Find pairs: Difference between revisions
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(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. ...") |
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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. | 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"> | ||
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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} | ||
Latest revision as of 06:31, 5 July 2011
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
- distance
- Selection operators within, around and expand