Provided by: cod-tools_3.4.0+dfsg-1build2_amd64 bug

NAME

       cif_filter  -  parse a CIF file and print out essential data values in the CIF format, the
       COD CIF style. This script has also many  capabilities  --  it  can  restore  space  group
       symbols  from  symmetry  operators  (consulting  predefined  tables),  parse  and  tidy-up
       _chemical_formula_sum, compute cell volume, exclude  unknown  or  "empty"  tags,  and  add
       specified bibliography data.

SYNOPSIS

       cif_filter --options input1.cif input*.cif

DESCRIPTION

       Parse a CIF file and print out essential data values in the CIF format, the COD CIF style.

       This script has also many capabilities -- it can restore space group symbols from symmetry
       operators (consulting predefined tables), parse and tidy-up _chemical_formula_sum, compute
       cell volume, exclude unknown or "empty" tags, and add specified bibliography data.

OPTIONS

       -a, --authors  'John Doe; Jane Doe; Joe Bloggs'

       -j, --journal 'Acta Cryst. A'

       -v, --volume    36

       -i, --issue      1

       -p, --page     123

       --start-page   123

       -e, --end-page 132

       -y, --year     1999

       -D, --doi      10.1010/xyz9999
                         Specify bibliographic data to be included into the output.

       -B, --bibliography bibliography.cif

       --bibliography bibliography.mrk
                         Provide a bibliography file with the bibliographic
                         information  to be included into the output. The
                         bibliography information can be provided in CIF format
                         or in a XML-like .mrk file with data items between
                         <authors>, <journal>, <volume>, <issue>, <year>,
                         <pages>123-132</pages> tags.

       --leave-bibliography
                         Combine bibliographies from various sources. Values of lower
                         precedence are overwritten, but never deleted. List of
                         bibliography sources in order of increasing precedence:
                           1) the bibliography tags of the original CIF file;
                           2) the optional bibliography file;
                           3) the user specified command line options.

       --discard-bibliography
                         Only retain the bibliography tags from the bibliography
                         source of highest precedence (see '--leave-bibliography'
                         option) (default).

       --leave-title
                         Do not delete the publication title obtained from the
                         source of lower precedence, even if the
                         '--discard-bibliography' option is enabled.

       -g, --global-priority
                         Assume bibliography found in 'data_global' data block
                         has precedence over bibliographies found in all the other
                         data blocks.

       -g-, --no-global-priority
                         Assume bibliography found in 'data_global' data block
                         does not have precedence over bibliographies found in
                         all the other data blocks. Only missing bibliographic
                         information will be copied from the 'data_global' data
                         block (default).

       --exclude-publication-details
                         Exclude potentially copyrighted and irrelevant tags.

       --dont-exclude-publication-details,

       --no-exclude-publication-details
                         Do not exclude potentially copyrighted and irrelevant tags.

       -h, --add-cif-header header_file.cif
                         Prepend each of the output files with the comments from
                         the beginning of the specified file.

       -s, --estimate-spacegroup
                         Estimate space group symbols from the symmetry operators
                         in the input.

       -s-, --dont-estimate-spacegroup, --no-estimate-spacegroup
                         Do not estimate space group symbols from the symmetry
                         operators in the input (default).

       --keep-unrecognised-spacegroups
                         This option is a modifier for the '--estimate-spacegroup'
                         option. Leave tags with unrecognised space group information
                         as they are.

       --dont-keep-unrecognised-spacegroups,

       --no-keep-unrecognised-spacegroups
                         This option is a modifier for the '--estimate-spacegroup'
                         option. Replace the values of tags with unrecognised space
                         group information with unknown values (represented as '?')
                         and store the unrecognised space group information in
                         '_cod_original_sg_*' tags (default).

       --reformat-space-group, --reformat-spacegroup
                         Correct the formatting of Hermann-Mauguin symmetry
                         space group symbol.

       --dont-reformat-space-group, --leave-space-group

       --dont-reformat-spacegroup, --leave-spacegroup
                         Leave the Hermann-Mauguin symmetry space group symbol
                         as is (default).

       --exclude-empty-tags
                         Remove data items that contain only empty values.
                         A value is considered empty if it is equal to a
                         single question mark ('?') or a single period ('.').

       --dont-exclude-empty-tags, --no-exclude-empty-tags
                         Disable the '--exclude-empty-tags' option (default).

       --placeholder-tag-list '_chemical_name_common,_chemical_name_systematic'
                         A comma-separated list of data items that should be
                         checked for placeholder values (default:
                         '_chemical_name_common,_chemical_name_systematic').

       --exclude-placeholder-tags
                         Remove data items that contain common placeholder values
                         (i.e. multiline value consisting only of white spaces
                         and question marks. Only data items specified using
                         the --placeholder-tag-list are affected by this option.

       --dont-exclude-placeholder-tags, --no-exclude-placeholder-tags
                         Disable the '--exclude-placeholder-tags' option (default).

       --exclude-redundant-chemical-names
                         Remove data items related to various chemical names
                         (systematic, common, mineral) if the stored values
                         match the chemical formula.

       --dont-exclude-redundant-chemical-names,

       --no-exclude-redundant-chemical-names
                         Disable the '--exclude-redundant-chemical-names'
                         option (default).

       --exclude-empty-non-loop-tags
                         Remove tags that contain empty values and are not
                         contained within the CIF _loop structure. For the
                         definition of empty values, see '--exclude-empty-tags'
                         option. This option does not override the
                         '--exclude-empty-tags' option.

       --dont-exclude-non-loop-empty-tags,

       --no-exclude-non-loop-empty-tags
                         Disable the '--exclude-empty-non-loop-tags' option (default).

