molstar
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A comprehensive macromolecular library.
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JavaScript
"use strict";
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
*
* @author molstar/ciftools package
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.mmCIF_Schema = void 0;
var db_1 = require("../../../../mol-data/db");
var Schema = db_1.Column.Schema;
var str = Schema.str;
var int = Schema.int;
var float = Schema.float;
var coord = Schema.coord;
var Aliased = Schema.Aliased;
var Matrix = Schema.Matrix;
var Vector = Schema.Vector;
var List = Schema.List;
exports.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: 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: 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: 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: 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: 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: coord,
/**
* 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: coord,
/**
* 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: coord,
/**
* 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: Aliased(str),
/**
* 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: 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: 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: 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: 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: str,
/**
* This data item is a pointer to _entity.id in the ENTITY category.
*/
label_entity_id: str,
/**
* This data item is a pointer to _entity_poly_seq.num in the
* ENTITY_POLY_SEQ category.
*/
label_seq_id: 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: float,
/**
* This data item is a pointer to _atom_type.symbol in the
* ATOM_TYPE category.
*/
type_symbol: str,
/**
* PDB insertion code.
*/
pdbx_PDB_ins_code: str,
/**
* PDB model number.
*/
pdbx_PDB_model_num: int,
/**
* The net integer charge assigned to this atom. This is the
* formal charge assignment normally found in chemical diagrams.
*/
pdbx_formal_charge: int,
/**
* 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: 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: int,
/**
* This data item is a pointer to _atom_type.symbol in the
* ATOM_TYPE category.
*/
type_symbol: 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: Matrix(3, 3),
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site_anisotrop.U.
*/
U_esd: Matrix(3, 3),
/**
* Pointer to _atom_site.auth_seq_id
*/
pdbx_auth_seq_id: str,
/**
* Pointer to _atom_site.auth_asym_id
*/
pdbx_auth_asym_id: str,
/**
* Pointer to _atom_site.auth_atom_id
*/
pdbx_auth_atom_id: str,
/**
* Pointer to _atom_site.auth_comp_id
*/
pdbx_auth_comp_id: str,
/**
* Pointer to _atom_site.label_seq_id
*/
pdbx_label_seq_id: int,
/**
* Pointer to _atom_site.label_alt_id.
*/
pdbx_label_alt_id: str,
/**
* Pointer to _atom_site.label_asym_id
*/
pdbx_label_asym_id: str,
/**
* Pointer to _atom_site.label_atom_id
*/
pdbx_label_atom_id: str,
/**
* Pointer to _atom_site.label_comp_id
*/
pdbx_label_comp_id: str,
/**
* Pointer to _atom_site.pdbx_PDB_ins_code
*/
pdbx_PDB_ins_code: 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: 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: Matrix(3, 3),
/**
* 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: Vector(3),
},
/**
* 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: str,
/**
* This data item defines the order of the author's name in the
* list of audit authors.
*/
pdbx_ordinal: int,
/**
* The Open Researcher and Contributor ID (ORCID).
*/
identifier_ORCID: 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: str,
/**
* The string identifying the highest-level dictionary defining
* data names used in this file.
*/
dict_name: str,
/**
* The version number of the dictionary to which the current
* data block conforms.
*/
dict_version: 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: float,
/**
* Unit-cell angle beta of the reported structure in degrees.
*/
angle_beta: float,
/**
* Unit-cell angle gamma of the reported structure in degrees.
*/
angle_gamma: float,
/**
* This data item is a pointer to _entry.id in the ENTRY category.
*/
entry_id: str,
/**
* Unit-cell length a corresponding to the structure reported in
* angstroms.
*/
length_a: float,
/**
* Unit-cell length b corresponding to the structure reported in
* angstroms.
*/
length_b: float,
/**
* Unit-cell length c corresponding to the structure reported in
* angstroms.
*/
length_c: 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: 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: 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: str,
/**
* Formula mass in daltons of the chemical component.
