Anything with a dispose method, used to despose of data assets or webgl resources
assignable ArrayLike version
Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
Index of a chain in the model data
RGB color triplet expressed as a single number
Index of an element in the model data
Index of an entity in the model data
Exclude from T those types that are assignable to U
Extract from T those types that are assignable to U
A File or Blob object or a URL string
Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
Maps groups to data, range for group i is offsets[i] to offsets[i + 1]
Labels from providers with higher priority are shown first
Exclude null and undefined from T
Construct a type with the properties of T except for those in type K.
Make all properties in T optional
From T, pick a set of properties whose keys are in the union K
Make all properties in T readonly
Construct a type with a set of properties K of type T
Make all properties in T required
Index of a residue in the model data
Obtain the return type of a function type
Pairs of min and max indices of sorted, non-overlapping ranges
Internal structure state
A group of units that differ only by symmetry operators.
Hash based on unit.invariantId which is the same for all units in the group
Hash based on all unit.id values in the group, reflecting the units transformation
Maps unit.id to index of unit in units array
A collection of columns
Extend selection to whole chain, by default only the first residue is selected. This is used by the oligoInteraction preset in rcsb-sierra, which should focus the whole oligo chain. Not wanted for the ligandInteraction preset, which would otherwise focus alternative conformations and symmetry mates.
Mol*-internal UUID of a model.
Mol*-internal representation, like 'ASM_2'. Enumerated in the order of appearance in the source file. If possible, specify the assemblyId when using this selector.
Strucmotif-/BioJava-specific representation, like 'Px42'. This is a single 'pdbx_struct_oper_list.id' value or a combination thereof. Specify the assemblyId when using this selector. Order matters, use order as specified in the source CIF file.
Numbers are shortcuts for color attachment
final per-instance transform calculated for instance i as
aTransform[i] = matrix * transform[i] * extraTransform[i]
additional per-instance transform, see aTransform
global transform, see aTransform
base per-instance transform, see aTransform
A UUID, either standard 36 characters or 22 characters base64 encoded.
A building block of a structure that corresponds to an atomic or a coarse grained representation 'conveniently grouped together'.
Index into Unit.elements
Lookup for triplets of atoms in delocalized bonds.
Does not include triplets that are part of aromatic rings.
Return index into triplets or undefined if a is not part of any triplet
An immutable value box that also holds a version of the attribute. Optionally includes automatically propadated "metadata".
Unique identifier in the range 0 to 0x7FFFFFFF
An immutable box stored inside a mutable cell.
This is required for params with optional values
set both the RGB blend equation and alpha blend equation to a single equation, determines how a new pixel is combined with an existing
set the RGB blend equation and alpha blend equation separately, determines how a new pixel is combined with an existing
defines which function is used for blending pixel arithmetic
defines which function is used for blending pixel arithmetic for RGB and alpha components separately
specifies the color values used when clearing color buffers, used when calling gl.clear, clamped to [0, 1]
sets which color components to enable or to disable
specifies whether or not front- and/or back-facing polygons can be culled
sets whether writing into the depth buffer is enabled or disabled
specifies which WebGL capability to disable
gl.BLEND: blending of the computed fragment color valuesgl.CULL_FACE: culling of polygonsgl.DEPTH_TEST: depth comparisons and updates to the depth buffergl.DITHER: dithering of color components before they get written to the color buffergl.POLYGON_OFFSET_FILL: adding an offset to depth values of polygon's fragmentsgl.SAMPLE_ALPHA_TO_COVERAGE: computation of a temporary coverage value determined by the alpha valuegl.SAMPLE_COVERAGE: ANDing the fragment's coverage with the temporary coverage valuegl.SCISSOR_TEST: scissor test that discards fragments that are outside of the scissor rectanglegl.STENCIL_TEST: stencil testing and updates to the stencil bufferspecifies which WebGL capability to enable
gl.BLEND: blending of the computed fragment color valuesgl.CULL_FACE: culling of polygonsgl.DEPTH_TEST: depth comparisons and updates to the depth buffergl.DITHER: dithering of color components before they get written to the color buffergl.POLYGON_OFFSET_FILL: adding an offset to depth values of polygon's fragmentsgl.SAMPLE_ALPHA_TO_COVERAGE: computation of a temporary coverage value determined by the alpha valuegl.SAMPLE_COVERAGE: ANDing the fragment's coverage with the temporary coverage valuegl.SCISSOR_TEST: scissor test that discards fragments that are outside of the scissor rectanglegl.STENCIL_TEST: stencil testing and updates to the stencil bufferspecifies whether polygons are front- or back-facing by setting a winding orientation
final per-instance transform calculated for instance i as
aTransform[i] = matrix * transform[i] * extraTransform[i]
base alpha, see uAlpha
bounding sphere taking aTransform into account and encompases all instances
additional per-instance transform, see aTransform
denotes reflection in transform
bounding sphere NOT taking aTransform into account
global transform, see aTransform
base per-instance transform, see aTransform
final alpha, calculated as values.alpha * state.alpha
Needed when running outside of sierra. If set to true, the strucmotif UI will use an absolute URL to sierra-prod. Otherwise, the link will be relative on the current host.
