Pymol-script-repo - Revision history

Cchem: 31 revisions

2018-12-10T03:24:51Z

31 revisions

Speleo3 at 12:36, 13 November 2018

2018-11-13T12:36:57Z

Speleo3: Speleo3 moved page Git intro to Pymol-script-repo over redirect

2018-11-13T12:33:12Z

Speleo3 moved page Git intro to Pymol-script-repo over redirect

Bell: 1 revision

2014-03-28T03:08:52Z

1 revision

Speleo3: clean up some misleading statements

2012-01-13T11:20:06Z

clean up some misleading statements

Speleo3: Redirected page to Git intro

2011-12-18T12:11:01Z

Redirected page to Git intro

Speleo3: simplify page, remove redundancy

2011-12-12T09:22:27Z

simplify page, remove redundancy

Tlinnet: /* Know problems */

2011-12-10T18:04:39Z

Know problems

Tlinnet: /* External modules - numeric */

2011-12-07T01:41:18Z

External modules - numeric

Tlinnet: /* The slash "\" and "/" problem */

2011-12-07T01:25:29Z

The slash "\" and "/" problem

@@ Line 1: / Line 1: @@
-== Introduction ==
+The [[Pymol-script-repo]] is the preferred place to host scripts which are published on the PyMOLWiki.
 == Benefits ==
-The benefits from this project, is
+# A convenient way, to let PyMOL users download all scripts at the PyMOLWiki, with a minimum of effort.
 # The possibility to let script authors push changes to their script out to PyMOL users.
 # Easier requiring assistance from the PyMOL [http://sourceforge.net/mail/?group_id=4546 mailing list].

← Older revision		Revision as of 12:33, 13 November 2018
Line 1:		Line 1:
−	#~~REDIRECT~~ [[Git ~~intro~~]]	+	== Introduction ==
		+	In November 2011, a group of PyMOL users initiated together with Jason Vertrees, a project to let PyMOL scripts be
		+	under version control system (VCS) called Git.
		+
		+	We hope that script authors and PyMOL users would be interested in this option.
		+
		+	== Benefits ==
		+	The benefits from this project, is
		+	# A convenient way, to let PyMOL users download all scripts at the PyMOL wiki, with a minimum of effort.
		+	# The possibility to let script authors push changes to their script out to PyMOL users.
		+	# Easier requiring assistance from the PyMOL [http://sourceforge.net/mail/?group_id=4546 mailing list].
		+
		+	== Official repository ==
		+	The repository is located at:
		+	: https://github.com/Pymol-Scripts/Pymol-script-repo
		+
		+	== Naming convention ==
		+	We recommend that the name for script filename and pagename at the PyMOLWiki are the same.
		+	All letters should also be lower case.
		+
		+	Example: '''colorbydisplacement'''
		+
		+	{\| class="wikitable"
		+	\| For a description of use
		+	\| http://pymolwiki.org/index.php/colorbydisplacement
		+	\|-
		+	\| For a color coded view
		+	\| https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
		+	\|-
		+	\| Raw download
		+	\| https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
		+	\|-
		+	\| In the users local script library
		+	\| /home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py
		+	\|-
		+	\| To import in PyMOL
		+	\| <code>import colorbydisplacement</code>
		+	\|-
		+	\| To print the available functions in PyMOL
		+	\| <code>help(colorbydisplacement)</code>
		+	\|}
		+
		+	== Read more here ==
		+
		+	* [[git install\|Git install instructions]]
		+	* [[git authors\|Information how to contribute scripts to the repository]].
		+	* [[git script guidelines\|Guidelines how to make a good PyMOL wiki script page]]
		+	* [[git admin\|Information how Repository admins handle the contributions]]

