---
name: "cif_distances"
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_distances"
---

# cif\_distances(1)

calculate minimal distance between atoms read from a CIF file.

## 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