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@@ -1,7 +1,7 @@
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/**
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* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.296, IHM 0.132.
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+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
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*
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* @author mol-star package (src/apps/schema-generator/generate)
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*/
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@@ -22,686 +22,3278 @@ const List = Schema.List;
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export const mmCIF_Schema = {
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atom_site: {
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+ /**
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+ * An alternative identifier for _atom_site.label_asym_id that
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+ * may be provided by an author in order to match the identification
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+ * used in the publication that describes the structure.
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+ */
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auth_asym_id: str,
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+ /**
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+ * An alternative identifier for _atom_site.label_atom_id that
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+ * may be provided by an author in order to match the identification
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+ * used in the publication that describes the structure.
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+ */
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auth_atom_id: str,
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+ /**
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+ * An alternative identifier for _atom_site.label_comp_id that
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+ * may be provided by an author in order to match the identification
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+ * used in the publication that describes the structure.
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+ */
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auth_comp_id: str,
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+ /**
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+ * An alternative identifier for _atom_site.label_seq_id that
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+ * may be provided by an author in order to match the identification
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+ * used in the publication that describes the structure.
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+ *
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+ * Note that this is not necessarily a number, that the values do
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+ * not have to be positive, and that the value does not have to
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+ * correspond to the value of _atom_site.label_seq_id. The value
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+ * of _atom_site.label_seq_id is required to be a sequential list
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+ * of positive integers.
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+ *
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+ * The author may assign values to _atom_site.auth_seq_id in any
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+ * desired way. For instance, the values may be used to relate
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+ * this structure to a numbering scheme in a homologous structure,
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+ * including sequence gaps or insertion codes. Alternatively, a
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+ * scheme may be used for a truncated polymer that maintains the
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+ * numbering scheme of the full length polymer. In all cases, the
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+ * scheme used here must match the scheme used in the publication
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+ * that describes the structure.
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+ */
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auth_seq_id: int,
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+ /**
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+ * Isotropic atomic displacement parameter, or equivalent isotropic
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+ * atomic displacement parameter, B~eq~, calculated from the
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+ * anisotropic displacement parameters.
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+ *
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+ * B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)]
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+ *
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+ * A = the real space cell lengths
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+ * a* = the reciprocal space cell lengths
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+ * B^ij^ = 8 pi^2^ U^ij^
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+ *
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+ * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
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+ * 775-776.
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+ *
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+ * The IUCr Commission on Nomenclature recommends against the use
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+ * of B for reporting atomic displacement parameters. U, being
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+ * directly proportional to B, is preferred.
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+ *
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+ * Note -
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+ *
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+ * The particular type of ADP stored in this item is qualified
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+ * by item _refine.pdbx_adp_type.
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+ */
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B_iso_or_equiv: float,
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+ /**
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+ * The x atom-site coordinate in angstroms specified according to
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+ * a set of orthogonal Cartesian axes related to the cell axes as
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+ * specified by the description given in
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+ * _atom_sites.Cartn_transform_axes.
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+ */
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Cartn_x: coord,
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+ /**
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+ * The y atom-site coordinate in angstroms specified according to
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+ * a set of orthogonal Cartesian axes related to the cell axes as
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+ * specified by the description given in
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+ * _atom_sites.Cartn_transform_axes.
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+ */
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Cartn_y: coord,
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+ /**
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+ * The z atom-site coordinate in angstroms specified according to
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+ * a set of orthogonal Cartesian axes related to the cell axes as
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+ * specified by the description given in
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+ * _atom_sites.Cartn_transform_axes.
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+ */
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Cartn_z: coord,
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+ /**
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+ * The group of atoms to which the atom site belongs. This data
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+ * item is provided for compatibility with the original Protein
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+ * Data Bank format, and only for that purpose.
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+ */
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group_PDB: Aliased<'ATOM' | 'HETATM'>(str),
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+ /**
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+ * The value of _atom_site.id must uniquely identify a record in the
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+ * ATOM_SITE list.
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+ *
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+ * Note that this item need not be a number; it can be any unique
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+ * identifier.
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+ *
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+ * This data item was introduced to provide compatibility between
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+ * small-molecule and macromolecular CIFs. In a small-molecule
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+ * CIF, _atom_site_label is the identifier for the atom. In a
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+ * macromolecular CIF, the atom identifier is the aggregate of
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+ * _atom_site.label_alt_id, _atom_site.label_asym_id,
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+ * _atom_site.label_atom_id, _atom_site.label_comp_id and
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+ * _atom_site.label_seq_id. For the two types of files to be
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+ * compatible, a formal identifier for the category had to be
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+ * introduced that was independent of the different modes of
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+ * identifying the atoms. For compatibility with older CIFs,
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+ * _atom_site_label is aliased to _atom_site.id.
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+ */
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id: int,
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+ /**
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+ * A component of the identifier for this atom site.
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+ * For further details, see the definition of the ATOM_SITE_ALT
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+ * category.
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+ *
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+ * This data item is a pointer to _atom_sites_alt.id in the
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+ * ATOM_SITES_ALT category.
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+ */
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label_alt_id: str,
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+ /**
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+ * A component of the identifier for this atom site.
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+ * For further details, see the definition of the STRUCT_ASYM
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+ * category.
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+ *
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+ * This data item is a pointer to _struct_asym.id in the
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+ * STRUCT_ASYM category.
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+ */
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label_asym_id: str,
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+ /**
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+ * A component of the identifier for this atom site.
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+ *
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+ * This data item is a pointer to _chem_comp_atom.atom_id in the
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+ * CHEM_COMP_ATOM category.
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+ */
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label_atom_id: str,
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+ /**
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+ * A component of the identifier for this atom site.
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+ *
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+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
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+ * category.
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+ */
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label_comp_id: str,
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+ /**
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+ * This data item is a pointer to _entity.id in the ENTITY category.
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+ */
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label_entity_id: str,
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+ /**
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+ * This data item is a pointer to _entity_poly_seq.num in the
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+ * ENTITY_POLY_SEQ category.
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+ */
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label_seq_id: int,
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+ /**
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+ * The fraction of the atom type present at this site.
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+ * The sum of the occupancies of all the atom types at this site
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+ * may not significantly exceed 1.0 unless it is a dummy site.
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+ */
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occupancy: float,
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+ /**
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+ * This data item is a pointer to _atom_type.symbol in the
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+ * ATOM_TYPE category.
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+ */
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type_symbol: str,
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+ /**
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+ * PDB insertion code.
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+ */
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pdbx_PDB_ins_code: str,
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+ /**
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+ * PDB model number.
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+ */
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pdbx_PDB_model_num: int,
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+ /**
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+ * The net integer charge assigned to this atom. This is the
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+ * formal charge assignment normally found in chemical diagrams.
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+ */
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pdbx_formal_charge: int,
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+ /**
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+ * The model id corresponding to the atom site.
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+ * This data item is a pointer to _ihm_model_list.model_id
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+ * in the IHM_MODEL_LIST category.
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+ */
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ihm_model_id: int,
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},
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atom_sites: {
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+ /**
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+ * This data item is a pointer to _entry.id in the ENTRY category.
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+ */
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entry_id: str,
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+ /**
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+ * The elements of the 3x3 matrix used to transform Cartesian
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+ * coordinates in the ATOM_SITE category to fractional coordinates
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+ * in the same category. The axial alignments of this
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+ * transformation are described in _atom_sites.Cartn_transform_axes.
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+ * The 3x1 translation is defined in
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+ * _atom_sites.fract_transf_vector[].
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+ *
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+ * |x'| |11 12 13| |x| |1|
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+ * |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
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+ * |z'| |31 32 33| |z| |3|
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+ */
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fract_transf_matrix: Matrix(3, 3),
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+ /**
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+ * The elements of the three-element vector used to transform
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+ * Cartesian coordinates in the ATOM_SITE category to fractional
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+ * coordinates in the same category. The axial alignments of this
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+ * transformation are described in _atom_sites.Cartn_transform_axes.
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+ * The 3x3 rotation is defined in
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+ * _atom_sites.fract_transf_matrix[][].
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+ *
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+ * |x'| |11 12 13| |x| |1|
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+ * |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
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+ * |z'| |31 32 33| |z| |3|
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+ */
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fract_transf_vector: Vector(3),
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},
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cell: {
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+ /**
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+ * Unit-cell angle alpha of the reported structure in degrees.
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+ */
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angle_alpha: float,
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+ /**
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+ * Unit-cell angle beta of the reported structure in degrees.
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+ */
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angle_beta: float,
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+ /**
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+ * Unit-cell angle gamma of the reported structure in degrees.
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+ */
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angle_gamma: float,
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+ /**
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+ * This data item is a pointer to _entry.id in the ENTRY category.
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+ */
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entry_id: str,
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+ /**
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+ * Unit-cell length a corresponding to the structure reported in
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+ * angstroms.
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+ */
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length_a: float,
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+ /**
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+ * Unit-cell length b corresponding to the structure reported in
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+ * angstroms.
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+ */
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length_b: float,
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+ /**
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+ * Unit-cell length c corresponding to the structure reported in
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+ * angstroms.
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+ */
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length_c: float,
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+ /**
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+ * The number of the polymeric chains in a unit cell. In the case
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+ * of heteropolymers, Z is the number of occurrences of the most
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+ * populous chain.
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+ *
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+ * This data item is provided for compatibility with the original
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+ * Protein Data Bank format, and only for that purpose.
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+ */
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Z_PDB: int,
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+ /**
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+ * To further identify unique axis if necessary. E.g., P 21 with
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+ * an unique C axis will have 'C' in this field.
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+ */
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pdbx_unique_axis: str,
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},
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chem_comp: {
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+ /**
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+ * The formula for the chemical component. Formulae are written
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+ * according to the following rules:
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+ *
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+ * (1) Only recognized element symbols may be used.
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+ *
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+ * (2) Each element symbol is followed by a 'count' number. A count
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+ * of '1' may be omitted.
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+ *
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+ * (3) A space or parenthesis must separate each cluster of
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+ * (element symbol + count), but in general parentheses are
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+ * not used.
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+ *
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+ * (4) The order of elements depends on whether carbon is
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+ * present or not. If carbon is present, the order should be:
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+ * C, then H, then the other elements in alphabetical order
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+ * of their symbol. If carbon is not present, the elements
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+ * are listed purely in alphabetic order of their symbol. This
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+ * is the 'Hill' system used by Chemical Abstracts.
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+ */
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formula: str,
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+ /**
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+ * Formula mass in daltons of the chemical component.
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+ */
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formula_weight: float,
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+ /**
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+ * The value of _chem_comp.id must uniquely identify each item in
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+ * the CHEM_COMP list.
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+ *
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+ * For protein polymer entities, this is the three-letter code for
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+ * the amino acid.
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+ *
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+ * For nucleic acid polymer entities, this is the one-letter code
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+ * for the base.
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+ */
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id: str,
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+ /**
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+ * 'yes' indicates that this is a 'standard' monomer, 'no'
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+ * indicates that it is 'nonstandard'. Nonstandard monomers
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+ * should be described in more detail using the
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+ * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
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+ * _chem_comp.mon_nstd_details data items.
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+ */
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mon_nstd_flag: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
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+ /**
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+ * The full name of the component.
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+ */
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name: str,
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+ /**
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+ * For standard polymer components, the type of the monomer.
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+ * Note that monomers that will form polymers are of three types:
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+ * linking monomers, monomers with some type of N-terminal (or 5')
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+ * cap and monomers with some type of C-terminal (or 3') cap.
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+ */
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type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
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+ /**
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+ * Synonym list for the component.
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+ */
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pdbx_synonyms: List(';', x => x),
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},
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chem_comp_bond: {
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+ /**
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+ * The ID of the first of the two atoms that define the bond.
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+ *
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+ * This data item is a pointer to _chem_comp_atom.atom_id in the
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+ * CHEM_COMP_ATOM category.
