Find pairs

From PyMOLWiki
Revision as of 04:33, 24 June 2011 by Speleo3 (talk | contribs) (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. ...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

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

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

  • 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