Hi Chimera Team, I’m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I’m only using it for `split`, but I’d like to first test whether a model is already split to avoid unnecessary invocation. I’m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn’t seem to be importable, as when I try:
from chimera import SplitMolecule Traceback (most recent call last): File "<pyshell#25>", line 2, in <module> ImportError: cannot import name SplitMolecule
I’m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I’ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I’m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ‘layer’ below `chimera` itself. Can you elighten me? I’m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps. If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1@warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738
Hi Joe, You need to use import SplitMolecule It is not a submodule of the chimera module. I am not sure why we made all the Chimera tools be top level modules instead of under the chimera module. Are you splitting to make each chain a separate model? If so then checking if a molecule needs splitting is the same as checking if it has one chain. Tom
On Feb 14, 2020, at 8:14 AM, Healey, Joseph <J.Healey.1@warwick.ac.uk> wrote:
Hi Chimera Team,
I’m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I’m only using it for `split`, but I’d like to first test whether a model is already split to avoid unnecessary invocation.
I’m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn’t seem to be importable, as when I try:
from chimera import SplitMolecule Traceback (most recent call last): File "<pyshell#25>", line 2, in <module> ImportError: cannot import name SplitMolecule
I’m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I’ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I’m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ‘layer’ below `chimera` itself. Can you elighten me?
I’m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps.
If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help.
Many thanks,
Joe
Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey | Website Email: J.Healey.1@warwick.ac.uk | ORCID: orcid.org/0000-0002-9569-6738
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Here is a bit a Python code to count the number of chains in a molecule m.
import chimera m = chimera.openModels.list()[0] m <_molecule.Molecule object at 0x7fb988fed620> len(set(r.id.chainId for r in m.residues)) 4
We have been working on ChimeraX the replacement for Chimera for a few years and it is quite a bit nicer. In ChimeraX the code would be m = session.models.list()[0] m.num_chains Tom
On Feb 14, 2020, at 2:09 AM, Healey, Joseph <J.Healey.1@warwick.ac.uk> wrote:
Hi Chimera Team,
I’m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I’m only using it for `split`, but I’d like to first test whether a model is already split to avoid unnecessary invocation.
I’m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn’t seem to be importable, as when I try:
from chimera import SplitMolecule Traceback (most recent call last): File "<pyshell#25>", line 2, in <module> ImportError: cannot import name SplitMolecule
I’m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I’ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I’m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ‘layer’ below `chimera` itself. Can you elighten me?
I’m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps.
If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help.
Many thanks,
Joe
Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey <https://twitter.com/JRJHealey> | Website <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1@warwick.ac.uk <mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Tom, Perfect – thanks for clearing up the confusion! I’m looking forward to moving over to scripting for ChimeraX (not least because I work on large structures), but it hasn’t quite got the featureset I need just yet… Many thanks for the help, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1@warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738 From: Tom Goddard <goddard@sonic.net> Date: Friday, 14 February 2020 at 18:34 To: "Healey, Joseph" <J.Healey.1@warwick.ac.uk> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] SplitCommand python Here is a bit a Python code to count the number of chains in a molecule m.
import chimera m = chimera.openModels.list()[0] m <_molecule.Molecule object at 0x7fb988fed620> len(set(r.id.chainId for r in m.residues)) 4
We have been working on ChimeraX the replacement for Chimera for a few years and it is quite a bit nicer. In ChimeraX the code would be m = session.models.list()[0] m.num_chains Tom On Feb 14, 2020, at 2:09 AM, Healey, Joseph <J.Healey.1@warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk>> wrote: Hi Chimera Team, I’m trying to reduce some overheads in one of my scripts part of which is coming from my use of `runCommand`. At the moment, I’m only using it for `split`, but I’d like to first test whether a model is already split to avoid unnecessary invocation. I’m aware the python equivalent of the command is buried inside chimera.SplitMolecule and the command split_command, however it doesn’t seem to be importable, as when I try:
from chimera import SplitMolecule Traceback (most recent call last): File "<pyshell#25>", line 2, in <module> ImportError: cannot import name SplitMolecule
I’m getting the above ImportError. I can import other members of the chimera class (e.g. chimera.openModels or chimera.Molecule and chimera itself without issue). I’ve seen in the source code that SplitMolecule gets imported elsewhere, and it has the __init__ file, so I assume I’m just doing something stupid with paths or similar. That said, SplitMolecule is clearly within the main chimera modules directory, so I would have expected it to only be one ‘layer’ below `chimera` itself. Can you elighten me? I’m currently on chimera production version 1.14 (build 42094) 2019-11-13 06:05:13 UTC if that helps. If you could point me in the right direction to understand how the code will check for multiple chains and decide to split by chain, that would also be a massive help. Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1@warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738<http://orcid.org/0000-0002-9569-6738> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Healey, Joseph -
Tom Goddard