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+ */
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atom_id_1: str,
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+ /**
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+ * The ID of the second of the two atoms that define the bond.
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+ *
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+ * This data item is a pointer to _chem_comp_atom.atom_id in the
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+ * CHEM_COMP_ATOM category.
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+ */
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atom_id_2: str,
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+ /**
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+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
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+ * category.
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+ */
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comp_id: str,
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+ /**
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+ * The value that should be taken as the target for the chemical
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+ * bond associated with the specified atoms, expressed as a bond
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+ * order.
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+ */
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value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
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+ /**
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+ * Ordinal index for the component bond list.
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+ */
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pdbx_ordinal: int,
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+ /**
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+ * Stereochemical configuration across a double bond.
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+ */
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pdbx_stereo_config: Aliased<'E' | 'Z' | 'N'>(str),
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+ /**
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+ * A flag indicating an aromatic bond.
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+ */
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pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
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},
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entity: {
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+ /**
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+ * A description of special aspects of the entity.
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+ */
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details: str,
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+ /**
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+ * Formula mass in daltons of the entity.
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+ */
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formula_weight: float,
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+ /**
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+ * The value of _entity.id must uniquely identify a record in the
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+ * ENTITY list.
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+ *
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+ * Note that this item need not be a number; it can be any unique
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+ * identifier.
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+ */
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id: str,
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+ /**
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+ * The method by which the sample for the entity was produced.
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+ * Entities isolated directly from natural sources (tissues, soil
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+ * samples etc.) are expected to have further information in the
|
|
|
+ * ENTITY_SRC_NAT category. Entities isolated from genetically
|
|
|
+ * manipulated sources are expected to have further information in
|
|
|
+ * the ENTITY_SRC_GEN category.
|
|
|
+ */
|
|
|
src_method: Aliased<'nat' | 'man' | 'syn'>(str),
|
|
|
+ /**
|
|
|
+ * Defines the type of the entity.
|
|
|
+ *
|
|
|
+ * Polymer entities are expected to have corresponding
|
|
|
+ * ENTITY_POLY and associated entries.
|
|
|
+ *
|
|
|
+ * Non-polymer entities are expected to have corresponding
|
|
|
+ * CHEM_COMP and associated entries.
|
|
|
+ *
|
|
|
+ * Water entities are not expected to have corresponding
|
|
|
+ * entries in the ENTITY category.
|
|
|
+ */
|
|
|
type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
|
|
|
+ /**
|
|
|
+ * A description of the entity.
|
|
|
+ *
|
|
|
+ * Corresponds to the compound name in the PDB format.
|
|
|
+ */
|
|
|
pdbx_description: str,
|
|
|
+ /**
|
|
|
+ * A place holder for the number of molecules of the entity in
|
|
|
+ * the entry.
|
|
|
+ */
|
|
|
pdbx_number_of_molecules: float,
|
|
|
+ /**
|
|
|
+ * Details about any entity mutation(s).
|
|
|
+ */
|
|
|
pdbx_mutation: str,
|
|
|
+ /**
|
|
|
+ * Entity fragment description(s).
|
|
|
+ */
|
|
|
pdbx_fragment: str,
|
|
|
+ /**
|
|
|
+ * Enzyme Commission (EC) number(s)
|
|
|
+ */
|
|
|
pdbx_ec: List(',', x => x),
|
|
|
},
|
|
|
entity_poly: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entity.id in the ENTITY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * A flag to indicate whether the polymer contains at least
|
|
|
+ * one monomer-to-monomer link different from that implied by
|
|
|
+ * _entity_poly.type.
|
|
|
+ */
|
|
|
nstd_linkage: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
|
|
|
+ /**
|
|
|
+ * A flag to indicate whether the polymer contains at least
|
|
|
+ * one monomer that is not considered standard.
|
|
|
+ */
|
|
|
nstd_monomer: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
|
|
|
+ /**
|
|
|
+ * The type of the polymer.
|
|
|
+ */
|
|
|
type: Aliased<'polypeptide(D)' | 'polypeptide(L)' | 'polydeoxyribonucleotide' | 'polyribonucleotide' | 'polysaccharide(D)' | 'polysaccharide(L)' | 'polydeoxyribonucleotide/polyribonucleotide hybrid' | 'cyclic-pseudo-peptide' | 'peptide nucleic acid' | 'other'>(str),
|
|
|
+ /**
|
|
|
+ * The PDB strand/chain id(s) corresponding to this polymer entity.
|
|
|
+ */
|
|
|
pdbx_strand_id: List(',', x => x),
|
|
|
+ /**
|
|
|
+ * Chemical sequence expressed as string of one-letter
|
|
|
+ * amino acid codes. Modifications and non-standard
|
|
|
+ * amino acids are coded as X.
|
|
|
+ */
|
|
|
pdbx_seq_one_letter_code: str,
|
|
|
+ /**
|
|
|
+ * Cannonical chemical sequence expressed as string of
|
|
|
+ * one-letter amino acid codes. Modifications are coded
|
|
|
+ * as the parent amino acid where possible.
|
|
|
+ *
|
|
|
+ * A for alanine or adenine
|
|
|
+ * B for ambiguous asparagine/aspartic-acid
|
|
|
+ * R for arginine
|
|
|
+ * N for asparagine
|
|
|
+ * D for aspartic-acid
|
|
|
+ * C for cysteine or cystine or cytosine
|
|
|
+ * Q for glutamine
|
|
|
+ * E for glutamic-acid
|
|
|
+ * Z for ambiguous glutamine/glutamic acid
|
|
|
+ * G for glycine or guanine
|
|
|
+ * H for histidine
|
|
|
+ * I for isoleucine
|
|
|
+ * L for leucine
|
|
|
+ * K for lysine
|
|
|
+ * M for methionine
|
|
|
+ * F for phenylalanine
|
|
|
+ * P for proline
|
|
|
+ * S for serine
|
|
|
+ * T for threonine or thymine
|
|
|
+ * W for tryptophan
|
|
|
+ * Y for tyrosine
|
|
|
+ * V for valine
|
|
|
+ * U for uracil
|
|
|
+ */
|
|
|
pdbx_seq_one_letter_code_can: str,
|
|
|
+ /**
|
|
|
+ * For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
|
|
|
+ */
|
|
|
pdbx_target_identifier: str,
|
|
|
},
|
|
|
entity_poly_seq: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entity.id in the ENTITY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * A flag to indicate whether this monomer in the polymer is
|
|
|
+ * heterogeneous in sequence.
|
|
|
+ */
|
|
|
hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
|
|
|
+ * category.
|
|
|
+ */
|
|
|
mon_id: str,
|
|
|
+ /**
|
|
|
+ * The value of _entity_poly_seq.num must uniquely and sequentially
|
|
|
+ * identify a record in the ENTITY_POLY_SEQ list.
|
|
|
+ *
|
|
|
+ * Note that this item must be a number and that the sequence
|
|
|
+ * numbers must progress in increasing numerical order.
|
|
|
+ */
|
|
|
num: int,
|
|
|
},
|
|
|
entry: {
|
|
|
+ /**
|
|
|
+ * The value of _entry.id identifies the data block.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
},
|
|
|
exptl: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entry.id in the ENTRY category.
|
|
|
+ */
|
|
|
entry_id: str,
|
|
|
+ /**
|
|
|
+ * The method used in the experiment.
|
|
|
+ */
|
|
|
method: Aliased<'X-RAY DIFFRACTION' | 'NEUTRON DIFFRACTION' | 'FIBER DIFFRACTION' | 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'SOLUTION NMR' | 'SOLID-STATE NMR' | 'SOLUTION SCATTERING' | 'POWDER DIFFRACTION' | 'INFRARED SPECTROSCOPY' | 'EPR' | 'FLUORESCENCE TRANSFER' | 'THEORETICAL MODEL'>(str),
|
|
|
},
|
|
|
struct: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entry.id in the ENTRY category.
|
|
|
+ */
|
|
|
entry_id: str,
|
|
|
+ /**
|
|
|
+ * A title for the data block. The author should attempt to convey
|
|
|
+ * the essence of the structure archived in the CIF in the title,
|
|
|
+ * and to distinguish this structural result from others.
|
|
|
+ */
|
|
|
title: str,
|
|
|
},
|
|
|
struct_asym: {
|
|
|
+ /**
|
|
|
+ * A description of special aspects of this portion of the contents
|
|
|
+ * of the asymmetric unit.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entity.id in the ENTITY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * The value of _struct_asym.id must uniquely identify a record in
|
|
|
+ * the STRUCT_ASYM list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * This data item indicates whether the structural elements are modified.
|
|
|
+ */
|
|
|
pdbx_modified: str,
|
|
|
+ /**
|
|
|
+ * A flag indicating that this entity was originally labeled
|
|
|
+ * with a blank PDB chain id.
|
|
|
+ */
|
|
|
pdbx_blank_PDB_chainid_flag: Aliased<'Y' | 'N'>(str),
|
|
|
},
|
|
|
struct_conf: {
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_comp_id in
|
|
|
+ * the ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in
|
|
|
+ * the ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _struct_conf_type.id in the
|
|
|
+ * STRUCT_CONF_TYPE category.
|
|
|
+ */
|
|
|
conf_type_id: Aliased<'HELX_P' | 'HELX_OT_P' | 'HELX_RH_P' | 'HELX_RH_OT_P' | 'HELX_RH_AL_P' | 'HELX_RH_GA_P' | 'HELX_RH_OM_P' | 'HELX_RH_PI_P' | 'HELX_RH_27_P' | 'HELX_RH_3T_P' | 'HELX_RH_PP_P' | 'HELX_LH_P' | 'HELX_LH_OT_P' | 'HELX_LH_AL_P' | 'HELX_LH_GA_P' | 'HELX_LH_OM_P' | 'HELX_LH_PI_P' | 'HELX_LH_27_P' | 'HELX_LH_3T_P' | 'HELX_LH_PP_P' | 'HELX_N' | 'HELX_OT_N' | 'HELX_RH_N' | 'HELX_RH_OT_N' | 'HELX_RH_A_N' | 'HELX_RH_B_N' | 'HELX_RH_Z_N' | 'HELX_LH_N' | 'HELX_LH_OT_N' | 'HELX_LH_A_N' | 'HELX_LH_B_N' | 'HELX_LH_Z_N' | 'TURN_P' | 'TURN_OT_P' | 'TURN_TY1_P' | 'TURN_TY1P_P' | 'TURN_TY2_P' | 'TURN_TY2P_P' | 'TURN_TY3_P' | 'TURN_TY3P_P' | 'STRN'>(str),
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the conformation assignment.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * The value of _struct_conf.id must uniquely identify a record in
|
|
|
+ * the STRUCT_CONF list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment starts.
|
|
|
+ */
|
|
|
pdbx_beg_PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * conformation segment ends.
|
|
|
+ */
|
|
|
pdbx_end_PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * This item is a place holder for the helix class used in the PDB
|
|
|
+ * HELIX record.
|
|
|
+ */
|
|
|
pdbx_PDB_helix_class: str,
|
|
|
+ /**
|
|
|
+ * A placeholder for the lengths of the helix of the PDB
|
|
|
+ * HELIX record.
|
|
|
+ */
|
|
|
pdbx_PDB_helix_length: int,
|
|
|
+ /**
|
|
|
+ * A placeholder for the helix identifier of the PDB
|
|
|
+ * HELIX record.
|
|
|
+ */
|
|
|
pdbx_PDB_helix_id: str,
|
|
|
},
|
|
|
struct_conn: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _struct_conn_type.id in the
|
|
|
+ * STRUCT_CONN_TYPE category.
|
|
|
+ */
|
|
|
conn_type_id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the connection.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The value of _struct_conn.id must uniquely identify a record in
|
|
|
+ * the STRUCT_CONN list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr1_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
ptnr1_label_atom_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr1_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr1_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr1_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr1_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr1_auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * Describes the symmetry operation that should be applied to the
|
|
|
+ * atom set specified by _struct_conn.ptnr1_label* to generate the
|
|
|
+ * first partner in the structure connection.
