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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>
| | Since version 1.5.0.5 PyMOL comes 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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| =Manual Setup= | | == Features == |
| 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= | |
| ===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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|
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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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|
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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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|
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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 '\' instead of '/', 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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|
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|
| | * Install/Uninstall plugins |
| | * Disable plugins and load them on demand to optimize PyMOL's startup time |
| | * Configure the plugin search path |
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| ===Appending additional paths to the Plugin Manager=== | | ===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> | | 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>
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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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|
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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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|
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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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|
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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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| | : Plugin > Plugin Manager > Settings > Add new directory... |
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| =If you don't have a Plugin Manager= | | == Screenshots == |
| 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
| | [[Image:plugin_manager_installed.png]] |
| cgo_arrow name N, name O # should work if it is loaded
| | [[Image:plugin_manager_install_new.png]] |
| </syntaxhighlight>
| | [[Image:plugin_manager_settings.png]] |
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| =SEE ALSO= | | == See Also == |
| [[Git install scripts]]
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| | * [[Pymol-script-repo]] |
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| [[Category:Launching]] | | [[Category:Launching]] |
| | [[Category:Plugins]] |
