OPTIMADE provider "Crystallography Open Database" (id: cod
)
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General information
Short description: Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers
Project homepage: https://www.crystallography.net/cod
Index Meta-Database URL:
https://providers.optimade.org/index-metadbs/cod
Number of structures: 520,323
Detailed information
/info
)State of the /info
endpoint of the index meta-database
found
found
Index metaDB versionVersion of the index meta-database
v1
Index metaDB (/links
)State of the /links
endpoint of the index meta-database
found
found
Databases served by this provider
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Crystallography Open Database (
cod, default sub-database
)https://www.crystallography.net/cod/optimade
Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymersProperties served by this database:
By entry type (click to expand):-
references
- The full list of standard OPTIMADE properties.
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structures
- The full list of standard OPTIMADE properties.
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_cod_a
Description: The lattice parameter a of the crystal structure.
Type: float
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_cod_acce_code
Description: Acta Crystallographica Coeditor Code. Uniquely identifies a publication by IUCr journals and can be used to construct URL of the paper "landing page".
Type: string
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_cod_alpha
Description: The lattice parameter alpha of the crystal structure.
Type: float
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_cod_authors
Description: The authors that published the paper describing the crystal structure deposited in the COD database, or the authors of the personal communication to COD. NB.: The name syntax uses the BibTeX convention, which is slightly different from the IUCr convention described under the CIF:DescriptionUrl.
Type: string
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_cod_b
Description: The lattice parameter b of the crystal structure.
Type: float
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_cod_beta
Description: The lattice parameter beta of the crystal structure.
Type: float
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_cod_c
Description: The lattice parameter c of the crystal structure.
Type: float
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_cod_calcformula
Description: The summary (brutto) formula calculated from the crystal data by the 'cod-tools' package. Ideally, should be the same value as in 'formula'.
Type: string
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_cod_cellformula
Description: The summary (brutto) formula of the whole unit cell calculated from the crystal data by the 'cod-tools' package. The number of atoms for each element in the 'cellformula' is 'Z' times higher than the number of atoms for the same element in the 'calcformula'.
Type: string
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_cod_cellpressure
Description: The pressure in kilopascals at which the unit cell parameters were measured.
Type: float
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_cod_celltemp
Description: The temperature in kelvins at which the unit cell parameters were measured (not the temperature of synthesis).
Type: float
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_cod_chemname
Description: IUPAC or Chemical Abstracts full name of the compound.
Type: string
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_cod_commonname
Description: Trivial name by which the compound in the crystal is commonly known.
Type: string
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_cod_compoundsource
Description: The description of the source of the compound (or a parent molecule). Includes the place of discovery (for minerals) or the actual source (for natural products).
Type: string
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_cod_date
Description: The date the current row of the table was inserted to the COD database.
Type: string
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_cod_diffrpressure
Description: The mean hydrostatic pressure in kilopascals at which the intensities were measured.
Type: float
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_cod_diffrtemp
Description: The mean temperature in kelvins at which the diffraction intensities were measured.
Type: float
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_cod_doi
Description: The DOI that links to the online paper where the crystal was published.
Type: string
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_cod_duplicateof
Description: Specifies that the COD entry containing this data item is considered to be a duplicate of another entry. The COD number of this other entry, which is considered to be "primary" entry for the structure, is specified as a value of this column.
Type: integer
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_cod_firstpage
Description: The first page of the scientific paper where the crystal structure was published.
Type: string
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_cod_flags
Description: A set (as in SQL or Pascal) that describes various conditions of a COD record: "has coordinates": the entry has atomic coordinates specified; "has disorder": some atoms were modeled as disordered in the unit cell of this entry; "has Fobs": there is a corresponding X-ray reflection file (Fobs or Iobs data) in the COD for this entry, containing the original reflection intensities used to determine this structure.
Type: string
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_cod_gamma
Description: The lattice parameter gamma of the crystal structure.
Type: float
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_cod_gofall
Description: The least-squares goodness-of-fit parameter S for all reflections after the final cycle of refinement.
