---
name: "cod_predeposition_check"
section: "1"
platform: "linux"
package: "cod-tools"
version: "2.3+dfsg-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/cod_predeposition_check"
---

# cod\_predeposition\_check(1)

Filter and check pairs of CIF and Fobs files for suitability for deposition to COD database.

## NAME

cod\_predeposition\_check - Filter and check pairs of CIF and Fobs files for suitability for deposition to COD database.

## SYNOPSIS

cod\_predeposition\_check --options input.cif input\*.cif

## DESCRIPTION

Filter and check pairs of CIF and Fobs files for suitability for deposition to COD database.

## OPTIONS

\-d, --database  cod\
                   Use database "cod" to query for structures.

\-h, --host   www.crystallography.net

\-s, --server www.crystallography.net\
                   Query COD database on the host 'www.crystallography.net'.

\-l, --localhost\
                   Use database server on the localhost to query the COD\
                   database.

\-p, --port 3306\
                   Use use the specified port (default 3306) to query\
                   structures.

\-t, --table  data\
                   Use SQL table 'data' to query for structures.

\-u, --user cod\_reader\
                   Use user name 'cod\_reader' to access COD database;\
                   this reader should be granted SELECT privilege, i.e.\
                   should be able to read the COD database, without\
                   supplying a password.

\--password\
                   Use the specified password (default empty) to connect.

\--platform 'SQLite'\
                   Use the SQL database platform 'SQLite' to query\
                   structures (default 'mysql').

\--cif input1.cif\
                   Specify a CIF file to be deposited. Multiple CIF files\
                   can be provided in a way like this:\
                   cod\_predeposition\_check --cif input1.cif --cif input2.cif

\--hkl, --fobs input1.hkl\
                   Specify a Fobs file to be deposited. Multiple Fobs files\
                   can be provided in way like this:\
                   cod\_predeposition\_check --hkl input1.hkl --hkl input2.hkl\
                   The order of the files is important in order to pair CIF\
                   and Fobs files correctly.

\--type, --deposition-type 'prepublication'\
                   Specify the deposition type under which the structure\
                   is to be deposited (default 'published').

\--author-name 'Doe, J.'\
                   Use the specified name as the name of the person\
                   depositing the files.

\--journal 'The Journal'\
                   Use the specified journal name as if it was supplied\
                   by the depositor during the 'prepublication' type\
                   deposition.

\--hold-period 3\
                   Use the specified hold period as if it was supplied by\
                   the depositor.

\--replace\
                   Treat given files as replacements for previously\
                   deposited data.

\--no-replace, --dont-replace\
                   Do not treat given files as replacements for previously\
                   deposited data (default).

\--release\
                   Treat given files as if they were previously deposited\
                   as prepublication material and should now be released\
                   into the public domain.

\--no-release, --dont-release\
                   Do not treat given files as if they were previously\
                   deposited as prepublication material and should now\
                   be released into the public domain (default).

\--bypass-checks\
                   Do not check CIF files for compliance with COD\
                   requirements.

\--dont-bypass-checks, --no-bypass-checks\
                   Check CIF files for compliance with COD requirements\
                   (default).

\--split-pdcif\
                   Output powder diffraction data blocks as a HKL file.

\--dont-split-pdcif, --no-split-pdcif\
                   Output powder diffraction data blocks as part of the\
                   CIF file (default).

\--print-timestamps\
                   Print timestamps to STDOUT at the start and end of\
                   each CIF file deposition.

\--no-print-timestamps, --dont-print-timestamps\
                   Do not print timestamps to STDOUT at the start and end\
                   of each CIF file deposition (default)

\--tmp-dir, --temp-dir\
                   Use the specified temporary directory (default './').

\--use-perl-parser\
                   Use Perl parser to parse CIF files.

\--use-c-parser\
                   Use C parser to parse CIF files (default).

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

\--version\
                   Output version information and exit.

## REPORTING BUGS

Report cod\_predeposition\_check bugs using e-mail: cod-bugs@ibt.lt