dps contact

Calculate residue-level contact maps and contact-number time series.

Synopsis and options

usage: dps contact [-h] -s FILE -f FILE [-n FILE] [-ref REFERENCE_GROUP] [-sel SELECTION_GROUP]
                   -cs {global,residue} [-c CUTOFF] [-cm CUTOFF_MULTIPLIER] [-rd REMOVE_DIAGONAL]
                   [-b START_TIME] [-e END_TIME] [-dt DELTA_TIME] [-pbc] [-ors FILE] [-orr FILE]
                   [-oss FILE] [-or FILE] [-os FILE] [-otrs FILE] [-otrr FILE] [-otss FILE]
                   [-otr FILE] [-ots FILE] [-intraavg] [-otype {dat,xpm,xlsx}]

Calculate residue-level contact maps and contact-number time series.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing the system and simulation
                        settings. (required)
  -f FILE, --input FILE
                        Input trajectory file (.xtc). (required)
  -n FILE, --index FILE
                        Optional index file (.ndx) defining additional atom groups. (default:
                        None)

Output:
  -ors FILE, --output-inter-reference-selection FILE
                        Output inter-chain reference-selection contact map; the --output-type
                        extension is added if omitted. (default: None)
  -orr FILE, --output-inter-reference-reference FILE
                        Output inter-chain reference-reference contact map; the --output-type
                        extension is added if omitted. (default: None)
  -oss FILE, --output-inter-selection-selection FILE
                        Output inter-chain selection-selection contact map; the --output-type
                        extension is added if omitted. (default: None)
  -or FILE, --output-intra-reference FILE
                        Output intra-chain reference contact map; the --output-type extension is
                        added if omitted. (default: None)
  -os FILE, --output-intra-selection FILE
                        Output intra-chain selection contact map; the --output-type extension is
                        added if omitted. (default: None)
  -otrs FILE, --output-time-inter-reference-selection FILE
                        Output inter-chain reference-selection contact-number time series (.xvg);
                        the extension is added if omitted. (default: None)
  -otrr FILE, --output-time-inter-reference-reference FILE
                        Output inter-chain reference-reference contact-number time series (.xvg);
                        the extension is added if omitted. (default: None)
  -otss FILE, --output-time-inter-selection-selection FILE
                        Output inter-chain selection-selection contact-number time series (.xvg);
                        the extension is added if omitted. (default: None)
  -otr FILE, --output-time-intra-reference FILE
                        Output intra-chain reference contact-number time series (.xvg); the
                        extension is added if omitted. (default: None)
  -ots FILE, --output-time-intra-selection FILE
                        Output intra-chain selection contact-number time series (.xvg); the
                        extension is added if omitted. (default: None)
  -otype {dat,xpm,xlsx}, --output-type {dat,xpm,xlsx}
                        File format for contact-map outputs. (default: dat)

Parameters:
  -h, --help            Show this help message and exit.
  -ref REFERENCE_GROUP, --reference-group REFERENCE_GROUP
                        Reference index group forming the x axis of each contact map. (default:
                        None)
  -sel SELECTION_GROUP, --selection-group SELECTION_GROUP
                        Optional selection index group forming the y axis of cross-group maps.
                        (default: None)
  -cs {global,residue}, --cutoff-scheme {global,residue}
                        Contact-cutoff scheme: one global distance or residue-specific distances.
                        (required)
  -c CUTOFF, --cutoff CUTOFF
                        Global contact cutoff, in nm. (default: 0.7)
  -cm CUTOFF_MULTIPLIER, --cutoff-multiplier CUTOFF_MULTIPLIER
                        Multiplier applied to residue sigma values in the residue cutoff scheme.
                        (default: 1.2)
  -rd REMOVE_DIAGONAL, --remove-diagonal REMOVE_DIAGONAL
                        Number of main and neighboring diagonals removed from intra-chain maps.
                        (default: 2)
  -b START_TIME, --start-time START_TIME
                        First trajectory time to analyze, in ns. (default: None)
  -e END_TIME, --end-time END_TIME
                        Last trajectory time to analyze, in ns. (default: None)
  -dt DELTA_TIME, --delta-time DELTA_TIME
                        Approximate interval between analyzed frames, in ns. (default: None)
  -pbc, --treat-pbc     Apply periodic-boundary distances during contact calculation. (default:
                        False)
  -intraavg, --intra-average
                        Average intra-chain contact maps instead of summing them. (default: False)

At least one contact-map or contact-number output option is required.

Examples:
  dps contact -s run.tpr -f run.xtc -ref 0 -sel 1 -cs global -ors contacts.dat

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps contact -h in the installed environment for the same reference at the command line.