← Older revision		Revision as of 03:08, 28 March 2014
Line 1:		Line 1:
−	~~== Introduction ==~~	+	#REDIRECT [[Git intro]]
−	~~In November 2011, a group of PyMOL users initiated together with Jason Vertrees, a project to let PyMOL scripts be~~
−	~~under version control system (VCS) called Git.~~
−
−	~~We hope that script authors and PyMOL users would be interested in this option.~~
−
−	~~== Benefits ==~~
−	~~The benefits from this project, is~~
−	# ~~A convenient way, to let PyMOL users download all scripts at the PyMOL wiki, with a minimum of effort.~~
−	~~# The possibility to let script authors push changes to their script out to PyMOL users.~~
−	~~# Easier requiring assistance from the PyMOL~~ [~~http://sourceforge.net/mail/?group_id=4546 mailing list].~~
−
−	~~== Official repository ==~~
−	~~The repository is located at:~~
−	~~: https://github.com/Pymol-Scripts/Pymol-script-repo~~
−
−	~~== Naming convention ==~~
−	~~We recommend that the name for script filename and pagename at the PyMOLWiki are the same.~~
−	~~All letters should also be lower case.~~
−
−	~~Example: '''colorbydisplacement'''~~
−
−	~~{\| class="wikitable"~~
−	~~\| For a description of use~~
−	~~\| http://pymolwiki.org/index.php/colorbydisplacement~~
−	\|-
−	~~\| For a color coded view~~
−	~~\| https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py~~
−	\|-
−	~~\| Raw download~~
−	~~\| https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py~~
−	\|-
−	~~\| In the users local script library~~
−	~~\| /home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py~~
−	\|-
−	~~\| To import in PyMOL~~
−	~~\| <code>import colorbydisplacement</code>~~
−	\|-
−	~~\| To print the available functions in PyMOL~~
−	~~\| <code>help(colorbydisplacement)</code>~~
−	\|}
−
−	~~== Read more here ==~~
−
−	* [~~[git install\|~~Git ~~install instructions]]~~
−	* [[git authors\|Information how to contribute scripts to the repository]].
−	* [[git script guidelines\|Guidelines how to make a good PyMOL wiki script page]]
−	* [[git admin\|Information how Repository admins handle the contributions]]

← Older revision		Revision as of 11:20, 13 January 2012
Line 1:		Line 1:
−	#~~REDIRECT~~ [[Git ~~intro~~]]	+	== Introduction ==
		+	In November 2011, a group of PyMOL users initiated together with Jason Vertrees, a project to let PyMOL scripts be
		+	under version control system (VCS) called Git.
		+
		+	We hope that script authors and PyMOL users would be interested in this option.
		+
		+	== Benefits ==
		+	The benefits from this project, is
		+	# A convenient way, to let PyMOL users download all scripts at the PyMOL wiki, with a minimum of effort.
		+	# The possibility to let script authors push changes to their script out to PyMOL users.
		+	# Easier requiring assistance from the PyMOL [http://sourceforge.net/mail/?group_id=4546 mailing list].
		+
		+	== Official repository ==
		+	The repository is located at:
		+	: https://github.com/Pymol-Scripts/Pymol-script-repo
		+
		+	== Naming convention ==
		+	We recommend that the name for script filename and pagename at the PyMOLWiki are the same.
		+	All letters should also be lower case.
		+
		+	Example: '''colorbydisplacement'''
		+
		+	{\| class="wikitable"
		+	\| For a description of use
		+	\| http://pymolwiki.org/index.php/colorbydisplacement
		+	\|-
		+	\| For a color coded view
		+	\| https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
		+	\|-
		+	\| Raw download
		+	\| https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
		+	\|-
		+	\| In the users local script library
		+	\| /home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py
		+	\|-
		+	\| To import in PyMOL
		+	\| <code>import colorbydisplacement</code>
		+	\|-
		+	\| To print the available functions in PyMOL
		+	\| <code>help(colorbydisplacement)</code>
		+	\|}
		+
		+	== Read more here ==
		+
		+	* [[git install\|Git install instructions]]
		+	* [[git authors\|Information how to contribute scripts to the repository]].
		+	* [[git script guidelines\|Guidelines how to make a good PyMOL wiki script page]]
		+	* [[git admin\|Information how Repository admins handle the contributions]]

