01/2016 20:59, Greg Landrum wrote:
Hi Paul,
ctfile.pdf says: "entry in periodic table"
I interpret this to mean "Cl", since that's what one finds in the
typical periodic table.
The RDKit, curiously, agrees with me. ;-)
:-)
-greg
On Mon, Jan 18, 2016 at 8:45 AM, Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
Dear RDKitters,
Is is clear what the case of the second character of an atom symbol in
the atom block of a MolFile should be? i.e. "CL", "Cl" or either?
Thanks,
Paul.
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