|
|
|
+ */
|
|
|
ptnr1_symmetry: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr2_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
ptnr2_label_atom_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr2_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr2_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr2_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr2_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
ptnr2_auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * Describes the symmetry operation that should be applied to the
|
|
|
+ * atom set specified by _struct_conn.ptnr2_label* to generate the
|
|
|
+ * second partner in the structure connection.
|
|
|
+ */
|
|
|
ptnr2_symmetry: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr1_PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_alt_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr1_label_alt_id: str,
|
|
|
+ /**
|
|
|
+ * A placeholder for the standard residue name found in
|
|
|
+ * the MODRES record of a PDB file.
|
|
|
+ */
|
|
|
pdbx_ptnr1_standard_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the structure
|
|
|
+ * connection.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr2_PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 2 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_alt_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr2_label_alt_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 3 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr3_PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 3 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_alt_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr3_label_alt_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 3 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_asym_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr3_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 3 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_atom_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr3_label_atom_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 3 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_comp_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr3_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for partner 1 of the
|
|
|
+ * structure connection. This data item is a pointer to
|
|
|
+ * _atom_site.label_seq_id in the ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_ptnr3_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A placeholder for the PDB id in the case the category
|
|
|
+ * is used to hold the information of the MODRES record of
|
|
|
+ * a PDB file.
|
|
|
+ */
|
|
|
pdbx_PDB_id: str,
|
|
|
+ /**
|
|
|
+ * Distance value for this contact.
|
|
|
+ */
|
|
|
pdbx_dist_value: float,
|
|
|
+ /**
|
|
|
+ * The chemical bond order associated with the specified atoms in
|
|
|
+ * this contact.
|
|
|
+ */
|
|
|
pdbx_value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad'>(str),
|
|
|
},
|
|
|
struct_conn_type: {
|
|
|
+ /**
|
|
|
+ * The criteria used to define the interaction.
|
|
|
+ */
|
|
|
criteria: str,
|
|
|
+ /**
|
|
|
+ * The chemical or structural type of the interaction.
|
|
|
+ */
|
|
|
id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
|
|
|
+ /**
|
|
|
+ * A reference that specifies the criteria used to define the
|
|
|
+ * interaction.
|
|
|
+ */
|
|
|
reference: str,
|
|
|
},
|
|
|
struct_keywords: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entry.id in the ENTRY category.
|
|
|
+ */
|
|
|
entry_id: str,
|
|
|
+ /**
|
|
|
+ * Keywords describing this structure.
|
|
|
+ */
|
|
|
text: List(',', x => x),
|
|
|
+ /**
|
|
|
+ * Terms characterizing the macromolecular structure.
|
|
|
+ */
|
|
|
pdbx_keywords: str,
|
|
|
},
|
|
|
struct_ncs_oper: {
|
|
|
+ /**
|
|
|
+ * A code to indicate whether this operator describes a
|
|
|
+ * relationship between coordinates all of which are given in the
|
|
|
+ * data block (in which case the value of code is 'given'), or
|
|
|
+ * whether the operator is used to generate new coordinates from
|
|
|
+ * those that are given in the data block (in which case the value
|
|
|
+ * of code is 'generate').
|
|
|
+ */
|
|
|
code: Aliased<'given' | 'generate'>(str),
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the noncrystallographic
|
|
|
+ * symmetry operator.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The value of _struct_ncs_oper.id must uniquely identify a
|
|
|
+ * record in the STRUCT_NCS_OPER list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * The elements of the 3x3 matrix component of a
|
|
|
+ * noncrystallographic symmetry operation.
|
|
|
+ */
|
|
|
matrix: Matrix(3, 3),
|
|
|
+ /**
|
|
|
+ * The elements of the three-element vector component of a
|
|
|
+ * noncrystallographic symmetry operation.
|
|
|
+ */
|
|
|
vector: Vector(3),
|
|
|
},
|
|
|
struct_sheet_range: {
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
beg_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
|
|
|
+ * category.
|
|
|
+ */
|
|
|
beg_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
end_label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
|
|
|
+ * category.
|
|
|
+ */
|
|
|
end_label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in
|
|
|
+ * the ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range begins.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
beg_auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta-sheet range ends.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
end_auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * The value of _struct_sheet_range.id must uniquely identify a
|
|
|
+ * range in a given sheet in the STRUCT_SHEET_RANGE list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _struct_sheet.id in the
|
|
|
+ * STRUCT_SHEET category.
|
|
|
+ */
|
|
|
sheet_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta sheet range begins. Insertion code.
|
|
|
+ */
|
|
|
pdbx_beg_PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the residue at which the
|
|
|
+ * beta sheet range ends. Insertion code.
|
|
|
+ */
|
|
|
pdbx_end_PDB_ins_code: str,
|
|
|
},
|
|
|
struct_site: {
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the site.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The value of _struct_site.id must uniquely identify a record in
|
|
|
+ * the STRUCT_SITE list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * Number of residues in the site.
|
|
|
+ */
|
|
|
pdbx_num_residues: int,
|
|
|
+ /**
|
|
|
+ * Source of evidence supporting the assignment of this site.
|
|
|
+ */
|
|
|
pdbx_evidence_code: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the ligand in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the ligand in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for the ligand in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
pdbx_auth_seq_id: str,
|
|
|
+ /**
|
|
|
+ * PDB insertion code for the ligand in the site.
|
|
|
+ */
|
|
|
pdbx_auth_ins_code: str,
|
|
|
},
|
|
|
struct_site_gen: {
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the symmetry generation of
|
|
|
+ * this portion of the structural site.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The value of _struct_site_gen.id must uniquely identify a record
|
|
|
+ * in the STRUCT_SITE_GEN list.
|
|
|
+ *
|
|
|
+ * Note that this item need not be a number; it can be any unique
|
|
|
+ * identifier.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_sites_alt.id in the
|
|
|
+ * ATOM_SITES_ALT category.
|
|
|
+ */
|
|
|
label_alt_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
label_atom_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A component of the identifier for participants in the site.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
auth_seq_id: str,
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _struct_site.id in the STRUCT_SITE
|
|
|
+ * category.
|
|
|
+ */
|
|
|
site_id: str,
|
|
|
+ /**
|
|
|
+ * Describes the symmetry operation that should be applied to the
|
|
|
+ * atom set specified by _struct_site_gen.label* to generate a
|
|
|
+ * portion of the site.
|
|
|
+ */
|
|
|
symmetry: str,
|
|
|
+ /**
|
|
|
+ * PDB insertion code.
|
|
|
+ */
|
|
|
pdbx_auth_ins_code: str,
|
|
|
+ /**
|
|
|
+ * Number of residues in the site.
|
|
|
+ */
|
|
|
pdbx_num_res: int,
|
|
|
},
|
|
|
symmetry: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _entry.id in the ENTRY category.
|
|
|
+ */
|
|
|
entry_id: str,
|
|
|
+ /**
|
|
|
+ * The cell settings for this space-group symmetry.
|
|
|
+ */
|
|
|
cell_setting: Aliased<'triclinic' | 'monoclinic' | 'orthorhombic' | 'tetragonal' | 'rhombohedral' | 'trigonal' | 'hexagonal' | 'cubic'>(str),
|
|
|
+ /**
|
|
|
+ * Space-group number from International Tables for Crystallography
|
|
|
+ * Vol. A (2002).
|
|
|
+ */
|
|
|
Int_Tables_number: int,
|
|
|
+ /**
|
|
|
+ * Space-group symbol as described by Hall (1981). This symbol
|
|
|
+ * gives the space-group setting explicitly. Leave spaces between
|
|
|
+ * the separate components of the symbol.
|
|
|
+ *
|
|
|
+ * Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
|
|
|
+ * (1981) A37, 921.
|
|
|
+ */
|
|
|
space_group_name_Hall: str,
|
|
|
+ /**
|
|
|
+ * Hermann-Mauguin space-group symbol. Note that the
|
|
|
+ * Hermann-Mauguin symbol does not necessarily contain complete
|
|
|
+ * information about the symmetry and the space-group origin. If
|
|
|
+ * used, always supply the FULL symbol from International Tables
|
|
|
+ * for Crystallography Vol. A (2002) and indicate the origin and
|
|
|
+ * the setting if it is not implicit. If there is any doubt that
|
|
|
+ * the equivalent positions can be uniquely deduced from this
|
|
|
+ * symbol, specify the _symmetry_equiv.pos_as_xyz or
|
|
|
+ * _symmetry.space_group_name_Hall data items as well. Leave
|
|
|
+ * spaces between symbols referring to
|
|
|
+ * different axes.
|
|
|
+ */
|
|
|
'space_group_name_H-M': str,
|
|
|
},
|
|
|
pdbx_struct_assembly: {
|
|
|
+ /**
|
|
|
+ * Provides details of the method used to determine or
|
|
|
+ * compute the assembly.
|
|
|
+ */
|
|
|
method_details: str,
|
|
|
+ /**
|
|
|
+ * Provides the details of the oligomeric state of the assembly.
|
|
|
+ */
|
|
|
oligomeric_details: str,
|
|
|
+ /**
|
|
|
+ * The number of polymer molecules in the assembly.
|
|
|
+ */
|
|
|
oligomeric_count: int,
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the macromolecular assembly.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_struct_assembly.id must uniquely identify a record in
|
|
|
+ * the PDBX_STRUCT_ASSEMBLY list.
|
|
|
+ */
|
|
|
id: str,
|
|
|
},
|
|
|
pdbx_struct_mod_residue: {
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_struct_mod_residue.id must uniquely identify
|
|
|
+ * each item in the PDBX_STRUCT_MOD_RESIDUE list.
|
|
|
+ *
|
|
|
+ * This is an integer serial number.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the modified polymer component.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the modified polymer component.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
auth_comp_id: str,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the modified polymer component.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.auth_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
auth_seq_id: int,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the modified polymer component.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
PDB_ins_code: str,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the modified polymer component.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_asym_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
label_asym_id: str,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the modified polymer component.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_comp_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
label_comp_id: str,
|
|
|
+ /**
|
|
|
+ * Part of the identifier for the unobserved or zero occupancy residue.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _atom_site.label_seq_id in the
|
|
|
+ * ATOM_SITE category.
|
|
|
+ */
|
|
|
label_seq_id: int,
|
|
|
+ /**
|
|
|
+ * The parent component identifier for this modified polymer component.
|
|
|
+ */
|
|
|
parent_comp_id: str,
|
|
|
+ /**
|
|
|
+ * Details of the modification for this polymer component.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
pdbx_struct_oper_list: {
|
|
|
+ /**
|
|
|
+ * This identifier code must uniquely identify a
|
|
|
+ * record in the PDBX_STRUCT_OPER_LIST list.
|
|
|
+ */
|
|
|
id: str,
|
|
|
+ /**
|
|
|
+ * A code to indicate the type of operator.
|
|
|
+ */
|
|
|
type: Aliased<'identity operation' | 'point symmetry operation' | 'helical symmetry operation' | 'crystal symmetry operation' | '3D crystal symmetry operation' | '2D crystal symmetry operation' | 'transform to point frame' | 'transform to helical frame' | 'transform to crystal frame' | 'transform to 2D crystal frame' | 'transform to 3D crystal frame' | 'build point asymmetric unit' | 'build helical asymmetric unit' | 'build 2D crystal asymmetric unit' | 'build 3D crystal asymmetric unit'>(str),
|
|
|
+ /**
|
|
|
+ * A descriptive name for the transformation operation.
|
|
|
+ */
|
|
|
name: str,
|
|
|
+ /**
|
|
|
+ * The symmetry operation corresponding to the transformation operation.
|
|
|
+ */
|
|
|
symmetry_operation: str,
|
|
|
+ /**
|
|
|
+ * The elements of the 3x3 matrix component of the
|
|
|
+ * transformation operation.