Type: float
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_cod_gofgt
Description: NOTE: the field stores the same information as the "gofobs" field, however, it should not be removed in order to retain compatibility with existing software. The least-squares goodness-of-fit parameter S for significantly intense reflections (see _reflns_threshold_expression) after the final cycle of refinement.
Type: float
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_cod_gofobs
Description: NOTE: the field stores the same information as the "gofgt" field, however, it should not be removed in order to retain compatibility with existing software. The least-squares goodness-of-fit parameter S for significantly intense reflections (see _reflns_threshold_expression) after the final cycle of refinement.
Type: float
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_cod_gofref
Description: The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement.
Type: float
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_cod_issue
Description: The issue of the journal where the scientific paper describing the crystal structure was published.
Type: string
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_cod_journal
Description: The name of the journal in which the scientific paper describing the crystal structure was published.
Type: string
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_cod_lastpage
Description: The last page of the scientific paper where the crystal structure was published.
Type: string
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_cod_method
Description: The method that was used to determine the crystal structure.
Type: string
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_cod_mineral
Description: Mineral name accepted by the International Mineralogical Association.
Type: string
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_cod_onhold
Description: Specifies the date when the atomic coordinates of the entry, which might be currently on hold (not public), will become available publicly.
Type: string
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_cod_optimal
Description: Contains a COD database code for the COD entry that contains optimally solved structure for the crystal or compound under consideration. This optimal structure should be used for all inferences; the current suboptimal structure is provided for illustration purposes only.
Type: integer
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_cod_pressurehist
Description: The pressure history of the crystal (human-readable informal description).
Type: string
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_cod_radiation
Description: The type of radiation that was used to determine the crystal structure.
Type: string
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_cod_radsymbol
Description: The IUPAC symbol for the X-ray wavelength for the probe radiation.
Type: string
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_cod_radtype
Description: The type of the radiation used to determine the structure of the crystal. This is used to give a more detailed description than _diffrn_radiation_probe and is typically a description of the X-ray wavelength in Siegbahn notation.
Type: string
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_cod_rall
Description: Residual factor for all reflections satisfying the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low.
Type: float
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_cod_rfsqd
Description: Residual factor R(Fsqd), calculated on the squared amplitudes of the observed and calculated structure factors, for significantly intense reflections (satisfying _reflns_threshold_expression) and included in the refinement.
Type: float
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_cod_ri
Description: Residual factor R(I) for significantly intense reflections (satisfying _reflns_threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~.
Type: float
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_cod_robs
Description: Residual factor for the reflections (with number given by _reflns_number_gt) judged significantly intense (i.e. satisfying the threshold specified by _reflns_threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_d_res_high and _refine_ls_d_res_low. This is the conventional R factor.
Type: float
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_cod_rref
Description: This data value is not described in official IUCr dictionaries, but many CIF files use it. Should be roughly equivalent to Robs.
Type: float
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_cod_sg
Description: Space group symbol, Hermann-Mauguin or superspace group symbol.
Type: string
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_cod_sghall
Description: Space group symbol as described by Hall.
Type: string
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_cod_sgnumber
Description: The space group number as assigned in International Tables for Crystallography Vol. A.
Type: integer
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_cod_siga
Description: The standard uncertainty of the lattice parameter a of the crystal structure.
Type: float
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_cod_sigalpha
Description: The standard uncertainty of the lattice parameter alpha of the crystal structure.
Type: float
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_cod_sigb
Description: The standard uncertainty of the lattice parameter b of the crystal structure.
Type: float
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_cod_sigbeta
Description: The standard uncertainty of the lattice parameter beta of the crystal structure.
Type: float
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_cod_sigc
Description: The standard uncertainty of the lattice parameter c of the crystal structure.
Type: float
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_cod_sigcellpressure
Description: The standard uncertainty of the 'cellpressure' value.
Type: float
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_cod_sigcelltemp
Description: The standard uncertainty of the temperature at which the crystal structure was determined.