← Older revision		Revision as of 12:11, 18 December 2011
Line 1:		Line 1:
−	~~== Introduction ==~~	+	#REDIRECT [[Git intro]]
−	~~In November 2011, a group of PyMOL users initiated together with Jason Vertrees, a project to let PyMOL scripts be~~
−	~~under version control system (VCS) called Git.~~
−
−	~~We hope that script authors and PyMOL users would be interested in this option.~~
−
−	~~== Benefits ==~~
−	~~The benefits from this project, is~~
−	~~# A convenient way, to let PyMOL users download all scripts at the PyMOL wiki, with a minimum of effort.~~
−	~~# The possibility to let script authors push changes to their script out to PyMOL users.~~
−	# ~~Easier requiring assistance from the PyMOL~~ [~~http://sourceforge.net/mail/?group_id=4546 mailing list].~~
−	~~# Script will be tested for malicious code before added to the official repository.~~
−
−	~~Read here to install:~~ [~~[git install]]~~
−
−	~~== Official repository ==~~
−	~~The repository is located at:~~
−	~~https://github.com/Pymol-Scripts/Pymol-script-repo~~
−
−	~~== Naming convention ==~~
−	~~We recommend that the name for script filename and pagename at the PyMOLWiki are the same.~~
−	~~All letters should also be lower case.~~
−
−	~~Example: '''colorbydisplacement'''~~
−
−	~~{\| class="wikitable"~~
−	~~\| For a description of use~~
−	~~\| http://pymolwiki.org/index.php/colorbydisplacement~~
−	\|-
−	~~\| For a color coded view~~
−	~~\| https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py~~
−	\|-
−	~~\| Raw download~~
−	~~\| https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py~~
−	\|-
−	~~\| In the users local script library~~
−	~~\| /home/tlinnet/Software/pymol/Pymol-script-repo/colorbydisplacement.py~~
−	\|-
−	~~\| To import in PyMOL~~
−	~~\| <code>import colorbydisplacement</code>~~
−	\|-
−	~~\| To print the available functions in PyMOL~~
−	~~\| <code>help(colorbydisplacement)</code>~~
−	\|}
−
−	~~== Read more here ==~~
−
−	* [[git install\|Simple install instructions for all PyMOL users]]
−	* [[git authors\|Information how to contribute scripts to the repository]]. It's easy!
−	* [[git script guidelines\|Guidelines how to make a good PyMOL wiki script page]]
−	* [[git admin\|Information how Repository admins handle the contributions]]

← Older revision	Revision as of 03:24, 10 December 2018
(No difference)

@@ Line 12: / Line 12: @@
 # Script will be tested for malicious code before added to the official repository.
-Read here to install: http://www.pymolwiki.org/index.php/git_install
+Read here to install: [[git install]]
 == Official repository ==
-The official repository is located at:
+The repository is located at:
   https://github.com/Pymol-Scripts/Pymol-script-repo
-And the Git Read-Only access is:
+== Naming convention ==
- git://github.com/Pymol-Scripts/Pymol-script-repo.git
+We recommend that the name for script filename and pagename at the PyMOLWiki are the same.
-== Same namespace ==
+Example: '''colorbydisplacement'''
-Example: colorbydisplacement
+{| class="wikitable"
-=== Example of namespace ===
+== Read more here ==
-This means, that if a PyMOL user look in their local repo directory, and wonder what '''colorbydisplacement.py''' does.
+* [[git install|Simple install instructions for all PyMOL users]]
-Then user can write:
+* [[git authors|Information how to contribute scripts to the repository]]. It's easy!
-http://www.pymolwiki.org/index.php/colorbydisplacement
+* [[git script guidelines|Guidelines how to make a good PyMOL wiki script page]]
+* [[git admin|Information how Repository admins handle the contributions]]