|
|
|
+ */
|
|
|
matrix: Matrix(3, 3),
|
|
|
+ /**
|
|
|
+ * The elements of the three-element vector component of the
|
|
|
+ * transformation operation.
|
|
|
+ */
|
|
|
vector: Vector(3),
|
|
|
},
|
|
|
pdbx_struct_assembly_gen: {
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _struct_asym.id in
|
|
|
+ * the STRUCT_ASYM category.
|
|
|
+ *
|
|
|
+ * This item may be expressed as a comma separated list of identifiers.
|
|
|
+ */
|
|
|
asym_id_list: List(',', x => x),
|
|
|
+ /**
|
|
|
+ * This data item is a pointer to _pdbx_struct_assembly.id in the
|
|
|
+ * PDBX_STRUCT_ASSEMBLY category.
|
|
|
+ */
|
|
|
assembly_id: str,
|
|
|
+ /**
|
|
|
+ * Identifies the operation of collection of operations
|
|
|
+ * from category PDBX_STRUCT_OPER_LIST.
|
|
|
+ *
|
|
|
+ * Operation expressions may have the forms:
|
|
|
+ *
|
|
|
+ * (1) the single operation 1
|
|
|
+ * (1,2,5) the operations 1, 2, 5
|
|
|
+ * (1-4) the operations 1,2,3 and 4
|
|
|
+ * (1,2)(3,4) the combinations of operations
|
|
|
+ * 3 and 4 followed by 1 and 2 (i.e.
|
|
|
+ * the cartesian product of parenthetical
|
|
|
+ * groups applied from right to left)
|
|
|
+ */
|
|
|
oper_expression: str,
|
|
|
},
|
|
|
pdbx_reference_entity_list: {
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_reference_entity_list.prd_id is a reference
|
|
|
+ * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
|
|
|
+ */
|
|
|
prd_id: str,
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier
|
|
|
+ * the a constituent entity within this reference molecule.
|
|
|
+ */
|
|
|
ref_entity_id: str,
|
|
|
+ /**
|
|
|
+ * Defines the polymer characteristic of the entity.
|
|
|
+ */
|
|
|
type: str,
|
|
|
+ /**
|
|
|
+ * Additional details about this entity.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The component number of this entity within the molecule.
|
|
|
+ */
|
|
|
component_id: int,
|
|
|
},
|
|
|
pdbx_reference_entity_link: {
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_reference_entity_link.link_id uniquely identifies
|
|
|
+ * linkages between entities with a molecule.
|
|
|
+ */
|
|
|
link_id: int,
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_reference_entity_link.prd_id is a reference
|
|
|
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
|
|
|
+ */
|
|
|
prd_id: str,
|
|
|
+ /**
|
|
|
+ * A description of special aspects of a linkage between
|
|
|
+ * chemical components in the structure.
|
|
|
+ */
|
|
|
details: str,
|
|
|
+ /**
|
|
|
+ * The reference entity id of the first of the two entities joined by the
|
|
|
+ * linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_LIST category.
|
|
|
+ */
|
|
|
ref_entity_id_1: str,
|
|
|
+ /**
|
|
|
+ * The reference entity id of the second of the two entities joined by the
|
|
|
+ * linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_LIST category.
|
|
|
+ */
|
|
|
ref_entity_id_2: str,
|
|
|
+ /**
|
|
|
+ * For a polymer entity, the sequence number in the first of
|
|
|
+ * the two entities containing the linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_seq_num_1: int,
|
|
|
+ /**
|
|
|
+ * For a polymer entity, the sequence number in the second of
|
|
|
+ * the two entities containing the linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_seq_num_2: int,
|
|
|
+ /**
|
|
|
+ * The component identifier in the first of the two entities containing the linkage.
|
|
|
+ *
|
|
|
+ * For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ *
|
|
|
+ * For non-polymer entities, this data item is a pointer to
|
|
|
+ * _pdbx_reference_entity_nonpoly.chem_comp_id in the
|
|
|
+ * PDBX_REFERENCE_ENTITY_NONPOLY category.
|
|
|
+ */
|
|
|
comp_id_1: str,
|
|
|
+ /**
|
|
|
+ * The component identifier in the second of the two entities containing the linkage.
|
|
|
+ *
|
|
|
+ * For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ *
|
|
|
+ * For non-polymer entities, this data item is a pointer to
|
|
|
+ * _pdbx_reference_entity_nonpoly.chem_comp_id in the
|
|
|
+ * PDBX_REFERENCE_ENTITY_NONPOLY category.
|
|
|
+ */
|
|
|
comp_id_2: str,
|
|
|
+ /**
|
|
|
+ * The atom identifier/name in the first of the two entities containing the linkage.
|
|
|
+ */
|
|
|
atom_id_1: str,
|
|
|
+ /**
|
|
|
+ * The atom identifier/name in the second of the two entities containing the linkage.
|
|
|
+ */
|
|
|
atom_id_2: str,
|
|
|
+ /**
|
|
|
+ * The bond order target for the chemical linkage.
|
|
|
+ */
|
|
|
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
|
|
|
+ /**
|
|
|
+ * The entity component identifier for the first of two entities containing the linkage.
|
|
|
+ */
|
|
|
component_1: int,
|
|
|
+ /**
|
|
|
+ * The entity component identifier for the second of two entities containing the linkage.
|
|
|
+ */
|
|
|
component_2: int,
|
|
|
+ /**
|
|
|
+ * A code indicating the entity types involved in the linkage.
|
|
|
+ */
|
|
|
link_class: Aliased<'PP' | 'PN' | 'NP' | 'NN'>(str),
|
|
|
},
|
|
|
pdbx_reference_entity_poly_link: {
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
|
|
|
+ * a linkage within a polymer entity.
|
|
|
+ */
|
|
|
link_id: int,
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_reference_entity_poly_link.prd_id is a reference
|
|
|
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.
|
|
|
+ */
|
|
|
prd_id: str,
|
|
|
+ /**
|
|
|
+ * The reference entity id of the polymer entity containing the linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY category.
|
|
|
+ */
|
|
|
ref_entity_id: str,
|
|
|
+ /**
|
|
|
+ * The entity component identifier entity containing the linkage.
|
|
|
+ */
|
|
|
component_id: int,
|
|
|
+ /**
|
|
|
+ * For a polymer entity, the sequence number in the first of
|
|
|
+ * the two components making the linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_seq_num_1: int,
|
|
|
+ /**
|
|
|
+ * For a polymer entity, the sequence number in the second of
|
|
|
+ * the two components making the linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_seq_num_2: int,
|
|
|
+ /**
|
|
|
+ * The component identifier in the first of the two components making the
|
|
|
+ * linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_1: str,
|
|
|
+ /**
|
|
|
+ * The component identifier in the second of the two components making the
|
|
|
+ * linkage.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
|
|
|
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_2: str,
|
|
|
+ /**
|
|
|
+ * The atom identifier/name in the first of the two components making
|
|
|
+ * the linkage.
|
|
|
+ */
|
|
|
atom_id_1: str,
|
|
|
+ /**
|
|
|
+ * The atom identifier/name in the second of the two components making
|
|
|
+ * the linkage.
|
|
|
+ */
|
|
|
atom_id_2: str,
|
|
|
+ /**
|
|
|
+ * The bond order target for the non-standard linkage.
|
|
|
+ */
|
|
|
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
|
|
|
},
|
|
|
pdbx_molecule: {
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_molecule.prd_id is the PDB accession code for this
|
|
|
+ * reference molecule.
|
|
|
+ */
|
|
|
prd_id: str,
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_molecule.instance_id is identifies a particular molecule
|
|
|
+ * in the molecule list.
|
|
|
+ */
|
|
|
instance_id: int,
|
|
|
+ /**
|
|
|
+ * A reference to _struct_asym.id in the STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
},
|
|
|
pdbx_molecule_features: {
|
|
|
+ /**
|
|
|
+ * The value of _pdbx_molecule_features.prd_id is the PDB accession code for this
|
|
|
+ * reference molecule.
|
|
|
+ */
|
|
|
prd_id: str,
|
|
|
+ /**
|
|
|
+ * Broadly defines the function of the molecule.
|
|
|
+ */
|
|
|
class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Growth factor' | 'Immunosuppressant' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Oxidation-reduction' | 'Receptor' | 'Thrombin inhibitor' | 'Trypsin inhibitor' | 'Toxin' | 'Transport activator' | 'Unknown' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
|
|
|
+ /**
|
|
|
+ * Defines the structural classification of the molecule.
|
|
|
+ */
|
|
|
type: Aliased<'Amino acid' | 'Aminoglycoside' | 'Anthracycline' | 'Anthraquinone' | 'Ansamycin' | 'Chalkophore' | 'Chromophore' | 'Glycopeptide' | 'Cyclic depsipeptide' | 'Cyclic lipopeptide' | 'Cyclic peptide' | 'Heterocyclic' | 'Imino sugar' | 'Keto acid' | 'Lipoglycopeptide' | 'Lipopeptide' | 'Macrolide' | 'Non-polymer' | 'Nucleoside' | 'Oligopeptide' | 'Oligosaccharide' | 'Peptaibol' | 'Peptide-like' | 'Polycyclic' | 'Polypeptide' | 'Polysaccharide' | 'Quinolone' | 'Thiolactone' | 'Thiopeptide' | 'Siderophore' | 'Unknown' | 'Chalkophore, Polypeptide'>(str),
|
|
|
+ /**
|
|
|
+ * A name of the molecule.
|
|
|
+ */
|
|
|
name: str,
|
|
|
+ /**
|
|
|
+ * Additional details describing the molecule.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_starting_model_details: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the starting structural model.
|
|
|
+ */
|
|
|
starting_model_id: str,
|
|
|
+ /**
|
|
|
+ * A unique identifier for the distinct molecular entities.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * A text description of the molecular entity
|
|
|
+ */
|
|
|
entity_description: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the entity molecule.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The leading residue index for the sequence segment modeled using this starting model.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The trailing residue index for the sequence segment modeled using this starting model.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * The source of the starting model.
|
|
|
+ */
|
|
|
starting_model_source: Aliased<'comparative model' | 'experimental model' | 'integrative model' | 'ab initio model' | 'other'>(str),
|
|
|
+ /**
|
|
|
+ * The author assigned chainId/auth_asym_id corresponding to this starting model.
|
|
|
+ * This corresponds to the chainId/auth_asym_id of the experimental models in the
|
|
|
+ * PDB or comparative models in the Model Archive or the starting models referenced
|
|
|
+ * via a DOI. If starting models are included in IHM_STARTING_MODEL_COORD, then
|
|
|
+ * this will be the same as _ihm_starting_model_details.asym_id.
|
|
|
+ */
|
|
|
starting_model_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * The offset in residue numbering between the starting model and the deposited I/H model, if applicable.
|
|
|
+ * I/H model residue number = Starting model residue number + offset
|
|
|
+ */
|
|
|
starting_model_sequence_offset: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the starting model (comparative, experimental or integrative)
|
|
|
+ * used as input in the integrative modeling.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
},
|
|
|
ihm_starting_comparative_models: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the starting comparative model.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * The identifier for the starting structural model.
|
|
|
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id
|
|
|
+ * in the IHM_STARTING_MODEL_DETAILS category.
|
|
|
+ */
|
|
|
starting_model_id: str,
|
|
|
+ /**
|
|
|
+ * The chainId/auth_asym_id corresponding to the starting model.
|
|
|
+ */
|
|
|
starting_model_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * The starting residue index of the starting model.
|
|
|
+ */
|
|
|
starting_model_seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The ending residue index of the starting model.
|
|
|
+ */
|
|
|
starting_model_seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * The chainId/auth_asym_id corresponding to the template.
|
|
|
+ */
|
|
|
template_auth_asym_id: str,
|
|
|
+ /**
|
|
|
+ * The starting residue index of the template.
|
|
|
+ */
|
|
|
template_seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The ending residue index of the template.
