📦 cod-tools

100 pages

C

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.✨
cif2qg(1)parse CIF file and print out the quotient graph.✨
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. Accepts optional bibliography file in ref, xrf or plaintext format as the second command line argument.✨
cif2tsv(1)get specified data values from a CIF file(s).✨
cif2xyz(1)read CIF files and print atom coordinates in XYZ format. The default output format is as described in https://en.wikipedia.org/wiki/XYZ_file_format.✨
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. The following heuristic is applied: if journal volume starts with a letter, add…✨
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 crystal description.✨
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, https://www.iucr.org/__data/iucr/ftp/pub/dvntests or…✨
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. Discrepancies between corresponding enumeration sets, default values, permitted ranges as well as data items unique to…✨
cif_correct_tags(1)correct misspelt tags in a CIF file and output made changes into the standard I/O streams. By default, only tags from CIF Core and CIF COD dictionaries with extra '^_+' prefixes are corrected…✨
cif_create_AMCSD_pressure_temp_tags(1)parse a CIF file, determine pressure and temperature tag values from the values of other tags. Designed for CIFs from AMCSD.✨
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. the number of "chemical formula units" in the unit cell) using the provided cell volume, crystal density and molecular weight.✨
cif_eval_numbers(1)read a CIF file and convert those number values that are written as simple fractions (e.g. "1/4") into a single floating point number.✨
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. This script has also many capabilities -- it can restore space group symbols from symmetry operators…✨
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. In order to obtain correct results most of the time, all atoms of the unit cell should be present in the input. This can be…✨
cif_fix_AMCSD_aniso_labels(1)read the CIF file, assuming that it follows AMCSD atom naming conventions, and correct the _atom_site_aniso_label values using some heuristics.✨
cif_fix_AMCSD_atom_labels(1)read the CIF file, assuming that it follows AMCSD atom naming conventions, and correct duplicated _atom_site_label and _atom_site_aniso_label values.✨
cif_fix_values(1)correct various CIF file values and output the made changes into the standard I/O streams. The script is capable of making these corrections: - Converting temperature from degrees Celsius to kelvins…✨
cif_guess_AMCSD_atom_types(1)read the CIF file, assuming that it follows AMCSD atom naming conventions, and assign atom types and attached hydrogen counts as follows: - for 'Wat' atoms (with or without a number) assign atom type…✨
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 account.✨
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. Unique data items are combined into a single data block of the output CIF; data items with equivalent values are silently merged into one…✨
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. outputting atoms that are bonded at bond distances from each other).✨
cif_parse(1)parse CIF file and print out the structure generated by CIF parser.✨
cif_polymer_multiplicity(1)parse CIF file and print out multiplicity and dimensionality per each molecule. Input CIF files should represent labeled quotient graphs using data items from the topoCIF dictionary: _topol_net.id…✨
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(1)split CIF files into separate files with one data_ section each. This script parses given CIF files to separate the data blocks, so is capable of splitting non-correctly formatted and nested CIF…✨
cif_split_primitive(1)split CIF files into separate files with one data_ section each. This is a very naive and primitive version of the splitter, which expects each data_... section to start on a new line. It may fail on…✨
cif_supercell(1)generate a supercell from the input CIF file.✨
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. The first column signals whether the tag must be declared in a looped list ( '0'…✨
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.✨
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-tools-version(1)print the version of cod-tools package.✨
cod2rdf(1)describe (in RDF format) properties of COD structures.✨
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' dictionary.✨
codcif2sdf(1)convert CIFs with crystal description (similar to those obtained from the COD) to an SDF file with a molecule description. Intended to be suitable for upload to PubChem.✨
codxyz2fract(1)take an XYZ format [1] molecular file and convert orthogonal coordinates to fractional ones. Unit cell constants can be given as command line option parameters. [1]…✨
codxyz2ortho(1)take an XYZ format [1] molecular file and convert coordinates to orthogonal ones (assuming that they were fractional in the original file). Unit cell constants can be given as command line option…✨
cosets(1)generate and print out cosets of a subgroup in a group. Both the group and the subgroup can be given either as H-M symbols of crystallographic groups or as lists of (generating) symmetry operators.✨

D

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.✨

F

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.✨

J

json2cif(1)parse JSON CIF and print out CIF.✨

M

molcif2sdf(1)convert CIFs with multiple molecules (similar to those obtained from the 'cif_molecule' script) to an SDF file with a molecule description. Intended to be suitable for upload to PubChem.✨
msg_parse(1)parse COD error messages and output the results in the desired format.✨

O

oqmd2cif(1)retrieve structures from the Open Quantum Materials Database and write them out in CIF format.✨

S

sdf_add_cod_data(1)append COD-specific meta-information to an SDF file in a format suitable for PubChem.✨
spacegroup_properties(1)lookup or determine space group properties and write them out in TSV format.✨
ssg3d(1)build a three-dimensional space group from (N+1) dimensional superspace group operators.✨
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 for them.✨
ssg_symop_string(1)determine superspace group symmetry operators from symmetry matrices. Superspace group symmetry operators are output as parsable strings as described in the CIF…✨
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) algorithm.✨
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 those operators that do not belong to the group.✨

U

utf8-to-cif(1)convert Unicode characters into CIF escape sequences.✨