       --exclude-unknown-tags
                         Remove tags that contain only unknown values. A value is
                         considered unknown if it is equal to a single question
                         mark ('?').

       --dont-exclude-unknown-tags, --no-exclude-unknown-tags
                         Disable the '--exclude-unknown-tags' option (default).

       --exclude-unknown-non-loop-tags
                         Remove tags that contain unknown values and are not
                         contained within the CIF _loop structure. For the
                         definition of unknown values, see '--exclude-unknown-tags'
                         option. This option does not override the
                         '--exclude-unknown-tags' option.

       --dont-exclude-non-loop-unknown-tags,

       --no-exclude-non-loop-unknown-tags
                         Disable the '--exclude-unknown-non-loop-tags' option (default).

       -x, --extra-tag-list tag-list.lst
                         Add additional tags to the list of recognised CIF tags.
                         These extra tags are presented in a separate file, one
                         tag per line.

       --exclude-misspelled-tags
                         Remove tags that were not present in the recognised tag list.

       --dont-exclude-misspelled-tags,

       --no-exclude-misspelled-tags
                         Disable the '--exclude-misspelled-tags' option (default).

       --parse-formula-sum
                         Parse '_chemical_formula_sum' tag value and reformat it
                         according to the Hill system ordering. If the original and
                         reformatted formulae differ, replace the original value
                         with the reformatted one and store the original value as
                         the '_cod_original_formula_sum' tag value.

       --dont-parse-formula-sum, --no-parse-formula-sum
                         Do not parse '_chemical_formula_sum' tag value.

       --fix-syntax-errors
                         Try to fix syntax errors in the input CIF files that can
                         be corrected unambiguously.

       --dont-fix-syntax-errors, --no-fix-syntax-errors
                         Do not try to fix syntax errors in input CIF files (default).

       --retain-tag-order
                         Print tags in the same order they appeared in the
                         original file.

       --dont-retain-tag-order
                         Disregard original tag order while printing the tags (default).

       --preserve-loop-order
                         Print loops in the same order they appeared in the original
                         file.

       --use-internal-loop-order
                         Disregard original loop order while printing the tags
                         (default).

       --calculate-cell-volume
                         Calculate the unit cell volume from the cell constants.
                         If the calculated value differs from the one already
                         present in the CIF, replace the original value with
                         the calculated one and store the original value as
                         the '_cod_original_cell_volume' tag value.

       --dont-calculate-cell-volume
                         Do not calculate unit cell volume from the cell
                         constants (default).

       --original-filename data_source.cif
                         Use the provided string as the name of the original file.
                         (see --record-original-filename).

       --clear-original-filename
                         Do not use any previously provided strings as the name of
                         the original file.

       --record-original-filename
                         Record the original filename and the original data block
                         name for each data block as the '_cod_data_source_*' tag
                         values.

       --dont-record-original-filename
                         Do not record the original filename and the original data
                         block name (default).

       -S, --start-data-block-number 1234567
                         Use the provided number as the start number when renaming
                         data blocks (default: '7000001'). Setting this option
                         enables the '-R' option.

       -d, --datablock-format '%07d'
                         Use the provided format to determine new data block names
                         from the provided data block numbers (default: '%07d').

       -R, --renumber-data-blocks
                         Rename all data blocks. The new names are constructed by
                         taking a start number (specified by the '-S' option),
                         applying the string format (specified by the '-d' option)
                         and then incrementing the start number for each sequential
                         data block.

       -R-, --dont-renumber-data-blocks
                         Do not rename data blocks (default). Enabling this option
                         sets the '-S' option to default value.

       --original-filename-tag _cod_data_source_file

       --original-data-block-tag _cod_data_source_block
                         Use the provided tags to record original filename/data
                         block name (default: '_cod_data_source_file' and
                         '_cod_data_source_block').

       --database-code-tag _cod_database_code
                         Use the provided tag while adding or updating the
                         database code upon renaming the data blocks
                         (default: '_cod_database_code').

       --update-database-code
                         Update the database code tag value upon renaming the
                         data blocks (default).

       --dont-update-database-code
                         Do not update the database code tag value upon renaming
                         the data blocks.

       --use-datablocks-without-coordinates,

       --use-all-datablocks
                         Do not remove data blocks without coordinates.

       --do-not-use-datablocks-without-coordinates,

       --dont-use-datablocks-without-coordinates,

       --no-use-datablocks-without-coordinates,

       --skip-datablocks-without-coordinates
                         Remove data blocks without coordinates (default).

       --use-datablocks-with-structure-factors
                         Do not remove data blocks with structure factors (Fobs).

       --dont-use-datablocks-with-structure-factors,

       --no-use-datablocks-with-structure-factors,

       --skip-datablocks-with-structure-factors
                         Filter out data blocks with structure factors (Fobs)
                         (default).

       --folding-width 78
                         Specify the length of the longest unfolded line
                         (default: 76).

       --fold-title
                         Folds the title, if longer than folding width.

       --dont-fold-title
                         Do not fold the title (default).

       --fold-long-fields
                         Fold fields, longer than folding width.

       --dont-fold-long-fields
                         Do not fold fields (default).

       --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.

       --cif-output
                         Use CIF format for output (default).

       --json-output
                         Use JSON format for output.

       --cif
                         Use CIF format for both input and output (default).

       --json
                         Use JSON format for both input and output.

       --help, --usage
                         Output a short usage message (this message) and exit.

       --version
                         Output version information and exit.

REPORTING BUGS

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

                                                                                    CIF_FILTER(1)