|
|
|
+ */
|
|
|
template_seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * The percentage sequence identity between the template sequence and the comparative model sequence.
|
|
|
+ */
|
|
|
template_sequence_identity: float,
|
|
|
+ /**
|
|
|
+ * The denominator used while calculating the sequence identity provided in
|
|
|
+ * _ihm_starting_comparative_models.template_sequence_identity.
|
|
|
+ */
|
|
|
template_sequence_identity_denominator: Aliased<'1' | '2' | '3' | '4' | '5'>(int),
|
|
|
+ /**
|
|
|
+ * The dataset list id corresponding to the template used to obtain the comparative model.
|
|
|
+ * This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
template_dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * The file id corresponding to the sequence alignment of the template sequence and the comparative model sequence.
|
|
|
+ * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
|
|
|
+ */
|
|
|
alignment_file_id: int,
|
|
|
},
|
|
|
ihm_starting_model_seq_dif: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the entry.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * A unique identifier for the distinct molecular entities.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the entity molecule.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The residue index.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id: int,
|
|
|
+ /**
|
|
|
+ * The component identifier for the residue.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id: str,
|
|
|
+ /**
|
|
|
+ * Unique identifier for the starting model record.
|
|
|
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id in the
|
|
|
+ * IHM_STARTING_MODEL_DETAILS category.
|
|
|
+ */
|
|
|
starting_model_id: str,
|
|
|
+ /**
|
|
|
+ * The asym/strand identifier for the entity molecule of the database starting model.
|
|
|
+ */
|
|
|
db_asym_id: str,
|
|
|
+ /**
|
|
|
+ * The corresponding residue index of the database starting model.
|
|
|
+ */
|
|
|
db_seq_id: int,
|
|
|
+ /**
|
|
|
+ * The correspinding component identifier for the residue in the database starting model.
|
|
|
+ */
|
|
|
db_comp_id: str,
|
|
|
+ /**
|
|
|
+ * A description of special aspects of the point differences
|
|
|
+ * between the sequence of the entity or biological unit described
|
|
|
+ * in the data block and that in the starting model referenced
|
|
|
+ * from a database.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_model_representation: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the model details record.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier that collects or groups together a set of representations.
|
|
|
+ * This data item may be used to identify a complete model representation.
|
|
|
+ */
|
|
|
representation_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the residue range segment within the structural model.
|
|
|
+ */
|
|
|
segment_id: int,
|
|
|
+ /**
|
|
|
+ * A unique identifier distinct molecular entities.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the
|
|
|
+ * ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * A text description of the molecular entity
|
|
|
+ */
|
|
|
entity_description: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the entity molecule.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
entity_asym_id: str,
|
|
|
+ /**
|
|
|
+ * The leading residue index for the sequence segment modeled using this starting model.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The trailing residue index for the sequence segment modeled using this starting model.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * The primitive object used to model this segment.
|
|
|
+ */
|
|
|
model_object_primitive: Aliased<'atomistic' | 'sphere' | 'gaussian' | 'other'>(str),
|
|
|
+ /**
|
|
|
+ * The identifier for the starting structural model.
|
|
|
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id
|
|
|
+ * in the IHM_STARTING_MODEL_DETAILS category.
|
|
|
+ */
|
|
|
starting_model_id: str,
|
|
|
+ /**
|
|
|
+ * The manner in which the segment is modeled.
|
|
|
+ */
|
|
|
model_mode: Aliased<'rigid' | 'flexible'>(str),
|
|
|
+ /**
|
|
|
+ * The level of detail at which model primitive objects are applied to the structure.
|
|
|
+ */
|
|
|
model_granularity: Aliased<'by-atom' | 'by-residue' | 'multi-residue' | 'by-feature'>(str),
|
|
|
+ /**
|
|
|
+ * The number of primitive objects used to model a feature in the case of 'by-feature' granularity.
|
|
|
+ */
|
|
|
model_object_count: int,
|
|
|
},
|
|
|
ihm_struct_assembly: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the structural assembly description.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the structural assembly.
|
|
|
+ * This data item will remain the same for all components
|
|
|
+ * of an assembly.
|
|
|
+ */
|
|
|
assembly_id: int,
|
|
|
+ /**
|
|
|
+ * The parent of this assembly in a hierarchy.
|
|
|
+ * This data item is an internal category pointer to
|
|
|
+ * _ihm_struct_assembly.assembly_id
|
|
|
+ * This data item should point to the assembly id of the immediate
|
|
|
+ * parent in a hierarchy.
|
|
|
+ * By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).
|
|
|
+ * In case of assemblies that do not conform to a hierarchy,
|
|
|
+ * _ihm_struct_assembly.parent_assembly_id is the same as
|
|
|
+ * _ihm_struct_assembly.assembly_id indicating a self-parent.
|
|
|
+ */
|
|
|
parent_assembly_id: int,
|
|
|
+ /**
|
|
|
+ * A text description of the molecular entity
|
|
|
+ */
|
|
|
entity_description: str,
|
|
|
+ /**
|
|
|
+ * A unique identifier for distinct molecular entities.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the
|
|
|
+ * ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the component in the assembly.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The starting residue index for the sequence segment of the entity instance
|
|
|
+ * that is part of the assembly.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The ending residue index for the sequence segment of the entity instance
|
|
|
+ * that is part of the assembly.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
},
|
|
|
ihm_struct_assembly_details: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the structural assembly.
|
|
|
+ */
|
|
|
assembly_id: int,
|
|
|
+ /**
|
|
|
+ * A name for the structural assembly.
|
|
|
+ */
|
|
|
assembly_name: str,
|
|
|
+ /**
|
|
|
+ * Description of the structural assembly.
|
|
|
+ */
|
|
|
assembly_description: str,
|
|
|
},
|
|
|
ihm_modeling_protocol: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the modeling protocol/step combination.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An index for the modeling protocol carried out.
|
|
|
+ */
|
|
|
protocol_id: int,
|
|
|
+ /**
|
|
|
+ * An index for a particular step within the modeling protocol.
|
|
|
+ */
|
|
|
step_id: int,
|
|
|
+ /**
|
|
|
+ * An index for the structural assembly being modeled.
|
|
|
+ * This is an indicator to whether the whole assembly is modeled
|
|
|
+ * or if only a subset of the structural assembly is modeled.
|
|
|
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
|
|
|
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
|
|
|
+ * details regarding the different structural assemblies used in the modeling.
|
|
|
+ * The default value for this data item is "1", indicating that the entire
|
|
|
+ * assembly is being modeled.
|
|
|
+ */
|
|
|
struct_assembly_id: int,
|
|
|
+ /**
|
|
|
+ * An index for the dataset group being used in the modeling protocol.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_group.group_id in the
|
|
|
+ * IHM_DATASET_GROUP category.
|
|
|
+ */
|
|
|
dataset_group_id: int,
|
|
|
+ /**
|
|
|
+ * A textual description of the structural assembly being modeled.
|
|
|
+ */
|
|
|
struct_assembly_description: str,
|
|
|
+ /**
|
|
|
+ * The name for the modeling protocol.
|
|
|
+ */
|
|
|
protocol_name: str,
|
|
|
+ /**
|
|
|
+ * The name or type of the modeling step.
|
|
|
+ */
|
|
|
step_name: str,
|
|
|
+ /**
|
|
|
+ * Description of the method involved in the modeling step.
|
|
|
+ */
|
|
|
step_method: str,
|
|
|
+ /**
|
|
|
+ * The number of models in the beginning of the step.
|
|
|
+ */
|
|
|
num_models_begin: int,
|
|
|
+ /**
|
|
|
+ * The number of models at the end of the step.
|
|
|
+ */
|
|
|
num_models_end: int,
|
|
|
+ /**
|
|
|
+ * A flag to indicate if the modeling is multi scale.
|
|
|
+ */
|
|
|
multi_scale_flag: Aliased<'YES' | 'NO'>(str),
|
|
|
+ /**
|
|
|
+ * A flag to indicate if the modeling is multi state.
|
|
|
+ */
|
|
|
multi_state_flag: Aliased<'YES' | 'NO'>(str),
|
|
|
+ /**
|
|
|
+ * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
|
|
|
+ */
|
|
|
ordered_flag: Aliased<'YES' | 'NO'>(str),
|
|
|
},
|
|
|
ihm_multi_state_modeling: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the multiple states being described.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the particular state in the multi-state modeling.
|
|
|
+ */
|
|
|
state_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for a collections of states in the multi-state modeling.
|
|
|
+ * If the states do not need to be grouped into collections, then
|
|
|
+ * _ihm_multi_state_modeling.state_group_id is the same as
|
|
|
+ * _ihm_multi_state_modeling.state_id.
|
|
|
+ */
|
|
|
state_group_id: int,
|
|
|
+ /**
|
|
|
+ * A fraction representing the population of the particular state.
|
|
|
+ */
|
|
|
population_fraction: float,
|
|
|
+ /**
|
|
|
+ * The type that the multiple states being modeled belong to.
|
|
|
+ */
|
|
|
state_type: str,
|
|
|
+ /**
|
|
|
+ * A descriptive name for the state.
|
|
|
+ */
|
|
|
state_name: str,
|
|
|
+ /**
|
|
|
+ * The model group id corresponding to the particular state in the multi-state model.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_group_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ * If there is only a single model corresponding to a particular state, then the
|
|
|
+ * _ihm_model_list.model_group_id is the same as the _ihm_model_list.model_id.
|
|
|
+ */
|
|
|
model_group_id: int,
|
|
|
+ /**
|
|
|
+ * The type of multi-state modeling experiment carried out.
|
|
|
+ */
|
|
|
experiment_type: Aliased<'Fraction of bulk' | 'Single molecule'>(str),
|
|
|
+ /**
|
|
|
+ * Additional textual details of the multi-state modeling, if required.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_modeling_post_process: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the post modeling analysis/step combination.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the modeling protocol, whose post modeling analysis
|
|
|
+ * is being carried out.
|
|
|
+ * This data item is a pointer to the _ihm_modeling_protocol.protocol_id
|
|
|
+ * in the IHM_MODELING_PROTOCOL category.
|
|
|
+ */
|
|
|
protocol_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the post modeling analysis. This data item accounts for
|
|
|
+ * multiple post-modeling analyses that can be carried out.
|
|
|
+ */
|
|
|
analysis_id: int,
|
|
|
+ /**
|
|
|
+ * In a multi-step process, this identifier denotes the particular
|
|
|
+ * step in the post modeling analysis.
|
|
|
+ */
|
|
|
step_id: int,
|
|
|
+ /**
|
|
|
+ * The type of post modeling analysis being carried out.
|
|
|
+ */
|
|
|
type: Aliased<'filter' | 'cluster' | 'rescore' | 'validation' | 'other' | 'none'>(str),
|
|
|
+ /**
|
|
|
+ * The parameter/feature used in the post modeling analysis.
|
|
|
+ */
|
|
|
feature: Aliased<'energy/score' | 'RMSD' | 'dRMSD' | 'other' | 'none'>(str),
|
|
|
+ /**
|
|
|
+ * The number of models at the beginning of the post processing step.
|
|
|
+ */
|
|
|
num_models_begin: int,
|
|
|
+ /**
|
|
|
+ * The number of models the the end of the post processing step.
|
|
|
+ */
|
|
|
num_models_end: int,
|
|
|
},
|
|
|
ihm_ensemble_info: {
|
|
|
+ /**
|
|
|
+ * A unique id for the ensemble.
|
|
|
+ */
|
|
|
ensemble_id: int,
|
|
|
+ /**
|
|
|
+ * An optional name for the cluster or ensemble for better description.
|
|
|
+ */
|
|
|
ensemble_name: str,
|
|
|
+ /**
|
|
|
+ * An identifier for the post modeling analyses carried out.
|
|
|
+ * This data item is a pointer to _ihm_modeling_post_process.id in
|
|
|
+ * the IHM_MODELING_POST_PROCESS category.
