table of contents
| cif_validate() | cif_validate() |
NAME¶
cif_validate - Parse CIF file(s) and CIF dictionary(ies). Check CIF file against CIF dictionaries.SYNOPSIS¶
cif_validate --dictionaries 'cif_core.dic,cif_cod.dic' --options input1.cif input*.cifDESCRIPTION¶
Parse CIF file(s) and CIF dictionary(ies). Check CIF file against CIF dictionaries.OPTIONS¶
-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.