table of contents
cif2rdf() | cif2rdf() |
NAME¶
cif2rdf - Parse a CIF file and describe it's properties in RDF format.SYNOPSIS¶
cif2rdf --options input.cif inputs*.cifDESCRIPTION¶
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.
--dont-use-attached-hydrogens,
--no-use-attached-hydrogens,
--ignore-attached-hydrogens Ignore number of implicit hydrogens, specified using _atom_site_attached_hydrogens tag, in calculation of the formula sum. Default option.
--reformat-space-group Correct the formatting of Hermann-Mauguin symmetry space group symbol.
--dont-reformat-space-group,
--leave-space-group Do not correct the formatting of Hermann-Mauguin symmetry space group.
--use-datablocks-without-coordinates Do not filter out data blocks without coordinates.
--do-not-use-datablocks-without-coordinates, --use-all-datablocks
--dont-use-datablocks-without-coordinates
--no-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 option.
--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 option.
--html-utf-escapes Escape Unicode code points using HTML hexadecimal format corresponding to '&#x%04X;' formatted string. Default option.
--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.
--dont-continue-on-errors, --no-continue-on-errors,
--exit-on-errors, --do-not-continue-on-errors, --die-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 CIFs (default).
--help, --usage Output a short usage message (this message) and exit.
--version Output version information and exit.