Cod-Tools

• cif_adjust_journal_name_volume(1) parse a CIF file, update the journal name and journal volume based on heuristics and output the updated file to STDOUT.
• cif_automorphism(1) find automorphism orbits in CIF files.
• cif_bounding_box(1) transform non-crystal CIF file (missing cell parameters and symmetry information, Cartesian coordinates are given instead of fractional) into a
• cif_cell_contents(1) calculate cell contents from atom coordinates and symmetry information.
• cif_classify(1) classify a CIF structure -- find out if it is organic compound, inorganic, mineral, etc.
• cif_cod_check(1) parse a CIF file, check if certain data values match COD requirements and IUCr data validation criteria (Version: 2000.06.09,
• cif_cod_deposit(1) deposit CIFs into COD database using CGI deposition interface.
• cif_cod_numbers(1) find COD numbers for the CIF files in given directories of file lists.
• cif_CODify(1) extract essential data from the input CIF file and format it using the rules of the Crystallography Open Database (COD).
• cif_compare_dics(1) checks a pair of DDL1/DDLm dictionaries for compatibility breaking differences.
• cif_correct_tags(1) correct misspelt tags in a CIF file and output made changes into the standard I/O streams.
• cif_create_AMCSD_pressure_temp_tags(1) parse a CIF file, determine pressure and temperature tag values from the values of other tags.
• cif_ddl1_dic_check(1) check DDL1 dictionaries against a set of best practice rules.
• cif_ddlm_dic_check(1) check DDLm dictionaries against a set of best practice rules.
• cif_ddlm_dic_print(1) pretty-print a DDLm dictionary file.
• cif_dictionary_tags(1) generate a list of all tags in a CIF dictionary.
• cif_diff(1) parse two CIF files and compare their content
• cif_distances(1) calculate minimal distance between atoms read from a CIF file.
• cif_estimate_Z(1) calculate Z value (i.e.
• cif_eval_numbers(1) read a CIF file and convert those number values that are written as simple fractions (e.g.
• cif_Fcalc(1) compute the structure factors from CIF files.
• cif_fillcell(1) generate symmetric atoms from a CIF file.
• cif_filter(1) parse a CIF file and print out essential data values in the CIF format, the COD CIF style.
• cif_find_duplicates(1) find COD numbers for the .cif files in given directories of file lists.
• cif_find_symmetry(1) find the symmetry of the atoms in the unit cell of a CIF crystal structure.
• cif_fix_values(1) correct various CIF file values and output the made changes into the standard I/O streams.
• cif_hkl_check(1) check the correspondence between CIF and diffraction data files, taking data block names, cell parameters, author lists and symmetry group names into
• cif_hkl_COD_number(1) parse a CIF file and print out the essential information in the COD CIF format
• cif_list_tags(1) parse CIF file(s) and output a list of CIF data items.
• cif_mark_disorder(1) mark disorder in CIF files judging by distance and occupancy.
• cif_merge(1) merge data values in identical data blocks of multiple CIFs.
• cif_molecule(1) restore molecules from a CIF file.
• cif_mpod_v1_to_v2(1) convert MPOD structures from MPOD dictionary V1 to MPOD dict. V2 based data names.
• cif_mpod_v1_to_v3(1) convert MPOD structures from MPOD dictionary V1 to MPOD dict. V3 based data names.
• cif_mpod_v2_to_v1(1) convert MPOD structures from MPOD dictionary V2 to MPOD dict. V1 based data names.
• cif_mpod_v3_to_v1(1) convert MPOD structures from MPOD dictionary V1 to MPOD dict. V3 based data names.
• cif_overlay(1) overlay atoms from each pair of CIFs given on the command line.
• cif_p1(1) expand atoms in CIF to the P1 space group, preserving molecules (i.e.
• cif_parse(1) parse CIF file and print out the structure generated by CIF parser.
• cif_reduce_cell(1) perform reductions of the unit cell using different algorithms.
• cif_reduce_Niggli(1) perform Niggli cell reduction of CIF files.
• cif_reformat_AMCSD_author_names(1) parse a CIF file, reformat author names in AMCSD convention into COD format.
• cif_reformat_pubmed_author_names(1) parse a CIF file, reformat author names in PubMed convention into COD format.
• cif_reformat_uppercase_author_names(1) parse a CIF file, reformat author names in AMCSD convention into COD format.