A Loci that is empty
A Loci that includes every loci
Returns a new IDBKeyRange spanning from lower to upper. If lowerOpen is true, lower is not included in the range. If upperOpen is true, upper is not included in the range.
Returns a new IDBKeyRange starting at key with no upper bound. If open is true, key is not included in the range.
Returns a new IDBKeyRange spanning only key.
Returns a new IDBKeyRange with no lower bound and ending at key. If open is true, key is not included in the range.
node is a CDATASection node.
node is a Comment node.
node is a DocumentFragment node.
node is a document.
Set when other is a descendant of node.
Set when other is an ancestor of node.
Set when node and other are not in the same tree.
Set when other is following node.
Set when other is preceding node.
node is a doctype.
node is an element.
node is a ProcessingInstruction node.
node is a Text node.
A null value Location
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.
Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, Beq, calculated from the
anisotropic displacement parameters.
Beq = (1/3) sumi[sumj(B^ij^ Ai Aj 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.
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.
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.
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.
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.
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.
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.
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.
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.
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 '.'.
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.
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.
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.
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.
A component of the identifier for this atom site.
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
This data item is a pointer to _entity.id in the ENTITY category.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
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.
PDB insertion code.
PDB model number.
The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
This data item is an ordinal which identifies distinct chemical components in the atom_site category, both polymeric and non-polymeric.
The accession code related to the additional external database entry.
The name of additional external databases with residue level mapping.
The sequence position of the external database entry that corresponds to the residue mapping defined by the SIFTS process.
Describes the residue type of the given UniProt match
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
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.
The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as:
T = exp{-2 pi^2^ sumi[sumj(U^ij^ hi hj 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.
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U.
This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Pointer to _atom_site.pdbx_PDB_ins_code
Pointer to _atom_site.auth_asym_id
Pointer to _atom_site.auth_atom_id
Pointer to _atom_site.auth_comp_id
Pointer to _atom_site.auth_seq_id
Pointer to _atom_site.label_alt_id.
Pointer to _atom_site.label_asym_id
Pointer to _atom_site.label_atom_id
Pointer to _atom_site.label_comp_id
Pointer to _atom_site.label_seq_id
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.
This data item is a pointer to _entry.id in the ENTRY category.
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|
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|
Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block.
The Open Researcher and Contributor ID (ORCID).
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).
This data item defines the order of the author's name in the list of audit authors.
Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.
A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms.
The string identifying the highest-level dictionary defining data names used in this file.
The version number of the dictionary to which the current data block conforms.
Data items in the CELL category record details about the crystallographic cell parameters.
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.
Unit-cell angle alpha of the reported structure in degrees.
Unit-cell angle beta of the reported structure in degrees.
Unit-cell angle gamma of the reported structure in degrees.
This data item is a pointer to _entry.id in the ENTRY category.
Unit-cell length a corresponding to the structure reported in angstroms.
Unit-cell length b corresponding to the structure reported in angstroms.
Unit-cell length c corresponding to the structure reported in angstroms.
To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field.
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.
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 mass in daltons of the chemical component.
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.
'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.
The full name of the component.
Synonym list for the component.
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.
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.
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.
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.
