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