--- name: "cif_cod_check" 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_cod_check" --- # cif\_cod\_check(1) parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, https://www.iucr.org/\_\_data/iucr/ftp/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests) ## NAME cif\_cod\_check - parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, https://www.iucr.org/\_\_data/iucr/ftp/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests) ## SYNOPSIS cif\_cod\_check --options input1.cif input\*.cif ## DESCRIPTION Parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09, https://www.iucr.org/\_\_data/iucr/ftp/pub/dvntests or ftp://ftp.iucr.org/pub/dvntests) ## OPTIONS \-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. \--use-perl-parser\ Use Perl parser for CIF parsing. \--use-c-parser\ Use Perl & C parser for CIF parsing (default). \--cif-input\ Use CIF format for input (default). \--json-input\ Use JSON format for input. For every --check-xyz option, there are the following corresponding related options: \--check-only-xyz\ Switch off any other checks and check ONLY xyz\ (the last option on the command line wins). \--no-check-xyz, --do-not-check-xyz, --dont-check-xyz\ Switch off checks of xyz condition. The check options are: \--check-authors\ Check if the author names comply with the COD name\ syntax requirements. Default. \--check-bibliography\ Check if the bibliographical information referring to\ the original source is present in the file. Default. \--require-only-doi\ Treat the presence of the DOI as sufficient bibliographic\ information. \--require-full-bibliography\ Require a more detailed set of bibliographic information\ containing items such as publication journal, year,\ volume, page numbers, etc. Default. \--check-chemical-formula-sum\ Check if the summary chemical formula complies with\ the chemical formula syntax requirements. This check\ uses a simple syntax that does not take into account\ things such as chemical element types, chemical element\ order, etc. Default. \--check-pd-block-relations\ Check if the relations between powder diffractogram\ and phase data blocks are properly described. Default. \--check-spacegroup-info \--check-operators, --check-symmetry-operators \--check-unit-cell \--check-symmetry \--check-simultaneous-presence\ Check if data items from a certain data item grouping\ (e.g. atomic coordinates, anisotropic displacement\ parameters, etc.) are all simultaneously present in\ a data block. Missing data items are reported only\ if at least one data item from the grouping is already\ present in the data block. Default. \--check-limits \--print-limits \--add-limits limits.lst \--limits-file limits.lst \--reset-limits \--check-adp-presence\ Check if each data block contains the atomic\ displacement parameters. The check may optionally\ be applied only to data files that were published after\ a certain year (see --max-year-adp-presence-is-optional).\ Default. \--max-year-adp-presence-is-optional 1969\ Check the presence of atomic displacement parameters\ only in data files published after the specified year.\ Modifies the behaviour of --check-adp-presence.\ Use --no-max-year-adp-presence-is-optional to\ override this option. Default: 1969. \--no-max-year-adp-presence-is-optional\ Check the presence of atomic displacement parameters\ in all data files regardless of the publication year.\ Modifies the behaviour of --check-adp-presence. \--check-temperature-factors\ Alias of the --check-adp-presence option.\ Deprecated. \--max-year-temperature-factors-optional 1969\ Alias of the --max-year-adp-presence-is-optional option.\ Deprecated. \--no-max-year-temperature-factors-optional\ Alias of the --no-max-year-adp-presence-is-optional option.\ Deprecated. \--check-shelx-checksums\ Validate the checksums of embedded SHELX files.\ Default. \--check-embedded-file-integrity \--check-z \--check-disorder \--check-unquoted-strings\ Check if unquoted strings start or end with unusual\ characters such as ";" or "'". The presence of such\ features is a likely indication of an incorrectly\ formatted multi-line text field or a quoted string.\ Disabled by default. \--check-all\ Enable all available checks. \--check-none, --dont-check-any, \--do-not-check-any, --no-check-any\ Disable all available checks. \--help, --usage\ Output a short usage message (this message) and exit. \--version\ Output version information and exit. ## REPORTING BUGS Report cif\_cod\_check bugs using e-mail: cod-bugs@ibt.lt