table of contents
| cif_cod_deposit() | cif_cod_deposit() |
NAME¶
cif_cod_deposit - Deposit CIFs into COD database using CGI deposition interface.SYNOPSIS¶
cif_cod_deposit --options structure1.cif structure*.cifDESCRIPTION¶
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 host to commit structures 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 http:// protocol and /).
-d, --deposition-type published Specify the deposition type under which the structure is to be deposited (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 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 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 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 can not 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, --dont-use-wipe, --use-rm Specifies whether to use 'wipe' command (if present) or 'rm' command to remove temporary password files.
--common-cif-header Use a standard COD CIF header (default).
--iucr-cif-header Use a COD CIF header agreed with IUCr.
--amcsd-cif-header Use a COD CIF header agreed with R.D.
--crystaleye-cif-header Use a COD CIF header agreed with P.M.-R.
--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.
-P, --progress Ask cif-deposit.pl to report progress of the deposition.
-P-, --no-progress Silence cif-deposit.pl deposition progress report messages.
--output-mode html Specify the output mode (from "html" and "stdout").
-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.