Find pairs - Revision history

Pyadmin: 3 revisions

2014-03-28T01:46:42Z

3 revisions

Speleo3: state-index

2011-07-05T11:31:27Z

state-index

Speleo3: PyMOL API

2011-06-24T08:34:33Z

PyMOL API

Speleo3: Created page with "'''find_pairs''' is an API only function which returns a list of atom pairs. Atoms are represented as (model,index) tuples. Can be restricted to hydrogen-bonding-like contacts. ..."

2011-06-24T08:33:46Z

Created page with "'''find_pairs''' is an API only function which returns a list of atom pairs. Atoms are represented as (model,index) tuples. Can be restricted to hydrogen-bonding-like contacts. ..."

New page

'''find_pairs''' is an API only function which returns a list of atom pairs. Atoms are represented as (model,index) tuples.

Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks atom orientation, not atom type (so would hydrogen bond between carbons for example), so make sure to provide appropriate atom selections.

== API ==

<source lang="python">
list cmd.find_pairs(string selection1, string selection2, int state1=1, int state2=1,
float cutoff=3.5, int mode=0, float angle=45)
</source>

== ARGUMENTS ==

* cutoff = float: distance cutoff {default: 3.5}

* mode = integer: if mode=1, do coarse hydrogen bonding assessment {default: 0}

* angle = float: hydrogen bond angle cutoff, only if mode=1 {default: 45.0}

== NOTE ==

Although this does a similar job like "[[distance]]", it uses a completely different routine and the "mode" argument has different meanings!

== SEE ALSO ==

* [[distance]]
* Selection operators [[Selection_Algebra|within, around and expand]]

[[Category:Scripting]]

← Older revision		Revision as of 11:31, 5 July 2011
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	== ARGUMENTS ==		== ARGUMENTS ==
		+
		+	* selection1, selection2 = string: atom selections
		+
		+	* state1, state2 = integer: state-index (only positive values allowed) {default: 1}

	* cutoff = float: distance cutoff {default: 3.5}		* cutoff = float: distance cutoff {default: 3.5}

← Older revision	Revision as of 01:46, 28 March 2014
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 Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks atom orientation, not atom type (so would hydrogen bond between carbons for example), so make sure to provide appropriate atom selections.
-== API ==
+== PyMOL API ==
 <source lang="python">