Re: [PyMOL] Custom menus and shortcuts?
Hi Boris, Boris Kheyfets wrote, On 10/23/12 19:28: [...] But I want bk_hides_W to be a toggler. So I need a way to set a state of my defun. If I do def bk_toggles_W (): Hides W molecules. if cmd.get(bk_toggles_W): cmd.hide(all) cmd.show(spheres, not (resn W)) cmd.set(bk_toggles_W, 0) else: cmd.show(spheres, resn W) cmd.set(bk_toggles_W, 1) pymol is upset -- I think it is because it doesn't know bk_toggles_W setting: If you need a global variable, use pymol.stored: from pymol import stored stored.bk_toggles_W = 0 def bk_toggles_W (): Hides W molecules. if stored.bk_toggles_W: cmd.hide(all) cmd.show(spheres, not (resn W)) stored.bk_toggles_W = 0 else: cmd.show(spheres, resn W) stored.bk_toggles_W = 1 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ 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] Custom menus and shortcuts?
If you need a global variable, use pymol.stored
Thank You Thomas -- that solves it.
Boris.
On Tue, Oct 23, 2012 at 9:28 PM, Boris Kheyfets kheyfbo...@gmail.comwrote:
Found a solution.
Basically it is to add
pmg_tk/startup/newmenu.py
file with the following content:
from Tkinter import *
from pymol import cmd
def __init__(self):
self.menuBar.addmenu('NewMenu', 'Sample Menu')
self.menuBar.addmenuitem('NewMenu', 'command',
'White background',
label='White Background',
command = lambda : cmd.set(bg_rgb,[1,1,1]))
self.menuBar.addmenuitem('NewMenu', 'command',
'Black background',
label='Black Background',
command = lambda : cmd.set(bg_rgb,[0,0,0]))
This adds the menu.
I got what I wanted with:
- .pymolrc:
# custom scripts:
import imp
imp.load_source('bk_pymols', os.path.expanduser('~/.pymolrc.py'))
- .pymolrc.py
from pymol import cmd
def bk_notW ():
Makes notW selection.
cmd.select(notW, not (resn W))
def bk_hides_W ():
Hides W molecules.
cmd.hide(all)
cmd.show(spheres, not (resn W))
cmd.set_key('ALT-N', bk_notW)
cmd.set_key('ALT-W', bk_hides_W)
- and finally -- pmg_tk/startup/BK.py:
from Tkinter import *
from pymol import cmd
# custom scripts:
import imp, os
imp.load_source('bk_pymols', os.path.expanduser('~/.pymolrc.py'))
from bk_pymols import bk_notW, bk_hides_W
def __init__(self):
self.menuBar.addmenu('BK', 'My menus!')
self.menuBar.addmenuitem('BK', 'command',
'Makes notW [Alt-n]',
label='Makes notW [Alt-n]',
command = bk_notW)
self.menuBar.addmenuitem('BK', 'command',
'Hides W mols [Alt-w]',
label='Hides W mols [Alt-w]',
command = bk_hides_W)
Works like a charm: I have custom menus and I can bind any of its entries
to a key.
But I want bk_hides_W to be a toggler. So I need a way to set a state of
my defun.
If I do
def bk_toggles_W ():
Hides W molecules.
if cmd.get(bk_toggles_W):
cmd.hide(all)
cmd.show(spheres, not (resn W))
cmd.set(bk_toggles_W, 0)
else:
cmd.show(spheres, resn W)
cmd.set(bk_toggles_W, 1)
pymol is upset -- I think it is because it doesn't know bk_toggles_Wsetting:
Error: 1
QuietException Exception in Tk callback
Function: function bk_toggles_W at 0x7ff02d90cb90 (type: type
'function')
Args: ()
Traceback (innermost last):
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
1747, in __call__
return apply(self.func, args)
File /home/boris/.pymolrc.py, line 67, in bk_toggles_W
if cmd.get(bk_toggles_W):
File /home/boris/.local/lib/python2.7/site-packages/pymol/setting.py,
line 1300, in get
raise QuietException
QuietException: pymol.parsing.QuietException instance at 0x7ff018698518
How can I add the setting to pymol?
--
Boris.
On Tue, Oct 23, 2012 at 5:17 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Boris,
David Hall's suggestions are perfect.
