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