*/
formula_weight: 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: 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: Aliased(str),
/**
* The full name of the component.
*/
name: 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: Aliased(str),
/**
* Synonym list for the component.
*/
pdbx_synonyms: List(';', function (x) { return x; }),
},
/**
* 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: 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: str,
/**
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
* category.
*/
comp_id: 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: Aliased(str),
/**
* Ordinal index for the component bond list.
*/
pdbx_ordinal: int,
/**
* Stereochemical configuration across a double bond.
*/
pdbx_stereo_config: Aliased(str),
/**
* A flag indicating an aromatic bond.
*/
pdbx_aromatic_flag: Aliased(str),
},
/**
* 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: str,
/**
* The country/region of publication; relevant for books
* and book chapters.
*/
country: 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: str,
/**
* Abbreviated name of the cited journal as given in the
* Chemical Abstracts Service Source Index.
*/
journal_abbrev: 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: 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: str,
/**
* The International Standard Serial Number (ISSN) code assigned to
* the journal cited; relevant for journal articles.
*/
journal_id_ISSN: str,
/**
* Volume number of the journal cited; relevant for journal
* articles.
*/
journal_volume: str,
/**
* The first page of the citation; relevant for journal
* articles, books and book chapters.
*/
page_first: str,
/**
* The last page of the citation; relevant for journal
* articles, books and book chapters.
*/
page_last: str,
/**
* The title of the citation; relevant for journal articles, books
* and book chapters.
*/
title: str,
/**
* The year of the citation; relevant for journal articles, books
* and book chapters.
*/
year: int,
/**
* Document Object Identifier used by doi.org to uniquely
* specify bibliographic entry.
*/
pdbx_database_id_DOI: str,
/**
* Ascession number used by PubMed to categorize a specific
* bibliographic entry.
*/
pdbx_database_id_PubMed: 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: 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: str,
/**
* This data item defines the order of the author's name in the
* list of authors of a citation.
*/
ordinal: 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: Aliased(str),
/**
* The code assigned by the database identified in
* _database_2.database_id.
*/
database_code: 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: str,
/**
* Formula mass in daltons of the entity.
*/
formula_weight: 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: 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: Aliased(str),
/**
* Defines the type of the entity.
*
* Polymer entities are expected to have corresponding
* ENTITY_POLY and associated entries.
*
* Non-polymer entities are expected to have corresponding
* CHEM_COMP and associated entries.
*
* Water entities are not expected to have corresponding
* entries in the ENTITY category.
*/
type: Aliased(str),
/**
* A description of the entity.
*
* Corresponds to the compound name in the PDB format.
*/
pdbx_description: List(',', function (x) { return x; }),
/**
* A place holder for the number of molecules of the entity in
* the entry.
*/
pdbx_number_of_molecules: int,
/**
* Details about any entity mutation(s).
*/
pdbx_mutation: str,
/**
* Entity fragment description(s).
*/
pdbx_fragment: str,
/**
* Enzyme Commission (EC) number(s)
*/
pdbx_ec: List(',', function (x) { return x; }),
},
/**
* 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: str,
/**
* A flag to indicate whether the polymer contains at least
* one monomer-to-monomer link different from that implied by
* _entity_poly.type.
*/
nstd_linkage: Aliased(str),
/**
* A flag to indicate whether the polymer contains at least
* one monomer that is not considered standard.
*/
nstd_monomer: Aliased(str),
/**
* The type of the polymer.
*/
type: Aliased(str),
/**
* The PDB strand/chain id(s) corresponding to this polymer entity.
*/
pdbx_strand_id: List(',', function (x) { return x; }),
/**
* 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
* (PTO) 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: 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.
*/
pdbx_seq_one_letter_code_can: str,
/**
* For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
*/
pdbx_target_identifier: str,
},
/**
* 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_poly.entity_id in the
* ENTITY_POLY category.