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
A flag indicating an aromatic bond.
Ordinal index for the component bond list.
Stereochemical configuration across a double bond.
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order.
Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.
The name of the publisher of the citation; relevant for books or book chapters.
The country/region of publication; relevant for books and book chapters.
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.
Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index.
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.
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).
The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles.
Volume number of the journal cited; relevant for journal articles.
The first page of the citation; relevant for journal articles, books and book chapters.
The last page of the citation; relevant for journal articles, books and book chapters.
Document Object Identifier used by doi.org to uniquely specify bibliographic entry.
Ascession number used by PubMed to categorize a specific bibliographic entry.
The title of the citation; relevant for journal articles, books and book chapters.
The year of the citation; relevant for journal articles, books and book chapters.
Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list.
This data item is a pointer to _citation.id in the CITATION category.
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).
This data item defines the order of the author's name in the list of authors of a citation.
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.
The code assigned by the database identified in _database_2.database_id.
An abbreviation that identifies the database.
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.
A description of special aspects of the entity.
Formula mass in daltons of the entity.
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.
A description of the entity.
Corresponds to the compound name in the PDB format.
Enzyme Commission (EC) number(s)
Entity fragment description(s).
Details about any entity mutation(s).
A place holder for the number of molecules of the entity in the entry.
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.
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.
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.
This data item is a pointer to _entity.id in the ENTITY category.
A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by _entity_poly.type.
A flag to indicate whether the polymer contains at least one monomer that is not considered standard.
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
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).
The PDB strand/chain id(s) corresponding to this polymer entity.
For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
The type of the polymer.
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.
This data item is a pointer to _entity_poly.entity_id in the ENTITY_POLY category.
A flag to indicate whether this monomer in the polymer is heterogeneous in sequence.
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
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.
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).
This data item is a pointer to _entity.id in the ENTITY category.
The beginning polymer sequence position for the polymer section corresponding to this source.
A reference to the sequence position in the entity_poly category.
The ending polymer sequence position for the polymer section corresponding to this source.
A reference to the sequence position in the entity_poly category.
Identifies the gene.
Scientific name of the organism.
This data item is an ordinal identifier for entity_src_gen data records.
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.
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.
This data item is a pointer to _entity.id in the ENTITY category.
The beginning polymer sequence position for the polymer section corresponding to this source.
A reference to the sequence position in the entity_poly category.
The ending polymer sequence position for the polymer section corresponding to this source.
A reference to the sequence position in the entity_poly category.
Scientific name of the organism of the natural source.
The plasmid containing the gene.
This data item is an ordinal identifier for entity_src_nat data records.
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.
The value of _entry.id identifies the data block.
Note that this item need not be a number; it can be any unique identifier.
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.
This data item is a pointer to _entry.id in the ENTRY category.
The method used in the experiment.
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 cross correlation coefficient corresponding to the model to image fitting.
A unique identifier for the 2dem class average fitting data.
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.
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.
Data item of the rotation matrix used in the fitting of the model to the image.
Data item of the tranlation vector used in the fitting of the model to the image.
Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the details of the 2DEM class averages used in the IHM modeling.
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.
Details of how the 2DEM restraint is applied in the modeling algorithm.
A unique identifier for the 2dem class average.
Resolution of the 2dem class average.
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.
Number of 2D projections of the model used in the fitting.
The number of raw micrographs used to obtain the class average.
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 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.
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.
Data items in the IHM_3DEM_RESTRAINT category records the details of the 3DEM maps used as restraints in the IHM modeling.
The cross correlation coefficient corresponding to the model to map fitting.
Identifier to the 3DEM map used. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category.
Method used to fit the model to the 3DEM map.
A unique identifier for the 3DEM restraint description.
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.
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.
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.
Data items in the IHM_CROSS_LINK_LIST category records the list of spatial restraints derived from chemical crosslinking experiment.
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.
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.
Identifier to the crosslinking dataset. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category.
A text description of molecular entity 1.
A text description of molecular entity 2.
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.
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.
An identifier for a set of ambiguous crosslink restraints. Handles experimental uncertainties in the identities of crosslinked residues.
A unique identifier for the cross link restraint.