|
|
|
+ */
|
|
|
post_process_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the cluster or group of models being deposited.
|
|
|
+ * This data item is a pointer to the _ihm_model_list.model_group_id
|
|
|
+ * in the IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_group_id: int,
|
|
|
+ /**
|
|
|
+ * The clustering method used to obtain the ensemble, if applicable.
|
|
|
+ */
|
|
|
ensemble_clustering_method: Aliased<'Hierarchical' | 'Partitioning (k-means)' | 'Other'>(str),
|
|
|
+ /**
|
|
|
+ * The parameter/feature used for clustering the models, if applicable.
|
|
|
+ */
|
|
|
ensemble_clustering_feature: Aliased<'RMSD' | 'dRMSD' | 'other'>(str),
|
|
|
+ /**
|
|
|
+ * The number of models in the current ensemble being described.
|
|
|
+ */
|
|
|
num_ensemble_models: int,
|
|
|
+ /**
|
|
|
+ * The number of models from the current ensemble that is deposited.
|
|
|
+ */
|
|
|
num_ensemble_models_deposited: int,
|
|
|
+ /**
|
|
|
+ * The precision of each cluster or ensemble is calculated as dRMSD, which
|
|
|
+ * is the average C-alpha distance root mean square deviation (dRMSD)
|
|
|
+ * between the individual models in the cluster and the cluster centroid.
|
|
|
+ * The cluster centroid is defined as the model with the minimal sum of
|
|
|
+ * dRMSDs to the other models in the cluster or ensemble.
|
|
|
+ */
|
|
|
ensemble_precision_value: float,
|
|
|
+ /**
|
|
|
+ * A reference to the external file containing the structural models
|
|
|
+ * in the ensemble. The number of models in the external file should
|
|
|
+ * correspond to the number of models in the ensemble. This data item
|
|
|
+ * is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES
|
|
|
+ * category.
|
|
|
+ * It is recommended that the large ensemble files be stored as separate
|
|
|
+ * zip files within the same DOI. It is also recommended that large sphere
|
|
|
+ * model ensembles be in binary format, which facilitates faster access.
|
|
|
+ * Currently, a binary dump of co-ordinates in dcd format is suggested.
|
|
|
+ * The topology can be inferred from the IHM_SPHERE_OBJ_SITE and the
|
|
|
+ * ATOM_SITE categories in the corresponding mmCIF file.
|
|
|
+ */
|
|
|
ensemble_file_id: int,
|
|
|
},
|
|
|
ihm_model_list: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the model / model group combination.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * A unique identifier for the structural model being deposited.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier to group structural models into collections or sets.
|
|
|
+ * This data item can be used to group models into structural clusters
|
|
|
+ * or using other criteria based on experimental data or other
|
|
|
+ * relationships such as those belonging to the same state or time stamp.
|
|
|
+ * An ensemble of models and its representative can either be grouped together
|
|
|
+ * or can be separate groups in the ihm_model_list table. The choice between
|
|
|
+ * the two options should be decided based on how the modeling was carried out
|
|
|
+ * and how the representative was chosen. If the representative is a member of
|
|
|
+ * the ensemble (i.e., best scoring model), then it is recommended that the
|
|
|
+ * representative and the ensemble belong to the same model group. If the
|
|
|
+ * representative is calculated from the ensemble (i.e., centroid), then it is
|
|
|
+ * recommended that the representative be separated into a different group.
|
|
|
+ * If the models do not need to be grouped into collections, then the
|
|
|
+ * _ihm_model_list.model_group_id is the same as _ihm_model_list.model_id.
|
|
|
+ */
|
|
|
model_group_id: int,
|
|
|
+ /**
|
|
|
+ * A decsriptive name for the model.
|
|
|
+ */
|
|
|
model_name: str,
|
|
|
+ /**
|
|
|
+ * A decsriptive name for the model group.
|
|
|
+ */
|
|
|
model_group_name: str,
|
|
|
+ /**
|
|
|
+ * An identifier to the structure assembly corresponding to the model.
|
|
|
+ * This data item is a pointer to the _ihm_struct_assembly.assembly_id
|
|
|
+ * in the IHM_STRUCT_ASSEMBLY category.
|
|
|
+ */
|
|
|
assembly_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier to the modeling protocol that produced the model.
|
|
|
+ * This data item is a pointer to the _ihm_modeling_protocol.protocol_id
|
|
|
+ * in the IHM_MODELING_PROTOCOL category.
|
|
|
+ */
|
|
|
protocol_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier to the multi-scale model representation id of the model.
|
|
|
+ * This data item is a pointer to the _ihm_model_representation.representation_id
|
|
|
+ * in the IHM_MODEL_REPRESENTATION category.
|
|
|
+ */
|
|
|
representation_id: int,
|
|
|
},
|
|
|
ihm_model_representative: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the representative of the model group.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * The model group identifier corresponding to the representative model.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_group_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_group_id: int,
|
|
|
+ /**
|
|
|
+ * The model identifier corresponding to the representative model.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
+ /**
|
|
|
+ * The selection criteria based on which the representative is chosen.
|
|
|
+ */
|
|
|
selection_criteria: Aliased<'medoid' | 'closest to the average' | 'lowest energy' | 'target function' | 'fewest violations' | 'minimized average structure' | 'best scoring model' | 'centroid' | 'other selction criteria'>(str),
|
|
|
},
|
|
|
ihm_dataset_list: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the dataset.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * The type of data held in the dataset.
|
|
|
+ */
|
|
|
data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Yeast two-hybrid screening data' | 'Other'>(str),
|
|
|
+ /**
|
|
|
+ * A flag that indicates whether the dataset is archived in
|
|
|
+ * an IHM related database or elsewhere.
|
|
|
+ */
|
|
|
database_hosted: Aliased<'YES' | 'NO'>(str),
|
|
|
},
|
|
|
ihm_dataset_group: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the entry.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the dataset group.
|
|
|
+ */
|
|
|
group_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier to the dataset. This data item is a pointer to
|
|
|
+ * _ihm_dataset_list.id in the IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
},
|
|
|
ihm_related_datasets: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the entry.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * The dataset list id corresponding to the derived dataset.
|
|
|
+ * This data item is a pointer to _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id_derived: int,
|
|
|
+ /**
|
|
|
+ * The primary dataset list id from which the corresponding derived dataset is obtained.
|
|
|
+ * This data item is a pointer to _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id_primary: int,
|
|
|
},
|
|
|
ihm_dataset_related_db_reference: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the related database entry.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the dataset list used in the IHM modeling.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * The name of the database containing the dataset entry.
|
|
|
+ */
|
|
|
db_name: Aliased<'PDB' | 'BMRB' | 'EMDB' | 'EMPIAR' | 'SASBDB' | 'PRIDE' | 'MODEL ARCHIVE' | 'MASSIVE' | 'BioGRID' | 'Other'>(str),
|
|
|
+ /**
|
|
|
+ * The accession code for the database entry.
|
|
|
+ */
|
|
|
accession_code: str,
|
|
|
+ /**
|
|
|
+ * Version of the database entry, if the database allows versioning.
|
|
|
+ */
|
|
|
version: str,
|
|
|
+ /**
|
|
|
+ * Details regarding the dataset entry.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_external_reference_info: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the external reference.
|
|
|
+ */
|
|
|
reference_id: int,
|
|
|
+ /**
|
|
|
+ * The name of the reference provider.
|
|
|
+ */
|
|
|
reference_provider: str,
|
|
|
+ /**
|
|
|
+ * The type of external reference.
|
|
|
+ * Currently, only Digital Object Identifiers (DOIs) and supplementary files
|
|
|
+ * stored locally are supported.
|
|
|
+ */
|
|
|
reference_type: Aliased<'DOI' | 'Supplementary Files'>(str),
|
|
|
+ /**
|
|
|
+ * The external reference or the Digital Object Identifier (DOI).
|
|
|
+ * This field is not relevant for local files.
|
|
|
+ */
|
|
|
reference: str,
|
|
|
+ /**
|
|
|
+ * The type of object that the external reference points to, usually
|
|
|
+ * a single file or an archive.
|
|
|
+ */
|
|
|
refers_to: Aliased<'File' | 'Archive' | 'Publication' | 'Other'>(str),
|
|
|
+ /**
|
|
|
+ * The Uniform Resource Locator (URL) corresponding to the external reference (DOI).
|
|
|
+ * This URL should link to the corresponding downloadable file or archive and is provided
|
|
|
+ * to enable automated software to download the referenced file or archive.
|
|
|
+ */
|
|
|
associated_url: str,
|
|
|
},
|
|
|
ihm_external_files: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for each external file.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * A pointer to the source of the external file - either DOI or locally stored.
|
|
|
+ * This data item is a pointer to _ihm_external_reference_info.reference_id in the
|
|
|
+ * IHM_EXTERNAL_REFERENCE_INFO category.
|
|
|
+ */
|
|
|
reference_id: int,
|
|
|
+ /**
|
|
|
+ * The relative path (including filename) for each external file.
|
|
|
+ * Absolute paths (starting with "/") are not permitted.
|
|
|
+ * This is required for identifying individual files from within
|
|
|
+ * a tar-zipped archive file or for identifying supplementary local
|
|
|
+ * files organized within a directory structure.
|
|
|
+ * This data item assumes a POSIX-like directory structure or file path.
|
|
|
+ */
|
|
|
file_path: str,
|
|
|
+ /**
|
|
|
+ * The type of content in the file.
|
|
|
+ */
|
|
|
content_type: Aliased<'Input data or restraints' | 'Modeling or post-processing output' | 'Modeling workflow or script' | 'Visualization script' | 'Other'>(str),
|
|
|
+ /**
|
|
|
+ * Storage size of the external file in bytes.
|
|
|
+ */
|
|
|
file_size_bytes: float,
|
|
|
+ /**
|
|
|
+ * Textual description of what the external file is.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_dataset_external_reference: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the external data.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the dataset list used in the I/H modeling.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * The file id corresponding to this external data file.
|
|
|
+ * This data item is a pointer to _ihm_external_files.id
|
|
|
+ * in the IHM_EXTERNAL_FILES category.
|
|
|
+ */
|
|
|
file_id: int,
|
|
|
},
|
|
|
ihm_localization_density_files: {
|
|
|
+ /**
|
|
|
+ * A unique identifier.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * The file id for the externally stored localization density file.
|
|
|
+ * This data item is a pointer to _ihm_external_files.id
|
|
|
+ * in the IHM_EXTERNAL_FILES category.
|
|
|
+ */
|
|
|
file_id: int,
|
|
|
+ /**
|
|
|
+ * The ensemble identifier for the ensemble, for which the localization density is provided.
|
|
|
+ * This data item is a pointer to _ihm_ensemble_info.ensemble_id in the IHM_ENSEMBLE_INFO category.
|
|
|
+ */
|
|
|
ensemble_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier corresponding to this localization density.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * The leading sequence index corresponding to this localization density.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The trailing sequence index corresponding to this localization density.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier corresponding to this localization density.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
},
|
|
|
ihm_predicted_contact_restraint: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the predicted contact restraint.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * An identifier to group the predicted contacts.
|
|
|
+ */
|
|
|
group_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier for the first monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id_1: str,
|
|
|
+ /**
|
|
|
+ * The entity identifier for the second monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id_2: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the first monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id_1: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the second monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id_2: str,
|
|
|
+ /**
|
|
|
+ * The component identifier for the first monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_1: str,
|
|
|
+ /**
|
|
|
+ * The component identifier for the second monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_2: str,
|
|
|
+ /**
|
|
|
+ * The sequence index for the first monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_1: int,
|
|
|
+ /**
|
|
|
+ * The sequence index for the second monomer partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_2: int,
|
|
|
+ /**
|
|
|
+ * The atom id of the first partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
atom_id_1: str,
|
|
|
+ /**
|
|
|
+ * The atom id of the second partner in the predicted contact.
