| cif_validate() | cif_validate() |
cif_validate - Parse CIF file(s) and CIF dictionary(ies). Check CIF file against CIF dictionaries.
cif_validate --dictionaries 'cif_core.dic,cif_cod.dic' --options input1.cif input*.cif
Parse CIF file(s) and CIF dictionary(ies). Check CIF file against CIF dictionaries.
-d, --dictionaries 'cif_core.dic,cif_cod.dic'
A list of CIF dictionary files (according to DDL2)
to be used in CIF file validation. List elements
are separated either by ',' or by ' '. To include
dictionaries with filenames containing these symbols,
the --add-dictionary option is used.
-D, --add-dictionary 'cif new dictionary.dic'
Add additional CIF dictionary to the list.
--clear-dictionaries
Remove all CIF dictionaries from the list.
--treat-as-set _atom_site_refinement_flags
Treat values of given data items as a set. For example,
more than one enumeration value could be defined
for a single element. Any number of data item tags can
be provided in the following way:
cif_validate --treat-as-set _tag_1 --treat-as-set _tag_2
Default is the '_atom_site_refinement_flags' data item.
--no-treat-as-set
Do not treat values of any data items as sets.
(see --treat-as-set).
--report-local-tags
Validate data items having tags prefixed with
the '_[local]' prefix. The prefix was used in the COD
to denote locally used data items prior to the creation
of cif_cod.dic. The default is to ignore these data items.
--no-report-local-tags, --ignore-local-tags
Ignore data items having tags prefixed with '_[local]'
prefix. Default.
--ignore-case
Ignore letter case while validating enumeration values.
For example, even though '_atom_site_adp_type' is
restricted to values ('Uani', 'Uiso', 'Uovl', ...),
value 'UANI' would still be treated as valid.
--respect-case, --case-sensitive, --dont-ignore-case
Respect letter case while validating enumeration
values. Default.
--report-deprecated
Report data items that are marked as deprecated in the
dictionaries. Data item deprecation usually means that
it has been replaced with an another data item(s).
--ignore-deprecated
Do not report data items that are marked as deprecated
in the dictionaries (default).
--use-perl-parser
Use Perl parser to parse CIF files.
--use-c-parser
Use C parser to parse CIF files (default)
-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 (default).
--die-on-errors
Terminate script immediately if errors are raised.
--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.
--debug
Output extra information for debugging purposes.
--help, --usage
Output a short usage message (this message) and exit.
-v, --version
Output version information and exit.
Report cif_validate bugs using e-mail: cod-bugs@ibt.lt