Provided by: cod-tools_3.7.0+dfsg-1build1_amd64 bug

NAME

       cif_validate - validate CIF files against CIF dictionaries (DDL1 or DDLm).

SYNOPSIS

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

DESCRIPTION

       Validate CIF files against CIF dictionaries (DDL1 or DDLm).

OPTIONS

       -d, --dictionaries 'cif_core.dic,cif_cod.dic'
                         A list of CIF dictionaries that the CIF files should
                         be validated against. May include DDL1 and DDLm
                         dictionaries. The order of DDL1 dictionaries
                         in the list is important (see --ddl1-dictionaries).
                         List elements are separated either by ',' or by ' '.
                         To include dictionaries with filenames containing
                         these symbols, the --add-dictionary option should
                         be used.

       -D, --add-dictionary 'cif new dictionary.dic'
                         Add an additional CIF dictionary to the end of the list.

       --clear-dictionaries
                         Remove all CIF dictionaries from the list.

       --ddl1-dictionaries 'cif_core.dic,cif_cod.dic'
                         A list of DDL1 dictionaries that the CIF files should
                         be validated against. The order of dictionaries in
                         the list is important as it determines the dictionary
                         merge order. The first DDL1 dictionary serves as the
                         base while the remaining ones are merged sequentially
                         using the OVERLAY mode. DDL1 dictionaries provided in
                         the generic dictionary list (see --dictionaries) are
                         appended to the end of this list.
                         List elements are separated either by ',' or by ' '.
                         To include dictionaries with filenames containing
                         these symbols, the --ddl1-add-dictionary option
                         should be used.

       --ddl1-add-dictionary
                         Add an additional dictionary to the end of DDL1
                         dictionary list.

       --ddl1-clear-dictionaries
                         Remove all dictionaries from the DDL1 dictionary list.

       --merge-ddl1-dictionaries
                         Merge all DDL1 dictionaries into a single virtual
                         dictionary prior to validation. Default.

       --no-merge-ddl1-dictionaries
                         Do not merge DDL1 dictionaries into a single virtual
                         dictionary prior to validation. Using this option
                         may result in incorrect validation results.

       --ddlm-dictionaries
                         A list of DDLm dictionaries that the CIF files should
                         be validated against. DDLm dictionaries provided in
                         the generic dictionary list (see --dictionaries) are
                         appended to the end of this list.
                         List elements are separated either by ',' or by ' '.
                         To include dictionaries with filenames containing
                         these symbols, the --ddlm-add-dictionary option
                         should be used.

       --ddlm-add-dictionary
                         Add an additional dictionary to the end of DDLm
                         dictionary list.

       --ddlm-clear-dictionaries
                         Remove all dictionaries from the DDLm dictionary list.

       -I, --add-ddlm-import-path './ddlm/cod/'
                         Prepend an additional directory to the dictionary
                         import path. The dictionary import path specifies
                         a list of directories in which to look for files
                         that are imported by DDLm-compliant CIF dictionaries.
                         Directories provided using this option are assigned
                         the highest priority and are searched prior to
                         the directories listed in the COD_TOOLS_DDLM_IMPORT_PATH
                         environment variable or the default import path
                         (directory of the importing dictionary).

       --clear-ddlm-import-path
                         Remove all directories from the dictionary import path
                         that were added using the --add-ddlm-import-path option.
                         Neither COD_TOOLS_DDLM_IMPORT_PATH environment variable
                         nor the default import path is affected by this option.

       --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 (e.g. -1)
                         to output all of the generated validation messages.
                         Default: -1.

       --range-su-multiplier 3.5
                          Multiplier that should be applied to the standard
                          uncertainty (s.u.) when determining if a numeric
                          value resides in the specified range. For example,
                          a multiplier of 3.5 means that the value is treated
                          as valid if it falls in the interval of
                          [lower bound - 3.5 * s.u.; upper bound + 3.5 * s.u.].
                          Default: 3.

       --treat-as-set _atom_site_refinement_flags
                         Treat values of given data items as a set. Due to
                         historical reasons data values of some data items
                         are sometimes formed by concatenating several of
                         the available enumeration values. Any number of data
                         items can be provided in the following way:
                         cif_validate --treat-as-set _tag_1 --treat-as-set _tag_2
                         Default: '_atom_site_refinement_flags'.

       --no-treat-as-set
                         Do not treat values of any data items as sets.
                         (see --treat-as-set).

       --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.

       --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.
                         Applies only to DDL1 dictionaries.

       --respect-case, --case-sensitive, --dont-ignore-case
                         Respect letter case while validating enumeration
                         values. Default.
                         Applies only to DDL1 dictionaries.

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

       --no-allow-double-precision-notation
                         Treat numbers expressed using the double precision
                         notation (e.g. 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.
                         Applies only to DDL1 dictionaries.

       --report-missing-su
                         Report measurand data items that are not accompanied by
                         the mandatory standard uncertainty values.
                         Applies only to DDLm dictionaries.

       --no-report-missing-su, --ignore-missing-su
                         Do not report measurand data items that are not
                         accompanied by the mandatory standard uncertainty
                         values. Default.
                         Applies only to DDLm dictionaries.

       --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.

       --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.

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

       -v, --version
                         Output version information and exit.

ENVIRONMENT

       COD_TOOLS_DDLM_IMPORT_PATH
                         A list of directories in which to look for the
                         DDLm-compliant CIF dictionaries that are imported
                         by other DDLm-compliant CIF dictionaries. List
                         elements are separated by the colon symbol (':').
                         Directories listed in COD_TOOLS_DDLM_IMPORT_PATH
                         have a lower priority than those provided using
                         the command line option (--add-dictionary-import-path),
                         but higher than the default import path directory
                         (directory of the importing dictionary).

REPORTING BUGS

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

                                                                                  CIF_VALIDATE(1)