| cif_fix_values() | cif_fix_values() |
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').
cif_fix_values --options input1.cif input*.cif
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').
--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.
Report cif_fix_values bugs using e-mail: cod-bugs@ibt.lt