Provided by: cod-tools_2.4+dfsg-1_amd64 bug

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*.cif

DESCRIPTION

       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 a
                         built-in table derived from the 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 a built-in table derived from the 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.

REPORTING BUGS

       Report cif_fix_values bugs using e-mail: cod-bugs@ibt.lt

                                                                                 cif_fix_values()