• cif_select(1) read CIFs and print out selected tags with their values.
• cif_set_value(1) set specified CIF data items to the given values.
• cif_sort_atoms(1) sort atoms in a CIF file in given order. Accepts more than one sorting criterion.
• cif_split_primitive(1) split CIF files into separate files with one data_ section each.
• cif_split(1) split CIF files into separate files with one data_ section each.
• cif_symop_apply(1) apply symmetry operator(s) to all atoms in a CIF.
• cif_tags_in_list(1) parse a DDL1 CIF dictionary file and generate a list of tags with additional information about their loop constraints.
• cif_tcod_tree(1) prepare a calculation tree from descriptions in TCOD CIF file.
• cif_validate(1) validate CIF files against CIF dictionaries (DDL1 or DDLm).
• cif_values(1) read CIFs and print out requested tag values in a tabular form.
• cif-to-utf8(1) convert CIF escape sequences into Unicode characters.
• cif2cod(1) parse a CIF file, prepare a COD database table entry from it.
• cif2csv(1) convert a CIF file into a CSV file.
• cif2json(1) parse CIF file and print out the structure generated by CIF parser.
• cif2rdf(1) parse a CIF file and describe its properties in RDF format.
• cif2ref(1) parse a CIF file and print out the essential information in the COD REF format.
• cif2xyz(1) read CIF files and print atom coordinates in XYZ format.
• cifparse(1) parse CIF file(s), check syntax, and optionally output pretty-printed data.
• cifvalues(1) get specified data values from a CIF file(s).
• cod_fetch(1) query COD server using the Perl DBD::mysql interface.
• cod_manage_related(1) embed provided relationships between databases into a CIF file using the COD notation described in the 'cod_cif.dic'
• cod-tools-version(1) print the version of cod-tools package.
• cod2rdf(1) describe (in RDF format) properties of COD structures.
• codcif2sdf(1) convert CIFs with crystal description (similar to those obtained from the COD) to an SDF file with a molecule description.
• codxyz2fract(1) take an XYZ format [1] molecular file and convert orthogonal coordinates to fractional ones.
• codxyz2ortho(1) take an XYZ format [1] molecular file and convert coordinates to orthogonal ones (assuming that they were fractional in the original file).
• cosets(1) generate and print out cosets of a subgroup in a group.
• ddl1-to-ddlm(1) convert DDL1 dictionaries to DDLm.
• ddlm_validate(1) validate CIF files against DDLm-compliant CIF dictionaries.
• dic2markdown(1) generate textual descriptions for DDLm dictionaries.
• fetch_cif_dict(1) fetch cif_core.dic from the IUCr FTP site if non-expired local copy does not exist.
• find_numbers(1) find COD numbers for the .cif files in given directories of file lists.
• formula_sum(1) parse and print the chemical formula sum as described in the CIF _chemical_formula_sum data item.
• json2cif(1) parse JSON CIF and print out CIF.
• molcif2sdf(1) convert CIFs with multiple molecules (similar to those obtained from the 'cif_molecule' script) to an SDF file with a molecule description.
• msg_parse(1) parse COD error messages and output the results in the desired format.
• oqmd2cif(1) retrieve structures from the Open Quantum Materials Database and write them out in CIF format.
• sdf_add_cod_data(1) append COD-specific meta-information to an SDF file in a format suitable for PubChem.
• ssg_symop_canonical(1) canonicalise superspace group symmetry operator strings.
• ssg_symop_check(1) check superspace group symmetry operator syntax.
• ssg_symop_matrices(1) parse superspace group symmetry operators as described in the CIF _space_group_symop_ssg_operation_algebraic data items and produce symmetry matrices
• ssg_symop_string(1) determine superspace group symmetry operators from symmetry matrices.
• ssg3d(1) build a three-dimensional space group from (N+1) dimensional superspace group operators.
• syminv(1) invert a symmetry operator provided on the command line.
• symmul(1) multiply all symmetry operators provided on the command line.
• symop_build_spacegroup(1) determine a space group from a list of symmetry operators (generators), using the Ralf's (Ralf Grosse-Kunstleve)
• symops(1) print out symmetry operators for a given space group, or print out those symmetry operators that belong to the group, while diagnosing as errors
• utf8-to-cif(1) convert Unicode characters into CIF escape sequences.