Older version of nativecontacts, retained for backwards compatibility.

contacts [ first | reference | ref <ref> | refindex <#> ] [byresidue] [out <filename>] [time <interval>] [distance <cutoff>] [<mask>]

NOTE: Users are encouraged to try the nativecontacts command, an update version of this command.

For each atom given in mask, calculate the number of other atoms (contacts) within the distance cutoff. The default cutoff is 7.0 A. Only atoms in mask are potential interaction partners (e.g., a mask @CA will evaluate only contacts between CA atoms). The results are dumped to filename if the keyword “out” is specified. Thereby, the time between snapshots is taken to be interval. In addition to the number of overall contacts, the number of native contacts is also determined.

Native contacts are those that have been found either in the first snapshot of the trajectory (if the keyword “first” is specified) or in a reference structure (if the keyword “reference” is specified). Finally, if the keyword “byresidue” is provided, results are output on a per-residue basis for each snapshot, whereby the number of native contacts is written to filename.native.