*/
entity_id: str,
/**
* A flag to indicate whether this monomer in the polymer is
* heterogeneous in sequence.
*/
hetero: Aliased(str),
/**
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
* category.
*/
mon_id: str,
/**
* The value of _entity_poly_seq.num must uniquely and sequentially
* identify a record in the ENTITY_POLY_SEQ list.
*
* Note that this item must be a number and that the sequence
* numbers must progress in increasing numerical order.
*/
num: int,
},
/**
* 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: 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: str,
/**
* The method used in the experiment.
*/
method: Aliased(str),
},
/**
* 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: str,
/**
* A title for the data block. The author should attempt to convey
* the essence of the structure archived in the CIF in the title,
* and to distinguish this structural result from others.
*/
title: str,
/**
* An automatically generated descriptor for an NDB structure or
* the unstructured content of the PDB COMPND record.
*/
pdbx_descriptor: 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: str,
/**
* This data item is a pointer to _entity.id in the ENTITY category.
*/
entity_id: str,
/**
* The value of _struct_asym.id must uniquely identify a record in
* the STRUCT_ASYM list.
*
* Note that this item need not be a number; it can be any unique
* identifier.
*/
id: str,
/**
* This data item indicates whether the structural elements are modified.
*/
pdbx_modified: str,
/**
* A flag indicating that this entity was originally labeled
* with a blank PDB chain id.
*/
pdbx_blank_PDB_chainid_flag: Aliased(str),
},
/**
* 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: str,
/**
* A component of the identifier for the residue at which the
* conformation segment begins.
*
* This data item is a pointer to _atom_site.label_comp_id in
* the ATOM_SITE category.
*/
beg_label_comp_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment begins.
*
* This data item is a pointer to _atom_site.label_seq_id in the
* ATOM_SITE category.
*/
beg_label_seq_id: int,
/**
* A component of the identifier for the residue at which the
* conformation segment begins.
*
* This data item is a pointer to _atom_site.auth_asym_id in the
* ATOM_SITE category.
*/
beg_auth_asym_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment begins.
*
* This data item is a pointer to _atom_site.auth_comp_id in
* the ATOM_SITE category.
*/
beg_auth_comp_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment begins.
*
* This data item is a pointer to _atom_site.auth_seq_id in the
* ATOM_SITE category.
*/
beg_auth_seq_id: int,
/**
* This data item is a pointer to _struct_conf_type.id in the
* STRUCT_CONF_TYPE category.
*/
conf_type_id: Aliased(str),
/**
* A description of special aspects of the conformation assignment.
*/
details: str,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*
* This data item is a pointer to _atom_site.label_asym_id in the
* ATOM_SITE category.
*/
end_label_asym_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*
* This data item is a pointer to _atom_site.label_comp_id in the
* ATOM_SITE category.
*/
end_label_comp_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*
* This data item is a pointer to _atom_site.label_seq_id in the
* ATOM_SITE category.
*/
end_label_seq_id: int,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*
* This data item is a pointer to _atom_site.auth_asym_id in the
* ATOM_SITE category.
*/
end_auth_asym_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*
* This data item is a pointer to _atom_site.auth_comp_id in the
* ATOM_SITE category.
*/
end_auth_comp_id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*
* This data item is a pointer to _atom_site.auth_seq_id in the
* ATOM_SITE category.
*/
end_auth_seq_id: int,
/**
* The value of _struct_conf.id must uniquely identify a record in
* the STRUCT_CONF list.
*
* Note that this item need not be a number; it can be any unique
* identifier.
*/
id: str,
/**
* A component of the identifier for the residue at which the
* conformation segment starts.
*/
pdbx_beg_PDB_ins_code: str,
/**
* A component of the identifier for the residue at which the
* conformation segment ends.
*/
pdbx_end_PDB_ins_code: str,
/**
* This item is a place holder for the helix class used in the PDB
* HELIX record.
*/
pdbx_PDB_helix_class: str,
/**
* A placeholder for the lengths of the helix of the PDB
* HELIX record.
