Iterate State - Revision history

Bell: 1 revision

2016-01-03T07:02:35Z

1 revision

Speleo3: redirect iterate

2015-12-23T21:02:49Z

redirect iterate

Pyadmin: 13 revisions

2014-03-28T01:47:12Z

13 revisions

Speleo3: arguments space and atomic

2012-03-27T17:53:32Z

arguments space and atomic

Speleo3: ARGUMENTS

2011-07-05T11:09:43Z

ARGUMENTS

Speleo3: space argument

2011-03-31T16:20:13Z

space argument

New page

Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position 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.

===USAGE===
iterate_state state,(selection),expression

===EXAMPLES===
==From PyMOL command line==
To get the sum of x coordinates:
<source lang="python">
stored.sum_x = 0.0
iterate_state 1,(all),stored.sum_x = stored.sum_x + x
</source>
To get a list of the positions in a selection
<source lang="python">
stored.pos = []
iterate_state 1, (all), stored.pos.append((x,y,z))
</source>
==From Python==
To get a list of positions
<source lang="python">
# either with global stored object
from pymol import stored
stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')

# or with local object, passed with space argument
pos = []
cmd.iterate_state(1, 'all', 'pos.append((x,y,z))', space={'pos': pos})
</source>

===SEE ALSO===
[[iterate]], [[alter]], [[Alter_State]]

[[Category:Commands|Iterate State]]
[[Category:States|Iterate State]]

Vinnyrose at 14:09, 20 June 2009

2009-06-20T14:09:26Z

New page

===DESCRIPTION===
Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position 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.

===USAGE===
iterate_state state,(selection),expression

===EXAMPLES===
==From PyMOL command line==
To get the sum of x coordinates:
<source lang="python">
stored.sum_x = 0.0
iterate_state 1,(all),stored.sum_x = stored.sum_x + x
</source>
To get a list of the positions in a selection
<source lang="python">
stored.pos = []
iterate_state 1, (all), stored.pos.append((x,y,z))
</source>
==From Python==
To get a list of positions (import stored first)
<source lang="python">
from pymol import stored

stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')
</source>

===SEE ALSO===
[[iterate]], [[alter]], [[Alter_State]]

[[Category:Commands|Iterate State]]
[[Category:States|Iterate State]]

James: /* From Python */

2007-04-09T11:13:03Z

From Python

James: /* From Python */

2007-04-09T11:11:30Z

From Python

AdShea: Made this useful

2006-07-06T12:39:58Z

Made this useful

New page

===DESCRIPTION===
Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position 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.

===USAGE===
iterate_state state,(selection),expression

===EXAMPLES===
==From PyMOL command line==
To get the sum of x coordinates:
<source lang="python">
stored.sum_x = 0.0
iterate_state 1,(all),stored.sum_x = stored.sum_x + x
</source>
To get a list of the positions in a selection
<source lang="python">
stored.pos = []
iterate_state 1, (all), stored.pos.append((x,y,z))
</source>
==From Python==
To get a list of positions
<source lang="python">
stored.pos = []
cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')
</source>

===SEE ALSO===
[[Cmd iterate]], [[Cmd alter]], [[Cmd alter_state]]

[[Category:Commands|iterate_state]]

← Older revision		Revision as of 21:02, 23 December 2015
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		+	#REDIRECT [[iterate]]
		+
	Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position 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.		Iterate state can be used to extract position data from an object or selection. The expression can use the variables x, y, and z which are the position 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.

@@ Line 11: / Line 11: @@
 * selection = string: atom selection
 * expression = string: expression in valid [http://en.wikipedia.org/wiki/Python_syntax_and_semantics python syntax]
 ===EXAMPLES===

← Older revision	Revision as of 07:02, 3 January 2016
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← Older revision	Revision as of 01:47, 28 March 2014
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@@ Line 2: / Line 2: @@
 ===USAGE===
-iterate_state state,(selection),expression
+ iterate_state state, (selection), expression
 ===EXAMPLES===

@@ Line 18: / Line 18: @@
 </source>
 ==From Python==
-To get a list of positions
+To get a list of positions (import stored first)
 <source lang="python">
 from pymol import stored

@@ Line 20: / Line 20: @@
 To get a list of positions
 <source lang="python">
 stored.pos = []
 cmd.iterate_state(1, 'all', 'stored.pos.append((x,y,z))')