← Older revision		Revision as of 18:04, 10 December 2011
Line 62:		Line 62:
	# Information how Repository admins handle the contributions		# Information how Repository admins handle the contributions
	#:http://www.pymolwiki.org/index.php/git_admin		#:http://www.pymolwiki.org/index.php/git_admin
−
−	~~= Know problems =~~
−
−	~~== The slash "\" and "/" problem ==~~
−	~~Windows uses backslash '''\''', and Linux uses forwardslash '''/''' in folder and path definitions. <br>~~
−	~~This give sometimes problems, when joining paths in script and plugins, if the author has not foreseen this. <br>~~
−	~~We hope windows users can help report this suggest a solution, so scripts can be used on both systems.~~
−
−	~~It could get solved, by implementing something like this~~
−	~~<syntaxhighlight lang="python">~~
−	~~import sys,os,platform~~
−	~~print sys.path~~
−	~~for path in sys.path:~~
−	~~if platform.system() == 'Windows':~~
−	~~path_desc = "\\"~~
−	~~if platform.system() == 'Linux':~~
−	~~path_desc = "/"~~
−	~~else:~~
−	~~pass~~
−	~~sys.path.append(os.getcwd()+path_desc+"Pymol-script-repo")~~
−	~~print sys.path~~
−
−	~~def add_to_path():~~
−	~~for path in sys.path:~~
−	~~if 'Pymol-script-repo' in path:~~
−	~~if platform.system() == 'Windows':~~
−	~~modules_path = path + "\\modules"~~
−	~~path_desc = "\\"~~
−	~~if platform.system() == 'Linux':~~
−	~~modules_path = path + "/modules"~~
−	~~path_desc = "/"~~
−	~~break~~
−	~~else:~~
−	~~pass~~
−	~~return(modules_path,path_desc)~~
−
−	~~print "\n", add_to_path()~~
−	~~</syntaxhighlight>~~
−
−	~~== External modules - numeric ==~~
−	~~Numeric is sometimes used in scripts. This module is easy to install in Linux, but not so easy to make part of a~~
−	~~PyMOL installation.~~
−
−	~~One could put in some "try" statements, to solve the problem.~~
−	~~<syntaxhighlight lang="python">~~
−	~~import os,sys~~
−	~~os.chdir("/home/tlinnet/Software/pymol/Pymol-script-repo")~~
−	~~sys.path.append(os.getcwd())~~
−	~~try:~~
−	~~import mechanize~~
−	~~except ImportError:~~
−	~~print("Could not import mechanize, trying again")~~
−	~~try:~~
−	~~import modules.mechanize~~
−	~~print("I succeded importing mechanize")~~
−	~~except:~~
−	~~print("I am sorry, no mechanize for you today")~~
−	~~#help(modules.mechanize)~~
−	~~</syntaxhighlight>~~

← Older revision		Revision as of 01:41, 7 December 2011
Line 102:		Line 102:

	== External modules - numeric ==		== External modules - numeric ==
−	Numeric is sometimes used in scripts. This module is	+	Numeric is sometimes used in scripts. This module is easy to install in Linux, but not so easy to make part of a
		+	PyMOL installation.
		+
		+	One could put in some "try" statements, to solve the problem.
		+	<syntaxhighlight lang="python">
		+	import os,sys
		+	os.chdir("/home/tlinnet/Software/pymol/Pymol-script-repo")
		+	sys.path.append(os.getcwd())
		+	try:
		+	import mechanize
		+	except ImportError:
		+	print("Could not import mechanize, trying again")
		+	try:
		+	import modules.mechanize
		+	print("I succeded importing mechanize")
		+	except:
		+	print("I am sorry, no mechanize for you today")
		+	#help(modules.mechanize)
		+	</syntaxhighlight>

@@ Line 68: / Line 68: @@
 Windows uses backslash '''\''', and Linux uses forwardslash '''/''' in folder and path definitions. <br>
 This give sometimes problems, when joining paths in script and plugins, if the author has not foreseen this. <br>
-We hope windows users can help report this of find a solution, so scripts can be used on both systems.
+We hope windows users can help report this suggest a solution, so scripts can be used on both systems.
 It could get solved, by implementing something like this