A collection of CLI tools for editing and filtering docking results made by CmDock or similar software.
To build every tool run:
cargo build --release
Returns number of SDF records in file or stdin.
USAGE:
sdcount <INPUT>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
-z, --zip Input file is a zip container (currently only
supports zips with a single file)
ARGS:
<INPUT> Sets input file. If missing
reads from stdin.
Distills values of a specified data field in SD records.
USAGE:
sddistill [FLAGS] [OPTIONS] --input <INPUT> --output <OUTPUT>
FLAGS:
-h, --help Prints help information
-r, --recursive Enables recursive directory crawling
-V, --version Prints version information
-z, --zip Input file is a zip container (currently only
supports zips with a single file)
OPTIONS:
-i, --input <INPUT> Sets input. Can be file or directory.
Reads from stdin if set to -
-o, --output <OUTPUT> Sets output directory. Must not be
. as the output filename is the
same as the input filename.
-p, --pattern <PATTERN> SDF field to write out. [default: SCORE]
Outputs file(s) with records that fits specified criterium.
USAGE:
sdfilter [FLAGS] --field <FIELD> --input <INPUT> --operand <operand>
--output <OUTPUT> --value <VALUE>
FLAGS:
-c, --concat Gathers results in a single file.
-h, --help Prints help information
-V, --version Prints version information
-z, --zip Input file is a zip container (currently only supports
zips with a single file)
OPTIONS:
-i, --input <INPUT> Sets input. Can be file or directory.
- reads from stdin
-o, --output <OUTPUT> Sets output directory. Must not be
. as the output filename is the
same as the input filename.
-f, --field <FIELD> SDF field to check. [default: SCORE]
-O, --operand <operand> [values: lt, le, eq, ne, ge, gt]
-v, --value <VALUE> Value to be compared to.
Produces text summaries of SD records.
USAGE:
sdreport [FLAGS] [OPTIONS]
FLAGS:
-l, --list List format: output all data fields for each record.
-t, --table Table format: tabulate selected fields for each record
as processed.
-c, --csv CSV format: comma delimited output of selected fields
for each record as processed.
-s, --summary Summary format: output summary statistics for each
unique value of ligand ID.
-n, --norm Use normalised score field names as default columns in
-t and -c formats (normalised = score / #ligand heavy atoms).
-o, --old Use old (v3.00) score field names as default columns
in -t and -c formats, else use v4.00 field names.
--no-head Don't output column headings in -t and -c formats.
-h, --help Prints help information
-V, --version Prints version information
-z, --zip Input file is a zip container (currently only supports
zips with a single file)
OPTIONS:
-i, --input <input> Sets input file. If missing or - reads from
stdin. [default: -]
-I, --idfield <idfield> Data field to use as ligand ID. [default:
_TITLE1]
-f, --fields <fields> Fields to include in report (idfield is
always included)
Separates file by id field
USAGE:
sdseparate [FLAGS] [OPTIONS] --input <INPUT>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
-z, --zip Input file is a zip container (currently only supports
zips with a single file)
OPTIONS:
-i, --input <INPUT> Sets input file. - reads from stdin.
-o, --output <OUTPUT> Sets output directory. [default: . ]
-f, --field <FIELD> Specifies id field. [default: _TITLE1]
Sorts SD records by given data field.
USAGE:
sdsort [FLAGS] [OPTIONS] --input <INPUT>
FLAGS:
-n, --num Numeric sort (default is text sort).
-r, --reverse Descending sort (default is ascending sort).
-z, --zip Input file is a zip container (currently only supports
zips with a single file).
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-i, --input <INPUT> Sets input file. - reads from stdin.
-o, --output <OUTPUT> Sets output directory. - writes to stdout.
[default: -]
-f, --field <SORT FIELD> Specifies sort field. [default: SCORE]
-g, --group <ID FIELD> Sort results by group. Group by
specified data field. [default: _TITLE1]
Splits SDF file into a specified number of equal files or files with an equal number of records.
USAGE:
sdsplit [OPTIONS] --input <INPUT> --output <OUTPUT>
[--files <NUM OF PACKAGES>/--size <PACKAGE SIZE>]
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
-z, --zip Input file is a zip container (currently only
supports zips with a single file)
OPTIONS:
-i, --input <INPUT> Sets input file. - reads from stdin.
-f, --files <NUM OF PACKAGES> Sets nr of packeges to split input into.
-s, --size <PACKAGE SIZE> Sets size of packages to split input into.
-o, --output <OUTPUT> Sets output directory. [default: .]
-n, --name <NAME> Sets output file names. This is
always suffixed with _# [default: temp]
--files and --size are incompatible, but at least one must be specified
Converts between CRLF and LF line separators. Replaces any non-UTF8 data with �.
USAGE:
lineconv [FLAGS] [OPTIONS] --crlf --lf
FLAGS:
--lf Sets EoL sequence to LF (unix)
--crlf Sets EoL sequence to CRLF (DOS)
-n, --non-destructive Keeps non-UTF8 data untouched
-h, --help Prints help information
-V, --version Prints version information
-z, --zip Input file is a zip container
(currently only supports zips
with a single file)
OPTIONS:
-i, --input <INPUT> Sets input file. If missing
reads from stdin.
-o, --output <OUTPUT> Sets output file. If missing
writes to stdout.