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  • Python
    ...). It's pseudo-interactive in that you don't get feedback until you type "python end," upon which your code is run the output appears. <source lang="python">
    1 KB (237 words) - 04:30, 3 March 2020
  • Python Integration
    ==Launching Python programs from PyMOL == Running a Python script from PyMOL, usually the command:
    1 KB (213 words) - 04:30, 3 March 2020

Page text matches

  • Python
    ...). It's pseudo-interactive in that you don't get feedback until you type "python end," upon which your code is run the output appears. <source lang="python">
    1 KB (237 words) - 04:30, 3 March 2020
  • Quit
    == Python API == <source lang="python">
    304 bytes (37 words) - 04:05, 7 December 2020
  • Python Integration
    ==Launching Python programs from PyMOL == Running a Python script from PyMOL, usually the command:
    1 KB (213 words) - 04:30, 3 March 2020
  • RPC
    Connect from any client, using python: <source lang="python">
    644 bytes (91 words) - 03:15, 5 March 2018
  • Intra rms cur
    ...ed state without performing any fitting. The rms values are returned as a python array. <source lang="python">
    721 bytes (106 words) - 03:06, 28 March 2014
  • List Colors
    <source lang="python"> #! /usr/bin/python
    384 bytes (59 words) - 02:16, 28 March 2014
  • Git include
    ...//raw.github.com/Pymol-Scripts/Pymol-script-repo/master/README" highlight="python" /> </nowiki> == Python Code ==
    1 KB (181 words) - 02:16, 28 March 2014
  • Unset
    == Python API == <source lang="python">
    651 bytes (89 words) - 03:05, 1 March 2021
  • Centerofmass
    == Python API == <syntaxhighlight lang="python" inline>cmd.centerofmass()</syntaxhighlight>
    757 bytes (92 words) - 00:06, 17 October 2016
  • Get colors
    |type = Python Module <source lang="python">
    2 KB (231 words) - 15:24, 26 November 2014
  • Get raw alignment
    <source lang="python"> # start a python block
    2 KB (255 words) - 03:14, 7 January 2019
  • AAindex
    This script is a python parser for the AAindex flat files which will be downloaded from ftp://ftp.g == Python Example ==
    2 KB (229 words) - 03:58, 4 March 2019
  • Speleo3/test1
    |type = Python Module
    162 bytes (18 words) - 01:44, 28 March 2014
  • Iterate State
    ...on of the current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state. ...ression in valid [http://en.wikipedia.org/wiki/Python_syntax_and_semantics python syntax]
    2 KB (253 words) - 07:02, 3 January 2016
  • Super
    ...' If super ever tells you no matched atoms, then instead of <source lang="python"> </source> try <source lang="python">
    2 KB (387 words) - 15:53, 30 October 2015
  • Editing atoms
    <source lang="python"> <source lang="python">
    2 KB (350 words) - 02:16, 28 March 2014
  • Intra fit
    ...to an atom selection in the specified state. It returns the rms values to python as an array. <source lang="python">
    2 KB (222 words) - 04:31, 26 June 2017
  • Mpng
    ...clusive interval over which to render frames. Thus, you can write a smart Python program that will automatically distribute rendering over a cluster of work == Python API ==
    2 KB (232 words) - 04:20, 4 February 2019
  • PYMOL PATH
    * '''<tt>PYMOL_PATH/examples/</tt>''' Example PyMOL and Python scripts * '''<tt>PYMOL_PATH/run_on_startup.py</tt>''' A python script run at startup, before <tt>.pymolrc</tt>. See [[Plugin Manager]] for
    1 KB (175 words) - 02:04, 27 June 2016
  • Leap Motion
    ...ww.leapmotion.com Leap Motion Controller] working in PyMOL, using the Leap Python API. == Using PyMOL 2.0 (Anaconda Python) ==
    3 KB (433 words) - 04:50, 11 December 2017
  • Pml2py
    This script converts a pml script to a python script. ...d=27331786 pymol-users mailing list] (Subject: Convert pml script to Pymol Python script, Fri, 8 Apr 2011).
    4 KB (467 words) - 04:30, 3 March 2020
  • 2to3
    ...about porting your existing scripts and plugins to Python 3, while keeping Python 2 compatibility. ...We'll exclude all <code>import</code> fixes here, because we want to use a Python 2 compatible fix instead.
    6 KB (838 words) - 18:47, 19 September 2019
  • Jupyter
    ...hould run in the same interpreter, they need to be installed into the same Python environment. [[RPC]] also works with two independent environments. [[Linux Install|Compile and install]] PyMOL with the same Python that you use with Jupyter, into the same environment.
    3 KB (392 words) - 03:43, 6 December 2021
  • Linux Install
    * [http://www.python.org/ Python] 3.6+ * [https://github.com/schrodinger/pmw-patched Pmw] (Python Megawidgets, for legacy GUI/plugins)
    5 KB (713 words) - 05:01, 22 June 2020
  • Plugins
    Plugins can be single Python files (*.py) or directories with an <code>__init__.py</code> file (see [[Pl Plugins were limited to single Python files, directories were not supported yet.