The type of crosslinker used.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The cross link conditionality.
The distance threshold applied to this crosslink in the integrative modeling task.
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.
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.
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.
A unique identifier for the cross link record.
The coarse-graining information for the crosslink implementation.
The uncertainty in the crosslinking experimental data; may be approximated to the false positive rate.
The type of the cross link restraint applied.
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.
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.
The uncertainty in the position of residue 1 in the crosslink arising due to the multi-scale nature of the model represention.
The uncertainty in the position of residue 2 in the crosslink arising due to the multi-scale nature of the model represention.
Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the results of the crosslinking restraint parameters in the IHM modeling.
A unique identifier for the restraint/model combination.
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.
The uncertainty in the crosslinking experimental data; May be approximated to the false positive rate.
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.
The uncertainty in the position of residue 1 in the crosslink arising due to the multi-scale nature of the model represention.
The uncertainty in the position of residue 2 in the crosslink arising due to the multi-scale nature of the model represention.
Category provides additional details regarding input data hosted externally at other resources.
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.
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.
A unique identifier for the external data.
Category to define groups or collections of input datasets.
The application / utilization of the dataset group in modeling.
Additional details regarding the dataset group.
A unique identifier for the dataset group.
A name for the dataset group.
IHM_DATASET_GROUP_LINK category provides the list of datasets present in a particular group.
An identifier for the dataset. This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category.
An identifier for the dataset group. This data item is a pointer to _ihm_dataset_group.id in the IHM_DATASET_GROUP category.
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.
The type of data held in the dataset.
A flag that indicates whether the dataset is archived in an IHM related database or elsewhere.
A unique identifier for the dataset.
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.
The accession code for the database entry.
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.
The name of the database containing the dataset entry.
Details regarding the dataset entry.
A unique identifier for the related database entry.
Version of the database entry, if the database allows versioning.
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.
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.
The upper limit to the distance threshold applied to this distance restraint in the integrative modeling task.
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.
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.
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.
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.
A unique identifier for the derived distance restraint.
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.
The type of distance restraint applied.
Data items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling.
The parameter/feature used for clustering the models, if applicable.
The clustering method used to obtain the ensemble, if applicable.
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.
A unique id for the ensemble.
An optional name for the cluster or ensemble for better description.
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.
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.
The number of models in the current ensemble being described.
The number of models from the current ensemble that is deposited.
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.
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.
The type of content in the file.
Additional textual details regarding the external file.
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.
Storage size of the external file in bytes.
A unique identifier for each external file.
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.
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).
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.
The external reference or the Digital Object Identifier (DOI). This field is not relevant for local files.
A unique identifier for the external reference.
The name of the reference provider.
The type of external reference. Currently, only Digital Object Identifiers (DOIs) and supplementary files stored locally are supported.
The type of object that the external reference points to, usually a single file or an archive.
IHM_FEATURE_LIST is the high level category that provides defintions to select atoms/residues from polymeric and non-polymeric entities.
The type of entity.
A unique identifier for the feature.
The type of feature.
Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details of the gaussian objects representing an ensemble or cluster of models.
An asym/strand identifier corresponding to this gaussian object. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
Data item of the covariance matrix representing the Gaussian object.
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.
The entity identifier corresponding to this gaussian object. This data item is a pointer to _entity.id in the ENTITY category.
A unique identifier for this gaussian object.
The mean Cartesian X component corresponding to this gaussian object.
The mean Cartesian Y component corresponding to this gaussian object.
The mean Cartesian Z component corresponding to this gaussian object.
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.
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.
The weight of the gaussian object.
Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details of the gaussian objects modeled in the integrative structural model.
An asym/strand identifier corresponding to this gaussian object. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
Data item of the covariance matrix representing the Gaussian object.
The entity identifier corresponding to this gaussian object. This data item is a pointer to _entity.id in the ENTITY category.
A unique identifier for this gaussian object in the model.
The mean Cartesian X component corresponding to this gaussian object.
The mean Cartesian Y component corresponding to this gaussian object.
The mean Cartesian Z component corresponding to this gaussian object.
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.
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.
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.
The weight of the gaussian object.
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.).
An asym/strand identifier corresponding to this localization density. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
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.
