NAME

       cif_distances - calculate minimal distance between atoms read from a CIF file.

SYNOPSIS

       cif_distances --options input1.cif input*.cif

DESCRIPTION

       Calculate minimal distance between atoms read from a CIF file.

OPTIONS

       -P, --pairwise-distance
                         Set pairwise distance output format (default).

       -M, --distance-matrix
                         Set distance matrix output format.

       --format "%8.6f"
                         Use the specified format for distance matrix
                         and pairwise printout format (default: "%-11.3f"
                         for matrix, "%-6.3f" for pairwise).

       -l, --matrix-line-length "80"
                         Maximum length of an output line in distance
                         matrix format (default: 80).

       -F, --add-filename
                         Add a filename field at the end of pairwise
                         distance format lines.

       --no-add-filename, --do-not-add-filename
                         Do not add a filename field at the end of
                         pairwise distance format lines (default).

       --process-disordered-structures,

       --include-disordered-structures
                         Force processing of disordered structures (default).

       --no-process-disordered-structures,

       --exclude-disordered-structures,

       --skip-disordered-structures
                         Skip disordered structures.

       --process-duplicate-structures,

       --include-duplicate-structures,
                         Force processing of structures, that are flagged
                         as duplicates with '_cod_duplicate_entry' or
                         '_[local]_cod_duplicate_entry' tags.

       --no-process-duplicate-structures,

       --exclude-duplicate-structures,

       --skip-duplicate-structures
                         Skip duplicate structures (default).

       --include-null-distances
                         Include entries of null distance relationship between
                         atoms from different disorder groups of the same
                         disorder assembly in pairwise distances output format.

       --no-null-distances, --exclude-null-distances
                         Exclude entries of null distance relationship between
                         atoms from different disorder groups of the same
                         disorder assembly in pairwise distances output format
                         (default).

       --include-self-distances
                         Include entries of distances between symmetry-related
                         instances of the same atom (default).

       --no-self-distances, --exclude-self-distances
                         Exclude entries of distances between symmetry-related
                         instances of the same atom.

       -U, --include-unknown-types
                         Include entries containing atoms of undetermined
                         chemical type. Atom type will be marked as 'UN'.

       --no-unknown-types, --exclude-unknown-types
                         Exclude entries containing atoms of undetermined
                         chemical type (default).

       --uniquify-atoms
                         Make atom labels unique (default).

       --no-uniquify-atoms
                         Do not make atom labels unique.

       --use-perl-parser
                         Use Perl parser to parse CIF files.

       --use-c-parser
                         Use C parser to parse CIF files (default).

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

       --version
                         Output version information and exit.

REPORTING BUGS

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

                                                                                 CIF_DISTANCES(1)