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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
• Pymol.stored
  ...ds by default expose the '''pymol''' module namespace as the [https://docs.python.org/2/library/functions.html#eval globals] dictionary, so '''pymol.stored'' <syntaxhighlight lang="python">
  1 KB (163 words) - 02:44, 1 May 2017
• Practical Pymol for Beginners
  #* or just type, <source lang="python">fetch 1bl8</source> and you can skip the next step (see [[Fetch]] command) <source lang="python">
  12 KB (1,971 words) - 02:46, 3 April 2017
• CCTBX-fedora32
  CCTBX and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible. cctbx.python setup.py install
  1 KB (184 words) - 02:13, 14 September 2020
• Plugin manager
  28 bytes (3 words) - 15:24, 26 November 2014
• Command Line Options
  -l file run python script in thread (spawn) -r file run python script
  5 KB (729 words) - 04:31, 26 June 2017
• Script Highlighting
  ...make it more clear when both reading and writing scripts. Highlighting of python scripts is available by default on most text editors, but support for highl
  2 KB (231 words) - 22:50, 21 April 2015
• Iterate
  ...local namespace exposes all atomic identifiers and properties as read-only Python variables. The global namespace by default is the '''pymol''' module namesp * '''expression''' = str: expression in Python language
  7 KB (1,031 words) - 04:03, 8 January 2018
• Movie color fade
  |type = Python Module <source lang="python">
  1 KB (204 words) - 15:24, 26 November 2014
• AngleBetweenHelices
  |type = Python Module <syntaxhighlight lang="python">
  2 KB (226 words) - 05:54, 9 January 2017
• Movie fade
  |type = Python Module <source lang="python">
  1 KB (193 words) - 02:46, 3 April 2017
• Main Page
  ! Python 3 | New [[2to3|Python 3 compatibility guide]] for scripts and plugins
  4 KB (525 words) - 03:21, 22 June 2021
• Psico
  |type = Python Module [[psico]] is a python module which extends PyMOL with many commands. It was developed as an in-ho
  5 KB (689 words) - 03:58, 4 March 2019
• FocalBlur
  <source lang="python"> or using python syntax:
  4 KB (591 words) - 15:34, 11 July 2014
• Tiff2ccp4
  Note: requires Python 2.7 or later (for argparse). <source lang="python">
  16 KB (1,394 words) - 02:06, 22 August 2016
• Set Key
  '''set_key''' binds a Python function or PyMOL command to a key press. <source lang="python">
  2 KB (273 words) - 03:47, 7 March 2016
• MAC Install
  <source lang="python"> ...or Homebrew to install the dependencies. Make sure you use the appropriate python interpreter (e.g. '''/sw/bin/python2.7''' when using Fink).
  5 KB (752 words) - 04:22, 12 November 2018
• TMalign
  '''tmalign''' is a python module (or script) that provides wrappers to TMalign, TMscore and MMalign. <syntaxhighlight lang="python">
  2 KB (271 words) - 03:27, 13 November 2017
• Color
  <source lang="python"> <source lang="python">color yellow, (name C*)</source>
  6 KB (1,020 words) - 02:11, 24 November 2019
• Cheshift
  ...stall it. In Ubuntu/Debian you could do "sudo apt-get install python-numpy python-scipy". .... Probably the easiest way to do this on a Windows machine is to install a Python Distribution like [[https://store.continuum.io/cshop/anaconda/ Anaconda]] o
  9 KB (1,428 words) - 03:04, 6 February 2017
• Pytms
  <syntaxhighlight lang="python"> <syntaxhighlight lang="python">
  9 KB (1,151 words) - 04:40, 14 December 2015
• MovieSchool 4
  <source lang="python"> <source lang="python">
  4 KB (625 words) - 02:16, 28 March 2014
• RmsdByResidue
  **Python *run this Python script inside PyMOL
  6 KB (869 words) - 03:24, 10 December 2018
• Forster distance calculator
  ...o calculation of proteins in pymol, but is made as a "hack/shortcut" for a python script. <br /> ...rt of pymol to do the calculations, so a student would not need to install python at home, but simply pymol. <br />
  7 KB (1,098 words) - 02:16, 28 March 2014
• Geo Measures Plugin
  You need to install python packages.
  2 KB (289 words) - 03:06, 1 March 2021
• MtsslTrilaterate
  The mtsslTrilaterate program is a python code and it works as a plugin for the PyMOL program. It is a part of the mt ...led. It can be downloaded free of charge from official web site http://www.python.org/.
