Plugin manager - Revision history

Bell: 1 revision

2014-11-26T15:24:48Z

1 revision

Sbliven: moved Plugin manager to Plugin Manager: Fixing capitalization

2014-11-24T09:21:25Z

moved Plugin manager to Plugin Manager: Fixing capitalization

Bell: 4 revisions

2014-06-09T14:21:54Z

4 revisions

Andwar: corrected path for windows

2014-06-06T22:50:30Z

corrected path for windows

Andwar: some editing pointing out differences to the old plugin management

2014-06-06T19:14:11Z

some editing pointing out differences to the old plugin management

Andwar: links to pymolrc page

2014-06-06T17:53:45Z

links to pymolrc page

Andwar: Created a page describing the Plugin Manager for PyMOL

2014-06-06T10:06:06Z

Created a page describing the Plugin Manager for PyMOL

New page

Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as the [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo].

=Manual Setup=
In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' 
Here you can manually add directories or scripts that will be loaded upon startup.

=Scripted setup during PyMOL launching=
===Creating run_on_startup.py===
'''run_on_startup.py''' can easily be created using a text editor such as notepad. 

The '''run_on_startup.py''' is handled similar to pymolrc files and is executed every time PyMOL launches. 
An important distinction is that '''run_on_startup.py''' is executed before the pymolrc files and is purely written in python. 
The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\'). 
An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).

<syntaxhighlight lang="python">
#this can be copy-pasted to create run_on_startup.py in the home directory

# Add paths to sys.path so PyMOL can find modules and scripts
import sys
import os

pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])

# Make setting changes to Plugin Manager
import pymol.plugins

#THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])

pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
pymol.plugins.autoload = {'apbs_tools': False}
pymol.plugins.preferences = {'instantsave': True, 'verbose': False}

# This can be used to trace if PyMOL executed the file correctly. Otherwise remove this part
print 'Loaded run_on_stratup.py'
</syntaxhighlight>

If the '''Pymol-script-repo''' is located somewhere else the first section of the file will be different. 
E.g. in the USER directory:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

E.g. in any other path:
<syntaxhighlight lang="python">
# This would replace the first section in '''run_on_startup.py'''.
import sys
import os

pymol_git = os.path.realpath('D:\MY\RANDOM\PATH\TO\Pymol-script-repo') # Adjust this line
# Note the '\' instead of '/', beware Windows users!

os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
sys.path.append(pymol_git)
sys.path.append(os.environ['PYMOL_GIT_MOD'])
</syntaxhighlight>

===Appending additional paths to the Plugin Manager===
Should your scripts be located in several alternative locations, it is possible to append additional directories to the '''Plugin Manager'''. 
In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger. 
Should the folder be somewhere else the example below can be adjusted as outlined above. 
<syntaxhighlight lang="python">
#copy paste into PyMOL's command line or into the pymolrc

python
import os
import sys
import pymol.plugins

PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))
startupdirectories=list(pymol.plugins.get_startup_path(True))
if PRIVATE_PATH not in startupdirectories:
startupdirectories.append(PRIVATE_PATH)
if PRIVATE_PATH not in sys.path:
sys.path.append(PRIVATE_PATH)
pymol.plugins.set_startup_path(startupdirectories)
python end
</syntaxhighlight>

Note that the '''Plugin Manager''' supports loading entire folders with scripts ('modules'). 
If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.

