.TH CIF_VALIDATE 1 .SH NAME cif_validate \- validate CIF files against CIF dictionaries (DDL1 or DDLm). .SH SYNOPSIS cif_validate \-\-dictionaries 'cif_core.dic,cif_cod.dic' \-\-options input1.cif input*.cif .SH DESCRIPTION Validate CIF files against CIF dictionaries (DDL1 or DDLm). .SH 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 (i.e. \-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. 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: '_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 (i.e. 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 (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). 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. .SH "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). .SH "REPORTING BUGS" Report cif_validate bugs using e\-mail: cod\-bugs@ibt.lt