.TH cif-grep 1 "2022-11-20" "version 1.0.5" "User Commands"
.if n .ad l
.nh
.SH NAME
cif\-grep \- A tool like grep to print fields in mmCIF files that match patterns
.SH SYNOPSIS
cif\-grep [OPTION] pattern file1 [file2..]
.SH DESCRIPTION
This tool tries to work in a similar way as \fIgrep\fR by searching mmCIF files
comparing the content of fields to patterns.
.SH OPTIONS
Multiple files can be specified to search. If a directory name if specified, all
files in that directory will be searched. Use the \fI--recursive\fR flag to do
a recursive search.
.TP
\fB--item\fR=<item>, \fB-i\fR <item>
Limit the search to only the item specified in \fI<item>\fR. Default is to search
all items. Item should be of the form \fB'_category.item'\fR with the leading
underscore.
.TP
\fB--quiet\fR, \fB-q\fR
Print only the file names that match the pattern.
.TP
\fB--count\fR, \fB-c\fR
Only show the number of hits.
.TP
\fB--invert-match\fR, \fB-v\fR
Only select the fields that do \fBnot\fR match the pattern.
.TP
\fB--line-number\fR, \fB-n\fR
Print the line numbers.
.TP
\fB--no-filename\fR, \fB-h\fR
Do not print the filename.
.TP
\fB--with-filename\fR, \fB-H\fR
Do print the filename.
.TP
\fB--files-with-matches\fR, \fB-l\fR
Print only the names of the files containing matches.
.TP
\fB--recursive\fR, \fB-r\fR
Search recursively.
.TP
\fB--verbose\fR,\fB-V\fR
Be more verbose, useful to diagnose validation errors.
.SH AUTHOR
Written by Maarten L. Hekkelman <maarten@hekkelman.com>
.SH "REPORTING BUGS"
Report bugs at https://github.com/PDB-REDO/cif-tools/issues
.SH "SEE ALSO"
\fBcif-diff\fR, \fBcif-merge\fR, \fBcif-validate\fR, 
\fBcif2pdb\fR, \fBmmCQL\fR, \fBpdb2cif\fR.