This is a read-only mirror of pymolwiki.org

Difference between revisions of "Find pairs"

From PyMOL Wiki
Jump to navigation Jump to search
(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. ...")
 
m (3 revisions)
 
(2 intermediate revisions by one other user not shown)
Line 3: Line 3:
 
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.
 
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">
 
<source lang="python">
Line 11: Line 11:
  
 
== 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}

Latest revision as of 01:46, 28 March 2014

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.

PyMOL API

list cmd.find_pairs(string selection1, string selection2, int state1=1, int state2=1,
    float cutoff=3.5, int mode=0, float angle=45)

ARGUMENTS

  • selection1, selection2 = string: atom selections
  • state1, state2 = integer: state-index (only positive values allowed) {default: 1}
  • 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