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
atom_id_2: str,
|
|
|
+ /**
|
|
|
+ * The lower limit to the distance threshold applied to this predicted contact restraint
|
|
|
+ * in the integrative modeling task.
|
|
|
+ */
|
|
|
distance_lower_limit: float,
|
|
|
+ /**
|
|
|
+ * The upper limit to the distance threshold applied to this predicted contact restraint
|
|
|
+ * in the integrative modeling task.
|
|
|
+ */
|
|
|
distance_upper_limit: float,
|
|
|
+ /**
|
|
|
+ * The real number that indicates the probability that the predicted distance restraint
|
|
|
+ * is correct. This number should fall between 0.0 and 1.0.
|
|
|
+ */
|
|
|
probability: float,
|
|
|
+ /**
|
|
|
+ * The type of distance restraint applied.
|
|
|
+ */
|
|
|
restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
|
|
|
+ /**
|
|
|
+ * The granularity of the predicted contact as applied to the multi-scale model.
|
|
|
+ */
|
|
|
model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
|
|
|
+ /**
|
|
|
+ * Identifier to the predicted contacts dataset.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the software used to obtain the predicted contacts dataset.
|
|
|
+ * This data item is a pointer to the _software.pdbx_ordinal in the
|
|
|
+ * SOFTWARE category.
|
|
|
+ */
|
|
|
software_id: int,
|
|
|
},
|
|
|
ihm_cross_link_list: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the cross link restraint.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for a set of ambiguous crosslink restraints.
|
|
|
+ * Handles experimental uncertainties in the identities of
|
|
|
+ * crosslinked residues.
|
|
|
+ */
|
|
|
group_id: int,
|
|
|
+ /**
|
|
|
+ * A text description of molecular entity 1.
|
|
|
+ */
|
|
|
entity_description_1: str,
|
|
|
+ /**
|
|
|
+ * A text description of molecular entity 2.
|
|
|
+ */
|
|
|
entity_description_2: str,
|
|
|
+ /**
|
|
|
+ * The entity identifier for the first monomer partner in the cross link
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id_1: str,
|
|
|
+ /**
|
|
|
+ * The entity identifier for the second monomer partner in the cross link
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id_2: str,
|
|
|
+ /**
|
|
|
+ * The component identifier for the first monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_1: str,
|
|
|
+ /**
|
|
|
+ * The component identifier for the second monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_2: str,
|
|
|
+ /**
|
|
|
+ * The sequence index for the first monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_1: int,
|
|
|
+ /**
|
|
|
+ * The sequence index for the second monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_2: int,
|
|
|
+ /**
|
|
|
+ * The type of crosslinker used.
|
|
|
+ */
|
|
|
linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'Other'>(str),
|
|
|
+ /**
|
|
|
+ * Identifier to the crosslinking dataset.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
},
|
|
|
ihm_cross_link_restraint: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the cross link record.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for a set of ambiguous cross-links.
|
|
|
+ * Handles implementation uncertainties related to multiple copies of subunit.
|
|
|
+ * This data item is a pointer to _ihm_cross_link_list.id in the
|
|
|
+ * IHM_CROSS_LINK_LIST category.
|
|
|
+ */
|
|
|
group_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier for the first monomer partner in the cross link
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category
|
|
|
+ * and the _ihm_cross_link_restraint.entity_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
entity_id_1: str,
|
|
|
+ /**
|
|
|
+ * The entity identifier for the second monomer partner in the cross link
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category
|
|
|
+ * and the _ihm_cross_link_restraint.entity_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
entity_id_2: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the first monomer partner in the cross-link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id_1: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the second monomer partner in the cross-link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id_2: str,
|
|
|
+ /**
|
|
|
+ * The component identifier for the first monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category
|
|
|
+ * and the _ihm_cross_link_restraint.comp_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
comp_id_1: str,
|
|
|
+ /**
|
|
|
+ * The component identifier for the second monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category
|
|
|
+ * and the _ihm_cross_link_restraint.comp_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
comp_id_2: str,
|
|
|
+ /**
|
|
|
+ * The sequence index for the first monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category
|
|
|
+ * and the _ihm_cross_link_restraint.seq_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
seq_id_1: int,
|
|
|
+ /**
|
|
|
+ * The sequence index for the second monomer partner in the cross link.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category
|
|
|
+ * and the _ihm_cross_link_restraint.seq_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
seq_id_2: int,
|
|
|
+ /**
|
|
|
+ * The atom identifier for the first monomer partner in the cross link.
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
atom_id_1: str,
|
|
|
+ /**
|
|
|
+ * The atom identifier for the second monomer partner in the cross link.
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
atom_id_2: str,
|
|
|
+ /**
|
|
|
+ * The type of the cross link restraint applied.
|
|
|
+ */
|
|
|
restraint_type: Aliased<'harmonic' | 'upper bound' | 'lower bound'>(str),
|
|
|
+ /**
|
|
|
+ * The cross link conditionality.
|
|
|
+ */
|
|
|
conditional_crosslink_flag: Aliased<'ALL' | 'ANY'>(str),
|
|
|
+ /**
|
|
|
+ * The coarse-graining information for the crosslink implementation.
|
|
|
+ */
|
|
|
model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
|
|
|
+ /**
|
|
|
+ * The distance threshold applied to this crosslink in the integrative modeling task.
|
|
|
+ */
|
|
|
distance_threshold: float,
|
|
|
+ /**
|
|
|
+ * The uncertainty in the crosslinking experimental data;
|
|
|
+ * may be approximated to the false positive rate.
|
|
|
+ */
|
|
|
psi: float,
|
|
|
+ /**
|
|
|
+ * The uncertainty in the position of residue 1 in the crosslink
|
|
|
+ * arising due to the multi-scale nature of the model represention.
|
|
|
+ */
|
|
|
sigma_1: float,
|
|
|
+ /**
|
|
|
+ * The uncertainty in the position of residue 2 in the crosslink
|
|
|
+ * arising due to the multi-scale nature of the model represention.
|
|
|
+ */
|
|
|
sigma_2: float,
|
|
|
},
|
|
|
ihm_cross_link_result_parameters: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the restraint/model combination.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the crosslink restraint between a pair of residues.
|
|
|
+ * This data item is a pointer to _ihm_cross_link_restraint.id in the
|
|
|
+ * IHM_CROSS_LINK_RESTRAINT category.
|
|
|
+ */
|
|
|
restraint_id: int,
|
|
|
+ /**
|
|
|
+ * The model number corresponding to the cross link result presented.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
+ /**
|
|
|
+ * The uncertainty in the crosslinking experimental data;
|
|
|
+ * May be approximated to the false positive rate.
|
|
|
+ */
|
|
|
psi: float,
|
|
|
+ /**
|
|
|
+ * The uncertainty in the position of residue 1 in the crosslink
|
|
|
+ * arising due to the multi-scale nature of the model represention.
|
|
|
+ */
|
|
|
sigma_1: float,
|
|
|
+ /**
|
|
|
+ * The uncertainty in the position of residue 2 in the crosslink
|
|
|
+ * arising due to the multi-scale nature of the model represention.
|
|
|
+ */
|
|
|
sigma_2: float,
|
|
|
},
|
|
|
ihm_2dem_class_average_restraint: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the 2dem class average.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the 2dem class average dataset.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * The number of raw micrographs used to obtain the class average.
|
|
|
+ */
|
|
|
number_raw_micrographs: int,
|
|
|
+ /**
|
|
|
+ * Pixel size width of the 2dem class average image.
|
|
|
+ * While fitting the model to the image, _ihm_2dem_class_average_restraint.pixel_size_width
|
|
|
+ * is used along with _ihm_2dem_class_average_restraint.pixel_size_height to scale the image.
|
|
|
+ */
|
|
|
pixel_size_width: float,
|
|
|
+ /**
|
|
|
+ * Pixel size height of the 2dem class average image.
|
|
|
+ * While fitting the model to the image, _ihm_2dem_class_average_restraint.pixel_size_height
|
|
|
+ * is used along with _ihm_2dem_class_average_restraint.pixel_size_width to scale the image.
|
|
|
+ */
|
|
|
pixel_size_height: float,
|
|
|
+ /**
|
|
|
+ * Resolution of the 2dem class average.
|
|
|
+ */
|
|
|
image_resolution: float,
|
|
|
+ /**
|
|
|
+ * A flag that indicates whether or not the 2DEM class average image is segmented i.e.,
|
|
|
+ * whether the whole image is used or only a portion of it is used (by masking
|
|
|
+ * or by other means) as restraint in the modeling.
|
|
|
+ */
|
|
|
image_segment_flag: Aliased<'YES' | 'NO'>(str),
|
|
|
+ /**
|
|
|
+ * Number of 2D projections of the model used in the fitting.
|
|
|
+ */
|
|
|
number_of_projections: int,
|
|
|
+ /**
|
|
|
+ * An indicator to whether the whole assembly that is modeled is fit into the image
|
|
|
+ * or if only a subset of the structural assembly is fit into the image.
|
|
|
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
|
|
|
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
|
|
|
+ * details regarding the different structural assemblies used in the modeling.
|
|
|
+ * The default value for this data item is "1" indicating that the entire assembly
|
|
|
+ * being modeled is fit into the EM data.
|
|
|
+ */
|
|
|
struct_assembly_id: int,
|
|
|
+ /**
|
|
|
+ * Details of how the 2DEM restraint is applied in the modeling algorithm.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_2dem_class_average_fitting: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the 2dem class average fitting data.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the 2dem class average restraint.
|
|
|
+ * This data item is a pointer to the _ihm_2dem_class_average_restraint.id in the
|
|
|
+ * IHM_2DEM_CLASS_AVERAGE_RESTRAINT category.
|
|
|
+ */
|
|
|
restraint_id: int,
|
|
|
+ /**
|
|
|
+ * The model number corresponding to the 2DEM fitting result presented.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
+ /**
|
|
|
+ * The cross correlation coefficient corresponding to the model to image fitting.
|
|
|
+ */
|
|
|
cross_correlation_coefficient: float,
|
|
|
+ /**
|
|
|
+ * Data item of the rotation matrix used in the fitting of the model to the image.
|
|
|
+ */
|
|
|
rot_matrix: Matrix(3, 3),
|
|
|
+ /**
|
|
|
+ * Data item of the tranlation vector used in the fitting of the model to the image.
|
|
|
+ */
|
|
|
tr_vector: Vector(3),
|
|
|
},
|
|
|
ihm_3dem_restraint: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the 3DEM restraint description.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the 3DEM map used.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * The model number corresponding to the 3DEM fitting result presented.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
+ /**
|
|
|
+ * An indicator to whether the whole assembly that is modeled is fit into the 3DEM map
|
|
|
+ * or if only a subset of the structural assembly is fit into the map.
|
|
|
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
|
|
|
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
|
|
|
+ * details regarding the different structural assemblies used in the modeling.
|
|
|
+ * The default value for this data item is "1" indicating that the entire assembly
|
|
|
+ * being modeled is fit into the EM map.
|
|
|
+ */
|
|
|
struct_assembly_id: int,
|
|
|
+ /**
|
|
|
+ * Method used to fit the model to the 3DEM map.
|
|
|
+ */
|
|
|
fitting_method: str,
|
|
|
+ /**
|
|
|
+ * In case of Gaussian mixture models, the number of gaussians
|
|
|
+ * is a parameter used to covert the 3DEM maps and models into
|
|
|
+ * GMMs. This captures the level of granularity used in
|
|
|
+ * representing the maps and/or models as 3D Gaussians.
|
|
|
+ */
|
|
|
number_of_gaussians: int,
|
|
|
+ /**
|
|
|
+ * The cross correlation coefficient corresponding to the model to map fitting.
|
|
|
+ */
|
|
|
cross_correlation_coefficient: float,
|
|
|
},
|
|
|
ihm_sas_restraint: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the SAS restraint description.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * Identifier to the SAS data used.