Let me offer one more. If you can put up with programming a little
Python, check out pymol/modules/pymol/menu.py and
pymol/modules/pymol/preset.py. In menu.py you could add a No W menu
option (or similar) to the A Preset
Cheers,
-- Jason
On Tue, Oct 23, 2012 at 6:02 AM, Boris Kheyfets kheyfbo...@gmail.com
wrote:
Hello PyMOL users,
Menus
=
Is there a way I can add custom menu in PyMOL?
Ideally I'd like to be able to call both
* pml scripts, as well as
* full python pymol scrpts
Shortcuts
=
Similarly -- is there a way I can bind exectution of given
* pml script, or
* full python pymol script
to a given key?
The problem
===
The basic problem
-
The basic problem is to automate tasks one repeats frequenlty. For
example I
had to type::
select notW, not (resn W)
hide all
show spheres, notW
frequently.
The problem which leads to the need of menu
---
So I make a pml or full-python pymol script and load it.
But then I have to remember the name of the script. Which is terrible --
because I have custom scripts in each and every program that I use.
The problem which leads to the need of custom shortcuts
---
Having custom menu us great as a reminder of what scripts have You
written.
But it's terrible to click through the menus. One is much better with
shorcuts (hotkeys).
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
[PyMOL] Custom menus and shortcuts?
Hello PyMOL users, Menus = Is there a way I can add custom menu in PyMOL? Ideally I'd like to be able to call both * pml scripts, as well as * full python pymol scrpts Shortcuts = Similarly -- is there a way I can bind exectution of given * pml script, or * full python pymol script to a given key? The problem === The basic problem - The basic problem is to automate tasks one repeats frequenlty. For example I had to type:: select notW, not (resn W) hide all show spheres, notW frequently. The problem which leads to the need of menu --- So I make a pml or full-python pymol script and load it. But then I have to remember the name of the script. Which is terrible -- because I have custom scripts in each and every program that I use. The problem which leads to the need of custom shortcuts --- Having custom menu us great as a reminder of what scripts have You written. But it's terrible to click through the menus. One is much better with shorcuts (hotkeys). -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ 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] Custom menus and shortcuts?
http://pymolwiki.org/index.php/Set_Key http://pymolwiki.org/index.php/Extend is also useful. -David On Tuesday, October 23, 2012 at 6:02 AM, Boris Kheyfets wrote: Hello PyMOL users, Menus = Is there a way I can add custom menu in PyMOL? Ideally I'd like to be able to call both * pml scripts, as well as * full python pymol scrpts Shortcuts = Similarly -- is there a way I can bind exectution of given * pml script, or * full python pymol script to a given key? The problem === The basic problem - The basic problem is to automate tasks one repeats frequenlty. For example I had to type:: select notW, not (resn W) hide all show spheres, notW frequently. The problem which leads to the need of menu --- So I make a pml or full-python pymol script and load it. But then I have to remember the name of the script. Which is terrible -- because I have custom scripts in each and every program that I use. The problem which leads to the need of custom shortcuts --- Having custom menu us great as a reminder of what scripts have You written. But it's terrible to click through the menus. One is much better with shorcuts (hotkeys). -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net (mailto: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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ 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] Custom menus and shortcuts?
Found a solution.
Basically it is to add
pmg_tk/startup/newmenu.py
file with the following content:
from Tkinter import *
from pymol import cmd
def __init__(self):
self.menuBar.addmenu('NewMenu', 'Sample Menu')
self.menuBar.addmenuitem('NewMenu', 'command',
'White background',
label='White Background',
command = lambda : cmd.set(bg_rgb,[1,1,1]))
self.menuBar.addmenuitem('NewMenu', 'command',
'Black background',
label='Black Background',
command = lambda : cmd.set(bg_rgb,[0,0,0]))
This adds the menu.
I got what I wanted with:
- .pymolrc:
# custom scripts:
import imp
imp.load_source('bk_pymols', os.path.expanduser('~/.pymolrc.py'))
- .pymolrc.py
from pymol import cmd
def bk_notW ():
Makes notW selection.
cmd.select(notW, not (resn W))
def bk_hides_W ():
Hides W molecules.
cmd.hide(all)
cmd.show(spheres, not (resn W))
cmd.set_key('ALT-N', bk_notW)
cmd.set_key('ALT-W', bk_hides_W)
- and finally -- pmg_tk/startup/BK.py:
from Tkinter import *
from pymol import cmd
# custom scripts:
import imp, os
imp.load_source('bk_pymols', os.path.expanduser('~/.pymolrc.py'))
from bk_pymols import bk_notW, bk_hides_W
def __init__(self):
self.menuBar.addmenu('BK', 'My menus!')
self.menuBar.addmenuitem('BK', 'command',
'Makes notW [Alt-n]',
label='Makes notW [Alt-n]',
command = bk_notW)
self.menuBar.addmenuitem('BK', 'command',
'Hides W mols [Alt-w]',
label='Hides W mols [Alt-w]',
command = bk_hides_W)
Works like a charm: I have custom menus and I can bind any of its entries
to a key.