=If you don't have a Plugin Manager=
If you are running an older PyMOL without '''Plugin Manager''' you can either upgrade to the newest version or load plugins the traditional way. 
For detailed instructions see: [[Git install scripts]] 
Essentially, make sure that the folder is added to PyMOL's search paths.
<syntaxhighlight lang="python">
import sys
import os
pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
sys.path.append(pymol_git)
</syntaxhighlight>
Import a plugin manually:
<syntaxhighlight lang="python">
# EXAMPLE
delete all
frag LYS
cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded

import cgo_arrow # PyMOL will look for this file and load it
cgo_arrow name N, name O # should work if it is loaded
</syntaxhighlight>

=SEE ALSO=
[[Git install scripts]]

[[Category:Launching]]

← Older revision		Revision as of 09:21, 24 November 2014
Line 1:		Line 1:
−	~~Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as those in the [https://github.com/Pymol-Scripts/Pymol-script-repo~~# ~~PyMOL Script Repo].<br>~~	+	#REDIRECT [[Plugin Manager]]
−
−	~~=Manual Setup=~~
−	~~In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' <br>~~
−	~~Here you can manually add directories or scripts that will be loaded upon startup.<br>~~
−	~~Older versions have a basic version of this manager: '''Plugin''' > '''Manage Plugins''', however, here the scripts need to be added individually.<br>~~
−
−
−	~~=Scripted setup during PyMOL launching=~~
−	~~===Creating run_on_startup.py===~~
−	~~'''run_on_startup.py''' can easily be created using a text editor such as notepad.<br>~~
−
−	~~The '''run_on_startup.py''' is handled similar to [~~[~~Pymolrc\|pymolrc]] files and is executed every time PyMOL launches.<br>~~
−	~~An important distinction is that '''run_on_startup.py''' is executed before the~~ [~~[Pymolrc\|pymolrc]] files and is purely written in python.<br>~~
−	~~The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\').<br>~~
−	~~An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).<br>~~
−
−	~~<syntaxhighlight lang="python">~~
−	~~#this can be copy-pasted to create run_on_startup.py in the home directory~~
−
−	~~# Add paths to sys.path so PyMOL can find modules and scripts~~
−	~~import sys~~
−	~~import os~~
−
−	~~pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))~~
−
−	~~os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')~~
−	~~sys.path.append(pymol_git)~~
−	~~sys.path.append(os.environ['PYMOL_GIT_MOD'])~~
−
−	~~# Make setting changes to~~ Plugin Manager
−	~~try: # in case the PyMOL is older and doe not have the module pymol.plugins~~
−	~~import pymol.plugins~~
−
−	~~#THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER~~
−	~~pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])~~
−
−	~~pymol.plugins.preferences = {'instantsave': False, 'verbose': False}~~
−	~~pymol.plugins.autoload = {'apbs_tools': False}~~
−	~~pymol.plugins.preferences = {'instantsave': True, 'verbose': False}~~
−	~~# This can be used to trace if PyMOL executed the file correctly~~
−	~~print 'Loaded run_on_stratup.py'~~
−	~~except:~~
−	~~print 'NB! Plugin Manager not present!'~~
−	~~</syntaxhighlight>~~
−	~~Note that this block will also add the '''Pymol-script-repo''' and the subfolder '''Pymol-script-repo/modules''' to PyMOL's search path.<br>~~
−	~~This is something that is required in earlier PyMOL version to allow import of scripts. Thus this version of '''run_on_startup.py''' can be used for older versions, too.<br>~~
