---
name: "cif2cod"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif2cod"
---

# cif2cod(1)

parse a CIF file, prepare a COD database table entry from it.

## NAME

cif2cod - parse a CIF file, prepare a COD database table entry from it.

## SYNOPSIS

cif2cod --options input.cif inputs\*.cif

## DESCRIPTION

Parse a CIF file, prepare a COD database table entry from it.

## OPTIONS

\-C, --cod-number 1000000\
                   Use the specified number, 1000000 in this example, as\
                   a COD number for this structure; do not take the number\
                   from the data block name.

\-c, --always-continue\
                   Continue processing and return successful return status\
                   even if errors are diagnosed.

\-c-, --always-die\
                   Stop and return error status if errors are diagnosed.

\-h, --print-header\
                   Print header with data column names at the first line\
                   for CSV output format. Default.

\-h-, --no-print-header, --dont-print-header\
                   Do not print column names on the first (header) line\
                   for CSV output format.

\-k, --keywords\
                   Print values in separate lines prefixed with keywords.

\--include-keywords-with-undefined-values\
                   Print the keyword line with an empty value even if the\
                   value is undefined.

\--exclude-keywords-with-undefined-values\
                   Do not print the keyword line at all if the value is\
                   undefined. Default.

\--use-attached-hydrogens\
                   Include number of implicit hydrogen atoms, specified\
                   using the \_atom\_site\_attached\_hydrogens data item, into\
                   the formula sum. Default.

\--no-use-attached-hydrogens,

\--dont-use-attached-hydrogens,

\--ignore-attached-hydrogens\
                   Ignore number of implicit hydrogen atoms, specified\
                   using the \_atom\_site\_attached\_hydrogens data item, in\
                   calculation of the formula sum.

\--reformat-space-group\
                   Correct the formatting of Hermann-Mauguin space group\
                   symbol.

\--no-reformat-space-group,

\--dont-reformat-space-group,

\--leave-space-group\
                   Do not correct the formatting of Hermann-Mauguin\
                   space group symbol. Default.

\--use-datablocks-without-coordinates,

\--use-all-datablocks\
                   Do not filter out data blocks without coordinates.

\--no-use-datablocks-without-coordinates,

\--do-not-use-datablocks-without-coordinates,

\--dont-use-datablocks-without-coordinates,

\--skip-datablocks-without-coordinates\
                   Filter out data blocks without coordinates. Default.

\--require-only-doi\
                   Do not require all bibliographic details (authors,\
                   journal name, title, year, volume and first page of\
                   the publication) to be present if publication DOI is\
                   specified.

\--require-full-bibliography\
                   Require author names, journal name, volume, publication\
                   title, year and first page to be present. Default.

\--columns file,flags,Robs

\--columns "file flags Robs"\
                   Print only columns specified in this option.

\--validate-by-schema doc/CODDictionary.xml\
                   Validate the output by supplied XML schema, where the\
                   SQL data types are given in the following manner:

                  \<CODDictionary\>\
                     \<CODParameter name="file"\>\
                       \<SQLDataType\>mediumint(7) unsigned\</SQLDataType\>\
                       ...\
                     \</CODParameter\>\
                   \</CODDictionary\>

\--continue-on-errors\
                   Do not terminate script if errors are raised.

\--die-on-errors,

\--no-continue-on-errors,

\--do-not-continue-on-errors,

\--dont-continue-on-errors,

\--exit-on-errors\
                   Terminate script immediately if errors are raised. Default.

\--continue-on-warnings\
                   Do not terminate script if warnings are raised. Default.

\--die-on-warnings\
                   Terminate script immediately if warnings are raised.

\--continue-on-notes\
                   Do not terminate script if notes are raised. Default.

\--die-on-notes\
                   Terminate script immediately if notes are raised.

\--use-perl-parser\
                   Use the Perl parser for parsing CIFs.

\--use-c-parser\
                   Use the faster C parser for parsing CIFs. Default.

\--cif-input\
                   Use CIF format for input. Default.

\--json-input\
                   Use JSON format for input.

\--help, --usage\
                   Output a short usage message (this message) and exit.

\--version\
                   Output version information and exit.

## REPORTING BUGS

Report cif2cod bugs using e-mail: cod-bugs@ibt.lt