NAME¶

cif_cod_check - parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, ftp://ftp.iucr.ac.uk/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests)

SYNOPSIS¶

cif_cod_check --options input1.cif input*.cif

DESCRIPTION¶

Parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, ftp://ftp.iucr.ac.uk/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests)

OPTIONS¶

-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.

--continue-on-errors
Do not terminate script if errors are raised.

--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 Perl parser for CIF parsing.

--use-c-parser
Use Perl & C parser for CIF parsing (default).

--cif-input
Use CIF format for input (default).

--json-input
Use JSON format for input.

For every --check-xyz option, there are the following corresponding related options:

--check-only-xyz
Switch off any other checks and check ONLY xyz
(the last option on the command line wins).

--no-check-xyz, --do-not-check-xyz, --dont-check-xyz
Switch off checks of xyz condition.

The check options are:

--check-authors
Check if the author names comply with the COD name
syntax requirements. Default.

--check-bibliography
Check if the bibliographical information referring to
the original source is present in the file. Default.

--require-only-doi
Treat the presence of the DOI as sufficient bibliographic
information.

--require-full-bibliography
Require a more detailed set of bibliographic information
containing items such as publication journal, year,
volume, page numbers, etc. Default.

--check-chemical-formula-sum
Check if the summary chemical formula complies with
the chemical formula syntax requirements. This check
uses a simple syntax that does not take into account
things such as chemical element types, chemical element
order, etc. Default.

--check-pd-block-relations
Check if the relations between powder diffractogram
and phase data blocks are properly described. Default.

--check-spacegroup-info

--check-operators, --check-symmetry-operators

--check-unit-cell

--check-symmetry

--check-simultaneous-presence
Check if data items from a certain data item grouping
(e.g. atomic coordinates, anisotropic displacement
parameters, etc.) are all simultaneously present in
a data block. Missing data items are reported only
if at least one data item from the grouping is already
present in the data block. Default.

--check-limits

--print-limits

--add-limits limits.lst

--limits-file limits.lst

--reset-limits

--check-adp-presence
Check if each data block contains the atomic
displacement parameters. The check may optionally
be applied only to data files that were published after
a certain year (see --max-year-adp-presence-is-optional).
Default.

--max-year-adp-presence-is-optional 1969
Check the presence of atomic displacement parameters
only in data files published after the specified year.
Modifies the behaviour of --check-adp-presence.
Use --no-max-year-adp-presence-is-optional to
override this option. Default: 1969.

--no-max-year-adp-presence-is-optional
Check the presence of atomic displacement parameters
in all data files regardless of the publication year.
Modifies the behaviour of --check-adp-presence.

--check-temperature-factors
Alias of the --check-adp-presence option.
Deprecated.

--max-year-temperature-factors-optional 1969
Alias of the --max-year-adp-presence-is-optional option.
Deprecated.

--no-max-year-temperature-factors-optional
Alias of the --no-max-year-adp-presence-is-optional option.
Deprecated.

--check-shelx-checksums
Validate the checksums of embedded SHELX files.
Default.

--check-embedded-file-integrity

--check-z

--check-disorder

--check-all
Enable all available checks.

--check-none, --dont-check-any,

--do-not-check-any, --no-check-any
Disable all available checks.

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

--version
Output version information and exit.

REPORTING BUGS¶

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