The entity identifier corresponding to this localization density. This data item is a pointer to _entity.id in the ENTITY category.
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.
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.
A unique identifier.
IHM_MODEL_GROUP category defines collections or groups of integrative structural models.
Additional details about the collection of models.
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.
A name for the collection of models.
IHM_MODEL_GROUP_LINK category provides the list of models present in a particular model group.
An identifier for the structural model group. This data item is a pointer to _ihm_model_group.id in the IHM_MODEL_GROUP category.
An identifier for the structural model. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category.
Data items in the IHM_MODEL_LIST category record the details of the models being deposited.
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.
A unique identifier for the structural model being deposited.
A decsriptive name for the model.
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.
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.
Data items in the IHM_MODEL_REPRESENTATION category lists the various mono or multi-scale model representations used in the integrative modeling study.
Additional details about the model representation.
A unique identifier for the model representation.
Name/brief description for the model representation.
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.
An asym/strand identifier for the entity molecule. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
A text description of the molecular entity
A unique identifier distinct molecular entities. This data item is a pointer to _entity.id in the ENTITY category.
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.
A unique identifier for the category.
The level of detail at which model primitive objects are applied to the structure.
The manner in which the segment is modeled.
The number of primitive objects used to model a feature in the case of 'by-feature' granularity.
The primitive object used to model this segment.
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.
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.
Data items in the IHM_MODEL_REPRESENTATIVE category record the details of the representative model in an ensemble or cluster.
A unique identifier for the representative of the model group.
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.
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.
The selection criteria based on which the representative is chosen.
Data items in the IHM_MODELING_POST_PROCESS category records the details of the post processing of the models/results of the modeling protocol.
An identifier for the post modeling analysis. This data item accounts for multiple post-modeling analyses that can be carried out.
The parameter/feature used in the post modeling analysis.
A unique identifier for the post modeling analysis/step combination.
The number of models at the beginning of the post processing step.
The number of models the the end of the post processing step.
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.
In a multi-step process, this identifier denotes the particular step in the post modeling analysis.
The type of post modeling analysis being carried out.
Data items in the IHM_MODELING_PROTOCOL category lists all modeling protocols used in the integrative modeling study.
A unique identifier for the modeling protocol.
Number of independent steps in the modeling protocol.
The name for the modeling protocol.
Data items in the IHM_MODELING_PROTOCOL_DETAILS category records the step-wise details of the integrative modeling workflow.
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.
A unique identifier for the modeling protocol/step combination.
A flag to indicate if the modeling is multi scale.
A flag to indicate if the modeling is multi state.
The number of models in the beginning of the step.
The number of models at the end of the step.
A flag to indicate if the modeling involves an ensemble ordered by time or other order.
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.
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.
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.
An index for a particular step within the modeling protocol.
Description of the method involved in the modeling step.
The name or type of the modeling step.
A textual description of the structural assembly being modeled.
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.
Data items in the IHM_MULTI_STATE_MODELING category records the details of the multi-state modeling protocol, if applicable.
Additional textual details of the multi-state modeling, if required.
The type of multi-state modeling experiment carried out.
A fraction representing the population of the particular state.
The standard deviation of the population fraction.
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.
A unique identifier for a particular state in the multi-state modeling.
A descriptive name for the state.
The type that the multiple states being modeled belong to.
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.
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.
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.
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.
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.
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.
A unique identifier for the category.
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.
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.
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.
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.
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.
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.
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.
Identifier to the predicted contacts dataset. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category.
The lower limit to the distance threshold applied to this predicted contact restraint in the integrative modeling task.
The upper limit to the distance threshold applied to this predicted contact restraint in the integrative modeling task.
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.
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.
An identifier to group the predicted contacts.
A unique identifier for the predicted contact restraint.
The granularity of the predicted contact as applied to the multi-scale model.
The real number that indicates the probability that the predicted distance restraint is correct. This number should fall between 0.0 and 1.0.
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.
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.
The type of distance restraint applied.
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.
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.
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.
Category holds information about related datasets, where one is derived from the other.
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.
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.
Data items in the IHM_SAS_RESTRAINT category records the details of the SAS data used as restraints in the IHM modeling.
