NAME¶

cif-grep - A tool like grep to print fields in mmCIF files that match patterns

SYNOPSIS¶

cif-grep [OPTION] pattern file1 [file2..]

DESCRIPTION¶

This tool tries to work in a similar way as grep by searching mmCIF files comparing the content of fields to patterns.

OPTIONS¶

Multiple files can be specified to search. If a directory name if specified, all files in that directory will be searched. Use the --recursive flag to do a recursive search.

--item=<item>, -i <item>

Limit the search to only the item specified in <item>. Default is to search all items. Item should be of the form '_category.item' with the leading underscore.

--quiet, -q

Print only the file names that match the pattern.

--count, -c

Only show the number of hits.

--invert-match, -v

Only select the fields that do not match the pattern.

--line-number, -n

Print the line numbers.

--no-filename, -h

Do not print the filename.

--with-filename, -H

Do print the filename.

--files-with-matches, -l

Print only the names of the files containing matches.

--recursive, -r

Search recursively.

--verbose,-V

Be more verbose, useful to diagnose validation errors.

AUTHOR¶

Written by Maarten L. Hekkelman <maarten@hekkelman.com>

REPORTING BUGS¶

Report bugs at https://github.com/PDB-REDO/cif-tools/issues

SEE ALSO¶

cif-diff, cif-merge, cif-validate, cif2pdb, mmCQL, pdb2cif.