Re: [PyMOL] Multiple PyMOL Instances in Python Script
> On Apr 24, 2018, at 7:17 PM, Yang Su wrote: > > OK, thanks. If you don't mind, I can add it to the wiki: > https://pymolwiki.org/index.php/Launching_From_a_Script Sure, that would be great. Thanks a lot! Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
OK, thanks. If you don't mind, I can add it to the wiki: https://pymolwiki.org/index.php/Launching_From_a_Script Best, Yang On Tue, Apr 24, 2018 at 6:47 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Yang, > > Very good questions. I don't think that it's documented anywhere. > Reference counting is maintained, I fixed that up as best as I could before > the PyMOL 2.0 release (in PyMOL 1.x it leaks references). Looks like there > is no way to introspect whether start() has been called already. > > Cheers, > Thomas > > > On Apr 24, 2018, at 6:16 PM, Yang Su wrote: > > > > Thanks Thomas. The code snippet works. Does start(), stop() maintain > reference counting? Is there a way to know if it's already started/stopped? > Is this API documented somewhere? > > > > Thanks, > > Yang > > > > > > On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder < > thomas.hol...@schrodinger.com> wrote: > > Hi Yang, > > > > Yes it's possible to have independent instances. The API has actually > been around for a long time. For some reason it was never widely adopted > and thus is not very thoroughly tested. Please report any bugs you > encounter. > > > > Example: > > > > import pymol2 > > p = pymol2.PyMOL() > > p.start() > > p.cmd.fragment('ala') > > p.cmd.show_as('sticks') > > p.cmd.zoom() > > p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1) > > p.stop() > > > > Cheers, > > Thomas > > > > > On Apr 19, 2018, at 3:33 PM, Yang Su wrote: > > > > > > Hi, > > > > > > Is it possible to start multiple independent pymol backend processes > in a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import > pymol' and call a pymol.cmd function to start a backend process, but this > is kind of 'global'. I'm looking for a way to manage multiple PyMOL > sessions in parallel, each manipulating its own structures. > > > > > > Thanks, > > > Yang > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
Hi Yang, Very good questions. I don't think that it's documented anywhere. Reference counting is maintained, I fixed that up as best as I could before the PyMOL 2.0 release (in PyMOL 1.x it leaks references). Looks like there is no way to introspect whether start() has been called already. Cheers, Thomas > On Apr 24, 2018, at 6:16 PM, Yang Su wrote: > > Thanks Thomas. The code snippet works. Does start(), stop() maintain > reference counting? Is there a way to know if it's already started/stopped? > Is this API documented somewhere? > > Thanks, > Yang > > > On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder > wrote: > Hi Yang, > > Yes it's possible to have independent instances. The API has actually been > around for a long time. For some reason it was never widely adopted and thus > is not very thoroughly tested. Please report any bugs you encounter. > > Example: > > import pymol2 > p = pymol2.PyMOL() > p.start() > p.cmd.fragment('ala') > p.cmd.show_as('sticks') > p.cmd.zoom() > p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1) > p.stop() > > Cheers, > Thomas > > > On Apr 19, 2018, at 3:33 PM, Yang Su wrote: > > > > Hi, > > > > Is it possible to start multiple independent pymol backend processes in a > > python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and > > call a pymol.cmd function to start a backend process, but this is kind of > > 'global'. I'm looking for a way to manage multiple PyMOL sessions in > > parallel, each manipulating its own structures. > > > > Thanks, > > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
Thanks Thomas. The code snippet works. Does start(), stop() maintain reference counting? Is there a way to know if it's already started/stopped? Is this API documented somewhere? Thanks, Yang On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Yang, > > Yes it's possible to have independent instances. The API has actually been > around for a long time. For some reason it was never widely adopted and > thus is not very thoroughly tested. Please report any bugs you encounter. > > Example: > > import pymol2 > p = pymol2.PyMOL() > p.start() > p.cmd.fragment('ala') > p.cmd.show_as('sticks') > p.cmd.zoom() > p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1) > p.stop() > > Cheers, > Thomas > > > On Apr 19, 2018, at 3:33 PM, Yang Su wrote: > > > > Hi, > > > > Is it possible to start multiple independent pymol backend processes in > a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' > and call a pymol.cmd function to start a backend process, but this is kind > of 'global'. I'm looking for a way to manage multiple PyMOL sessions in > parallel, each manipulating its own structures. > > > > Thanks, > > Yang > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Multiple PyMOL Instances in Python Script
Hi Yang, Yes it's possible to have independent instances. The API has actually been around for a long time. For some reason it was never widely adopted and thus is not very thoroughly tested. Please report any bugs you encounter. Example: import pymol2 p = pymol2.PyMOL() p.start() p.cmd.fragment('ala') p.cmd.show_as('sticks') p.cmd.zoom() p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1) p.stop() Cheers, Thomas > On Apr 19, 2018, at 3:33 PM, Yang Su wrote: > > Hi, > > Is it possible to start multiple independent pymol backend processes in a > python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and > call a pymol.cmd function to start a backend process, but this is kind of > 'global'. I'm looking for a way to manage multiple PyMOL sessions in > parallel, each manipulating its own structures. > > Thanks, > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Multiple PyMOL Instances in Python Script
Hi, Is it possible to start multiple independent pymol backend processes in a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and call a pymol.cmd function to start a backend process, but this is kind of 'global'. I'm looking for a way to manage multiple PyMOL sessions in parallel, each manipulating its own structures. Thanks, Yang -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net