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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: 516,399

Detailed information

(information checked on Saturday July 27, 2024 at 05:29 UTC)
Index metaDB (/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

  • 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 biopolymers

    Properties served by this database:

    By entry type (click to expand):
    • references
      • The full list of standard OPTIMADE properties.
    • structures
      • The full list of standard OPTIMADE properties.
      • _cod_a Description: The lattice parameter a of the crystal structure.
        Type: float
      • _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
      • _cod_alpha Description: The lattice parameter alpha of the crystal structure.
        Type: float
      • _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
      • _cod_b Description: The lattice parameter b of the crystal structure.
        Type: float
      • _cod_beta Description: The lattice parameter beta of the crystal structure.
        Type: float
      • _cod_c Description: The lattice parameter c of the crystal structure.
        Type: float
      • _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
      • _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
      • _cod_cellpressure Description: The pressure in kilopascals at which the unit cell parameters were measured.
        Type: float
      • _cod_celltemp Description: The temperature in kelvins at which the unit cell parameters were measured (not the temperature of synthesis).
        Type: float
      • _cod_chemname Description: IUPAC or Chemical Abstracts full name of the compound.
        Type: string
      • _cod_commonname Description: Trivial name by which the compound in the crystal is commonly known.
        Type: string
      • _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
      • _cod_date Description: The date the current row of the table was inserted to the COD database.
        Type: string
      • _cod_diffrpressure Description: The mean hydrostatic pressure in kilopascals at which the intensities were measured.
        Type: float
      • _cod_diffrtemp Description: The mean temperature in kelvins at which the diffraction intensities were measured.
        Type: float
      • _cod_doi Description: The DOI that links to the online paper where the crystal was published.
        Type: string
      • _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
      • _cod_firstpage Description: The first page of the scientific paper where the crystal structure was published.
        Type: string
      • _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
      • _cod_gamma Description: The lattice parameter gamma of the crystal structure.
        Type: float
      • _cod_gofall Description: The least-squares goodness-of-fit parameter S for all reflections after the final cycle of refinement.
        Type: float
      • _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
      • _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
      • _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
      • _cod_issue Description: The issue of the journal where the scientific paper describing the crystal structure was published.
        Type: string
      • _cod_journal Description: The name of the journal in which the scientific paper describing the crystal structure was published.
        Type: string
      • _cod_lastpage Description: The last page of the scientific paper where the crystal structure was published.
        Type: string
      • _cod_method Description: The method that was used to determine the crystal structure.
        Type: string
      • _cod_mineral Description: Mineral name accepted by the International Mineralogical Association.
        Type: string
      • _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
      • _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
      • _cod_pressurehist Description: The pressure history of the crystal (human-readable informal description).
        Type: string
      • _cod_radiation Description: The type of radiation that was used to determine the crystal structure.
        Type: string
      • _cod_radsymbol Description: The IUPAC symbol for the X-ray wavelength for the probe radiation.
        Type: string
      • _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
      • _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
      • _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
      • _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
      • _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
      • _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
      • _cod_sg Description: Space group symbol, Hermann-Mauguin or superspace group symbol.
        Type: string
      • _cod_sghall Description: Space group symbol as described by Hall.
        Type: string
      • _cod_sgnumber Description: The space group number as assigned in International Tables for Crystallography Vol. A.
        Type: integer
      • _cod_siga Description: The standard uncertainty of the lattice parameter a of the crystal structure.
        Type: float
      • _cod_sigalpha Description: The standard uncertainty of the lattice parameter alpha of the crystal structure.
        Type: float
      • _cod_sigb Description: The standard uncertainty of the lattice parameter b of the crystal structure.
        Type: float
      • _cod_sigbeta Description: The standard uncertainty of the lattice parameter beta of the crystal structure.
        Type: float
      • _cod_sigc Description: The standard uncertainty of the lattice parameter c of the crystal structure.
        Type: float
      • _cod_sigcellpressure Description: The standard uncertainty of the 'cellpressure' value.
        Type: float
      • _cod_sigcelltemp Description: The standard uncertainty of the temperature at which the crystal structure was determined.
        Type: float
      • _cod_sigdiffrpressure Description: The standard uncertainty of the 'diffrpressure' value.
        Type: float
      • _cod_sigdiffrtemp Description: The standard uncertainty of the 'diffrtemp' value.
        Type: float
      • _cod_siggamma Description: The standard uncertainty of the lattice parameter gamma of the crystal structure.
        Type: float
      • _cod_sigvol Description: The standard uncertainty of the volume of the crystal structure.
        Type: float
      • _cod_smiles Description: The SMILES (Simplified Molecular Input Line Entry Specification) descriptor for the structure.
        Type: string
      • _cod_status Description: Describes the severity of errors if such are detected in COD entries. Permitted values are: NULL, 'warnings', 'errors', 'retracted'.
        Type: string
      • _cod_svnrevision Description: The Subversion revision of the file that was used to produce the SQL table row.
        Type: integer
      • _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
      • _cod_thermalhist Description: The thermal history of the crystal (human-readable informal description).
        Type: string
      • _cod_time Description: The time the current row of the table was inserted to the COD database.
        Type: string
      • _cod_title Description: The title of the scientific paper where the crystal structure was published.
        Type: string
      • _cod_vol Description: The volume of the crystal structure (calculated by 'cod-tools' from the cell constants).
        Type: float
      • _cod_volume Description: The volume of the journal where the scientific paper describing the crystal structure was published.
        Type: integer
      • _cod_wavelength Description: The wavelength in ångströms that was used to determine the crystal structure.
        Type: float
      • _cod_wrall Description: Weighted residual factors for all reflections.
        Type: float
      • _cod_wrobs Description: Weighted residual factors for significantly intense reflections (satisfying _reflns_threshold_expression) included in the refinement.
        Type: float
      • _cod_wrref Description: Weighted residual factors for all reflections included in the refinement.
        Type: float
      • _cod_year Description: The year of publication of this crystal structure.
        Type: integer
      • _cod_z Description: The number of the formula units in the unit cell.
        Type: integer
      • _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,chemical_formula_anonymous,lattice_vectors,nperiodic_dimensions,assemblies,species,last_modified,cartesian_site_positions,dimension_types,immutable_id,elements_ratios,chemical_formula_reduced,elements,chemical_formula_hill,nsites,chemical_formula_descriptive,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/2.8/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/2.8/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.