Re: [PyMOL] Calling scripted functions within alter_state
Stuart,
Hmm...whoops, my mistake. Cmd.extend doesn't actually add a function to
the cmd module -- only to the command keyword dictionary.
So, instead, set it explicitly in your .py file:
from pymol import cmd
def my_fn(...):
cmd.my_fn = my_fn
# then later on, in the menu, etc.:
cmd.alter_state(..., "cmd.my_fn(...)")
Cheers,
Warren
From: Stuart Ballard [mailto:srball...@wisc.edu]
Sent: Monday, August 24, 2009 4:06 PM
To: Warren DeLano
Cc: pymol-users
Subject: Re: [PyMOL] Calling scripted functions within
alter_state
Hello Warren,
When adding in the "cmd." I get these error messages:
Traceback (most recent call last):
File "", line 1, in
AttributeError: 'module' object has no attribute 'sym_partner'
Traceback (most recent call last):
File "", line 1, in
AttributeError: 'module' object has no attribute
'cell_shift_helper'
Versus the error I get with the "cmd." not included:
Traceback (most recent call last):
File "", line 1, in
NameError: name 'sym_partner' is not defined
Traceback (most recent call last):
File "", line 1, in
NameError: name 'cell_shift_helper' is not defined
I'm pretty stumped at this point. Does it seem like the
pymol.cmd namespace isn't acquiring the new functions as it ought to be?
Stuart
2009/8/24 Warren DeLano
Hello Stuart,
By default, alter_state expressions are evaluated in the
"pymol" namespace of the current PyMOL instance, not the "cmd"
(pymol.cmd) namespace. The reason why it works with 'run' is that run
also executes in "pymol" by default, and thus, includes any functions
you define.
Try:
cmd.alter_state(1, copy, "x,y,z =
cmd.sym_partner([x,y,z], stored.tmpOp)")
instead, after using cmd.extend in your startup or GUI
script.
Cheers,
Warren
________
From: Stuart Ballard [mailto:srball...@wisc.edu]
Sent: Monday, August 24, 2009 3:38 PM
To: pymol-users
Subject: [PyMOL] Calling scripted functions within
alter_state
Hello Warren, all,
I've been working on a plugin for PyMOLX11Hybrid, in
which I have a few lines of code such as:
cmd.alter_state(1, copy, "x,y,z =
sym_partner([x,y,z], stored.tmpOp)")
AND
cmd.alter_state(1, object, "x,y,z =
cell_shift_helper([x,y,z],stored.shift)")
Both those functions (sym_partner and cell_shift_helper)
are extended through cmd.extend() function, along with several others
which work perfectly well. The issue arises only when I attempt to use
these functions through a menu added to PyMOL GUI, which does not
involve issuing the run /(filepath)/(script).py command in PyMOL, but
rather initializes necessary commands on startup. I've confirmed that
the cmd.extend() calls are made properly, but I can only fix the problem
by issuing the run command independent of my initialization scripts.
Because this script is planned to be incorporated into a
build of PyMOL which will be run from a variety of file paths, I'd like
to know how I can solve this problem without simply jury rigging a run
command. Is there a way to properly make commands available within an
alter_state command without using the run command?
Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison
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Re: [PyMOL] Calling scripted functions within alter_state
Hello Warren, When adding in the "cmd." I get these error messages: Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'sym_partner' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'cell_shift_helper' Versus the error I get with the "cmd." not included: Traceback (most recent call last): File "", line 1, in NameError: name 'sym_partner' is not defined Traceback (most recent call last): File "", line 1, in NameError: name 'cell_shift_helper' is not defined I'm pretty stumped at this point. Does it seem like the pymol.cmd namespace isn't acquiring the new functions as it ought to be? Stuart 2009/8/24 Warren DeLano > Hello Stuart, > > > > By default, alter_state expressions are evaluated in the “pymol” namespace > of the current PyMOL instance, not the “cmd” (pymol.cmd) namespace. The > reason why it works with ‘run’ is that run also executes in “pymol” by > default, and thus, includes any functions you define. > > > > Try: > > > > cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)") > > instead, after using cmd.extend in your startup or GUI script. > > > > Cheers, > > Warren > > > > > -- > > *From:* Stuart Ballard [mailto:srball...@wisc.edu] > *Sent:* Monday, August 24, 2009 3:38 PM > *To:* pymol-users > *Subject:* [PyMOL] Calling scripted functions within alter_state > > > > Hello Warren, all, > > > I've been working on a plugin for PyMOLX11Hybrid, in which I have a few > lines of code such as: > > cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], > stored.tmpOp)") > > AND > > cmd.alter_state(1, object, "x,y,z = > cell_shift_helper([x,y,z],stored.shift)") > > Both those functions (sym_partner and cell_shift_helper) are extended > through cmd.extend() function, along with several others which work > perfectly well. The issue arises only when I attempt to use these functions > through a menu added to PyMOL GUI, which does not involve issuing the run > /(filepath)/(script).py command in PyMOL, but rather initializes necessary > commands on startup. I've confirmed that the cmd.extend() calls are made > properly, but I can only fix the problem by issuing the run command > independent of my initialization scripts. > > Because this script is planned to be incorporated into a build of PyMOL > which will be run from a variety of file paths, I'd like to know how I can > solve this problem without simply jury rigging a run command. Is there a way > to properly make commands available within an alter_state command without > using the run command? > > > Thanks, > Stuart Ballard > Dept. of Biochemistry > UW-Madison > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] Calling scripted functions within alter_state
Hello Stuart, By default, alter_state expressions are evaluated in the "pymol" namespace of the current PyMOL instance, not the "cmd" (pymol.cmd) namespace. The reason why it works with 'run' is that run also executes in "pymol" by default, and thus, includes any functions you define. Try: cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)") instead, after using cmd.extend in your startup or GUI script. Cheers, Warren From: Stuart Ballard [mailto:srball...@wisc.edu] Sent: Monday, August 24, 2009 3:38 PM To: pymol-users Subject: [PyMOL] Calling scripted functions within alter_state Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], stored.tmpOp)") AND cmd.alter_state(1, object, "x,y,z = cell_shift_helper([x,y,z],stored.shift)") Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] Calling scripted functions within alter_state
Hello Warren, all, I've been working on a plugin for PyMOLX11Hybrid, in which I have a few lines of code such as: cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z], stored.tmpOp)") AND cmd.alter_state(1, object, "x,y,z = cell_shift_helper([x,y,z],stored.shift)") Both those functions (sym_partner and cell_shift_helper) are extended through cmd.extend() function, along with several others which work perfectly well. The issue arises only when I attempt to use these functions through a menu added to PyMOL GUI, which does not involve issuing the run /(filepath)/(script).py command in PyMOL, but rather initializes necessary commands on startup. I've confirmed that the cmd.extend() calls are made properly, but I can only fix the problem by issuing the run command independent of my initialization scripts. Because this script is planned to be incorporated into a build of PyMOL which will be run from a variety of file paths, I'd like to know how I can solve this problem without simply jury rigging a run command. Is there a way to properly make commands available within an alter_state command without using the run command? Thanks, Stuart Ballard Dept. of Biochemistry UW-Madison -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