−	~~Note that the settings specific for the ''new'' version of the '''Plugin Manager''' will not have an effect.<br>~~
−
−	~~===What if the 'Pymol-script-repo' is not in the PyMOL directory?===~~
−	~~If the '''Pymol-script-repo''' is located somewhere else the first section of the '''run_on_startup.py''' file will be different.<br>~~
−	~~E.g. in the USER directory:~~
−	~~<syntaxhighlight lang="python">~~
−	~~# This would replace the first section in '''run_on_startup.py'''.~~
−	~~import sys~~
−	~~import os~~
−
−	~~pymol_git = os.path.abspath(os.path.join(os.path.expanduser('~'), 'Pymol-script-repo'))~~
−
−	~~os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')~~
−	~~sys.path.append(pymol_git)~~
−	~~sys.path.append(os.environ['PYMOL_GIT_MOD'])~~
−	~~</syntaxhighlight>~~
−
−	~~E.g. in any other path:~~
−	~~<syntaxhighlight lang="python">~~
−	~~# This would replace the first section in '''run_on_startup.py'''.~~
−	~~import sys~~
−	~~import os~~
−
−	~~pymol_git = os.path.realpath('D:/MY/RANDOM/PATH/TO/Pymol-script-repo') # Adjust this line~~
−	~~# Note the slash ('/') instead of backslash ('\'), beware Windows users!~~
−
−	~~os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')~~
−	~~sys.path.append(pymol_git)~~
−	~~sys.path.append(os.environ['PYMOL_GIT_MOD'])~~
−	~~</syntaxhighlight>~~
−
−
−	~~===Appending additional paths to the Plugin Manager===~~
−	~~Should your scripts be located in several alternative locations, it is possible to append additional directories to the '''Plugin Manager'''.<br>~~
−	~~In the example below, a directory called 'plugins_private', which is located in the PyMOL directory, is added to the Plugin Manger.<br>~~
−	~~Should the folder be somewhere else the example below can be adjusted as outlined above.<br>~~
−	~~<syntaxhighlight lang="python">~~
−	~~#copy paste into PyMOL's command line or into the pymolrc~~
−
−	~~python~~
−	~~import os~~
−	~~import sys~~
−	~~import pymol.plugins # Note that this requires the 'new' Plugin Manager~~
−
−	~~PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))~~
−	~~startupdirectories=list(pymol.plugins.get_startup_path(True))~~
−	~~if PRIVATE_PATH not in startupdirectories:~~
−	~~startupdirectories.append(PRIVATE_PATH)~~
−	~~if PRIVATE_PATH not in sys.path:~~
−	~~sys.path.append(PRIVATE_PATH)~~
−	~~pymol.plugins.set_startup_path(startupdirectories)~~
−	~~python end~~
−	~~</syntaxhighlight>~~
−
−	~~Note that the '''Plugin Manager''' supports loading entire folders with scripts ('modules').<br>~~
−	~~If you have such a folder, make sure it contains a file called '__init__.py', which can be empty.~~
−
−
−	~~=If you don't have a Plugin Manager=~~
−	~~If you are running an older PyMOL without '''Plugin Manager''' you can either upgrade to the newest version or load plugins the traditional way. <br>~~
−	~~For detailed instructions see: [[Git install scripts]]<br>~~
−	~~Essentially, make sure that the folder is added to PyMOL's search paths.~~
−	~~<syntaxhighlight lang="python">~~
−	~~import sys~~
−	~~import os~~
−	~~pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))~~
−	~~sys.path.append(pymol_git)~~
−	~~</syntaxhighlight>~~
−	~~Import a plugin manually:~~
−	~~<syntaxhighlight lang="python">~~
−	~~# EXAMPLE~~
−	~~delete all~~
−	~~frag LYS~~
−	~~cgo_arrow name N, name O # will not work if 'cgo_arrow' is not loaded~~
−
−	~~import cgo_arrow # PyMOL will look for this file and load it~~
−	~~cgo_arrow name N, name O # should work if it is loaded~~
−	~~</syntaxhighlight>~~
−
−	~~=SEE ALSO=~~
−	~~[[Git install scripts]]~~
−
−
−	~~[[Category:Launching~~]]

