/** * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info. * * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.410, IHM 1.28, MA 1.4.9. * * @author molstar/ciftools package */ import { Database, Column } from '../../../../mol-data/db.js'; import Schema = Column.Schema; export declare const mmCIF_Schema: { /** * Data items in the ATOM_SITE category record details about * the atom sites in a macromolecular crystal structure, such as * the positional coordinates, atomic displacement parameters, * magnetic moments and directions. * * The data items for describing anisotropic atomic * displacement factors are only used if the corresponding items * are not given in the ATOM_SITE_ANISOTROP category. * * wwPDB recommends wwPDB-assigned residue number, residue ID, * and chain ID, _atom_site.auth_seq_id _atom_site.auth_comp_id, and * _atom_site.auth_asym_id, respectively, to be used for publication * materials. */ atom_site: { /** * An alternative identifier for _atom_site.label_asym_id that * may be provided by an author in order to match the identification * used in the publication that describes the structure. */ auth_asym_id: Schema.Str; /** * An alternative identifier for _atom_site.label_atom_id that * may be provided by an author in order to match the identification * used in the publication that describes the structure. */ auth_atom_id: Schema.Str; /** * An alternative identifier for _atom_site.label_comp_id that * may be provided by an author in order to match the identification * used in the publication that describes the structure. */ auth_comp_id: Schema.Str; /** * An alternative identifier for _atom_site.label_seq_id that * may be provided by an author in order to match the identification * used in the publication that describes the structure. * * Note that this is not necessarily a number, that the values do * not have to be positive, and that the value does not have to * correspond to the value of _atom_site.label_seq_id. The value * of _atom_site.label_seq_id is required to be a sequential list * of positive integers. * * The author may assign values to _atom_site.auth_seq_id in any * desired way. For instance, the values may be used to relate * this structure to a numbering scheme in a homologous structure, * including sequence gaps or insertion codes. Alternatively, a * scheme may be used for a truncated polymer that maintains the * numbering scheme of the full length polymer. In all cases, the * scheme used here must match the scheme used in the publication * that describes the structure. */ auth_seq_id: Schema.Int; /** * Isotropic atomic displacement parameter, or equivalent isotropic * atomic displacement parameter, B~eq~, calculated from the * anisotropic displacement parameters. * * B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] * * A = the real space cell lengths * a* = the reciprocal space cell lengths * B^ij^ = 8 pi^2^ U^ij^ * * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, * 775-776. * * The IUCr Commission on Nomenclature recommends against the use * of B for reporting atomic displacement parameters. U, being * directly proportional to B, is preferred. * * Note - * * The particular type of ADP stored in this item is qualified * by item _refine.pdbx_adp_type. */ B_iso_or_equiv: Schema.Float; /** * The x atom-site coordinate in angstroms specified according to * a set of orthogonal Cartesian axes related to the cell axes as * specified by the description given in * _atom_sites.Cartn_transform_axes. */ Cartn_x: Schema.Coordinate; /** * The y atom-site coordinate in angstroms specified according to * a set of orthogonal Cartesian axes related to the cell axes as * specified by the description given in * _atom_sites.Cartn_transform_axes. */ Cartn_y: Schema.Coordinate; /** * The z atom-site coordinate in angstroms specified according to * a set of orthogonal Cartesian axes related to the cell axes as * specified by the description given in * _atom_sites.Cartn_transform_axes. */ Cartn_z: Schema.Coordinate; /** * The group of atoms to which the atom site belongs. This data * item is provided for compatibility with the original Protein * Data Bank format, and only for that purpose. */ group_PDB: Schema.Aliased<"ATOM" | "HETATM">; /** * The value of _atom_site.id must uniquely identify a record in the * ATOM_SITE list. * * Note that this item need not be a number; it can be any unique * identifier. * * This data item was introduced to provide compatibility between * small-molecule and macromolecular CIFs. In a small-molecule * CIF, _atom_site_label is the identifier for the atom. In a * macromolecular CIF, the atom identifier is the aggregate of * _atom_site.label_alt_id, _atom_site.label_asym_id, * _atom_site.label_atom_id, _atom_site.label_comp_id and * _atom_site.label_seq_id. For the two types of files to be * compatible, a formal identifier for the category had to be * introduced that was independent of the different modes of * identifying the atoms. For compatibility with older CIFs, * _atom_site_label is aliased to _atom_site.id. * * In general, this aggregate identifier does not uniquely * identify an atom site as for non-polymers _atom_site.label_seq_id * is '.'. */ id: Schema.Int; /** * A place holder to indicate alternate conformation. The alternate conformation * can be an entire polymer chain, or several residues or * partial residue (several atoms within one residue). If * an atom is provided in more than one position, then a * non-blank alternate location indicator must be used for * each of the atomic positions. */ label_alt_id: Schema.Str; /** * A component of the identifier for this atom site. * For further details, see the definition of the STRUCT_ASYM * category. * * This data item is a pointer to _struct_asym.id in the * STRUCT_ASYM category. */ label_asym_id: Schema.Str; /** * A component of the identifier for this atom site. * * This data item is a pointer to _chem_comp_atom.atom_id in the * CHEM_COMP_ATOM category. */ label_atom_id: Schema.Str; /** * A component of the identifier for this atom site. * * This data item is a pointer to _chem_comp.id in the CHEM_COMP * category. */ label_comp_id: Schema.Str; /** * This data item is a pointer to _entity.id in the ENTITY category. */ label_entity_id: Schema.Str; /** * This data item is a pointer to _entity_poly_seq.num in the * ENTITY_POLY_SEQ category. */ label_seq_id: Schema.Int; /** * The fraction of the atom type present at this site. * The sum of the occupancies of all the atom types at this site * may not exceed 1.0 unless it is a dummy site. */ occupancy: Schema.Float; /** * This data item is a pointer to _atom_type.symbol in the * ATOM_TYPE category. */ type_symbol: Schema.Str; /** * PDB insertion code. */ pdbx_PDB_ins_code: Schema.Str; /** * PDB model number. */ pdbx_PDB_model_num: Schema.Int; /** * The net integer charge assigned to this atom. This is the * formal charge assignment normally found in chemical diagrams. */ pdbx_formal_charge: Schema.Int; /** * This data item is an ordinal which identifies distinct chemical components in the atom_site category, both * polymeric and non-polymeric. */ pdbx_label_index: Schema.Int; /** * The name of additional external databases with residue level mapping. */ pdbx_sifts_xref_db_name: Schema.Str; /** * The accession code related to the additional external database entry. */ pdbx_sifts_xref_db_acc: Schema.Str; /** * The sequence position of the external database entry that corresponds * to the residue mapping defined by the SIFTS process. */ pdbx_sifts_xref_db_num: Schema.Str; /** * Describes the residue type of the given UniProt match */ pdbx_sifts_xref_db_res: Schema.Str; /** * The model id corresponding to the atom site. * This data item is a pointer to _ihm_model_list.model_id * in the IHM_MODEL_LIST category. */ ihm_model_id: Schema.Int; }; /** * Data items in the ATOM_SITE_ANISOTROP category record details * about anisotropic displacement parameters. * If the ATOM_SITE_ANISOTROP category is used for storing these * data, the corresponding ATOM_SITE data items are not used. */ atom_site_anisotrop: { /** * This data item is a pointer to _atom_site.id in the ATOM_SITE * category. */ id: Schema.Int; /** * This data item is a pointer to _atom_type.symbol in the * ATOM_TYPE category. */ type_symbol: Schema.Str; /** * The elements of the standard anisotropic atomic * displacement matrix U, which appears in the structure-factor * term as: * * T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} * * h = the Miller indices * a* = the reciprocal space cell lengths * * These matrix elements may appear with atomic coordinates * in the ATOM_SITE category, or they may appear in the separate * ATOM_SITE_ANISOTROP category, but they may not appear in both * places. Similarly, anisotropic displacements may appear as * either B's or U's, but not as both. * * The unique elements of the real symmetric matrix are * entered by row. */ U: Schema.Tensor; /** * The standard uncertainty (estimated standard deviation) * of _atom_site_anisotrop.U. */ U_esd: Schema.Tensor; /** * Pointer to _atom_site.auth_seq_id */ pdbx_auth_seq_id: Schema.Int; /** * Pointer to _atom_site.auth_asym_id */ pdbx_auth_asym_id: Schema.Str; /** * Pointer to _atom_site.auth_atom_id */ pdbx_auth_atom_id: Schema.Str; /** * Pointer to _atom_site.auth_comp_id */ pdbx_auth_comp_id: Schema.Str; /** * Pointer to _atom_site.label_seq_id */ pdbx_label_seq_id: Schema.Int; /** * Pointer to _atom_site.label_alt_id. */ pdbx_label_alt_id: Schema.Str; /** * Pointer to _atom_site.label_asym_id */ pdbx_label_asym_id: Schema.Str; /** * Pointer to _atom_site.label_atom_id */ pdbx_label_atom_id: Schema.Str; /** * Pointer to _atom_site.label_comp_id */ pdbx_label_comp_id: Schema.Str; /** * Pointer to _atom_site.pdbx_PDB_ins_code */ pdbx_PDB_ins_code: Schema.Str; }; /** * Data items in the ATOM_SITES category record details about * the crystallographic cell and cell transformations, which are * common to all atom sites. */ atom_sites: { /** * This data item is a pointer to _entry.id in the ENTRY category. */ entry_id: Schema.Str; /** * The elements of the 3x3 matrix used to transform Cartesian * coordinates in the ATOM_SITE category to fractional coordinates * in the same category. The axial alignments of this * transformation are described in _atom_sites.Cartn_transform_axes. * The 3x1 translation is defined in * _atom_sites.fract_transf_vector[]. * * |x'| |11 12 13| |x| |1| * |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| * |z'| |31 32 33| |z| |3| */ fract_transf_matrix: Schema.Tensor; /** * The elements of the three-element vector used to transform * Cartesian coordinates in the ATOM_SITE category to fractional * coordinates in the same category. The axial alignments of this * transformation are described in _atom_sites.Cartn_transform_axes. * The 3x3 rotation is defined in * _atom_sites.fract_transf_matrix[][]. * * |x'| |11 12 13| |x| |1| * |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| * |z'| |31 32 33| |z| |3| */ fract_transf_vector: Schema.Tensor; }; /** * Data items in the AUDIT_AUTHOR category record details about * the author(s) of the data block. */ audit_author: { /** * The name of an author of this data block. If there are multiple * authors, _audit_author.name is looped with _audit_author.address. * The family name(s), followed by a comma and including any * dynastic components, precedes the first name(s) or initial(s). */ name: Schema.Str; /** * This data item defines the order of the author's name in the * list of audit authors. */ pdbx_ordinal: Schema.Int; /** * The Open Researcher and Contributor ID (ORCID). */ identifier_ORCID: Schema.Str; }; /** * Data items in the AUDIT_CONFORM category describe the * dictionary versions against which the data names appearing in * the current data block are conformant. */ audit_conform: { /** * A file name or uniform resource locator (URL) for the * dictionary to which the current data block conforms. */ dict_location: Schema.Str; /** * The string identifying the highest-level dictionary defining * data names used in this file. */ dict_name: Schema.Str; /** * The version number of the dictionary to which the current * data block conforms. */ dict_version: Schema.Str; }; /** * Data items in the CELL category record details about the * crystallographic cell parameters. */ cell: { /** * Unit-cell angle alpha of the reported structure in degrees. */ angle_alpha: Schema.Float; /** * Unit-cell angle beta of the reported structure in degrees. */ angle_beta: Schema.Float; /** * Unit-cell angle gamma of the reported structure in degrees. */ angle_gamma: Schema.Float; /** * This data item is a pointer to _entry.id in the ENTRY category. */ entry_id: Schema.Str; /** * Unit-cell length a corresponding to the structure reported in * angstroms. */ length_a: Schema.Float; /** * Unit-cell length b corresponding to the structure reported in * angstroms. */ length_b: Schema.Float; /** * Unit-cell length c corresponding to the structure reported in * angstroms. */ length_c: Schema.Float; /** * The number of the polymeric chains in a unit cell. In the case * of heteropolymers, Z is the number of occurrences of the most * populous chain. * * This data item is provided for compatibility with the original * Protein Data Bank format, and only for that purpose. */ Z_PDB: Schema.Int; /** * To further identify unique axis if necessary. E.g., P 21 with * an unique C axis will have 'C' in this field. */ pdbx_unique_axis: Schema.Str; }; /** * Data items in the CHEM_COMP category give details about each * of the chemical components from which the relevant chemical * structures can be constructed, such as name, mass or charge. * * The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, * CHEM_COMP_ANGLE etc. describe the detailed geometry of these * chemical components. */ chem_comp: { /** * The formula for the chemical component. Formulae are written * according to the following rules: * * (1) Only recognized element symbols may be used. * * (2) Each element symbol is followed by a 'count' number. A count * of '1' may be omitted. * * (3) A space or parenthesis must separate each cluster of * (element symbol + count), but in general parentheses are * not used. * * (4) The order of elements depends on whether carbon is * present or not. If carbon is present, the order should be: * C, then H, then the other elements in alphabetical order * of their symbol. If carbon is not present, the elements * are listed purely in alphabetic order of their symbol. This * is the 'Hill' system used by Chemical Abstracts. */ formula: Schema.Str; /** * Formula mass in daltons of the chemical component. */ formula_weight: Schema.Float; /** * The value of _chem_comp.id must uniquely identify each item in * the CHEM_COMP list. * * For protein polymer entities, this