NAME

cif2rdf - parse a CIF file and describe it's properties in RDF format.

SYNOPSIS

cif2rdf --options input.cif inputs*.cif

DESCRIPTION

Parse a CIF file and describe it's properties in RDF format.

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.

--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.

--vocabulary-namespace cod
Use vocabulary namespace "cod" to prefix properties
native to the queried database.

--vocabulary-url-prefix http://www.crystallography.net/cod/doc/rdf/
Specify URL prefix for database's native namespace.

--prefix, --db-url-prefix http://www.crystallography.net/cod/
Specify URL prefix for all objects in the queried database.

--postfix, --db-url-postfix .html
Specify URL postfix for all objects in the queried database.

--split-author-names
Split author names in internal database representation at
semicolons (';') to produce RDF-parsable list of author names.
Each author in such list is marked with "author" property
instead of "authors", which is used for non-split value
(default).

--no-split-author-names, --dont-split-author-names
Make no assumptions about internal database representation
of author list.

--xml-output
Output RDF in XML carrier format (default).

--n3-output
Output RDF in N3 (Notation3) carrier format.

--turtle-output
Output RDF in Turtle carrier format.

--ntriples-output, --n-triples-output
Output RDF in N-Triples carrier format.

--replace-utf-codepoints-from
Replace Unicode code points starting at specified
point with carrier format-specific entities.

--no-replace-utf-codepoints, --dont-replace-utf-code-points
Leave Unicode code points unescaped (default).

--html-utf-escapes
Escape Unicode code points using HTML hexadecimal
format corresponding to '&#x%04X;' formatted string
(default).

--internal-utf-escapes
Escape Unicode code points using internal format
corresponding to '\u%04X' formatted string.

--utf-escape-format
Escape Unicode code points using format
corresponding to the provided formatted string.

--no-header
Skip header of corresponding format. May be useful
for generation of catenable output.

--no-footer
Skip footer of corresponding format. May be useful
for generation of catenable output.

--only-header
Print header of corresponding format and exit.

--only-footer
Print footer of corresponding format and exit.

--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).

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

--version
Output version information and exit.

REPORTING BUGS

Report cif2rdf bugs using e-mail: cod-bugs@ibt.lt