.TH CIF2COD 1
.SH NAME
cif2cod \- parse a CIF file, prepare a COD database table entry from it.

.SH SYNOPSIS
cif2cod \-\-options input.cif inputs*.cif

.SH DESCRIPTION
Parse a CIF file, prepare a COD database table entry from it.

.SH 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.

.SH "REPORTING BUGS"
Report cif2cod bugs using e\-mail: cod\-bugs@ibt.lt