is the three-letter code for * the amino acid. * * For nucleic acid polymer entities, this is the one-letter code * for the base. */ id: Schema.Str; /** * 'yes' indicates that this is a 'standard' monomer, 'no' * indicates that it is 'nonstandard'. Nonstandard monomers * should be described in more detail using the * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and * _chem_comp.mon_nstd_details data items. */ mon_nstd_flag: Schema.Aliased<"y" | "yes" | "no" | "n">; /** * The full name of the component. */ name: Schema.Str; /** * For standard polymer components, the type of the monomer. * Note that monomers that will form polymers are of three types: * linking monomers, monomers with some type of N-terminal (or 5') * cap and monomers with some type of C-terminal (or 3') cap. */ type: Schema.Aliased<"other" | "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, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha 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">; /** * Synonym list for the component. */ pdbx_synonyms: Schema.List; }; /** * Data items in the CHEM_COMP_BOND category record details about * the bonds between atoms in a chemical component. Target values * may be specified as bond orders, as a distance between the two * atoms, or both. */ chem_comp_bond: { /** * The ID of the first of the two atoms that define the bond. * * This data item is a pointer to _chem_comp_atom.atom_id in the * CHEM_COMP_ATOM category. */ atom_id_1: Schema.Str; /** * The ID of the second of the two atoms that define the bond. * * This data item is a pointer to _chem_comp_atom.atom_id in the * CHEM_COMP_ATOM category. */ atom_id_2: Schema.Str; /** * This data item is a pointer to _chem_comp.id in the CHEM_COMP * category. */ comp_id: Schema.Str; /** * The value that should be taken as the target for the chemical * bond associated with the specified atoms, expressed as a bond * order. */ value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">; /** * Ordinal index for the component bond list. */ pdbx_ordinal: Schema.Int; /** * Stereochemical configuration across a double bond. */ pdbx_stereo_config: Schema.Aliased<"z" | "n" | "e">; /** * A flag indicating an aromatic bond. */ pdbx_aromatic_flag: Schema.Aliased<"y" | "n">; }; /** * Data items in the CITATION category record details about the * literature cited as being relevant to the contents of the data * block. */ citation: { /** * The name of the publisher of the citation; relevant * for books or book chapters. */ book_publisher: Schema.Str; /** * The country/region of publication; relevant for books * and book chapters. */ country: Schema.Str; /** * The value of _citation.id must uniquely identify a record in the * CITATION list. * * The _citation.id 'primary' should be used to indicate the * citation that the author(s) consider to be the most pertinent to * the contents of the data block. * * Note that this item need not be a number; it can be any unique * identifier. */ id: Schema.Str; /** * Abbreviated name of the cited journal as given in the * Chemical Abstracts Service Source Index. */ journal_abbrev: Schema.Str; /** * The American Society for Testing and Materials (ASTM) code * assigned to the journal cited (also referred to as the CODEN * designator of the Chemical Abstracts Service); relevant for * journal articles. */ journal_id_ASTM: Schema.Str; /** * The Cambridge Structural Database (CSD) code assigned to the * journal cited; relevant for journal articles. This is also the * system used at the Protein Data Bank (PDB). */ journal_id_CSD: Schema.Str; /** * The International Standard Serial Number (ISSN) code assigned to * the journal cited; relevant for journal articles. */ journal_id_ISSN: Schema.Str; /** * Volume number of the journal cited; relevant for journal * articles. */ journal_volume: Schema.Str; /** * The first page of the citation; relevant for journal * articles, books and book chapters. */ page_first: Schema.Str; /** * The last page of the citation; relevant for journal * articles, books and book chapters. */ page_last: Schema.Str; /** * The title of the citation; relevant for journal articles, books * and book chapters. */ title: Schema.Str; /** * The year of the citation; relevant for journal articles, books * and book chapters. */ year: Schema.Int; /** * Document Object Identifier used by doi.org to uniquely * specify bibliographic entry. */ pdbx_database_id_DOI: Schema.Str; /** * Ascession number used by PubMed to categorize a specific * bibliographic entry. */ pdbx_database_id_PubMed: Schema.Int; }; /** * Data items in the CITATION_AUTHOR category record details * about the authors associated with the citations in the * CITATION list. */ citation_author: { /** * This data item is a pointer to _citation.id in the CITATION * category. */ citation_id: Schema.Str; /** * Name of an author of the citation; relevant for journal * articles, books and book chapters. * * The family name(s), followed by a comma and including any * dynastic components, precedes the first name(s) or initial(s). */ name: Schema.Str; /** * This data item defines the order of the author's name in the * list of authors of a citation. */ ordinal: Schema.Int; }; /** * Data items in the DATABASE_2 category record details about the * database identifiers of the data block. * * These data items are assigned by database managers and should * only appear in a data block if they originate from that source. * * The name of this category, DATABASE_2, arose because the * category name DATABASE was already in use in the core CIF * dictionary, but was used differently from the way it needed * to be used in the mmCIF dictionary. Since CIF data names * cannot be changed once they have been adopted, a new category * had to be created. */ database_2: { /** * An abbreviation that identifies the database. */ database_id: Schema.Aliased<"alphafolddb" | "cas" | "csd" | "emdb" | "icsd" | "modelarchive" | "mdf" | "modbase" | "ndb" | "nbs" | "pdb" | "pdb-dev" | "pdf" | "rcsb" | "swiss-model_repository" | "ebi" | "pdbe" | "bmrb" | "wwpdb" | "pdb_acc">; /** * The code assigned by the database identified in * _database_2.database_id. */ database_code: Schema.Str; }; /** * Data items in the ENTITY category record details (such as * chemical composition, name and source) about the molecular * entities that are present in the crystallographic structure. * * Items in the various ENTITY subcategories provide a full * chemical description of these molecular entities. * * Entities are of three types: polymer, non-polymer and water. * Note that the water category includes only water; ordered * solvent such as sulfate ion or acetone would be described as * individual non-polymer entities. * * The ENTITY category is specific to macromolecular CIF * applications and replaces the function of the CHEMICAL category * in the CIF core. * * It is important to remember that the ENTITY data are not the * result of the crystallographic experiment; those results are * represented by the ATOM_SITE data items. ENTITY data items * describe the chemistry of the molecules under investigation * and can most usefully be thought of as the ideal groups to which * the structure is restrained or constrained during refinement. * * It is also important to remember that entities do not correspond * directly to the enumeration of the contents of the asymmetric * unit. Entities are described only once, even in those structures * that contain multiple observations of an entity. The * STRUCT_ASYM data items, which reference the entity list, * describe and label the contents of the asymmetric unit. */ entity: { /** * A description of special aspects of the entity. */ details: Schema.Str; /** * Formula mass in daltons of the entity. */ formula_weight: Schema.Float; /** * The value of _entity.id must uniquely identify a record in the * ENTITY list. * * Note that this item need not be a number; it can be any unique * identifier. */ id: Schema.Str; /** * The method by which the sample for the entity was produced. * Entities isolated directly from natural sources (tissues, soil * 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: Schema.Aliased<"nat" | "man" | "syn">; /** * 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: Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">; /** * A description of the entity. * * Corresponds to the compound name in the PDB format. */ pdbx_description: Schema.List; /** * A place holder for the number of molecules of the entity in * the entry. */ pdbx_number_of_molecules: Schema.Int; /** * An identifier for the parent entity if this entity * is part of a complex entity. For instance a chimeric * entity may be decomposed into several independent * chemical entities where each component entity was * obtained from a different source. */ pdbx_parent_entity_id: Schema.Str; /** * Details about any entity mutation(s). */ pdbx_mutation: Schema.Str; /** * Entity fragment description(s). */ pdbx_fragment: Schema.Str; /** * Enzyme Commission (EC) number(s) */ pdbx_ec: Schema.List; }; /** * Data items in the ENTITY_POLY category record details about the * polymer, such as the type of the polymer, the number of * monomers and whether it has nonstandard features. */ entity_poly: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.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: Schema.Aliased<"y" | "yes" | "no" | "n">; /** * A flag to indicate whether the polymer contains at least * one monomer that is not considered standard. */ nstd_monomer: Schema.Aliased<"y" | "yes" | "no" | "n">; /** * The type of the polymer. */ type: Schema.Aliased<"other" | "polypeptide(D)" | "polypeptide(L)" | "polydeoxyribonucleotide" | "polyribonucleotide" | "polydeoxyribonucleotide/polyribonucleotide hybrid" | "cyclic-pseudo-peptide" | "peptide nucleic acid">; /** * The PDB strand/chain id(s) corresponding to this polymer entity. */ pdbx_strand_id: Schema.List; /** * Sequence of protein or nucleic acid polymer in standard one-letter * codes of amino acids or nucleotides. Non-standard amino * acids/nucleotides are represented by their Chemical * Component Dictionary (CCD) codes in * parenthesis. Deoxynucleotides are represented by the * specially-assigned 2-letter CCD codes in parenthesis, * with 'D' prefix added to their ribonucleotide * counterparts. For hybrid polymer, each residue is * represented by the code of its individual type. A * cyclic polymer is represented in linear sequence from * the chosen start to end. * * A for Alanine or Adenosine-5'-monophosphate * C for Cysteine or Cytidine-5'-monophosphate * D for Aspartic acid * E for Glutamic acid * F for Phenylalanine * G for Glycine or Guanosine-5'-monophosphate * H for Histidine * I for Isoleucine or Inosinic Acid * L for Leucine * K for Lysine * M for Methionine * N for Asparagine or Unknown ribonucleotide * O for Pyrrolysine * P for Proline * Q for Glutamine * R for Arginine * S for Serine * T for Threonine * U for Selenocysteine or Uridine-5'-monophosphate * V for Valine * W for Tryptophan * Y for Tyrosine * (DA) for 2'-deoxyadenosine-5'-monophosphate * (DC) for 2'-deoxycytidine-5'-monophosphate * (DG) for 2'-deoxyguanosine-5'-monophosphate * (DT) for Thymidine-5'-monophosphate * (MSE) for Selenomethionine * (SEP) for Phosphoserine * (TPO) for Phosphothreonine * (PTR) for Phosphotyrosine * (PCA) for Pyroglutamic acid * (UNK) for Unknown amino acid * (ACE) for Acetylation cap * (NH2) for Amidation cap */ pdbx_seq_one_letter_code: Schema.Str; /** * Canonical sequence of protein or nucleic acid polymer in standard * one-letter codes of amino acids or nucleotides, * corresponding to the sequence in * _entity_poly.pdbx_seq_one_letter_code. Non-standard * amino acids/nucleotides are represented by the codes of * their parents if parent is specified in * _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if * parent is not specified. Deoxynucleotides are * represented by their canonical one-letter codes of A, * C, G, or T. * * For modifications with several parent amino acids, * all corresponding parent amino acid codes will be listed * (ex. chromophores). */ pdbx_seq_one_letter_code_can: Schema.Str; /** * For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database. */ pdbx_target_identifier: Schema.Str; }; /** * Data items in the ENTITY_POLY_SEQ category specify the sequence * of monomers in a polymer. Allowance is made for the possibility * of microheterogeneity in a sample by allowing a given sequence * number to be correlated with more than one monomer ID. The * corresponding ATOM_SITE entries should reflect this * heterogeneity. */ entity_poly_seq: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * A flag to indicate whether this monomer in the polymer is * heterogeneous in sequence. */ hetero: Schema.Aliased<"y" | "yes" | "no" | "n">; /** * This data item is a pointer to _chem_comp.id in the CHEM_COMP * category. */ mon_id: Schema.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: Schema.Int; }; /** * There is only one item in the ENTRY category, _entry.id. This * data item gives a name to this entry and is indirectly a key to * the categories (such as CELL, GEOM, EXPTL) that describe * information pertinent to the entire data block. */ 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: Schema.Str; }; /** * Data items in the EXPTL category record details about the * experimental work prior to the intensity measurements and * details about the absorption-correction technique employed. */ exptl: { /** * This data item is a pointer to _entry.id in the ENTRY category. */ entry_id: Schema.Str; /** * The method used in the experiment. */ method: Schema.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">; }; /** * Data items in the SOFTWARE category record details about * the software used in the structure analysis, which implies * any software used in the generation of any data items * associated with the structure determination and * structure representation. * * These data items allow computer programs to be referenced * in more detail than data items in the COMPUTING category do. */ software: { /** * The classification of the program according to its * major function. */ classification: Schema.Str; /** * The date the software was released. */ date: Schema.Str; /** * Description of the software. */ description: Schema.Str; /** * The name of the software. */ name: Schema.Str; /** * The classification of the software according to the most * common types. */ type: Schema.Aliased<"filter" | "other" | "program" | "library" | "package" | "jiffy">; /** * The version of the software. */ version: Schema.Str; /** * An ordinal index for this category */ pdbx_ordinal: Schema.Int; }; /** * Data items in the STRUCT category record details about the * description of the crystallographic structure. */ struct: { /** * This data item is a pointer to _entry.id in the ENTRY category. */ entry_id: Schema.