NAME

       cif_validate - validate CIF files against DDL1-compliant CIF dictionaries.

SYNOPSIS

       cif_validate --dictionaries 'cif_core.dic,cif_cod.dic' --options input1.cif input*.cif

DESCRIPTION

       Validate CIF files against DDL1-compliant 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.

       --max-message-count 5
                         Maximum number of validation messages that are reported
                         for each unique combination of validation criteria and
                         validated data items. Provide a negative value (i.e. -1)
                         to output all of the generated validation messages
                         (default: -1).

       --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).

       --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 the presence of data items that are marked as
                         deprecated in the dictionaries. Data item deprecation
                         usually means that it has been replaced with other
                         data items.

       --no-report-deprecated, --ignore-deprecated
                         Do not report presence of data items that are marked
                         as deprecated in the dictionaries (default).

       --report-local-tags
                         Report the presence of local data items.

       --no-report-local-tags, --ignore-local-tags
                         Do not report the presence of local data items (default).

       --allow-double-precision-notation
                         Treat numbers expressed using the double precision
                         notation (i.e. 0.42D+7) as proper numbers in a way
                         that is compatible with DDL1, but not the CIF_1.1
                         syntax.

       --no-allow-double-precision-notation
                         Treat numbers expressed using the double precision
                         notation (i.e. 0.42D+7) as character strings in a
                         way compatible with the CIF_1.1 syntax, but does not
                         cover the full extent of the DDL1 numbers variations
                         (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.

REPORTING BUGS

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

                                                                                                 CIF_VALIDATE(1)