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

Latest revision as of 15:24, 26 November 2014

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