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: Schema.Str; /** * Indicates if the structure was determined using experimental, computational, or integrative methods */ pdbx_structure_determination_methodology: Schema.Aliased<"experimental" | "integrative" | "computational">; /** * An automatically generated descriptor for an NDB structure or * the unstructured content of the PDB COMPND record. */ pdbx_descriptor: Schema.Str; }; /** * Data items in the STRUCT_ASYM category record details about the * structural elements in the asymmetric unit. */ struct_asym: { /** * A description of special aspects of this portion of the contents * of the asymmetric unit. */ details: Schema.Str; /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.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: Schema.Str; /** * This data item indicates whether the structural elements are modified. */ pdbx_modified: Schema.Str; /** * A flag indicating that this entity was originally labeled * with a blank PDB chain id. */ pdbx_blank_PDB_chainid_flag: Schema.Aliased<"Y" | "N">; }; /** * Data items in the STRUCT_CONF category record details about * the backbone conformation of a segment of polymer. * * Data items in the STRUCT_CONF_TYPE category define the * criteria used to identify the backbone conformations. */ 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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Int; /** * This data item is a pointer to _struct_conf_type.id in the * STRUCT_CONF_TYPE category. */ conf_type_id: Schema.Aliased<"other" | "bend" | "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">; /** * A description of special aspects of the conformation assignment. */ details: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * A component of the identifier for the residue at which the * conformation segment starts. */ pdbx_beg_PDB_ins_code: Schema.Str; /** * A component of the identifier for the residue at which the * conformation segment ends. */ pdbx_end_PDB_ins_code: Schema.Str; /** * This item is a place holder for the helix class used in the PDB * HELIX record. */ pdbx_PDB_helix_class: Schema.Str; /** * A placeholder for the lengths of the helix of the PDB * HELIX record. */ pdbx_PDB_helix_length: Schema.Int; /** * A placeholder for the helix identifier of the PDB * HELIX record. */ pdbx_PDB_helix_id: Schema.Str; }; /** * Data items in the STRUCT_CONN category record details about * the connections between portions of the structure. These can be * hydrogen bonds, salt bridges, disulfide bridges and so on. * * The STRUCT_CONN_TYPE records define the criteria used to * identify these connections. */ struct_conn: { /** * This data item is a pointer to _struct_conn_type.id in the * STRUCT_CONN_TYPE category. */ conn_type_id: Schema.Aliased<"covale" | "disulf" | "metalc" | "hydrog">; /** * A description of special aspects of the connection. */ details: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * A placeholder for the standard residue name found in * the MODRES record of a PDB file. */ pdbx_ptnr1_standard_comp_id: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * Distance value for this contact. */ pdbx_dist_value: Schema.Float; /** * The chemical bond order associated with the specified atoms in * this contact. */ pdbx_value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad">; }; /** * Data items in the STRUCT_CONN_TYPE category record details * about the criteria used to identify interactions between * portions of the structure. */ struct_conn_type: { /** * The criteria used to define the interaction. */ criteria: Schema.Str; /** * The chemical or structural type of the interaction. */ id: Schema.Aliased<"covale" | "disulf" | "metalc" | "hydrog" | "mismat" | "saltbr" | "modres" | "covale_base" | "covale_sugar" | "covale_phosphate">; /** * A reference that specifies the criteria used to define the * interaction. */ reference: Schema.Str; }; /** * Data items in the STRUCT_KEYWORDS category specify keywords * that describe the chemical structure in this entry. */ struct_keywords: { /** * This data item is a pointer to _entry.id in the ENTRY category. */ entry_id: Schema.Str; /** * Keywords describing this structure. */ text: Schema.List; /** * Terms characterizing the macromolecular structure. */ pdbx_keywords: Schema.Str; }; /** * Data items in the STRUCT_MON_PROT_CIS category identify * monomers that have been found to have the peptide bond in the cis * conformation. The criterion used to select residues to be * designated as containing cis peptide bonds is given in * _struct_mon_details.prot_cis. */ struct_mon_prot_cis: { /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_sites_alt.id in the * ATOM_SITES_ALT category. */ label_alt_id: Schema.Str; /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_site.label_asym_id in the * ATOM_SITE category. */ label_asym_id: Schema.Str; /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_site.label_comp_id in the * ATOM_SITE category. */ label_comp_id: Schema.Str; /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_site.label_seq_id in the * ATOM_SITE category. */ label_seq_id: Schema.Int; /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_site.auth_asym_id in the * ATOM_SITE category. */ auth_asym_id: Schema.Str; /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_site.auth_comp_id in the * ATOM_SITE category. */ auth_comp_id: Schema.Str; /** * A component of the identifier for the monomer. * * This data item is a pointer to _atom_site.auth_seq_id in the * ATOM_SITE category. */ auth_seq_id: Schema.Int; /** * Pointer to _atom_site.auth_asym_id. */ pdbx_auth_asym_id_2: Schema.Str; /** * Pointer to _atom_site.auth_comp_id. */ pdbx_auth_comp_id_2: Schema.Str; /** * Pointer to _atom_site.auth_seq_id */ pdbx_auth_seq_id_2: Schema.Int; /** * Pointer to _atom_site.label_asym_id. */ pdbx_label_asym_id_2: Schema.Str; /** * Pointer to _atom_site.label_comp_id. */ pdbx_label_comp_id_2: Schema.Str; /** * Pointer to _atom_site.label_seq_id */ pdbx_label_seq_id_2: Schema.Int; /** * Pointer to _atom_site.pdbx_PDB_ins_code */ pdbx_PDB_ins_code: Schema.Str; /** * Pointer to _atom_site.pdbx_PDB_ins_code */ pdbx_PDB_ins_code_2: Schema.Str; /** * Pointer to _atom_site.pdbx_PDB_model_num */ pdbx_PDB_model_num: Schema.Int; /** * omega torsion angle */ pdbx_omega_angle: Schema.Str; /** * ordinal index */ pdbx_id: Schema.Str; /** * PDB Insertion code */ pdbx_auth_ins_code: Schema.Str; /** * PDB Insertion code */ pdbx_auth_ins_code_2: Schema.Str; }; /** * Data items in the STRUCT_NCS_OPER category describe the * noncrystallographic symmetry operations. * * Each operator is specified as a matrix and a subsequent * translation vector. Operators need not represent proper * rotations. */ 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: Schema.Aliased<"given" | "generate">; /** * A description of special aspects of the noncrystallographic * symmetry operator. */ details: Schema.Str; /** * The value of _struct_ncs_oper.id must uniquely identify a * record in the STRUCT_NCS_OPER list. * * Note that for PDB _struct_ncs_oper.id must be a number. */ id: Schema.Int; /** * The elements of the 3x3 matrix component of a * noncrystallographic symmetry operation. */ matrix: Schema.Tensor; /** * The elements of the three-element vector component of a * noncrystallographic symmetry operation. */ vector: Schema.Tensor; }; /** * Data items in the STRUCT_SHEET_RANGE category record details * about the residue ranges that form a beta-sheet. Residues are * included in a range if they made beta-sheet-type hydrogen-bonding * interactions with at least one adjacent strand and if there are * at least two residues in the range. */ 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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * This data item is a pointer to _struct_sheet.id in the * STRUCT_SHEET category. */ sheet_id: Schema.Str; /** * A component of the identifier for the residue at which the * beta sheet range begins. Insertion code. */ pdbx_beg_PDB_ins_code: Schema.Str; /** * A component of the identifier for the residue at which the * beta sheet range ends. Insertion code. */ pdbx_end_PDB_ins_code: Schema.Str; }; /** * Data items in the STRUCT_SITE category record details about * portions of the structure that contribute to structurally * relevant sites (e.g. active sites, substrate-binding subsites, * metal-coordination sites). */ struct_site: { /** * A description of special aspects of the site. */ details: Schema.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: Schema.Str; /** * Number of residues in the site. */ pdbx_num_residues: Schema.Int; /** * Source of evidence supporting the assignment of this site. */ pdbx_evidence_code: Schema.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: Schema.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: Schema.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: Schema.Int; /** * PDB insertion code for the ligand in the site. */ pdbx_auth_ins_code: Schema.Str; }; /** * Data items in the STRUCT_SITE_GEN category record details about * the generation of portions of the structure that contribute to * structurally relevant sites. */ struct_site_gen: { /** * A description of special aspects of the symmetry generation of * this portion of the structural site. */ details: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * A component of the identifier for participants in the site. * * This data item is a pointer to _atom_site.auth_atom_id in the * ATOM_SITE category. */ auth_atom_id: Schema.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: Schema.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: Schema.Int; /** * This data item is a pointer to _struct_site.id in the STRUCT_SITE * category. */ site_id: Schema.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: Schema.Str; /** * PDB insertion code. */ pdbx_auth_ins_code: Schema.Str; /** * Number of residues in the site. */ pdbx_num_res: Schema.Int; }; /** * Data items in the STRUCT_SITE_KEYWORDS category record * keywords describing the site. */ struct_site_keywords: { /** * This data item is a pointer to _struct_site.id in the STRUCT_SITE * category. */ site_id: Schema.Str; /** * Keywords describing this site. */ text: Schema.Str; }; /** * Data items in the SYMMETRY category record details about the * space-group symmetry. */ symmetry: { /** * This data item is a pointer to _entry.id in the ENTRY category. */ entry_id: Schema.Str; /** * The cell settings for this space-group symmetry. */ cell_setting: Schema.Aliased<"triclinic" | "monoclinic" | "orthorhombic" | "tetragonal" | "rhombohedral" | "trigonal" | "hexagonal" | "cubic">; /** * Space-group number from International Tables for Crystallography * Vol. A (2002). */ Int_Tables_number: Schema.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: Schema.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': Schema.Str; }; /** * These are internal RCSB records to keep track of data processing * and status of the entry. */ pdbx_database_status: { /** * Code for status of file. */ status_code: Schema.Aliased<"PROC" | "WAIT" | "REL" | "HOLD" | "HPUB" | "REFI" | "OBS" | "WDRN" | "AUTH" | "POLC" | "REPL" | "AUCO" | "TRSF" | "RMVD" | "DEL" | "REV" | "UPD" | "BIB">; /** * Code for status of structure factor file. */ status_code_sf: Schema.Aliased<"PROC" | "WAIT" | "REL" | "HOLD" | "HPUB" | "OBS" | "WDRN" | "AUTH" | "POLC" | "REPL" | "RMVD">; /** * Code for status of NMR constraints file. */ status_code_mr: Schema.Aliased<"PROC" | "WAIT" | "REL" | "HOLD" | "HPUB" | "OBS" | "WDRN" | "AUTH" | "POLC" | "REPL" | "AUCO" | "RMVD">; /** * The value of _pdbx_database_status.entry_id identifies the data block. */ entry_id: Schema.Str; /** * The date of initial deposition. (The first message for * deposition has been received.) */ recvd_initial_deposition_date: Schema.Str; /** * This code indicates whether the entry belongs to * Structural Genomics Project. */ SG_entry: Schema.Aliased<"y" | "n">; /** * The site where the file was deposited. */ deposit_site: Schema.Aliased<"NDB" | "RCSB" | "PDBE" | "PDBJ" | "BMRB" | "BNL" | "PDBC">; /** * The site where the file was deposited. */ process_site: Schema.Aliased<"NDB" | "RCSB" | "PDBE" | "PDBJ" | "BNL" | "PDBC">; /** * Code for status of chemical shift data file. */ status_code_cs: Schema.Aliased<"PROC" | "WAIT" | "REL" | "HOLD" | "HPUB" | "OBS" | "WDRN" | "AUTH" | "POLC" | "REPL" | "AUCO" | "RMVD">; /** * The methods development category in which this * entry has been placed. */ methods_development_category: Schema.Aliased<"CAPRI" | "CASP" | "CASD-NMR" | "FoldIt" | "GPCR Dock" | "D3R" | "RNA-Puzzles">; /** * A flag indicating that the entry is compatible with the PDB format. * * A value of 'N' indicates that the no PDB format data file is * corresponding to this entry is available in the PDB archive. */ pdb_format_compatible: Schema.Aliased<"y" | "n">; }; /** * The PDBX_NONPOLY_SCHEME category provides residue level nomenclature * mapping for non-polymer entities. */ pdbx_nonpoly_scheme: { /** * Pointer to _atom_site.label_asym_id. */ asym_id: Schema.Str; /** * Pointer to _atom_site.label_entity_id. */ entity_id: Schema.Str; /** * Pointer to _atom_site.label_comp_id. */ mon_id: Schema.Str; /** * PDB strand/chain id. */ pdb_strand_id: Schema.Str; /** * NDB/RCSB residue number. */ ndb_seq_num: Schema.Str; /** * PDB residue number. */ pdb_seq_num: Schema.Str; /** * Author provided residue numbering. This value may differ from the PDB residue * number and may not correspond to residue numbering within the coordinate records. */ auth_seq_num: Schema.Str; /** * PDB residue identifier. */ pdb_mon_id: Schema.Str; /** * Author provided residue identifier. This value may differ from the PDB residue * identifier and may not correspond to residue identification within the coordinate records. */ auth_mon_id: Schema.Str; /** * PDB insertion code. */ pdb_ins_code: Schema.Str; }; /** * Data items in PDBX_DATABASE_RELATED contain references to entries * that are related to the this entry. */ pdbx_database_related: { /** * The name of the database containing the related entry. */ db_name: Schema.Aliased<"NDB" | "BMRB" | "BIOISIS" | "BMCD" | "EMDB" | "PDB" | "PDB-Dev" | "SASBDB" | "TargetDB" | "TargetTrack">; /** * A description of the related entry. */ details: Schema.Str; /** * The identifying code in the related database. */ db_id: Schema.Str; /** * The identifying content type of the related entry. */ content_type: Schema.Aliased<"split" | "other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "focused EM volume" | "consensus EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "re-refinement" | "complete structure" | "unspecified">; }; /** * The