On Tue, Jan 14, 2014 at 11:48 AM, Greg Landrum greg.land...@gmail.comwrote:
ok, it looks like something bad happened[1] when the PDB branch was merged
into trunk before the last release. Here's an example that worked properly
at the time of the UGM:
In [5]: m
Thanks Greg! Much appreciated.
-
Jean-Paul Ebejer
Early Stage Researcher
On 15 January 2014 08:38, Greg Landrum greg.land...@gmail.com wrote:
On Tue, Jan 14, 2014 at 11:48 AM, Greg Landrum greg.land...@gmail.comwrote:
ok, it looks like something bad happened[1] when the PDB branch was
Hi JP,
However I am unable to get bond orders for the protein side - am I doing
something wrong or is this the intended behaviour ?
I imagine I can use AssignBondOrdersFromTemplate() for the 20 amino acids
and set these myself -- or is there a better way to do this?
I don't know why your
RDKitters!
Finally back on the mailing list!
I am sure we've been through this at the UGM (my mind must have wandered
off!), but a quick question about the PDB reader and bond perception. Is
this supported with the current PDB reader? I remember that someone
(PaulE, perhaps?) was saying bond
Hi JP
I use this file from PDB Europe:
ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/pdb.tar.gz
Useful links followed from
http://www.ebi.ac.uk/pdbe-srv/pdbechem/
The pdb.tar.gz file has the standard residues and LOTS of others
with specific CONNECT records.
TJ
On Mon, Jan 13, 2014 at
On 13/01/14 17:54, JP wrote:
RDKitters!
Finally back on the mailing list!
I am sure we've been through this at the UGM (my mind must have
wandered off!), but a quick question about the PDB reader and bond
perception. Is this supported with the current PDB reader? I
remember that
Hi JP,
If you have also a SMILES of the molecule you want to read from PDB, you
can assign the bond orders based on this template:
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
Is this what you're
Thanks All - I think I am in a good place now.
I can get the SMILES from Paul's mmcif links and then I can use Sereina
magic three lines to do what I want. I'd cross my fingers - but with RDKit
you don't need to.
This works for all Chemical Components (or what other fashionable name they
go by
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