|
|
|
+ * This data item is a pointer to the _ihm_dataset_list.id in the
|
|
|
+ * IHM_DATASET_LIST category.
|
|
|
+ */
|
|
|
dataset_list_id: int,
|
|
|
+ /**
|
|
|
+ * The model number corresponding to the SAS fitting result presented.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id in the
|
|
|
+ * IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
+ /**
|
|
|
+ * An indicator to whether the whole assembly that is modeled is fit into the SAS data
|
|
|
+ * or if only a subset of the structural assembly is fit into the data.
|
|
|
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
|
|
|
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
|
|
|
+ * details regarding the different structural assemblies used in the modeling.
|
|
|
+ * The default value for this data item is "1" indicating that the entire assembly
|
|
|
+ * being modeled is fit into the SAS data.
|
|
|
+ */
|
|
|
struct_assembly_id: int,
|
|
|
+ /**
|
|
|
+ * A flag that indicates whether or not the SAS profile is segmented i.e.,
|
|
|
+ * whether the whole SAS profile is used or only a portion of it is used
|
|
|
+ * (by masking or by other means) as restraint in the modeling.
|
|
|
+ */
|
|
|
profile_segment_flag: Aliased<'YES' | 'NO'>(str),
|
|
|
+ /**
|
|
|
+ * The type of atoms in the model fit to the SAS data.
|
|
|
+ */
|
|
|
fitting_atom_type: str,
|
|
|
+ /**
|
|
|
+ * The method used for fitting the model to the SAS data.
|
|
|
+ */
|
|
|
fitting_method: str,
|
|
|
+ /**
|
|
|
+ * An indicator to single or multiple state fitting.
|
|
|
+ */
|
|
|
fitting_state: Aliased<'Single' | 'Multiple'>(str),
|
|
|
+ /**
|
|
|
+ * Radius of gyration obtained from the SAS profile, if used as input restraint.
|
|
|
+ */
|
|
|
radius_of_gyration: float,
|
|
|
+ /**
|
|
|
+ * The chi value resulting from fitting the model to the SAS data.
|
|
|
+ */
|
|
|
chi_value: float,
|
|
|
+ /**
|
|
|
+ * Additional details regarding the SAS restraint used.
|
|
|
+ */
|
|
|
details: str,
|
|
|
},
|
|
|
ihm_starting_model_coord: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for this coordinate position.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * The identifier for the starting structural model.
|
|
|
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id
|
|
|
+ * in the IHM_STARTING_MODEL_DETAILS category.
|
|
|
+ */
|
|
|
starting_model_id: str,
|
|
|
+ /**
|
|
|
+ * The group of atoms to which the atom site in the starting model belongs. This data
|
|
|
+ * item is provided for compatibility with the original Protein Data Bank format,
|
|
|
+ * and only for that purpose.
|
|
|
+ */
|
|
|
group_PDB: Aliased<'ATOM' | 'HETATM'>(str),
|
|
|
+ /**
|
|
|
+ * The serial number for this coordinate position.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * The atom type symbol(element symbol) corresponding to this coordinate position.
|
|
|
+ */
|
|
|
type_symbol: str,
|
|
|
+ /**
|
|
|
+ * The entity identifier corresponding to this coordinate position.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * The atom identifier/name corresponding to this coordinate position.
|
|
|
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
|
|
|
+ * CHEM_COMP_ATOM category.
|
|
|
+ */
|
|
|
atom_id: str,
|
|
|
+ /**
|
|
|
+ * The component identifier corresponding to this coordinate position.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
comp_id: str,
|
|
|
+ /**
|
|
|
+ * The sequence index corresponding this to coordinate position.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id: int,
|
|
|
+ /**
|
|
|
+ * The asym/strand id corresponding to this coordinate position.
|
|
|
+ *
|
|
|
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The Cartesian X component corresponding to this coordinate position.
|
|
|
+ */
|
|
|
Cartn_x: float,
|
|
|
+ /**
|
|
|
+ * The Cartesian Y component corresponding to this coordinate position.
|
|
|
+ */
|
|
|
Cartn_y: float,
|
|
|
+ /**
|
|
|
+ * The Cartesian Z component corresponding to this coordinate position.
|
|
|
+ */
|
|
|
Cartn_z: float,
|
|
|
+ /**
|
|
|
+ * The isotropic temperature factor corresponding to this coordinate position.
|
|
|
+ */
|
|
|
B_iso_or_equiv: float,
|
|
|
},
|
|
|
ihm_sphere_obj_site: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for this pseudo atom / sphere object.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier corresponding to this sphere object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * The leading sequence index corresponding to this sphere object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The trailing sequence index corresponding to this sphere object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier corresponding to this sphere object.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The Cartesian X component corresponding to this sphere object.
|
|
|
+ */
|
|
|
Cartn_x: float,
|
|
|
+ /**
|
|
|
+ * The Cartesian Y component corresponding to this sphere object.
|
|
|
+ */
|
|
|
Cartn_y: float,
|
|
|
+ /**
|
|
|
+ * The Cartesian Z component corresponding to this sphere object.
|
|
|
+ */
|
|
|
Cartn_z: float,
|
|
|
+ /**
|
|
|
+ * The radius associated with the primitive sphere object at this position.
|
|
|
+ */
|
|
|
object_radius: float,
|
|
|
+ /**
|
|
|
+ * The Root Mean Square Fluctuation (RMSF) observed in the primitive
|
|
|
+ * sphere object at this position.
|
|
|
+ */
|
|
|
rmsf: float,
|
|
|
+ /**
|
|
|
+ * The model id corresponding to the sphere object.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id
|
|
|
+ * in the IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
},
|
|
|
ihm_gaussian_obj_site: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for this gaussian object in the model.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * The leading sequence index corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The trailing sequence index corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The mean Cartesian X component corresponding to this gaussian object.
|
|
|
+ */
|
|
|
mean_Cartn_x: float,
|
|
|
+ /**
|
|
|
+ * The mean Cartesian Y component corresponding to this gaussian object.
|
|
|
+ */
|
|
|
mean_Cartn_y: float,
|
|
|
+ /**
|
|
|
+ * The mean Cartesian Z component corresponding to this gaussian object.
|
|
|
+ */
|
|
|
mean_Cartn_z: float,
|
|
|
+ /**
|
|
|
+ * The weight of the gaussian object.
|
|
|
+ */
|
|
|
weight: float,
|
|
|
+ /**
|
|
|
+ * Data item of the covariance matrix representing the Gaussian object.
|
|
|
+ */
|
|
|
covariance_matrix: Matrix(3, 3),
|
|
|
+ /**
|
|
|
+ * The model id corresponding to the gaussian object.
|
|
|
+ * This data item is a pointer to _ihm_model_list.model_id
|
|
|
+ * in the IHM_MODEL_LIST category.
|
|
|
+ */
|
|
|
model_id: int,
|
|
|
},
|
|
|
ihm_gaussian_obj_ensemble: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for this gaussian object.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * The leading sequence index corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The trailing sequence index corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier corresponding to this gaussian object.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The mean Cartesian X component corresponding to this gaussian object.
|
|
|
+ */
|
|
|
mean_Cartn_x: float,
|
|
|
+ /**
|
|
|
+ * The mean Cartesian Y component corresponding to this gaussian object.
|
|
|
+ */
|
|
|
mean_Cartn_y: float,
|
|
|
+ /**
|
|
|
+ * The mean Cartesian Z component corresponding to this gaussian object.
|
|
|
+ */
|
|
|
mean_Cartn_z: float,
|
|
|
+ /**
|
|
|
+ * The weight of the gaussian object.
|
|
|
+ */
|
|
|
weight: float,
|
|
|
+ /**
|
|
|
+ * Data item of the covariance matrix representing the Gaussian object.
|
|
|
+ */
|
|
|
covariance_matrix: Matrix(3, 3),
|
|
|
+ /**
|
|
|
+ * The ensemble id corresponding to the gaussian object.
|
|
|
+ * This data item is a pointer to _ihm_ensemble_info.ensemble_id
|
|
|
+ * in the IHM_ENSEMBLE_INFO category.
|
|
|
+ */
|
|
|
ensemble_id: int,
|
|
|
},
|
|
|
ihm_feature_list: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the feature.
|
|
|
+ */
|
|
|
feature_id: int,
|
|
|
+ /**
|
|
|
+ * The type of feature.
|
|
|
+ */
|
|
|
feature_type: Aliased<'atom' | 'residue' | 'residue range'>(str),
|
|
|
+ /**
|
|
|
+ * The type of entity.
|
|
|
+ * This data item is a pointer to _entity.type in the ENTITY category.
|
|
|
+ */
|
|
|
entity_type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
|
|
|
},
|
|
|
ihm_poly_residue_feature: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the category.
|
|
|
+ */
|
|
|
ordinal_id: int,
|
|
|
+ /**
|
|
|
+ * An identifier for the selected residue / residue range feature.
|
|
|
+ * This data item is a pointer to _ihm_feature_list.feature_id in the
|
|
|
+ * IHM_FEATURE_LIST category.
|
|
|
+ */
|
|
|
feature_id: int,
|
|
|
+ /**
|
|
|
+ * The entity identifier for residue / residue range.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.entity_id in the
|
|
|
+ * ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
entity_id: str,
|
|
|
+ /**
|
|
|
+ * An asym/strand identifier for the residue / residue range.
|
|
|
+ * This data item is a pointer to _struct_asym.id in the
|
|
|
+ * STRUCT_ASYM category.
|
|
|
+ */
|
|
|
asym_id: str,
|
|
|
+ /**
|
|
|
+ * The component identifier of the beginning residue / residue range.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_begin: str,
|
|
|
+ /**
|
|
|
+ * The component identifier of the ending residue / residue range.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
comp_id_end: str,
|
|
|
+ /**
|
|
|
+ * The sequence index of the beginning residue / residue range.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_begin: int,
|
|
|
+ /**
|
|
|
+ * The sequence index of the ending residue / residue range.
|
|
|
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
|
|
|
+ */
|
|
|
seq_id_end: int,
|
|
|
},
|
|
|
ihm_derived_distance_restraint: {
|
|
|
+ /**
|
|
|
+ * A unique identifier for the derived distance restraint.
|
|
|
+ */
|
|
|
id: int,
|
|
|
+ /**
|
|
|
+ * An identifier to group the distance restraints.
|
|
|
+ * This can be the same as the _ihm_derived_distance_restraint.id in case
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+ * the some of the restraints are not grouped.
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+ */
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group_id: int,
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+ /**
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+ * The feature identifier for the first partner in the distance restraint.
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+ * This data item is a pointer to _ihm_feature_list.feature_id in the
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+ * IHM_FEATURE_LIST category.
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+ */
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feature_id_1: int,
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+ /**
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+ * The feature identifier for the second partner in the distance restraint.
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+ * This data item is a pointer to _ihm_feature_list.feature_id in the
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+ * IHM_FEATURE_LIST category.
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+ */
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feature_id_2: int,
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+ /**
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+ * If a group of atoms or residues are restrained, this data item defines
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+ * the conditionality based on which the restraint is applied in the modeling.
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+ */
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group_conditionality: Aliased<'ALL' | 'ANY'>(str),
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+ /**
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+ * The fraction of randomly excluded distance restraints during modeling.
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+ * In HADDOCK, this is used along with ambiguous interface restraints (AIRs)
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+ * to account for uncertainties in AIRs.
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+ */
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random_exclusion_fraction: float,
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+ /**
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+ * The upper limit to the distance threshold applied to this distance restraint
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+ * in the integrative modeling task.
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+ */
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distance_upper_limit: float,
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+ /**
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+ * The type of distance restraint applied.
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+ */
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restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
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+ /**
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+ * Identifier to the input data from which the distance restraint is derived.
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+ * This data item is a pointer to the _ihm_dataset_list.id in the
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+ * IHM_DATASET_LIST category.
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+ */
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dataset_list_id: int,
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},
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}
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Alexander Rose