4.6.2. curp analyze pickup-respairs

curp analyze pickup-respairs [-h] -if FORMAT -p PRMTOP_FN -pf PRMTOP_FMT
                             [-i INTERVAL] [-m {com,nearest,farthest}]
                             [-c CUTOFF]
                             [-t [TRIM_RESNAMES [TRIM_RESNAMES ...]]]
                             [-f FORMAT] [-U]
                             [-e [FIRST:LAST [FIRST:LAST ...]]] [-b]
                             trj_fns [trj_fns ...]

Pick up the residue pair table to given file as a ndx format.

Positional arguments

trj_fns

The trajectory file names.

Options

-h, –help

Show this help message and exit.

-if FORMAT, –input-format FORMAT

Specify formats of trajectories.

-p PRMTOP_FN, –input-prmtop-file PRMTOP_FN

Specify the prmtop file to be amber format.

-pf PRMTOP_FMT, –input-prmtop-format PRMTOP_FMT

Specify the format of the prmtop file.

-i INTERVAL, –interval INTERVAL (type: int, default: 1)

Specify interval step to perform the calculation for trajectory.

-m {com,nearest,farthest}, –mode {com,nearest,farthest}

Cutoff method; com, nearest and farthest for residue. “com” is the distance between centers of mass of residues. “nearest” is the distance between nearest atoms of residues. “farthest” is the distance between farthest atoms of residues.

-c CUTOFF, –cutoff CUTOFF (default: 5.0)

Specify the cutoff to pick up.

-t [TRIM_RESNAMES [TRIM_RESNAMES …]], –trim-resnames [TRIM_RESNAMES [TRIM_RESNAMES …]] (default: [])

Residue names for trimming from the target residues.

-f FORMAT, –output-format FORMAT (default: {rid:05}_{rname})

Specify the format for representing residue identify.

-U, –disble-union

Whether residue pair table is calculated by union or intersection when collecting over trajectory specify

-e [FIRST:LAST [FIRST:LAST …]], –exclude-resids [FIRST:LAST [FIRST:LAST …]] (default: [])

Residues that you want to exclude. ex) 5:10 80:150

-b, –enable-residues-both-cxcluded

Whether to include residue pairs that exclude residues