Find pairs

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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.


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


  • 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}


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