PDBX_ENTITY_NONPOLY category provides a mapping between * entity and the nonpolymer component */ pdbx_entity_nonpoly: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * This data item is a pointer to _chem_comp.id in the CHEM_COMP category. */ comp_id: Schema.Str; /** * A name for the non-polymer entity */ name: Schema.Str; }; /** * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences. */ pdbx_chem_comp_synonyms: { /** * The synonym of this particular chemical component. */ name: Schema.Str; /** * The chemical component for which this synonym applies. */ comp_id: Schema.Str; /** * The provenance of this synonym. */ provenance: Schema.Aliased<"PDB" | "AUTHOR" | "DRUGBANK" | "CHEBI" | "CHEMBL" | "PUBCHEM">; }; /** * Data items in the CHEM_COMP_IDENTIFIER category provide * identifiers for chemical components. */ pdbx_chem_comp_identifier: { /** * This data item is a pointer to _chem_comp.id in the CHEM_COMP * category. */ comp_id: Schema.Str; /** * This data item contains the identifier value for this * component. */ identifier: Schema.Str; /** * This data item contains the identifier type. */ type: Schema.Aliased<"COMMON NAME" | "SYSTEMATIC NAME" | "CAS REGISTRY NUMBER" | "PUBCHEM Identifier" | "MDL Identifier" | "SYNONYM" | "CONDENSED IUPAC CARB SYMBOL" | "IUPAC CARB SYMBOL" | "SNFG CARB SYMBOL" | "CONDENSED IUPAC CARBOHYDRATE SYMBOL" | "IUPAC CARBOHYDRATE SYMBOL" | "SNFG CARBOHYDRATE SYMBOL">; /** * This data item contains the name of the program * or library used to compute the identifier. */ program: Schema.Str; /** * This data item contains the version of the program * or library used to compute the identifier. */ program_version: Schema.Str; }; /** * Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the * residues within the entry that are not observed or have zero occupancy. */ pdbx_unobs_or_zero_occ_residues: { /** * The value of _pdbx_unobs_or_zero_occ_residues.id must uniquely identify * each item in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES list. * * This is an integer serial number. */ id: Schema.Int; /** * The value of polymer flag indicates whether the unobserved or * zero occupancy residue is part of a polymer chain or not */ polymer_flag: Schema.Aliased<"y" | "n">; /** * The value of occupancy flag indicates whether the residue * is unobserved (= 1) or the coordinates have an occupancy of zero (=0) */ occupancy_flag: Schema.Aliased<"1" | "0">; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.pdbx_PDB_model_num in the * ATOM_SITE category. */ PDB_model_num: Schema.Int; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.auth_asym_id in the * ATOM_SITE category. */ auth_asym_id: Schema.Str; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.auth_comp_id in the * ATOM_SITE category. */ auth_comp_id: Schema.Str; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.auth_seq_id in the * ATOM_SITE category. */ auth_seq_id: Schema.Int; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the * ATOM_SITE category. */ PDB_ins_code: Schema.Str; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.label_asym_id in the * ATOM_SITE category. */ label_asym_id: Schema.Str; /** * Part of the identifier for the unobserved or zero occupancy residue. * * This data item is a pointer to _atom_site.label_comp_id in the * ATOM_SITE category. */ label_comp_id: Schema.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: Schema.Int; }; /** * Data items in the PDBX_STRUCT_MOD_RESIDUE category list the * modified polymer components in the entry and provide some * details describing the nature of the modification. */ 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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Int; /** * The parent component identifier for this modified polymer component. */ parent_comp_id: Schema.Str; /** * Details of the modification for this polymer component. */ details: Schema.Str; }; /** * Data items in the PDBX_STRUCT_OPER_LIST category describe * Cartesian rotation and translation operations required to * generate or transform the coordinates deposited with this entry. */ pdbx_struct_oper_list: { /** * This identifier code must uniquely identify a * record in the PDBX_STRUCT_OPER_LIST list. */ id: Schema.Str; /** * A code to indicate the type of operator. */ type: Schema.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">; /** * A descriptive name for the transformation operation. */ name: Schema.Str; /** * The symmetry operation corresponding to the transformation operation. */ symmetry_operation: Schema.Str; /** * The elements of the 3x3 matrix component of the * transformation operation. */ matrix: Schema.Tensor; /** * The elements of the three-element vector component of the * transformation operation. */ vector: Schema.Tensor; }; /** * Data items in the PDBX_STRUCT_ASSEMBLY category record details about * the structural elements that form macromolecular assemblies. */ pdbx_struct_assembly: { /** * Provides details of the method used to determine or * compute the assembly. */ method_details: Schema.Str; /** * Provides the details of the oligomeric state of the assembly. */ oligomeric_details: Schema.Str; /** * The number of polymer molecules in the assembly. */ oligomeric_count: Schema.Int; /** * A description of special aspects of the macromolecular assembly. * * In the PDB, 'representative helical assembly', 'complete point assembly', * 'complete icosahedral assembly', 'software_defined_assembly', 'author_defined_assembly', * and 'author_and_software_defined_assembly' are considered "biologically relevant assemblies. */ details: Schema.Str; /** * The value of _pdbx_struct_assembly.id must uniquely identify a record in * the PDBX_STRUCT_ASSEMBLY list. */ id: Schema.Str; }; /** * Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about * the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN * data items provide the specifications of the components that * constitute that assembly in terms of cartesian transformations. */ 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: Schema.List; /** * This data item is a pointer to _pdbx_struct_assembly.id in the * PDBX_STRUCT_ASSEMBLY category. */ assembly_id: Schema.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: Schema.Str; }; /** * Data items in the PDBX_REFERENCE_ENTITY_LIST category record * the list of entities within each reference molecule. */ 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: Schema.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: Schema.Str; /** * Defines the polymer characteristic of the entity. */ type: Schema.Aliased<"non-polymer" | "polymer" | "branched" | "polymer-like">; /** * Additional details about this entity. */ details: Schema.Str; /** * The component number of this entity within the molecule. */ component_id: Schema.Int; }; /** * Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about * the linkages between entities within reference molecules. */ pdbx_reference_entity_link: { /** * The value of _pdbx_reference_entity_link.link_id uniquely identifies * linkages between entities with a molecule. */ link_id: Schema.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: Schema.Str; /** * A description of special aspects of a linkage between * chemical components in the structure. */ details: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * The atom identifier/name in the first of the two entities containing the linkage. */ atom_id_1: Schema.Str; /** * The atom identifier/name in the second of the two entities containing the linkage. */ atom_id_2: Schema.Str; /** * The bond order target for the chemical linkage. */ value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">; /** * The entity component identifier for the first of two entities containing the linkage. */ component_1: Schema.Int; /** * The entity component identifier for the second of two entities containing the linkage. */ component_2: Schema.Int; /** * A code indicating the entity types involved in the linkage. */ link_class: Schema.Aliased<"PP" | "PN" | "NP" | "NN">; }; /** * Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about * polymer linkages including both standard and non-standard linkages between * polymer componnents. */ 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: Schema.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: Schema.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: Schema.Str; /** * The entity component identifier entity containing the linkage. */ component_id: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * The atom identifier/name in the first of the two components making * the linkage. */ atom_id_1: Schema.Str; /** * The atom identifier/name in the second of the two components making * the linkage. */ atom_id_2: Schema.Str; /** * The bond order target for the non-standard linkage. */ value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">; }; /** * Data items in the PDBX_MOLECULE category identify reference molecules * within a PDB entry. */ pdbx_molecule: { /** * The value of _pdbx_molecule.prd_id is the PDB accession code for this * reference molecule. */ prd_id: Schema.Str; /** * The value of _pdbx_molecule.instance_id is identifies a particular molecule * in the molecule list. */ instance_id: Schema.Int; /** * A reference to _struct_asym.id in the STRUCT_ASYM category. */ asym_id: Schema.Str; }; /** * Data items in the PDBX_MOLECULE_FEATURES category record features of molecules * within a PDB entry. */ pdbx_molecule_features: { /** * The value of _pdbx_molecule_features.prd_id is the accession code for this * reference molecule. */ prd_id: Schema.Str; /** * Broadly defines the function of the molecule. */ class: Schema.Aliased<"antagonist" | "antibiotic" | "anticancer" | "anticoagulant" | "antifungal" | "antigen" | "antiinflammatory" | "antimicrobial" | "antineoplastic" | "antiparasitic" | "antiretroviral" | "anthelmintic" | "antithrombotic" | "antitumor" | "antiviral" | "caspase inhibitor" | "chaperone binding" | "enzyme inhibitor" | "drug delivery" | "glycan component" | "growth factor" | "immunosuppressant" | "inducer" | "inhibitor" | "lantibiotic" | "metabolism" | "metal transport" | "nutrient" | "oxidation-reduction" | "protein binding" | "receptor" | "substrate analog" | "synthetic opioid" | "thrombin inhibitor" | "transition state mimetic" | "transport activator" | "trypsin inhibitor" | "toxin" | "unknown" | "water retention" | "anticoagulant, antithrombotic" | "antibiotic, antimicrobial" | "antibiotic, anthelmintic" | "antibiotic, antineoplastic" | "antimicrobial, antiretroviral" | "antimicrobial, antitumor" | "antimicrobial, antiparasitic, antibiotic" | "thrombin inhibitor, trypsin inhibitor">; /** * Defines the structural classification of the molecule. */ type: Schema.Aliased<"non-polymer" | "peptide-like" | "macrolide" | "unknown" | "amino acid" | "aminoglycoside" | "anthracycline" | "anthraquinone" | "ansamycin" | "chalkophore" | "chromophore" | "glycopeptide" | "cyclic depsipeptide" | "cyclic lipopeptide" | "cyclic peptide" | "heterocyclic" | "imino sugar" | "keto acid" | "lipoglycopeptide" | "lipopeptide" | "nucleoside" | "oligopeptide" | "oligosaccharide" | "peptaibol" | "polycyclic" | "polypeptide" | "polysaccharide" | "quinolone" | "thiolactone" | "thiopeptide" | "siderophore" | "chalkophore, polypeptide">; /** * A name of the molecule. */ name: Schema.Str; /** * Additional details describing the molecule. */ details: Schema.Str; }; /** * Data items in the ENTITY_SRC_NAT category record details of * the source from which the entity was obtained in cases * where the entity was isolated directly from a natural tissue. */ entity_src_nat: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * Scientific name of the organism of the natural source. */ pdbx_organism_scientific: Schema.Str; /** * The plasmid containing the gene. */ pdbx_plasmid_name: Schema.Str; /** * This data item is an ordinal identifier for entity_src_nat data records. */ pdbx_src_id: Schema.Int; /** * The beginning polymer sequence position for the polymer section corresponding * to this source. * * A reference to the sequence position in the entity_poly category. */ pdbx_beg_seq_num: Schema.Int; /** * The ending polymer sequence position for the polymer section corresponding * to this source. * * A reference to the sequence position in the entity_poly category. */ pdbx_end_seq_num: Schema.Int; }; /** * Data items in the ENTITY_SRC_GEN category record details of * the source from which the entity was obtained in cases * where the source was genetically manipulated. The * following are treated separately: items pertaining to the tissue * from which the gene was obtained, items pertaining to the host * organism for gene expression and items pertaining to the actual * producing organism (plasmid). */ entity_src_gen: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * Identifies the gene. */ pdbx_gene_src_gene: Schema.List; /** * Scientific name of the organism. */ pdbx_gene_src_scientific_name: Schema.Str; /** * The name of the plasmid that produced the entity in the host * organism. Where full details of the protein production are available * it would be expected that this item would be derived from * _pdbx_construct.name of the construct pointed to from * _entity_src_gen_express.plasmid_id. */ plasmid_name: Schema.Str; /** * This data item is an ordinal identifier for entity_src_gen data records. */ pdbx_src_id: Schema.Int; /** * The beginning polymer sequence position for the polymer section corresponding * to this source. * * A reference to the sequence position in the entity_poly category. */ pdbx_beg_seq_num: Schema.Int; /** * The ending polymer sequence position for the polymer section corresponding * to this source. * * A reference to the sequence position in the entity_poly category. */ pdbx_end_seq_num: Schema.Int; }; /** * The data items in category PDBX_ENTITY_SRC_SYN record the source details * about chemically synthesized molecules. */ pdbx_entity_src_syn: { /** * The scientific name of the organism from which the sequence of * the synthetic entity was derived. */ organism_scientific: Schema.Str; /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * This data item is an ordinal identifier for pdbx_entity_src_syn data records. */ pdbx_src_id: Schema.Int; /** * The beginning polymer sequence position for the polymer section corresponding * to this source. * * A reference to the sequence position in the entity_poly category. */ pdbx_beg_seq_num: Schema.Int; /** * The ending polymer sequence position for the polymer section corresponding * to this source. * * A reference to the sequence position in the entity_poly category. */ pdbx_end_seq_num: Schema.Int; }; /** * Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide * string descriptors of entity chemical structure. */ pdbx_entity_branch_descriptor: { /** * This data item is a pointer to _entity_poly.entity_id in the ENTITY * category. */ entity_id: Schema.Str; /** * This data item contains the descriptor value for this * entity. */ descriptor: Schema.Str; /** * This data item contains the descriptor type. */ type: Schema.Aliased<"linucs" | "glycam condensed sequence" | "glycam condensed core sequence" | "wurcs">; /** * This data item contains the name of the program * or library used to compute the descriptor. */ program: Schema.Str; /** * This data item contains the version of the program * or library used to compute the descriptor. */ program_version: Schema.Str; /** * Ordinal index for this category. */ ordinal: Schema.Int; }; /** * Data items in the pdbx_entity_instance_feature category records * special features of selected entity instances. */ pdbx_entity_instance_feature: { /** * Special structural details about this entity instance. */ details: Schema.Str; /** * A feature type associated with entity instance. */ feature_type: Schema.Aliased<"SUBJECT OF INVESTIGATION" | "NO FUNCTIONAL ROLE" | "OTHER">; /** * Author instance identifier (formerly PDB Chain ID) */ auth_asym_id: Schema.Str; /** * Instance identifier for this entity. */ asym_id: Schema.Str; /** * Author provided residue number. */ auth_seq_num: Schema.Str; /** * Position in the sequence. */ seq_num: Schema.Int; /** * Chemical component identifier */ comp_id: Schema.Str; /** * The author provided chemical component identifier */ auth_comp_id: Schema.Str; /** * An ordinal index for this category */ ordinal: Schema.Int; }; /** * Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list * of monomers in a branched entity. Allowance is made for the possibility * of microheterogeneity in a sample by allowing a given sequence * number to be correlated with more than one monomer ID. The * corresponding ATOM_SITE entries should reflect this * heterogeneity. */ pdbx_entity_branch_list: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * A flag to indicate whether this monomer in the entity is * heterogeneous in sequence. */ hetero: Schema.Aliased<"y" | "yes" | "no" | "n">; /** * This data item is a pointer to _chem_comp.id in the CHEM_COMP * category. */ comp_id: Schema.Str; /** * The value pair _pdbx_entity_branch_list.num and _pdbx_entity_branch_list.comp_id * must uniquely identify a record in the PDBX_ENTITY_BRANCH_LIST list. */ num: Schema.Int; }; /** * Data items in the PDBX_ENTITY_BRANCH_LINK category give details about * the linkages between components within a branched entity. */ pdbx_entity_branch_link: { /** * The value of _pdbx_entity_branch_link.link_id uniquely identifies * linkages within the branched entity. */ link_id: Schema.Int; /** * A description of special aspects of this linkage. */ details: Schema.Str; /** * The entity id for this branched entity. * * This data item is a pointer to _pdbx_entity_branch_list.entity_id * in the PDBX_ENTITY_BRANCH_LIST category. */ entity_id: Schema.Str; /** * The component number for the first component making the linkage. * * This data item is a pointer to _pdbx_entity_branch_list.num * in the PDBX_ENTITY_BRANCH_LIST category. */ entity_branch_list_num_1: Schema.Int; /** * The component number for the second component making the linkage. * * This data item is a pointer to _pdbx_entity_branch_list.num * in the PDBX_ENTITY_BRANCH_LIST category. */ entity_branch_list_num_2: Schema.Int; /** * The component identifier for the first component making the linkage. * * This data item is a pointer to _pdbx_entity_branch_list.comp_id * in the PDBX_ENTITY_BRANCH_LIST category. */ comp_id_1: Schema.Str; /** * The component identifier for the second component making the linkage. * * This data item is a pointer to _pdbx_entity_branch_list.comp_id * in the PDBX_ENTITY_BRANCH_LIST category. */ comp_id_2: Schema.Str; /** * The atom identifier/name for the first atom making the linkage. */ atom_id_1: Schema.Str; /** * The leaving atom identifier/name bonded to the first atom making the linkage. */ leaving_atom_id_1: Schema.Str; /** * The chiral configuration of the first atom making the linkage. */ atom_stereo_config_1: Schema.Aliased<"r" | "s" | "n">; /** * The atom identifier/name for the second atom making the linkage. */ atom_id_2: Schema.Str; /** * The leaving atom identifier/name bonded to the second atom making the linkage. */ leaving_atom_id_2: Schema.Str; /** * The chiral configuration of the second atom making the linkage. */ atom_stereo_config_2: Schema.Aliased<"r" | "s" | "n">; /** * The bond order target for the chemical linkage. */ value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">; }; /** * Data items in the PDBX_ENTITY_BRANCH category specify the list * of branched entities and the type. */ pdbx_entity_branch: { /** * The entity id for this branched entity. * * This data item is a pointer to _entity.id */ entity_id: Schema.Str; /** * The type of this branched oligosaccharide. */ type: Schema.Aliased<"oligosaccharide">; }; /** * The PDBX_BRANCH_SCHEME category provides residue level nomenclature * mapping for branch chain entities. */ pdbx_branch_scheme: { /** * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * A flag to indicate whether this monomer in the entity is * heterogeneous in sequence. */ hetero: Schema.Aliased<"y" | "yes" | "no" | "n">; /** * Pointer to _atom_site.label_asym_id. */ asym_id: Schema.Str; /** * This data item is a pointer to _atom_site.label_comp_id in the * PDBX_ENTITY_BRANCH_LIST category. */ mon_id: Schema.Str; /** * This data item is a pointer to _pdbx_entity_branch_list.num in the * PDBX_ENTITY_BRANCH_LIST category. */ num: Schema.Int; /** * This data item is a pointer to _atom_site.auth_asym_id in the * ATOM_SITE category. */ pdb_asym_id: Schema.Str; /** * This data item is a pointer to _atom_site.auth_seq_id in the * ATOM_SITE category. */ pdb_seq_num: Schema.Str; /** * This data item is a pointer to _atom_site.auth_comp_id in the * ATOM_SITE category. */ pdb_mon_id: Schema.Str; /** * This data item is a pointer to _atom_site.pdbx_auth_asym_id in the * ATOM_SITE category. */ auth_asym_id: Schema.Str; /** * This data item is a pointer to _atom_site.pdbx_auth_seq_id in the * ATOM_SITE category. */ auth_seq_num: Schema.Str; /** * This data item is a pointer to _atom_site.pdbx_auth_comp_id in the * ATOM_SITE category. */ auth_mon_id: Schema.Str; }; /** * PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components. */ pdbx_chem_comp_related: { /** * The chemical component for which this relationship applies. */ comp_id: Schema.Str; /** * The related chemical component for which this chemical component is based. */ related_comp_id: Schema.Str; /** * Describes the type of relationship */ relationship_type: Schema.Aliased<"Carbohydrate core" | "Precursor">; /** * Describes the type of relationship */ details: Schema.Str; }; /** * Data items in the IHM_STARTING_MODEL_DETAILS category records the * details about structural models used as starting inputs in * the integrative model building process. */ ihm_starting_model_details: { /** * A unique identifier for the starting structural model. */ starting_model_id: Schema.Str; /** * A unique identifier for the distinct molecular entities. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * A text description of the molecular entity */ entity_description: Schema.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: Schema.Str; /** * The identifier for the polymeric segment modeled using this starting model. * This data item is a pointer to _ihm_entity_poly_segment.id in the * IHM_ENTITY_POLY_SEGMENT category. */ entity_poly_segment_id: Schema.Int; /** * The source of the starting model. */ starting_model_source: Schema.Aliased<"other" | "comparative model" | "experimental model" | "integrative model" | "ab initio model">; /** * 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: Schema.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: Schema.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: Schema.Int; }; /** * Data items in the IHM_STARTING_COMPARATIVE_MODELS category records * additional details about comparative models used as starting inputs in * the integrative model building process. */ ihm_starting_comparative_models: { /** * A unique identifier for the starting comparative model. */ id: Schema.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: Schema.Str; /** * The chainId/auth_asym_id corresponding to the starting model. */ starting_model_auth_asym_id: Schema.Str; /** * The starting residue index of the starting model. */ starting_model_seq_id_begin: Schema.Int; /** * The ending residue index of the starting model. */ starting_model_seq_id_end: Schema.Int; /** * The chainId/auth_asym_id corresponding to the template. */ template_auth_asym_id: Schema.Str; /** * The starting residue index of the template. */ template_seq_id_begin: Schema.Int; /** * The ending residue index of the template. */ template_seq_id_end: Schema.Int; /** * The percentage sequence identity between the template sequence and the comparative model sequence. */ template_sequence_identity: Schema.Float; /** * The denominator used while calculating the sequence identity provided in * _ihm_starting_comparative_models.template_sequence_identity. */ template_sequence_identity_denominator: Schema.Aliased<"1" | "2" | "3" | "4" | "5">; /** * 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: Schema.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: Schema.Int; }; /** * Data items in the IHM_STARTING_MODEL_SEQ_DIF category provide a * mechanism for indicating and annotating point differences * between the sequence of the entity or biological unit described * in the data block and the sequence of the starting model used in * the integrative modeling referenced from a database. The point * differences may be due to point mutations introduced in the * starting model or the presence of modified amino acid residues. */ ihm_starting_model_seq_dif: { /** * A unique identifier for the entry. */ id: Schema.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: Schema.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: Schema.Str; /** * The residue index. * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. */ seq_id: Schema.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: Schema.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: Schema.Str; /** * The asym/strand identifier for the entity molecule of the database starting model. */ db_asym_id: Schema.Str; /** * The corresponding residue index of the database starting model. */ db_seq_id: Schema.Int; /** * The correspinding component identifier for the residue in the database starting model. */ db_comp_id: Schema.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: Schema.Str; }; /** * Data items in the IHM_MODEL_REPRESENTATION category lists the * various mono or multi-scale model representations used in the * integrative modeling study. */ ihm_model_representation: { /** * A unique identifier for the model representation. */ id: Schema.Int; /** * Name/brief description for the model representation. */ name: Schema.Str; /** * Additional details about the model representation. */ details: Schema.Str; }; /** * Data items in the IHM_MODEL_REPRESENTATION_DETAILS category records the * details about the architecture and representation of structural * models involved in the integrative modeling study. */ ihm_model_representation_details: { /** * A unique identifier for the category. */ id: Schema.Int; /** * An identifier that collects or groups together a set of representations. * This data item is a pointer to _ihm_model_representation.id in the * IHM_MODEL_REPRESENTATION category. */ representation_id: Schema.Int; /** * The identifier for the polymeric segment in the representation. * This data item is a pointer to _ihm_entity_poly_segment.id in the * IHM_ENTITY_POLY_SEGMENT category. */ entity_poly_segment_id: Schema.Int; /** * A unique identifier distinct molecular entities. * This data item is a pointer to _entity.id in the * ENTITY category. */ entity_id: Schema.Str; /** * A text description of the molecular entity */ entity_description: Schema.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: Schema.Str; /** * The primitive object used to model this segment. */ model_object_primitive: Schema.Aliased<"other" | "atomistic" | "sphere" | "gaussian">; /** * 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: Schema.Str; /** * The manner in which the segment is modeled. */ model_mode: Schema.Aliased<"rigid" | "flexible">; /** * The level of detail at which model primitive objects are applied to the structure. */ model_granularity: Schema.Aliased<"by-atom" | "by-residue" | "multi-residue" | "by-feature">; /** * The number of primitive objects used to model a feature in the case of 'by-feature' granularity. */ model_object_count: Schema.Int; }; /** * Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category records * the details of the structural assemblies and used in the * integrative modeling. */ ihm_struct_assembly_details: { /** * A unique identifier for the structural assembly description. */ id: Schema.Int; /** * An identifier for the structural assembly. * This data item will remain the same for all components * of an assembly. * This data item is a pointer to _ihm_struct_assembly.id * in the IHM_STRUCT_ASSEMBLY category. */ assembly_id: Schema.Int; /** * The parent of this assembly in a hierarchy. * This data item is a pointer to _ihm_struct_assembly.id in the * IHM_STRUCT_ASSEMBLY category. * 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_details.parent_assembly_id is the same as * _ihm_struct_assembly_details.assembly_id indicating a self-parent. */ parent_assembly_id: Schema.Int; /** * A text description of the molecular entity */ entity_description: Schema.Str; /** * A unique identifier for distinct molecular entities. * This data item is a pointer to _entity.id in the * ENTITY category. */ entity_id: Schema.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: Schema.Str; /** * The identifier for the polymeric segment in the assembly. * This data item is a pointer to _ihm_entity_poly_segment.id in the * IHM_ENTITY_POLY_SEGMENT category. */ entity_poly_segment_id: Schema.Int; }; /** * Data items in the IHM_STRUCT_ASSEMBLY category lists * all the structural assemblies used in the integrative * modeling study. */ ihm_struct_assembly: { /** * A unique identifier for the structural assembly. */ id: Schema.Int; /** * A name for the structural assembly. */ name: Schema.Str; /** * Description of the structural assembly. */ description: Schema.Str; }; /** * Data items in the IHM_MODELING_PROTOCOL category lists all * modeling protocols used in the integrative modeling study. */ ihm_modeling_protocol: { /** * A unique identifier for the modeling protocol. */ id: Schema.Int; /** * Number of independent steps in the modeling protocol. */ num_steps: Schema.Int; /** * The name for the modeling protocol. */ protocol_name: Schema.Str; }; /** * Data items in the IHM_MODELING_PROTOCOL_DETAILS category records the * step-wise details of the integrative modeling workflow. */ ihm_modeling_protocol_details: { /** * A unique identifier for the modeling protocol/step combination. */ id: Schema.Int; /** * An index for the modeling protocol carried out. * This data item is a pointer to _ihm_modeling_protocol.id in the * IHM_MODELING_PROTOCOL category. */ protocol_id: Schema.Int; /** * An index for a particular step within the modeling protocol. */ step_id: Schema.