Topmask

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topmask: version 2.231.418d045(2020-03-01 18:49) [CATs - Conversion And Analysis Tools]

Name

topmask

Synopsis

topmask [OPTIONS] [--] PARM MASK

Description

Print the names of atoms or residues selected by the application of MASK. Current implementation fully supports ambmask syntax (see AMBER manual).

Arguments

PARM topology file name. If - is provided then topology is read from standard input stream.

MASK mask specification

Options

-c, --coords CRD optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)

-f, --maskfile read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.

-r, --residues perform selection on the level of residues. The mask specification cannot contains atom selectors (@ @ @%).

-o, --output FORMAT specify output format. Default format 'cats' prints atoms or residues as the list sorted into three colums. Format 'list' prints the same information as 'cats' but only to a single colum without any header. Format 'number' prints only the number of selected atoms or residues. Format 'amber' provides the same output as ambmask. Format 'bmask' write bitmap mask. (Default: cats)

-v, --verbose increase output verbosity

--version output version information and exit

-h, --help display this help and exit