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2014-04-08T04:32:37Z

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2014-04-05T16:03:21Z

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= Overview =
[[toGroup]] will convert a multistate object into a group of single-state objects. ''Be warned, by default it deletes your original object (since it's extracting a copy).

PyMOL does a great job at handling multistate objects and grouping them together. One thing that I found myself doing over and over again was
* loading a multistate object (say a PDBQT file with 100 ligand poses)
* splitting that object into all 100 states, with some given prefix
* then grouping them into their own group
* and then finally removing the original.

This became tedious, so I automated that with this script.

= Examples =
<source lang="python">
# A multistate object (20 NMR states)
fetch 1nmr

# Create the group called, "nmrEnsemble"
# from '1nmr' and name all the new states state1,
# state2, state3, etc.
toGroup nmrEnsemble, 1nmr, prefix=state
</source>

= The Code =
<source lang="python">
import pymol
from pymol import cmd

def toGroup(groupName,sel,prefix="",delOrig=True):
"""
DESCRIPTION
toGroup will take a multistate object and extract it
to a group with N objects all in state #1. It essentially
performs the following:

split_states myObj, prefix=somePrefix
group newGroup, somePrefix*
delete myObj

PARAMETERS:

groupName (string)
The name of the group to create

sel (string)
The name of the selection/object from which
to make the group

prefix (string)
The prefix of the names of each of split states.
For example, if your prefix is ''obj'' and is in
states 1 through 100 then the states will be labeled
obj1, obj2, obj3, ..., obj100.

delOrig (string/boolean)
If true then delete the original selection, otherwise not.

RETURN

Nothing, it makes a new group.

"""
if prefix=="":
prefix="grouped"

cmd.split_states(sel, prefix=prefix)
cmd.group(groupName,prefix+"*")

if delOrig:
cmd.delete(sel)

cmd.extend("toGroup", toGroup)
</source>

= See Also =
[[group]], [[saveGroup]], [[select]], [[Category:States]], [[split_states]], [[delete]], [[extend]].

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]

← Older revision		Revision as of 16:03, 5 April 2014
Line 1:		Line 1:
		+	{{Infobox script-repo
		+	\|type = script
		+	\|filename = togroup.py
		+	\|author = [[User:Inchoate\|Jason Vertrees]]
		+	\|license = -
		+	}}
	= Overview =		= Overview =
	[[toGroup]] will convert a multistate object into a group of single-state objects. ''Be warned, by default it deletes your original object (since it's extracting a copy).		[[toGroup]] will convert a multistate object into a group of single-state objects. ''Be warned, by default it deletes your original object (since it's extracting a copy).

← Older revision	Revision as of 04:32, 8 April 2014
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