table of contents
| cif_fix_values() | cif_fix_values() |
NAME¶
cif_fix_values - Corrects various CIF file values and outputs the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from Celsius degrees to Kelvins degrees, removing temperature units of measurement, processing other undefined temperature values; - Fixing misspelled values by using the provided replacement value file; - Fixing enumeration values in CIF file against CIF dictionaries; - Correcting values of '_exptl_crystal_density_meas' data item. All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').SYNOPSIS¶
cif_fix_values --options input1.cif input*.cifDESCRIPTION¶
Corrects various CIF file values and outputs the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from Celsius degrees to Kelvins degrees, removing temperature units of measurement, processing other undefined temperature values; - Fixing misspelled values by using the provided replacement value file; - Fixing enumeration values in CIF file against CIF dictionaries; - Correcting values of '_exptl_crystal_density_meas' data item.All described corrections are enabled by default, but can be disabled by prefixing the corresponding options by '--do-not', '--dont' or '--no' (for example, '--no-fix-temperature').
OPTIONS¶
--fix-temperature Corrects temperature values which have units specified or converts between Celsius degrees and Kelvins. Changes 'room/ambiante temperature' to the appropriate numeric value. Changes other undefined values ('none', 'not given') to '?' symbol.--fix-misspelled replacement_value.lst Corrects misspelled values in the CIF file. Provide a file for the check.
--fix-dois Removes URL or doi: prefixes from values of DOI data items.
--fix-enums Corrects enumeration values in the CIF against CIF dictionaries. Provide dictionaries using option --dictionary (or -d), otherwise script uses the built-in table from CIF Core dictionary.
--treat-as-set Treats certain enumeration values as set data type in the CIF against CIF dictionaries (default). Provide dictionaries using --dictionary (or -d) option, otherwise script uses the built-in table from CIF Core dictionary.
--fix-density-meas Corrects value of data item '_exptl_crystal_density_meas'. Values which are perceived as 'not measured' are changed to '?'. The correct units are deleted. The new data item is created if there are information about temperature.
--fix-weighting-scheme Changes the value of the data item '_refine_ls_weighting_scheme' to the value 'calc' if it contains details which seems to have a formula, and creates new data item '_refine_ls_weighting_details' to store that information. If value is equal to number one, then it is changed to the enumeration value 'unit'.
--fix-atom-sites-solution Corrects the most frequent mistakes in the values of data items '_atom_sites_solution_primary', '_atom_sites_solution_secondary' and '_atom_sites_solution_hydrogens'.
-d, --dictionary cif_core.dic Any valid CIF file, with CIF dictionary (according to DDL1). You can define any number of CIF dictionaries, in a way like this: cif_fix_values --dictionary cif_core.dic --dictionary cod_core.dic
-D, --add-dictionaries cif_core.dic You can add CIF dictionary, in a way like this: cif_fix_values --add-dictionaries cif_core.dic
--clear-dictionaries You can clear all dictionaries used for checking CIF file, in a way like this: cif_fix_values --clear-dictionaries
--use-perl-parser
--use-c-parser Specify parser to parse CIF files. C parser is default.
--help, --usage Output a short usage message (this message) and exit.
--version Output version information and exit.