*/
pdbx_PDB_helix_length: int,
/**
* A placeholder for the helix identifier of the PDB
* HELIX record.
*/
pdbx_PDB_helix_id: str,
},
/**
* 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: Aliased(str),
/**
* A description of special aspects of the connection.
*/
details: str,
/**
* The value of _struct_conn.id must uniquely identify a record in
* the STRUCT_CONN list.
*
* Note that this item need not be a number; it can be any unique
* identifier.
*/
id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.label_asym_id in the
* ATOM_SITE category.
*/
ptnr1_label_asym_id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _chem_comp_atom.atom_id in the
* CHEM_COMP_ATOM category.
*/
ptnr1_label_atom_id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.label_comp_id in the
* ATOM_SITE category.
*/
ptnr1_label_comp_id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.label_seq_id in the
* ATOM_SITE category.
*/
ptnr1_label_seq_id: int,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.auth_asym_id in the
* ATOM_SITE category.
*/
ptnr1_auth_asym_id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.auth_comp_id in the
* ATOM_SITE category.
*/
ptnr1_auth_comp_id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.auth_seq_id in the
* ATOM_SITE category.
*/
ptnr1_auth_seq_id: int,
/**
* Describes the symmetry operation that should be applied to the
* atom set specified by _struct_conn.ptnr1_label* to generate the
* first partner in the structure connection.
*/
ptnr1_symmetry: str,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _atom_site.label_asym_id in the
* ATOM_SITE category.
*/
ptnr2_label_asym_id: str,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _chem_comp_atom.atom_id in the
* CHEM_COMP_ATOM category.
*/
ptnr2_label_atom_id: str,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _atom_site.label_comp_id in the
* ATOM_SITE category.
*/
ptnr2_label_comp_id: str,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _atom_site.label_seq_id in the
* ATOM_SITE category.
*/
ptnr2_label_seq_id: int,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _atom_site.auth_asym_id in the
* ATOM_SITE category.
*/
ptnr2_auth_asym_id: str,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _atom_site.auth_comp_id in the
* ATOM_SITE category.
*/
ptnr2_auth_comp_id: str,
/**
* A component of the identifier for partner 2 of the structure
* connection.
*
* This data item is a pointer to _atom_site.auth_seq_id in the
* ATOM_SITE category.
*/
ptnr2_auth_seq_id: int,
/**
* Describes the symmetry operation that should be applied to the
* atom set specified by _struct_conn.ptnr2_label* to generate the
* second partner in the structure connection.
*/
ptnr2_symmetry: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
* ATOM_SITE category.
*/
pdbx_ptnr1_PDB_ins_code: str,
/**
* A component of the identifier for partner 1 of the
* structure connection. This data item is a pointer to
* _atom_site.label_alt_id in the ATOM_SITE category.
*/
pdbx_ptnr1_label_alt_id: str,
/**
* A placeholder for the standard residue name found in
* the MODRES record of a PDB file.
*/
pdbx_ptnr1_standard_comp_id: str,
/**
* A component of the identifier for partner 1 of the structure
* connection.
*
* This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
* ATOM_SITE category.
*/
pdbx_ptnr2_PDB_ins_code: str,
/**
* A component of the identifier for partner 2 of the
* structure connection. This data item is a pointer to
* _atom_site.label_alt_id in the ATOM_SITE category.
*/
pdbx_ptnr2_label_alt_id: str,
/**
* A component of the identifier for partner 3 of the
* structure connection. This data item is a pointer to
* _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
*/
pdbx_ptnr3_PDB_ins_code: str,
/**
* A component of the identifier for partner 3 of the
* structure connection. This data item is a pointer to
* _atom_site.label_alt_id in the ATOM_SITE category.
*/
pdbx_ptnr3_label_alt_id: str,
/**
* A component of the identifier for partner 3 of the
* structure connection. This data item is a pointer to
* _atom_site.labe