--- name: "cif_validate" section: "1" platform: "linux" package: "cod-tools" version: "3.11.0+dfsg-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/cif_validate" --- # cif\_validate(1) validate CIF files against CIF dictionaries (DDL1 or DDLm). ## 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