NAME¶

cif_cod_deposit - deposit CIFs into COD database using CGI deposition interface.

SYNOPSIS¶

cif_cod_deposit --options structure1.cif structure*.cif

DESCRIPTION¶

Deposit CIFs into COD database using CGI deposition interface.

OPTIONS¶

-c, --config config-file-with-password.cfg
Specify which file holds depositor user name and
password. Default: "~/.cod_deposit.cfg".

-h, --host test.crystallography.net
Specify the host to which the structure should be
deposited to.

-p, --path cgi-bin/cif-deposit.pl
Specify script path within the host to use for structure
upload.

-u, --url http://test.crystallography.net/cgi-bin/cif-deposit.pl
Specify the full URL to use for structure uploading.
Default: combine --host and --path values using
the "http://" protocol and "/".

-d, --deposition-type published
Specify the deposition type under which the structure
should be deposited. Accepted values:
["published", "personal", "prepublication"].
Default: "published".

-s, --separate-outputs folder-to-put-deposition-outputs/
Specify a folder to put deposition output for each
deposited file.

-r, --read-stdin
Read a list of CIF and Fobs file names from the standard
input in format
<CIF file> [<Fobs file> ]*
for example:
Ice.cif
bi5014sup1.cif all.hkl
bi5005sup1.cif bi50051sup2.hkl bi50052sup3.hkl

--cif "input1.cif input*.cif"
Specify a list of CIF files to be deposited.

--add-cif "input1.cif input*.cif"
Specify additional CIF files to be deposited.

--clear-cif
Clear the list of CIF files to be deposited.

--hkl, --fobs
Specify a list of Fobs files to be deposited.

--add-hkl, --add-fobs
Specify additional Fobs files to be deposited.

--clear-hkl, --clear-fobs
Clear the list of Fobs files to be deposited.

--replace
Specify that the given files are replacements for
previously deposited data.

--release-data
Specify that given files were previously deposited as
prepublication material and should be now released into
the public domain.

--log-message, --log-msg
Specify the log message for redeposited structures.

--script
Do not deposit, print the commands to be executed
on deposition instead.

--run
Enable the execution of deposition commands instead
of simply printing them. Default.

--strict,

--no-ignore-unpaired-datablocks, --dont-ignore-unpaired-datablocks
Stop the deposition if any CIF data block cannot be
paired to any Fobs data blocks (provided that any
unpaired data blocks exist). Default.

--silent, --ignore-unpaired-datablocks
Ignore unpaired CIF and Fobs data blocks.

--require-only-doi
Do not require any other bibliographic information to be
present if CIF data block contains resolvable DOI.

--require-full-bibliography
Require all bibliographic information to be present in
submitted CIF file. Default.

--use-wipe
Use the 'wipe' command to remove temporary password
files. Revert to using 'rm' if 'wipe' is not available.
Default.

--no-use-wipe, --dont-use-wipe, --use-rm
Use the 'rm' command to remove temporary password files.

--common-cif-header
Use the standard COD CIF header. Default.

--iucr-cif-header
Use the COD CIF header agreed with IUCr.

--amcsd-cif-header
Use the COD CIF header agreed with R.D.

--crystaleye-cif-header
Use the COD CIF header agreed with P.M.-R.

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

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

-P, --progress
Ask cif-deposit.pl to report progress of the deposition.

-P-, --no-progress
Silence cif-deposit.pl deposition progress report messages.
Default.

--output-mode html
Specify the output mode. Accepted values:
["html", "stdout"]. Default: "html".

-D, --debug
Request output of the progress information from
cif-deposit.pl to the HTTP server log.

-D-, --no-debug
Disable the output of the progress information from
cif-deposit.pl to the HTTP server log. Default.

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

--version
Output version information and exit.

REPORTING BUGS¶

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