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.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: Schema.Int; /** * An index for the dataset group being used in the modeling protocol. * This data item is a pointer to the _ihm_dataset_group.id in the * IHM_DATASET_GROUP category. */ dataset_group_id: Schema.Int; /** * A textual description of the structural assembly being modeled. */ struct_assembly_description: Schema.Str; /** * The name or type of the modeling step. */ step_name: Schema.Str; /** * Description of the method involved in the modeling step. */ step_method: Schema.Str; /** * The number of models in the beginning of the step. */ num_models_begin: Schema.Int; /** * The number of models at the end of the step. */ num_models_end: Schema.Int; /** * A flag to indicate if the modeling is multi scale. */ multi_scale_flag: Schema.Aliased<"yes" | "no">; /** * A flag to indicate if the modeling is multi state. */ multi_state_flag: Schema.Aliased<"yes" | "no">; /** * A flag to indicate if the modeling involves an ensemble ordered by time or other order. */ ordered_flag: Schema.Aliased<"yes" | "no">; /** * The file id corresponding to the script used in the modeling protocol step. * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category. */ script_file_id: Schema.Int; /** * Identifier to the software used in the modeling protocol step. * This data item is a pointer to the _software.pdbx_ordinal in the * SOFTWARE category. */ software_id: Schema.Int; }; /** * Data items in the IHM_MULTI_STATE_MODELING category records the * details of the multi-state modeling protocol, if applicable. */ ihm_multi_state_modeling: { /** * A unique identifier for a particular state in the multi-state modeling. */ state_id: Schema.Int; /** * An identifier for a collections of states in the multi-state modeling. * This data item can be used when structural models belong to diffent * multi-state modeling types. */ state_group_id: Schema.Int; /** * A fraction representing the population of the particular state. */ population_fraction: Schema.Float; /** * The standard deviation of the population fraction. */ population_fraction_sd: Schema.Float; /** * The type that the multiple states being modeled belong to. */ state_type: Schema.Str; /** * A descriptive name for the state. */ state_name: Schema.Str; /** * The type of multi-state modeling experiment carried out. */ experiment_type: Schema.Aliased<"Fraction of bulk" | "Single molecule">; /** * Additional textual details of the multi-state modeling, if required. */ details: Schema.Str; }; /** * Data items in the IHM_MODELING_POST_PROCESS category records * the details of the post processing of the models/results of * the modeling protocol. */ ihm_modeling_post_process: { /** * A unique identifier for the post modeling analysis/step combination. */ id: Schema.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.id * in the IHM_MODELING_PROTOCOL category. */ protocol_id: Schema.Int; /** * An identifier for the post modeling analysis. This data item accounts for * multiple post-modeling analyses that can be carried out. */ analysis_id: Schema.Int; /** * In a multi-step process, this identifier denotes the particular * step in the post modeling analysis. */ step_id: Schema.Int; /** * The type of post modeling analysis being carried out. */ type: Schema.Aliased<"none" | "filter" | "other" | "cluster" | "rescore" | "validation">; /** * The parameter/feature used in the post modeling analysis. */ feature: Schema.Aliased<"none" | "other" | "energy/score" | "RMSD" | "dRMSD">; /** * The number of models at the beginning of the post processing step. */ num_models_begin: Schema.Int; /** * The number of models the the end of the post processing step. */ num_models_end: Schema.Int; }; /** * Data items in the IHM_ENSEMBLE_INFO category records the * details of the model clusters or ensembles obtained after * sampling. */ ihm_ensemble_info: { /** * A unique id for the ensemble. */ ensemble_id: Schema.Int; /** * An optional name for the cluster or ensemble for better description. */ ensemble_name: Schema.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: Schema.Int; /** * An identifier for the cluster or group of models being deposited. * This data item is a pointer to the _ihm_model_group.id * in the IHM_MODEL_GROUP category. */ model_group_id: Schema.Int; /** * The clustering method used to obtain the ensemble, if applicable. */ ensemble_clustering_method: Schema.Aliased<"Hierarchical" | "Partitioning (k-means)" | "Density based threshold-clustering" | "Other">; /** * The parameter/feature used for clustering the models, if applicable. */ ensemble_clustering_feature: Schema.Aliased<"other" | "RMSD" | "dRMSD">; /** * The number of models in the current ensemble being described. */ num_ensemble_models: Schema.Int; /** * The number of models from the current ensemble that is deposited. */ num_ensemble_models_deposited: Schema.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: Schema.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: Schema.Int; }; /** * Data items in the IHM_MODEL_LIST category record the * details of the structure models being deposited. */ ihm_model_list: { /** * A unique identifier for the structural model being deposited. */ model_id: Schema.Int; /** * A decsriptive name for the model. */ model_name: Schema.Str; /** * An identifier to the structure assembly corresponding to the model. * This data item is a pointer to the _ihm_struct_assembly.id * in the IHM_STRUCT_ASSEMBLY category. */ assembly_id: Schema.Int; /** * An identifier to the modeling protocol that produced the model. * This data item is a pointer to the _ihm_modeling_protocol.id * in the IHM_MODELING_PROTOCOL category. */ protocol_id: Schema.Int; /** * An identifier to the multi-scale model representation id of the model. * This data item is a pointer to the _ihm_model_representation.id * in the IHM_MODEL_REPRESENTATION category. */ representation_id: Schema.Int; }; /** * IHM_MODEL_GROUP category defines collections or groups of integrative * structure models. */ ihm_model_group: { /** * A unique identifier for a collection or group of structural models. * 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_group 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. */ id: Schema.Int; /** * A name for the collection of models. */ name: Schema.Str; /** * Additional details about the collection of models. */ details: Schema.Str; }; /** * IHM_MODEL_GROUP_LINK category provides the list of structure models present in * a particular structure model group. */ ihm_model_group_link: { /** * An identifier for the structural model. * This data item is a pointer to _ihm_model_list.model_id in the * IHM_MODEL_LIST category. */ model_id: Schema.Int; /** * An identifier for the structural model group. * This data item is a pointer to _ihm_model_group.id in the * IHM_MODEL_GROUP category. */ group_id: Schema.Int; }; /** * Data items in the IHM_MODEL_REPRESENTATIVE category record the * details of the representative structure model in an ensemble or cluster. */ ihm_model_representative: { /** * A unique identifier for the representative of the model group. */ id: Schema.Int; /** * The model group identifier corresponding to the representative model. * This data item is a pointer to _ihm_model_group.id in the * IHM_MODEL_GROUP category. */ model_group_id: Schema.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: Schema.Int; /** * The selection criteria based on which the representative is chosen. */ selection_criteria: Schema.Aliased<"minimized average structure" | "medoid" | "closest to the average" | "lowest energy" | "target function" | "fewest violations" | "best scoring model" | "centroid" | "other selction criteria">; }; /** * Category holds the list of all datasets used in the IHM modeling. * These can be datasets archived in other related databases such as * BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc., or can be hosted in other * places such as the authors website, github etc. These datasets are * elaborated in detail in the IHM_DATASET_RELATED_DB_REFERENCE and/or * the IHM_DATASET_EXTERNAL_REFERENCE categories. This category * holds the list of all datasets used. */ ihm_dataset_list: { /** * A unique identifier for the dataset. */ id: Schema.Int; /** * The type of data held in the dataset. */ data_type: Schema.Aliased<"Other" | "NMR data" | "3DEM volume" | "2DEM class average" | "EM raw micrographs" | "X-ray diffraction data" | "SAS data" | "CX-MS data" | "Crosslinking-MS data" | "Mass Spectrometry data" | "EPR data" | "H/D exchange data" | "Single molecule FRET data" | "Ensemble FRET data" | "Experimental model" | "Comparative model" | "Integrative model" | "De Novo model" | "Predicted contacts" | "Mutagenesis data" | "DNA footprinting data" | "Hydroxyl radical footprinting data" | "Yeast two-hybrid screening data" | "Quantitative measurements of genetic interactions">; /** * A flag that indicates whether the dataset is archived in * an IHM related database or elsewhere. */ database_hosted: Schema.Aliased<"yes" | "no">; }; /** * Category to define groups or collections of input datasets. */ ihm_dataset_group: { /** * A unique identifier for the dataset group. */ id: Schema.Int; /** * A name for the dataset group. */ name: Schema.Str; /** * The application / utilization of the dataset group in modeling. */ application: Schema.Aliased<"filter" | "other" | "validation" | "restraint" | "representation" | "sampling" | "modeling">; /** * Additional details regarding the dataset group. */ details: Schema.Str; }; /** * IHM_DATASET_GROUP_LINK category provides the list of datasets present in * a particular group. */ ihm_dataset_group_link: { /** * An identifier for the dataset. * This data item is a pointer to _ihm_dataset_list.id in the * IHM_DATASET_LIST category. */ dataset_list_id: Schema.Int; /** * An identifier for the dataset group. * This data item is a pointer to _ihm_dataset_group.id in the * IHM_DATASET_GROUP category. */ group_id: Schema.Int; }; /** * Category holds information about related datasets, where one is derived from the other. */ ihm_related_datasets: { /** * 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: Schema.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: Schema.Int; }; /** * Category holds information related to data sources for the entry. * These can be datasets archived in other related databases such as * BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc. */ ihm_dataset_related_db_reference: { /** * A unique identifier for the related database entry. */ id: Schema.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: Schema.Int; /** * The name of the database containing the dataset entry. */ db_name: Schema.Aliased<"BMRB" | "EMDB" | "PDB" | "PDB-Dev" | "SASBDB" | "Other" | "EMPIAR" | "PRIDE" | "MODEL ARCHIVE" | "MASSIVE" | "BioGRID" | "ProXL" | "jPOSTrepo" | "iProX" | "AlphaFoldDB" | "ProteomeXchange" | "BMRbig">; /** * The accession code for the database entry. */ accession_code: Schema.Str; /** * Version of the database entry, if the database allows versioning. */ version: Schema.Str; /** * Details regarding the dataset entry. */ details: Schema.Str; }; /** * Category holds links to other external data sources for the I/H model entry. * Input datasets held in other databases such as EMDB, BMRB, SASBDB etc. * are referenced in the IHM_DATASET_RELATED_DB_REFERENCE category. * This data category, along with IHM_EXTERNAL_FILES category, holds information * regarding other non-database external data sources, such as DOIs (digital * object identifiers) or supplementary files stored locally. The DOIs can either * lead to the external data file(s) directly (as in case of DOIs provided by the PDB) * or might lead to an HTML landing page (as provided by Zenodo). In the latter case, * additional URL (Uniform Resource Locator) information is required to retrieve * the external data file(s). */ ihm_external_reference_info: { /** * A unique identifier for the external reference. */ reference_id: Schema.Int; /** * The name of the reference provider. */ reference_provider: Schema.Str; /** * The type of external reference. * Currently, only Digital Object Identifiers (DOIs) and supplementary files * stored locally are supported. */ reference_type: Schema.Aliased<"DOI" | "Supplementary Files">; /** * The external reference or the Digital Object Identifier (DOI). * This field is not relevant for local files. */ reference: Schema.Str; /** * The type of object that the external reference points to, usually * a single file or an archive. */ refers_to: Schema.Aliased<"Other" | "File" | "Archive" | "Publication">; /** * 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: Schema.Str; }; /** * Category provides details regarding external files. The IHM_EXTERNAL_REFERENCE_INFO * category captures the top-level details regarding external data sources. * This category captures the specific details regarding externally stored files * related to the particular I/H model entry. */ ihm_external_files: { /** * A unique identifier for each external file. */ id: Schema.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: Schema.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: Schema.Str; /** * The type of content in the file. */ content_type: Schema.Aliased<"Other" | "Input data or restraints" | "Modeling or post-processing output" | "Modeling workflow or script" | "Visualization script">; /** * Storage size of the external file in bytes. */ file_size_bytes: Schema.Float; /** * Additional textual details regarding the external file. */ details: Schema.Str; }; /** * Category provides additional details regarding input data hosted externally * at other resources. */ ihm_dataset_external_reference: { /** * A unique identifier for the external data. */ id: Schema.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: Schema.