@@ Line 10: / Line 10: @@
 '''run_on_startup.py''' can easily be created using a text editor such as notepad.<br>
-The '''run_on_startup.py''' is handled similar to pymolrc files and is executed every time PyMOL launches.<br>
+The '''run_on_startup.py''' is handled similar to [[Pymolrc|pymolrc]] files and is executed every time PyMOL launches.<br>
-An important distinction is that '''run_on_startup.py''' is executed before the pymolrc files and is purely written in python.<br>
+An important distinction is that '''run_on_startup.py''' is executed before the [[Pymolrc|pymolrc]] files and is purely written in python.<br>
 The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\').<br>
 An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).

← Older revision	Revision as of 15:24, 26 November 2014
(No difference)

← Older revision	Revision as of 14:21, 9 June 2014
(No difference)

@@ Line 69: / Line 69: @@
 import os
-pymol_git = os.path.realpath('D:\MY\RANDOM\PATH\TO\Pymol-script-repo') # Adjust this line
+pymol_git = os.path.realpath('D:/MY/RANDOM/PATH/TO/Pymol-script-repo') # Adjust this line
-# Note the '\' instead of '/', beware Windows users!
+# Note the slash ('/') instead of backslash ('\'), beware Windows users!
 os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')

@@ Line 1: / Line 1: @@
-Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as the  [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo].
+Newer versions of PyMOL come with a '''Plugin Manager''', which can be used to load plugins such as those in the [https://github.com/Pymol-Scripts/Pymol-script-repo# PyMOL Script Repo].<br>
 =Manual Setup=
 In the PyMOL menu naviagte to '''Plugins''' > '''Plugin Manager''' <br>
-Here you can manually add directories or scripts that will be loaded upon startup.
+Here you can manually add directories or scripts that will be loaded upon startup.<br>
@@ Line 13: / Line 14: @@
 An important distinction is that '''run_on_startup.py''' is executed before the [[Pymolrc|pymolrc]] files and is purely written in python.<br>
 The recommended location of '''run_on_startup.py''' is the PyMOL home directory (PYMOL_PATH, e.g. something like 'C:\Program Files \PyMOL\').<br>
-An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).
+An advantage is that should PyMOL be installed on a computer with several users, this will be run for all users, while the pymolrc files can be individual (e.g. in the USER directory).<br>
 <syntaxhighlight lang="python">
 #this can be copy-pasted to create run_on_startup.py in the home directory
-−
 # Add paths to sys.path so PyMOL can find modules and scripts
 import sys
 import os
-−
 pymol_git = os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'Pymol-script-repo'))
-−
 os.environ['PYMOL_GIT_MOD'] = os.path.join(pymol_git,'modules')
 sys.path.append(pymol_git)
 sys.path.append(os.environ['PYMOL_GIT_MOD'])
-−
 # Make setting changes to Plugin Manager
-import pymol.plugins
+try: # in case the PyMOL is older and doe not have the module pymol.plugins
+    import pymol.plugins
 #THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
-pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
+    #THIS IS WHERE THE PATH IS ADDED TO INITIALIZE PLUGINS USING THE PLUGIN MANAGER
+    pymol.plugins.set_startup_path([os.path.join(pymol_git, 'plugins'), os.path.join(sys.prefix, 'Lib', 'site-packages', 'pmg_tk', 'startup')])
 pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
-pymol.plugins.autoload = {'apbs_tools': False}
+    pymol.plugins.preferences = {'instantsave': False, 'verbose': False}
-pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
+    pymol.plugins.autoload = {'apbs_tools': False}
+    pymol.plugins.preferences = {'instantsave': True, 'verbose': False}
+    # This can be used to trace if PyMOL executed the file correctly
-# This can be used to trace if PyMOL executed the file correctly. Otherwise remove this part
+    print 'Loaded run_on_stratup.py'
-print 'Loaded run_on_stratup.py'
+except:
 </syntaxhighlight>
+===What if the 'Pymol-script-repo' is not in the PyMOL directory?===
-If the '''Pymol-script-repo''' is located somewhere else the first section of the file will be different.<br>
+If the '''Pymol-script-repo''' is located somewhere else the first section of the '''run_on_startup.py''' file will be different.<br>
 E.g. in the USER directory:
 <syntaxhighlight lang="python">
@@ Line 83: / Line 88: @@
 import os
 import sys
-import pymol.plugins
+import pymol.plugins # Note that this requires the 'new' Plugin Manager
 PRIVATE_PATH=os.path.realpath(os.path.join(os.environ['PYMOL_PATH'], 'plugins_private'))