Re: [Rdkit-discuss] RDKit to PyMol

[Robert D. <rkd...@gm...>]

Greg,

It worked with only one hiccup.

You mentioned replacing PyMol's xml-rpc server:

***
An aside: The version of the xml-rpc server that is distributed with
PyMol is somewhat out of date because I kept forgetting to send a new
version to Warren D. I remedied this this morning, so perhaps the next
version of PyMol will have an up-to-date rpc extension. Until then,
you can always copy $RDBASE/External/pymol/
>
> modules/pymol/rpc.py to pymol's modules/pymol directory if you want the
> newest functionality.

***

Prior to doing this I received some difficult to trace errors through
Python.  Once this was replaced, however, it worked perfectly.

Thank you for the head-start working with PyMol through RDKit.  I have a
number of projects that this will enable.

-Kirk




On Sat, Oct 18, 2008 at 12:15 AM, Greg Landrum <gre...@gm...>wrote:

> Dear Kirk,
>
> On Sat, Oct 18, 2008 at 1:18 AM, Robert DeLisle <rkd...@gm...>
> wrote:
> >
> > I notice within the Python API that RDKit has the ability to communicate
> > with PyMol.  I have not, however, been able to find an example and
> haven't
> > quite figured it out on my own.  Could you provide an example of opening
> a
> > file in PyMol through RDKit, please?
>
> Sure. There's a lot of functionality there, so I'll pick an arbitrary
> example get this started. If anyone has unanswered questions, please
> post. Once we have a somewhat refined set of examples, I'll post it to
> the wiki.
>
> The first thing you need to do is get PyMol started with the optional
> xml-rpc server running. You do this via the -R switch to PyMol. When
> PyMol starts, you should see a message about the xml-rpc server
> running on port 9123.
>
> From python (this actually ought to work for you as is if you run it
> in $RDBASE/Python/qtGui/Search3D/testData):
>
> import os
> import Chem
> from Chem import PyMol
> # start the viewer:
> s = PyMol.MolViewer()
> # have pymol display a pdb file, notice that we have to provide the full
> path:
> s.LoadFile(os.path.join(os.getcwd(),'1OIR-nowater.pdb'),'1oir')
> s.Zoom('1oir')
> s.SetDisplayStyle('1oir','cartoon')
> # create an RDKit molecule:
> m = Chem.MolFromMolFile('1oir-xtal.mol',removeHs=False)
> # have pymol display it:
> s.ShowMol(m,name='ligand',showOnly=False)
> s.Zoom('ligand')
> s.SetDisplayStyle('ligand','sticks')
> # select the protein neighborhood around the ligand and add a surface:
> s.SelectProteinNeighborhood('ligand','1oir',showSurface=True)
> # show h bonds and bumps:
> s.DisplayHBonds('hbonds','ligand','1oir')
> s.DisplayCollisions('bumps','ligand','1oir')
>
> s is an instance of the PyMol.MolViewer class and we have so far been
> using higher level methods of the class. To get more control (and see
> more functionality), you can work directly with the underlying xml-rpc
> server object, which the MolViewer carries around as a member named
> server.
>
> So, for example, we can use a raw pymol command to add a surface to the
> ligand:
> s.server.do('show surface, ligand')
>
> Or we can ask the server for its list of supported commands:
> s.server.help()
> or get more specific help about a particular command:
> print s.server.help('sphere')
>
> An aside: The version of the xml-rpc server that is distributed with
> PyMol is somewhat out of date because I kept forgetting to send a new
> version to Warren D. I remedied this this morning, so perhaps the next
> version of PyMol will have an up-to-date rpc extension. Until then,
> you can always copy $RDBASE/External/pymol/modules/pymol/rpc.py to
> pymol's modules/pymol directory if you want the newest functionality.
>
> Best Regards,
> -greg
>