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 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 hydrogens, specified using
                         _atom_site_attached_hydrogens tag, into the formula
                         sum (default).

       --no-use-attached-hydrogens,

       --dont-use-attached-hydrogens,

       --ignore-attached-hydrogens
                         Ignore number of implicit hydrogens, specified using
                         _atom_site_attached_hydrogens tag, in calculation of
                         the formula sum.

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

       --no-reformat-space-group,

       --dont-reformat-space-group,

       --leave-space-group
                         Do not correct the formatting of Hermann-Mauguin
                         symmetry 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

                                                                                       CIF2COD(1)