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: Schema.Int; }; /** * Data items in the IHM_LOCALIZATION_DENSITY_FILES category records the * details of files that provide information regarding localization densities * of ensembles. These may be stored externally as local files or linked via * DOI and can be in any accepted format that provides volume information * (CCP4, MRC, etc.). */ ihm_localization_density_files: { /** * A unique identifier. */ id: Schema.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: Schema.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: Schema.Int; /** * The entity identifier corresponding to this localization density. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * The identifier for the polymeric segment corresponding to this * localization density. * This data item is a pointer to _ihm_entity_poly_segment.id in the * IHM_ENTITY_POLY_SEGMENT category. */ entity_poly_segment_id: Schema.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: Schema.Str; }; /** * Data items in the IHM_PREDICTED_CONTACT_RESTRAINT category records the * list of predicted contacts used in the integrative modeling experiment. * This has been adapted from the widely used CASP RR format * (http://www.predictioncenter.org/casp8/index.cgi?page=format#RR). * These contacts may be derived from various computational tools. * The software information can be provided in the SOFTWARE category. */ ihm_predicted_contact_restraint: { /** * A unique identifier for the predicted contact restraint. */ id: Schema.Int; /** * An identifier to group the predicted contacts. */ group_id: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Int; /** * If _ihm_predicted_contact_restraint.model_granularity is by-residue, then indicate the atom * used to represent the first monomer partner in three-dimension. Default is the C-alpha atom. */ rep_atom_1: Schema.Aliased<"CA" | "CB">; /** * If _ihm_predicted_contact_restraint.model_granularity is by-residue, then indicate the atom * used to represent the second monomer partner in three-dimension. Default is the C-alpha atom. */ rep_atom_2: Schema.Aliased<"CA" | "CB">; /** * The lower limit to the distance threshold applied to this predicted contact restraint * in the integrative modeling task. */ distance_lower_limit: Schema.Float; /** * The upper limit to the distance threshold applied to this predicted contact restraint * in the integrative modeling task. */ distance_upper_limit: Schema.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: Schema.Float; /** * The type of distance restraint applied. */ restraint_type: Schema.Aliased<"lower bound" | "upper bound" | "lower and upper bound">; /** * The granularity of the predicted contact as applied to the multi-scale model. */ model_granularity: Schema.Aliased<"by-residue" | "by-feature">; /** * 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: Schema.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: Schema.Int; }; /** * Data items in the IHM_CROSS_LINK_LIST category records the * list of spatial restraints derived from chemical crosslinking * experiment. */ ihm_cross_link_list: { /** * A unique identifier for the cross link restraint. */ id: Schema.Int; /** * An identifier for a set of ambiguous crosslink restraints. * Handles experimental uncertainties in the identities of * crosslinked residues. */ group_id: Schema.Int; /** * A text description of molecular entity 1. */ entity_description_1: Schema.Str; /** * A text description of molecular entity 2. */ entity_description_2: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Int; /** * The type of crosslinker used. */ linker_type: Schema.Aliased<"Other" | "EDC" | "DSS" | "EGS" | "BS3" | "BS2G" | "DST" | "sulfo-SDA" | "sulfo-SMCC" | "DSSO" | "DSG" | "BSP" | "BMSO" | "DHSO" | "CYS" | "SDA" | "DSA" | "BrdU" | "LCSDA" | "CDI" | "ADH" | "L-Photo-Leucine" | "KArGO" | "BrEtY" | "DSBU" | "DSPP" | "TBDSPP" | "DMTMM" | "PDH">; /** * 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: Schema.Int; }; /** * Data items in the IHM_CROSS_LINK_RESTRAINT category enumerates the * implementation details of the chemical crosslinking restraints in * the integrative modeling. This category holds the details of how * the experimentally derived crosslinks are applied in the modeling. */ ihm_cross_link_restraint: { /** * A unique identifier for the cross link record. */ id: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Str; /** * The type of the cross link restraint applied. */ restraint_type: Schema.Aliased<"lower bound" | "upper bound" | "harmonic">; /** * The cross link conditionality. */ conditional_crosslink_flag: Schema.Aliased<"ALL" | "ANY">; /** * The coarse-graining information for the crosslink implementation. */ model_granularity: Schema.Aliased<"by-atom" | "by-residue" | "by-feature">; /** * The distance threshold applied to this crosslink in the integrative modeling task. */ distance_threshold: Schema.Float; /** * The uncertainty in the crosslinking experimental data; * may be approximated to the false positive rate. */ psi: Schema.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: Schema.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: Schema.Float; }; /** * Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the * results of the crosslinking restraint parameters in the IHM modeling. */ ihm_cross_link_result_parameters: { /** * A unique identifier for the restraint/model combination. */ id: Schema.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: Schema.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: Schema.Int; /** * The uncertainty in the crosslinking experimental data; * May be approximated to the false positive rate. */ psi: Schema.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: Schema.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: Schema.Float; }; /** * Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the * details of the 2DEM class averages used in the IHM modeling. */ ihm_2dem_class_average_restraint: { /** * A unique identifier for the 2dem class average. */ id: Schema.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: Schema.Int; /** * The number of raw micrographs used to obtain the class average. */ number_raw_micrographs: Schema.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: Schema.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: Schema.Float; /** * Resolution of the 2dem class average. */ image_resolution: Schema.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: Schema.Aliased<"yes" | "no">; /** * Number of 2D projections of the model used in the fitting. */ number_of_projections: Schema.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.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: Schema.Int; /** * Details of how the 2DEM restraint is applied in the modeling algorithm. */ details: Schema.Str; }; /** * Data items in the IHM_2DEM_CLASS_AVERAGE_FITTING category records the * details of the fitting of the model to the 2DEM class averages * used in the IHM modeling. The following conventions are recommended * while generating the rotation matrix and translation vector for * transformation. * * - The model is rotated and translated to fit to the 2DEM image. * - The 2DEM image should be in the XY plane. * - The lower left image corner (image pixel index 0,0) should be at x,y,z = (0,0,0). * - The 2D image is scaled by the _ihm_2dem_class_average_restraint.pixel_size_width * and _ihm_2dem_class_average_restraint.pixel_size_height from the * IHM_2DEM_CLASS_AVERAGE_RESTRAINT table. * - The transformation is applied after the scaling and hence the translation vector * should account for the scaling. * - There are no specifications for Z translations i.e., how far the image should be * from the model while projecting. It may be set to zero. */ ihm_2dem_class_average_fitting: { /** * A unique identifier for the 2dem class average fitting data. */ id: Schema.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: Schema.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: Schema.Int; /** * The cross correlation coefficient corresponding to the model to image fitting. */ cross_correlation_coefficient: Schema.Float; /** * Data item of the rotation matrix used in the fitting of the model to the image. */ rot_matrix: Schema.Tensor; /** * Data item of the tranlation vector used in the fitting of the model to the image. */ tr_vector: Schema.Tensor; }; /** * Data items in the IHM_3DEM_RESTRAINT category records the * details of the 3DEM maps used as restraints in the * IHM modeling. */ ihm_3dem_restraint: { /** * A unique identifier for the 3DEM restraint description. */ id: Schema.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: Schema.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: Schema.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.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: Schema.Int; /** * Method used to fit the model to the 3DEM map. */ fitting_method: Schema.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: Schema.Int; /** * The cross correlation coefficient corresponding to the model to map fitting. */ cross_correlation_coefficient: Schema.Float; }; /** * Data items in the IHM_SAS_RESTRAINT category records the * details of the SAS data used as restraints in the * IHM modeling. */ ihm_sas_restraint: { /** * A unique identifier for the SAS restraint description. */ id: Schema.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: Schema.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: Schema.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.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: Schema.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: Schema.Aliased<"yes" | "no">; /** * The type of atoms in the model fit to the SAS data. */ fitting_atom_type: Schema.Str; /** * The method used for fitting the model to the SAS data. */ fitting_method: Schema.Str; /** * An indicator to single or multiple state fitting. */ fitting_state: Schema.Aliased<"Single" | "Multiple">; /** * Radius of gyration obtained from the SAS profile, if used as input restraint. */ radius_of_gyration: Schema.Float; /** * The chi value resulting from fitting the model to the SAS data. */ chi_value: Schema.Float; /** * Additional details regarding the SAS restraint used. */ details: Schema.Str; }; /** * Data items in the IHM_STARTING_MODEL_COORD category records the coordinates * for structural templates used as starting inputs in the integrative model * building tasks. */ ihm_starting_model_coord: { /** * A unique identifier for this coordinate position. */ ordinal_id: Schema.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: Schema.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: Schema.Aliased<"ATOM" | "HETATM">; /** * The serial number for this coordinate position. */ id: Schema.Int; /** * The atom type symbol(element symbol) corresponding to this coordinate position. */ type_symbol: Schema.Str; /** * The entity identifier corresponding to this coordinate position. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.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: Schema.Str; /** * The component identifier corresponding to this coordinate position. * This data item is a pointer to _chem_comp.id in the * CHEM_COMP category. */ comp_id: Schema.Str; /** * The sequence index corresponding this to coordinate position. * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. */ seq_id: Schema.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: Schema.Str; /** * The Cartesian X component corresponding to this coordinate position. */ Cartn_x: Schema.Float; /** * The Cartesian Y component corresponding to this coordinate position. */ Cartn_y: Schema.Float; /** * The Cartesian Z component corresponding to this coordinate position. */ Cartn_z: Schema.Float; /** * The isotropic temperature factor corresponding to this coordinate position. */ B_iso_or_equiv: Schema.Float; }; /** * Data items in the IHM_SPHERE_OBJ_SITE category records the details * of the spherical objects modeled in the integrative structural model. */ ihm_sphere_obj_site: { /** * A unique identifier for this pseudo atom / sphere object. */ id: Schema.Int; /** * The entity identifier corresponding to this sphere object. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.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_SEQ category. */ seq_id_begin: Schema.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_SEQ category. */ seq_id_end: Schema.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: Schema.Str; /** * The Cartesian X component corresponding to this sphere object. */ Cartn_x: Schema.Float; /** * The Cartesian Y component corresponding to this sphere object. */ Cartn_y: Schema.Float; /** * The Cartesian Z component corresponding to this sphere object. */ Cartn_z: Schema.Float; /** * The radius associated with the primitive sphere object at this position. */ object_radius: Schema.Float; /** * The Root Mean Square Fluctuation (RMSF) observed in the primitive * sphere object at this position. */ rmsf: Schema.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: Schema.Int; }; /** * Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details * of the gaussian objects modeled in the integrative structural model. */ ihm_gaussian_obj_site: { /** * A unique identifier for this gaussian object in the model. */ id: Schema.Int; /** * The entity identifier corresponding to this gaussian object. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.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_SEQ category. */ seq_id_begin: Schema.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_SEQ category. */ seq_id_end: Schema.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: Schema.Str; /** * The mean Cartesian X component corresponding to this gaussian object. */ mean_Cartn_x: Schema.Float; /** * The mean Cartesian Y component corresponding to this gaussian object. */ mean_Cartn_y: Schema.Float; /** * The mean Cartesian Z component corresponding to this gaussian object. */ mean_Cartn_z: Schema.Float; /** * The weight of the gaussian object. */ weight: Schema.Float; /** * Data item of the covariance matrix representing the Gaussian object. */ covariance_matrix: Schema.Tensor; /** * 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: Schema.Int; }; /** * Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details * of the gaussian objects representing an ensemble or cluster of models. */ ihm_gaussian_obj_ensemble: { /** * A unique identifier for this gaussian object. */ id: Schema.Int; /** * The entity identifier corresponding to this gaussian object. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.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_SEQ category. */ seq_id_begin: Schema.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_SEQ category. */ seq_id_end: Schema.