But I want bk_hides_W to be a toggler. So I need a way to set a state of my
defun.
If I do
def bk_toggles_W ():
Hides W molecules.
if cmd.get(bk_toggles_W):
cmd.hide(all)
cmd.show(spheres, not (resn W))
cmd.set(bk_toggles_W, 0)
else:
cmd.show(spheres, resn W)
cmd.set(bk_toggles_W, 1)
pymol is upset -- I think it is because it doesn't know bk_toggles_Wsetting:
Error: 1
QuietException Exception in Tk callback
Function: function bk_toggles_W at 0x7ff02d90cb90 (type: type
'function')
Args: ()
Traceback (innermost last):
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
1747, in __call__
return apply(self.func, args)
File /home/boris/.pymolrc.py, line 67, in bk_toggles_W
if cmd.get(bk_toggles_W):
File /home/boris/.local/lib/python2.7/site-packages/pymol/setting.py,
line 1300, in get
raise QuietException
QuietException: pymol.parsing.QuietException instance at 0x7ff018698518
How can I add the setting to pymol?
--
Boris.
On Tue, Oct 23, 2012 at 5:17 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Boris,
David Hall's suggestions are perfect.
Let me offer one more. If you can put up with programming a little
Python, check out pymol/modules/pymol/menu.py and
pymol/modules/pymol/preset.py. In menu.py you could add a No W menu
option (or similar) to the A Preset
Cheers,
-- Jason
On Tue, Oct 23, 2012 at 6:02 AM, Boris Kheyfets kheyfbo...@gmail.com
wrote:
Hello PyMOL users,
Menus
=
Is there a way I can add custom menu in PyMOL?
Ideally I'd like to be able to call both
* pml scripts, as well as
* full python pymol scrpts
Shortcuts
=
Similarly -- is there a way I can bind exectution of given
* pml script, or
* full python pymol script
to a given key?
The problem
===
The basic problem
-
The basic problem is to automate tasks one repeats frequenlty. For
example I
had to type::
select notW, not (resn W)
hide all
show spheres, notW
frequently.
The problem which leads to the need of menu
---
So I make a pml or full-python pymol script and load it.
But then I have to remember the name of the script. Which is terrible --
because I have custom scripts in each and every program that I use.
The problem which leads to the need of custom shortcuts
---
Having custom menu us great as a reminder of what scripts have You
written.
But it's terrible to click through the menus. One is much better with
shorcuts (hotkeys).
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_sfd2d_oct
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives:
Re: [PyMOL] Custom menus and shortcuts?
Hi Boris, David Hall's suggestions are perfect. Let me offer one more. If you can put up with programming a little Python, check out pymol/modules/pymol/menu.py and pymol/modules/pymol/preset.py. In menu.py you could add a No W menu option (or similar) to the A Preset Cheers, -- Jason On Tue, Oct 23, 2012 at 6:02 AM, Boris Kheyfets kheyfbo...@gmail.com wrote: Hello PyMOL users, Menus = Is there a way I can add custom menu in PyMOL? Ideally I'd like to be able to call both * pml scripts, as well as * full python pymol scrpts Shortcuts = Similarly -- is there a way I can bind exectution of given * pml script, or * full python pymol script to a given key? The problem === The basic problem - The basic problem is to automate tasks one repeats frequenlty. For example I had to type:: select notW, not (resn W) hide all show spheres, notW frequently. The problem which leads to the need of menu --- So I make a pml or full-python pymol script and load it. But then I have to remember the name of the script. Which is terrible -- because I have custom scripts in each and every program that I use. The problem which leads to the need of custom shortcuts --- Having custom menu us great as a reminder of what scripts have You written. But it's terrible to click through the menus. One is much better with shorcuts (hotkeys). -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ 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
