Nick,
On Fri, Jan 25, 2013 at 11:42 AM, Nicholas Firth
<[email protected]>wrote:
> Hi RDKitters,
>
> I've been looking at using RDKit to view molecules in PyMol as Greg showed
> at the UGM. I found the test file in the source and started firstly to
> replicate this, which threw and error so I then tried to run the test
> "python Code/RDKit/RDKit_2012_06_1/rdkit/Chem/Subshape/testCombined.py" and
> this also threw the same error which is below
>
when you start pymol, you need to tell it to run the xmlrpc server: via the
-R argument.
There's some info about using this here:
http://www.pymolwiki.org/index.php/XML-RPC_server
> So first question is, can anyone help me to get this working? Second
> question, is there a way to push RDKit molecules from C++ programs into
> PyMol?
>
>
You would just need an xmlrpc client library for C++. The interface is
quite simple once you have the library (take a look at
$RDBASE/rdkit/Chem/PyMol.py to see it).
> Also while I'm bothering you Greg (as I assume you will read this),
> currently the smiles reader will read dummy atoms if they are [*] however
> neither [R] or [A]. Is there anyway the smiles reader can read [R]
> molecules? It's pretty simple to work round, but I thought it might be nice
> to go in RDKit
>
[R] isn't part of SMILES (either Daylight's smiles spec or OpenSmiles). You
could, if you really wanted to, add it by patching
$RDBASE/Code/GraphMol/SmilesParse/smiles.ll to add a rule for [R], but it's
probably better to just use [*].
-greg
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