  7 KB (1,169 words) - 15:24, 26 November 2014
• Cart to frac
  <source lang="python"> <source lang="python">
  2 KB (331 words) - 02:19, 19 September 2016
• ColorByDistance
  *run this Python script inside PyMOL
  2 KB (302 words) - 03:24, 10 December 2018
• MtsslDock
  ...s it is usually the system-wide installation, on my Mac PyMOL uses its own Python: /Applications/PyMOLX11Hybrid.app/pymol/ext/lib/python2.7/site-packages
  5 KB (840 words) - 05:13, 26 May 2020
• Rigimol.morph
  <syntaxhighlight lang="python"> <syntaxhighlight lang="python">
  2 KB (307 words) - 20:53, 9 April 2014
• Ray
  <source lang="python">cmd.ray(int width,int height,int renderer=-1,float shift=0)</source> <source lang="python">
  8 KB (1,344 words) - 15:32, 20 October 2014
• Fetching scripts
  <source lang="python"> <source lang="python">
  6 KB (959 words) - 02:16, 28 March 2014
• 3DNA
  The pdb_get python script comes from [http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/p <source lang="python">
  3 KB (388 words) - 05:26, 8 February 2016
• Dssr block
  The script can be [[run]], imported as a Python module, or installed with the [[Plugin Manager]]. <source lang="python">
  2 KB (353 words) - 05:13, 26 May 2020
• Cealign plugin
  ...nted in C (and another in C++) with the rotations finally done by Numpy in Python (or C++ in version 0.9). Because the computationally complex portion of th <source lang="python">
  22 KB (3,321 words) - 18:50, 31 October 2015
• Flatten obj
  The <code>flatten_obj</code> python script combines multiple objects or states into a single object,
  3 KB (366 words) - 05:01, 16 November 2015
• Lisica
  To work properly, the plugin requires Python with Tkinter and PyMOL. The plugin was mainly tested with PyMOL 1.7.x. ...me directory. This folder contains the executables, log files, icon files, python modules etc.
  10 KB (1,511 words) - 02:19, 19 September 2016
• Ideas
  Always start with Python and only delve down into the C code when absolutely necessary. Although Py ...le to extend PyMOL safely and quickly. Even when performance is critical, Python should be the interface between external C, C++, and Java code and PyMOL's
  17 KB (2,322 words) - 01:04, 19 October 2015
• OLD TOPTOC
  # [[Python_Integration|Python Integration]]
  4 KB (451 words) - 02:16, 28 March 2014
• Kabsch
  ...al space as to minimize the RMSD between them. The following program is a Python implementation of the Kabsch algorithm. ...s on all PyMols 0.97 and newer (haven't tested earlier versions) and I use Python 2.3's Numeric Version 23.3.
  26 KB (4,053 words) - 03:23, 29 April 2019
• MovieSchool 2
  ...to whichever you desire. To use it, just issue the command, <source lang="python">frame X</source> where '''X''' is some integer number indicating the frame <source lang="python">
  11 KB (1,845 words) - 02:16, 28 March 2014
• PyANM
  ...see any error messages, you now have NumPy ready for Pymol! <source lang="python"> import numpy </source>
  7 KB (1,240 words) - 15:32, 20 October 2014
• Apropos
  <source lang="python"> <source lang="python">
  5 KB (730 words) - 03:58, 4 March 2019
• Alter
  '''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in <source lang="python">
  3 KB (413 words) - 07:02, 3 January 2016
• Cluster mols
  The results of 1 and 2 are saved to python pickle files so you do not have to recompute them in subsequent runs. Python packages (install using easy_install or pip)
  8 KB (1,334 words) - 18:29, 25 May 2022
• Align
  ...thus not doing any outlier rejection. The RMSD can also be captured with a python script, see the [[#PyMOL API|API paragraph]] below. Note that the output pr <syntaxhighlight lang="python">
  4 KB (558 words) - 04:50, 11 December 2017
• Fetch
  ...that: !quiet, which means 1 for the PyMOL command language, and 0 for the Python API} <syntaxhighlight lang="python">
  4 KB (590 words) - 03:58, 4 March 2019
• Plugins Tutorial
  <source lang="Python"> └── __init__.py (defines "__init_plugin__(app=None)" function)
  4 KB (636 words) - 03:42, 24 June 2019
• AKMT Lys pred
  <syntaxhighlight lang="python"> python
  8 KB (1,074 words) - 02:39, 24 July 2017
• Distancetoatom
  |type = Python Module <source lang="python">
  4 KB (603 words) - 15:24, 26 November 2014
• TOPTOC
  # [[Python_Integration|Python Integration]]
  6 KB (682 words) - 21:17, 28 March 2014

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