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