.TH CIF_DISTANCES 1
.SH NAME
cif_distances \- calculate minimal distance between atoms read from a CIF file.

.SH SYNOPSIS
cif_distances \-\-options input1.cif input*.cif

.SH DESCRIPTION
Calculate minimal distance between atoms read from a CIF file.

.SH 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.

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