Man page - cif_distances(1)
Packages contas this manual
- cif2qg(1)
- cif2csv(1)
- cif2cod(1)
- msg_parse(1)
- cif_overlay(1)
- cif_merge(1)
- cif_fillcell(1)
- cifvalues(1)
- cif_cod_numbers(1)
- cif_adjust_journal_name_volume(1)
- codxyz2ortho(1)
- syminv(1)
- cif_bounding_box(1)
- cif_distances(1)
- cif2xyz(1)
- cod_fetch(1)
- cif2rdf(1)
- cif_mpod_v1_to_v3(1)
- cif-to-utf8(1)
- cif_filter(1)
- cif_find_duplicates(1)
- cif_dictionary_tags(1)
- cif_mpod_v3_to_v1(1)
- symops(1)
- oqmd2cif(1)
- ssg_symop_matrices(1)
- cif_molecule(1)
- ssg_symop_check(1)
- cif_cod_check(1)
- cif2json(1)
- cif_values(1)
- cif_reduce_cell(1)
- json2cif(1)
- cif_ddlm_dic_print(1)
- utf8-to-cif(1)
- ddl1-to-ddlm(1)
- cif_mpod_v1_to_v2(1)
- cod-tools-version(1)
- cif_mpod_v2_to_v1(1)
- cif_polymer_multiplicity(1)
- cif_reformat_pubmed_author_names(1)
- symop_build_spacegroup(1)
- cif_cod_deposit(1)
- cif_mark_disorder(1)
- ssg3d(1)
- cif_symop_apply(1)
- cif_set_value(1)
- cif_split(1)
- cif_validate(1)
- cif_split_primitive(1)
- cif_ddlm_dic_check(1)
- spacegroup_properties(1)
- symmul(1)
- cif_eval_numbers(1)
- cif_tcod_tree(1)
- formula_sum(1)
- codcif2sdf(1)
- cosets(1)
- cif2ref(1)
- cif_list_tags(1)
- sdf_add_cod_data(1)
- cif_tags_in_list(1)
- cif_hkl_check(1)
- cif_automorphism(1)
- cif_p1(1)
- dic2markdown(1)
- ssg_symop_string(1)
- cif_diff(1)
- cif_classify(1)
- cif_select(1)
- cif_correct_tags(1)
- cif_compare_dics(1)
- ssg_symop_canonical(1)
- cif_ddl1_dic_check(1)
- find_numbers(1)
- cifparse(1)
- ddlm_validate(1)
- molcif2sdf(1)
- codxyz2fract(1)
- cif_reformat_uppercase_author_names(1)
- cod_manage_related(1)
- cif_sort_atoms(1)
- cif2tsv(1)
- cif_find_symmetry(1)
- cif_parse(1)
- cod2rdf(1)
- cif_cell_contents(1)
- cif_fix_values(1)
- fetch_cif_dict(1)
apt-get install cod-tools
Manual
| CIF_DISTANCES(1) | General Commands Manual | CIF_DISTANCES(1) |
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