--- name: "cif_filter" section: "1" platform: "linux" package: "cod-tools" version: "3.11.0+dfsg-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/cif_filter" --- # cif\_filter(1) 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. ## 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\ \, \, \, \, \,\ \123-132\ 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. \--no-exclude-publication-details, \--dont-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-space-group, --estimate-spacegroup\ Estimate space group symbols from the symmetry operators\ in the input. \-s-, --no-estimate-space-group, --dont-estimate-space-group, \--no-estimate-spacegroup, --dont-estimate-spacegroup\ Do not estimate space group symbols from the symmetry\ operators in the input. Default. \--keep-unrecognised-space-groups, --keep-unrecognised-spacegroups\ This option is a modifier for the '--estimate-space-group'\ option. Leave tags with unrecognised space group information\ as they are. \--no-keep-unrecognised-space-groups, --dont-keep-unrecognised-space-groups, \--no-keep-unrecognised-spacegroups, --dont-keep-unrecognised-spacegroups\ This option is a modifier for the '--estimate-space-group'\ 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 ('.'). \--no-exclude-empty-tags, --dont-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. \--no-exclude-placeholder-tags, --dont-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. \--no-exclude-redundant-chemical-names, \--dont-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. \--no-exclude-non-loop-empty-tags, \--dont-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 ('?'). \--no-exclude-unknown-tags, --dont-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. \--no-exclude-non-loop-unknown-tags, \--dont-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. \--no-exclude-misspelled-tags, \--dont-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. Default. \--no-parse-formula-sum, --dont-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. \--no-fix-syntax-errors, --dont-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. \--no-use-datablocks-without-coordinates, \--do-not-use-datablocks-without-coordinates, \--dont-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). \--no-use-datablocks-with-structure-factors, \--dont-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