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: Schema.Str; /** * The mean Cartesian X component corresponding to this gaussian object. */ mean_Cartn_x: Schema.Float; /** * The mean Cartesian Y component corresponding to this gaussian object. */ mean_Cartn_y: Schema.Float; /** * The mean Cartesian Z component corresponding to this gaussian object. */ mean_Cartn_z: Schema.Float; /** * The weight of the gaussian object. */ weight: Schema.Float; /** * Data item of the covariance matrix representing the Gaussian object. */ covariance_matrix: Schema.Tensor; /** * 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: Schema.Int; }; /** * IHM_FEATURE_LIST is the high level category that provides defintions * to select atoms/residues from polymeric and non-polymeric entities. */ ihm_feature_list: { /** * A unique identifier for the feature. */ feature_id: Schema.Int; /** * The type of feature. */ feature_type: Schema.Aliased<"atom" | "residue" | "residue range" | "ligand" | "pseudo site">; /** * The type of entity. */ entity_type: Schema.Aliased<"other" | "non-polymer" | "polymer" | "water">; }; /** * Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions * required to select a specific residue or a set of residues that may or may not be * in a contiguous range. */ ihm_poly_residue_feature: { /** * A unique identifier for the category. */ ordinal_id: Schema.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: Schema.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: Schema.Str; /** * An asym/strand identifier for the residue / residue range, if applicable. * This data item is a pointer to _struct_asym.id in the * STRUCT_ASYM category. */ asym_id: Schema.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: Schema.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: Schema.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: Schema.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: Schema.Int; }; /** * Data items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the * list of distance restraints used in the integrative modeling experiment. * These distance redistance restraints may be derived from various kinds of experiments. */ ihm_derived_distance_restraint: { /** * A unique identifier for the derived distance restraint. */ id: Schema.Int; /** * An identifier to group the distance restraints. * This can be the same as the _ihm_derived_distance_restraint.id in case * the some of the restraints are not grouped. */ group_id: Schema.Int; /** * The feature identifier for the first partner in the distance restraint. * This data item is a pointer to _ihm_feature_list.feature_id in the * IHM_FEATURE_LIST category. */ feature_id_1: Schema.Int; /** * The feature identifier for the second partner in the distance restraint. * This data item is a pointer to _ihm_feature_list.feature_id in the * IHM_FEATURE_LIST category. */ feature_id_2: Schema.Int; /** * If a group of atoms or residues are restrained, this data item defines * the conditionality based on which the restraint is applied in the modeling. */ group_conditionality: Schema.Aliased<"ALL" | "ANY">; /** * The fraction of randomly excluded distance restraints during modeling. * In HADDOCK, this is used along with ambiguous interface restraints (AIRs) * to account for uncertainties in AIRs. */ random_exclusion_fraction: Schema.Float; /** * The upper limit to the distance threshold applied to this distance restraint * in the integrative modeling task. */ distance_upper_limit: Schema.Float; /** * The type of distance restraint applied. */ restraint_type: Schema.Aliased<"lower bound" | "upper bound" | "lower and upper bound" | "harmonic">; /** * Identifier to the input data from which the distance restraint is derived. * This data item is a pointer to the _ihm_dataset_list.id in the * IHM_DATASET_LIST category. * This data item may not be applicable for all cases. For example, in case of * ambiguous interface restraints where the interface residues are identified * from multiple experiments, the reference to the _ihm_dataset_list.id is * handled in the IHM_INTERFACE_RESIDUE_FEATURE category rather than here. */ dataset_list_id: Schema.Int; }; /** * Data items in the MA_MODEL_LIST category record the * details of the models being deposited. */ ma_model_list: { /** * A unique identifier for the structural model being deposited. */ ordinal_id: Schema.Int; /** * A unique identifier for the structural model being deposited. * This data item was practically a duplicate of _ma_model_list.ordinal_id * and has been deprecated with dictionary version 1.4.7. */ model_id: Schema.Int; /** * An identifier to group structural models into collections or sets. * This data item has been deprecated with dictionary version 1.4.7. * See ma_model_group category. */ model_group_id: Schema.Int; /** * A decsriptive name for the model. */ model_name: Schema.Str; /** * A decsriptive name for the model group. * This data item has been deprecated with dictionary version 1.4.7. * See ma_model_group category. */ model_group_name: Schema.Str; /** * The type of model. */ model_type: Schema.Aliased<"Other" | "Homology model" | "Ab initio model">; /** * The data_id identifier. This data item is a pointer to * _ma_data.id in the MA_DATA category. */ data_id: Schema.Int; }; /** * Data items in the MA_TARGET_ENTITY category record details about * the target entities. The details are provided for each entity * being modeled. */ ma_target_entity: { /** * A unique identifier for the distinct molecular entity of the target. * This data item is a pointer to _entity.id in the ENTITY category. */ entity_id: Schema.Str; /** * The data_id identifier. This data item is a pointer to * _ma_data.id in the MA_DATA category. */ data_id: Schema.Int; /** * The origin of the target entity. */ origin: Schema.Aliased<"reference database" | "designed">; }; /** * Data items in the MA_TARGET_ENTITY_INSTANCE category record details about * the instances of target entities modeled. */ ma_target_entity_instance: { /** * A unique identifier for the instance of the entity. */ asym_id: Schema.Str; /** * A unique identifier for the distinct molecular entity of the target. * This data item is a pointer to _ma_target_entity.entity_id in the * MA_TARGET_ENTITY category. */ entity_id: Schema.Str; /** * Additional details about the entity instance. */ details: Schema.Str; }; /** * Data items in the MA_TARGET_REF_DB_DETAILS category record details about * the reference databases for the target sequences. */ ma_target_ref_db_details: { /** * An identifier for the target entity. */ target_entity_id: Schema.Str; /** * The name of the database containing reference information about * this entity or biological unit. */ db_name: Schema.Aliased<"GB" | "Other" | "UNP" | "OrthoDB" | "NCBI" | "JGI" | "Phytozyme">; /** * The code for this entity or biological unit or for a closely * related entity or biological unit in the named database. * This can include the version number. */ db_code: Schema.Str; /** * Accession code assigned by the reference database. */ db_accession: Schema.Str; /** * Database code assigned by the reference database for a sequence isoform. An isoform sequence is an * alternative protein sequence that can be generated from the same gene by a single or by a combination of * biological events such as: alternative promoter usage, alternative splicing, alternative initiation * and ribosomal frameshifting. */ seq_db_isoform: Schema.Str; /** * Beginning index in the chemical sequence from the * reference database. */ seq_db_align_begin: Schema.Str; /** * Ending index in the chemical sequence from the * reference database. */ seq_db_align_end: Schema.Str; /** * Taxonomy identifier provided by NCBI. */ ncbi_taxonomy_id: Schema.Str; /** * Scientific name of the organism. */ organism_scientific: Schema.Str; }; /** * Data items in the MA_DATA category capture the different kinds of * data used in the modeling. These can be multiple sequence * alignments, spatial restraints, template structures etc. */ ma_data: { /** * A unique identifier for the data. */ id: Schema.Int; /** * The type of data held in the dataset. */ content_type: Schema.Aliased<"target" | "other" | "reference database" | "template structure" | "polymeric template library" | "spatial restraints" | "target-template alignment" | "coevolution MSA" | "model coordinates" | "input structure" | "intermediate backbone" | "intermediate sequence" | "model quality assessment scores" | "energy estimate" | "experimental validation">; /** * Details for other content types. */ content_type_other_details: Schema.Str; /** * An author-given name for the content held in the dataset. */ name: Schema.Str; }; /** * Data items in the MA_SOFTWARE_GROUP category describes the * collection of software into groups so that they can be used * efficiently in the MA_PROTOCOL_STEP category. */ ma_software_group: { /** * A unique identifier for the category. */ ordinal_id: Schema.Int; /** * An identifier for the group entry. * If data does not need to be grouped, then _ma_software_group.group_id * is the same as _ma_software_group.software_id. */ group_id: Schema.Int; /** * The identifier for the software. * This data item is a pointer to _software.pdbx_ordinal * in the SOFTWARE category. */ software_id: Schema.Int; }; /** * Data items in the MA_QA_METRIC category record the * details of the metrics use to assess model quality. */ ma_qa_metric: { /** * An identifier for the QA metric. */ id: Schema.Int; /** * Name of the QA metric. */ name: Schema.Str; /** * The type of QA metric. */ type: Schema.Aliased<"boolean" | "other" | "zscore" | "energy" | "distance" | "normalized score" | "pLDDT" | "pLDDT in [0,1]" | "pLDDT all-atom" | "pLDDT all-atom in [0,1]" | "pLDDT to polymer" | "PAE" | "pTM" | "ipTM" | "contact probability">; /** * The mode of calculation of the QA metric. */ mode: Schema.Aliased<"local" | "global" | "local-pairwise" | "per-feature" | "per-feature-pair" | "dihedral">; /** * Identifier to the set of software used to calculate the QA metric. * This data item is a pointer to the _ma_software_group.group_id in the * MA_SOFTWARE_GROUP category. */ software_group_id: Schema.Int; }; /** * Data items in the MA_QA_METRIC_GLOBAL category captures the * details of the global QA metrics, calculated at the model-level. */ ma_qa_metric_global: { /** * A unique identifier for the category. */ ordinal_id: Schema.Int; /** * The identifier for the structural model, for which global QA metric is provided. * This data item is a pointer to _ma_model_list.ordinal_id * in the MA_MODEL_LIST category. */ model_id: Schema.Int; /** * The identifier for the QA metric. * This data item is a pointer to _ma_qa_metric.id in the * MA_QA_METRIC category. */ metric_id: Schema.Int; /** * The value of the global QA metric. */ metric_value: Schema.Float; }; /** * Data items in the MA_QA_METRIC_LOCAL category captures the * details of the local QA metrics, calculated at the residue-level. * Data in this category can be extracted into a separate file which * is linked to the main file using the categories * ma_associated_archive_file_details or ma_entry_associated_files * with file_content set to "QA metrics". */ ma_qa_metric_local: { /** * A unique identifier for the category. */ ordinal_id: Schema.Int; /** * The identifier for the structural model, for which local QA metric is provided. * This data item is a pointer to _ma_model_list.ordinal_id * in the MA_MODEL_LIST category. */ model_id: Schema.Int; /** * The identifier for the asym id of the residue in the * structural model, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_asym_id * in the ATOM_SITE category. */ label_asym_id: Schema.Str; /** * The identifier for the sequence index of the residue * in the structural model, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_seq_id * in the ATOM_SITE category. */ label_seq_id: Schema.Int; /** * The component identifier for the residue in the * structural model, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_comp_id * in the ATOM_SITE category. */ label_comp_id: Schema.Str; /** * The identifier for the QA metric. * This data item is a pointer to _ma_qa_metric.id in the * MA_QA_METRIC category. */ metric_id: Schema.Int; /** * The value of the local QA metric. */ metric_value: Schema.Float; }; /** * Data items in the MA_QA_METRIC_LOCAL_PAIRWISE category captures the * details of the local QA metrics, calculated at the pairwise residue level. * In cases where the metric is symmetric, it is enough to store just one value per pair. * For asymmetric metrics, the order of residues is expected to be meaningful * (e.g. PAE where PAE_ij is defined by aligning residue i (label_*_1) and measuring * the error on residue j (label_*_2)). * In all cases, it is perfectly valid to only provide values for a subset of residue pairs. * Data in this category is expected to be very large and can be extracted into a * separate file which is linked to the main file using the categories * ma_associated_archive_file_details or ma_entry_associated_files with file_content * set to "QA metrics". */ ma_qa_metric_local_pairwise: { /** * A unique identifier for the category. */ ordinal_id: Schema.Int; /** * The identifier for the structural model, for which local QA metric is provided. * This data item is a pointer to _ma_model_list.ordinal_id * in the MA_MODEL_LIST category. */ model_id: Schema.Int; /** * The identifier for the asym id of the first residue in the * pair, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_asym_id * in the ATOM_SITE category. */ label_asym_id_1: Schema.Str; /** * The identifier for the sequence index of the first residue * in the pair, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_seq_id * in the ATOM_SITE category. */ label_seq_id_1: Schema.Int; /** * The component identifier for the first residue in the * pair, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_comp_id * in the ATOM_SITE category. */ label_comp_id_1: Schema.Str; /** * The identifier for the asym id of the second residue in the * pair, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_asym_id * in the ATOM_SITE category. */ label_asym_id_2: Schema.Str; /** * The identifier for the sequence index of the second residue * in the pair, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_seq_id * in the ATOM_SITE category. */ label_seq_id_2: Schema.Int; /** * The component identifier for the second residue in the * pair, for which local QA metric is provided. * This data item is a pointer to _atom_site.label_comp_id * in the ATOM_SITE category. */ label_comp_id_2: Schema.Str; /** * The identifier for the QA metric. * This data item is a pointer to _ma_qa_metric.id in the * MA_QA_METRIC category. */ metric_id: Schema.Int; /** * The value of the local QA metric. */ metric_value: Schema.Float; }; }; export type mmCIF_Schema = typeof mmCIF_Schema; export interface mmCIF_Database extends Database { }