    1 KB (211 words) - 03:24, 10 December 2018
  • Line smooth
    <source lang="python"> <source lang="python">
    534 bytes (77 words) - 02:16, 28 March 2014
  • Wizard
    '''wizard''' launches one of the built-in wizards. There are special Python scripts which work with PyMOL in order to obtain direct user interaction an <source lang="python">
    557 bytes (75 words) - 04:07, 28 March 2014
  • Launching PyMOL
    PyMOL can be started from the command line or from a Python script. Also, PyMOL has lots of [[Command_Line_Options|command line option <source lang="python">
    6 KB (991 words) - 02:16, 28 March 2014
  • Light
    <source lang="python"> <source lang="python">
    2 KB (261 words) - 02:16, 28 March 2014
  • Windows Install
    ...n directory is most likely C:\Users\<Your Username>\AppData\Local\Programs\Python\Python38). Make sure the option to add environment variables is selected. Navigate to the installation directory in a CMD window <source lang = python>cd C:\Users\<Your Username>\Downloads\PyMOL_installation</source> (or where
    5 KB (746 words) - 03:21, 22 June 2021
  • Map set
    <source lang="python"> <source lang="python">
    2 KB (281 words) - 02:16, 28 March 2014
  • Chempy
    Chempy is a python-importable module that can be used to write PyMOL-executable [[scripts]]. <source lang="python">
    5 KB (326 words) - 01:43, 28 March 2014
  • PluginArchitecture
    A plugin is a Python module which uses PyMOL's API. The following entrypoints add functionality <syntaxhighlight lang="python">
    4 KB (547 words) - 03:24, 10 December 2018
  • Launching From a Script
    The recommended way to run PyMOL-Python scripts is by using PyMOL as the interpreter. This is supported by all vers ...ers, the following PyMOL versions also allow to run PyMOL from an existing Python process:
    4 KB (675 words) - 05:13, 26 May 2020
  • Alter State
    ...er_state''' changes the atomic coordinates of a particular state using the python evaluator with a separate name space for each atom. The symbols defined in <source lang="python">
    634 bytes (92 words) - 07:02, 3 January 2016
  • PyMOLWiki:Community Portal
    ** Example 1: Python Code | style="padding: 3em;" |<nowiki><source lang="python"></nowiki><br />
    6 KB (928 words) - 00:49, 28 March 2014
  • CCTBX
    cctbx and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.
    948 bytes (119 words) - 04:05, 7 December 2020
  • Extend
    * All command arguments are passed as strings to the Python function. This may require type conversion before those arguments can be us ...fault '''quiet=1''' argument and have no (or little) output when used in a Python script, but would print a more verbose feedback when invoked as a command.
    4 KB (556 words) - 05:40, 25 July 2018
  • Label font id
    <source lang="python"> ...red with [https://docs.python.org/2/howto/unicode.html#unicode-literals-in-python-source-code unicode literals] as 4-digit hexadecimal escape sequences.
    2 KB (330 words) - 01:14, 28 August 2017
  • Uniprot features
    |type = Python Module <syntaxhighlight lang="python">
    971 bytes (124 words) - 04:07, 28 March 2014
  • Cif keepinmemory
    ...rsed file is kept in memory and made accessible like a dictionary from the Python API. <syntaxhighlight lang="python">
    957 bytes (125 words) - 03:11, 1 April 2019
  • Get Coordinates I
    ...are several ways to extract or load atomic coordinates in PyMOL using the python API. <source lang="python">
    3 KB (407 words) - 07:02, 3 January 2016
  • Contact map visualizer
    * [http://wiki.python.org/moin/TkInter Tkinter] (optional and usually included with PyMOL) sudo apt-get install python-tk python-imaging python-pygame
    4 KB (589 words) - 03:43, 6 December 2021
  • Inertia tensor
    |type = Python Module <source lang="python">
    981 bytes (140 words) - 02:16, 28 March 2014
  • Transform selection
    ...estCOM2 is for molecule two. '''pyU''' becomes '''rotMat'''. The call in Python is then, <source lang="python">
    2 KB (349 words) - 20:24, 9 July 2015
  • ColorByGroup
    *run this Python script inside PyMOL
    937 bytes (125 words) - 03:24, 10 December 2018
  • Grepsel
    Create selections matching motifs, using python regular expression syntax. <source lang="python">
    3 KB (416 words) - 03:06, 28 March 2014
  • CMPyMOL
    * Python 2.7 * Python module dependency
    8 KB (1,116 words) - 05:42, 31 May 2016
  • Pymolrc
    ...file, if it exists. This is simply a script in PyMOL command syntax or in python syntax, depending on the suffix.<br> * Files ending on '''.py''' (or .pym) will be parsed as python scripts, files ending on '''.pml''' or without suffix will be parsed as PyM
    3 KB (420 words) - 05:40, 25 July 2018
  • Gyration tensor
    * [http://wiki.python.org/moin/TkInter Tkinter] and sudo apt-get install python-tk python-numpy
    3 KB (393 words) - 02:16, 28 March 2014

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