.TH cif_fix_values
.SH 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'). 
.SH SYNOPSIS
cif_fix_values \-\-options input1.cif input*.cif


.SH 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').

.SH 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.
.SH "REPORTING BUGS"
Report cif_fix_values bugs using e\-mail: cod\-bugs@ibt.lt