On Sat, Apr 23, 2016 at 8:37 PM, Robert DeLisle <rkdeli...@gmail.com> wrote:
>
>
> In working with this, I found myself wanting to save some PyMOL files
> programatically, but I see that there is not a Save option in the RDKit
> PyMOL code. I added the snip below to the MolViewer class and it seems to
> work nicely. I don't know if it is generally useful or if it should be
> added to the code base - I'll let Greg make that decision.
>
>
Makes sense. It not being there is an oversight.
Thanks for the addition!
-greg
> -Kirk
>
>
> def SaveFile(self, filename):
> id = self.server.save(filename)
> return id
>
>
>
> I've attached my modified PyMol.py file as well.
>
>
>
>
> On Fri, Apr 22, 2016 at 3:08 PM, Paolo Tosco <paolo.to...@unito.it> wrote:
>
>> Dear Robert,
>>
>> I have just built the latest PyMOL 1.8.2.0 on CentOS 7, I started it:
>>
>> pymol -R
>>
>> and then I ran the following Python script:
>>
>> #!/usr/bin/env python
>>
>> import os
>> import rdkit
>> from rdkit import Chem
>> from rdkit.Chem import PyMol
>> from rdkit.Chem import AllChem
>>
>> s = PyMol.MolViewer()
>> mol = Chem.MolFromSmiles \
>> ('CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2ccccc21')
>> mol = AllChem.AddHs(mol)
>> AllChem.EmbedMolecule(mol)
>> AllChem.MMFFOptimizeMolecule(mol)
>> s.ShowMol(mol, name = 'bilastine', showOnly = False)
>> s.Zoom('bilastine')
>> s.SetDisplayStyle('bilastine', 'sticks')
>>
>> I obtained the expected display:
>>
>>
>>
>> Cheers,
>> p.
>>
>>
>> On 04/22/2016 09:09 PM, Robert DeLisle wrote:
>>
>> Back again!
>>
>> I apologize for resurrecting an old topic, but I'm once again trying to
>> work with PyMOL through RDKit. I've been following the approach in this
>> thread (
>> http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html)
>> but it seems not to work any longer. I'm using PyMOL 1.8 on Fedora and I
>> see that the xml-rpc file is current, so that's no longer a problem. When
>> I step through the process and hit this step:
>>
>> s.ShowMol(m,name='ligand',showOnly=False)
>>
>>
>> nothing happens in the PyMOL viewer. It just remains blank.
>>
>> Any updates on operating with PyMOL?
>>
>> -Kirk
>>
>>
>>
>>
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>>
>
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