Type: float
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_cod_sigdiffrpressure
Description: The standard uncertainty of the 'diffrpressure' value.
Type: float
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_cod_sigdiffrtemp
Description: The standard uncertainty of the 'diffrtemp' value.
Type: float
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_cod_siggamma
Description: The standard uncertainty of the lattice parameter gamma of the crystal structure.
Type: float
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_cod_sigvol
Description: The standard uncertainty of the volume of the crystal structure.
Type: float
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_cod_smiles
Description: The SMILES (Simplified Molecular Input Line Entry Specification) descriptor for the structure.
Type: string
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_cod_status
Description: Describes the severity of errors if such are detected in COD entries. Permitted values are: NULL, 'warnings', 'errors', 'retracted'.
Type: string
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_cod_svnrevision
Description: The Subversion revision of the file that was used to produce the SQL table row.
Type: integer
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_cod_text
Description: A concatenation of all descriptive fields in the table: my $text = join( '\n', map { Unicode2:cif2unicode($_) } ( $authors, $title, $journal, $volume . ( $issue? ( $volume ? "($issue)" : "(issue $issue)") : "" ), "(" . $year . ")", ( $last_page ? $first_page . "-" . $last_page : $first_page )) ); Retained here for compatibility with the first version of the COD.
Type: string
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_cod_thermalhist
Description: The thermal history of the crystal (human-readable informal description).
Type: string
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_cod_time
Description: The time the current row of the table was inserted to the COD database.
Type: string
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_cod_title
Description: The title of the scientific paper where the crystal structure was published.
Type: string
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_cod_vol
Description: The volume of the crystal structure (calculated by 'cod-tools' from the cell constants).
Type: float
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_cod_volume
Description: The volume of the journal where the scientific paper describing the crystal structure was published.
Type: integer
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_cod_wavelength
Description: The wavelength in ångströms that was used to determine the crystal structure.
Type: float
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_cod_wrall
Description: Weighted residual factors for all reflections.
Type: float
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_cod_wrobs
Description: Weighted residual factors for significantly intense reflections (satisfying _reflns_threshold_expression) included in the refinement.
Type: float
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_cod_wrref
Description: Weighted residual factors for all reflections included in the refinement.
Type: float
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_cod_year
Description: The year of publication of this crystal structure.
Type: integer
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_cod_z
Description: The number of the formula units in the unit cell.
Type: integer
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_cod_zprime
Description: The number of the formula units in the unit cell ('Z') divided by the number of independent general positions.
Type: float
Validation
ValidationResults of validation Passed 57 / 59
❌ https://www.crystallography.net/cod/optimade/v1/structures?page_limit=4&response_fields=structure_features,nelements,lattice_vectors,dimension_types,immutable_id,nperiodic_dimensions,nsites,cartesian_site_positions,assemblies,chemical_formula_descriptive,chemical_formula_reduced,species,chemical_formula_hill,last_modified,elements,elements_ratios,chemical_formula_anonymous,species_at_sites
ValidationError: 2 validation errors for ValidatorStructureResponseMany
data.2.attributes.chemical_formula_reduced
Value error, Cannot use unknown chemical symbols ['D'] in 'chemical_formula_reduced' [type=value_error, input_value='C3D3O7Sr', input_type=str]
For further information visit https://errors.pydantic.dev/2.10/v/value_error
data.2.attributes.chemical_formula_hill
Value error, Cannot use unknown chemical symbols ['D'] in 'chemical_formula_hill' [type=value_error, input_value='C3D3O7Sr', input_type=str]
For further information visit https://errors.pydantic.dev/2.10/v/value_error
❌ https://www.crystallography.net/cod/optimade/v1/;%20testing%20queries%20for%20structures-%3Estructure_features
ResponseError: Chosen entry had no value for 'structure_features' with support level SupportLevel.MUST and queryability SupportLevel.MUST, so cannot construct test queries. This field should potentially be removed from the `/info/structures` endpoint response.
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