The chi value resulting from fitting the model to the SAS data.
Identifier to the SAS data used. This data item is a pointer to the _ihm_dataset_list.id in the IHM_DATASET_LIST category.
Additional details regarding the SAS restraint used.
The type of atoms in the model fit to the SAS data.
The method used for fitting the model to the SAS data.
An indicator to single or multiple state fitting.
A unique identifier for the SAS restraint description.
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.
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.
Radius of gyration obtained from the SAS profile, if used as input restraint.
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.
Data items in the IHM_SPHERE_OBJ_SITE category records the details of the spherical objects modeled in the integrative structural model.
The Cartesian X component corresponding to this sphere object.
The Cartesian Y component corresponding to this sphere object.
The Cartesian Z component corresponding to this sphere object.
An asym/strand identifier corresponding to this sphere object. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
The entity identifier corresponding to this sphere object. This data item is a pointer to _entity.id in the ENTITY category.
A unique identifier for this pseudo atom / sphere object.
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.
The radius associated with the primitive sphere object at this position.
The Root Mean Square Fluctuation (RMSF) observed in the primitive sphere object at this position.
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.
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.
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.
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.
A unique identifier for the starting comparative model.
The chainId/auth_asym_id corresponding to the starting model.
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.
The starting residue index of the starting model.
The ending residue index of the starting model.
The chainId/auth_asym_id corresponding to the template.
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.
The starting residue index of the template.
The ending residue index of the template.
The percentage sequence identity between the template sequence and the comparative model sequence.
The denominator used while calculating the sequence identity provided in _ihm_starting_comparative_models.template_sequence_identity.
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.
The isotropic temperature factor corresponding to this coordinate position.
The Cartesian X component corresponding to this coordinate position.
The Cartesian Y component corresponding to this coordinate position.
The Cartesian Z component corresponding to this coordinate position.
The asym/strand id corresponding to this coordinate position.
This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
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.
The component identifier corresponding to this coordinate position. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
The entity identifier corresponding to this coordinate position. This data item is a pointer to _entity.id in the ENTITY category.
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.
The serial number for this coordinate position.
A unique identifier for this coordinate position.
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.
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.
The atom type symbol(element symbol) corresponding to this coordinate position.
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.
An asym/strand identifier for the entity molecule. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
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.
A text description of the molecular entity
A unique identifier for the distinct molecular entities. This data item is a pointer to _entity.id in the ENTITY category.
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.
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.
A unique identifier for the starting structural model.
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
The source of the starting model.
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.
An asym/strand identifier for the entity molecule. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
The component identifier for the residue. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
The asym/strand identifier for the entity molecule of the database starting model.
The correspinding component identifier for the residue in the database starting model.
The corresponding residue index of the database starting model.
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.
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.
A unique identifier for the entry.
The residue index. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
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.
Data items in the IHM_STRUCT_ASSEMBLY category lists all the structural assemblies used in the integrative modeling study.
Description of the structural assembly.
A unique identifier for the structural assembly.
A name for the structural assembly.
Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category records the details of the structural assemblies and used in the integrative modeling.
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.
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.
A text description of the molecular entity
A unique identifier for distinct molecular entities. This data item is a pointer to _entity.id in the ENTITY category.
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.
A unique identifier for the structural assembly description.
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.
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.
The type of data held in the dataset.
Details for other content types.
A unique identifier for the data.
An author-given name for the content held in the dataset.
Data items in the MA_MODEL_LIST category record the details of the models being deposited.
The data_id identifier. This data item is a pointer to _ma_data.id in the MA_DATA category.
An identifier to group structural models into collections or sets. A cluster of models and its representative can either be grouped together or can be separate groups in the ma_model_list table. The choice between the two options should be decided based on how the modeling was carried out and how the representative was chosen. If the representative is a member of the ensemble (i.e., best scoring model), then it is recommended that the representative and the ensemble belong to the same model group. If the representative is calculated from the ensemble (i.e., centroid), then it is recommended that the representative be separated into a different group. If the models do not need to be grouped into collections, then the _ma_model_list.model_group_id is the same as _ma_model_list.model_id.
A decsriptive name for the model group.
A unique identifier for the structural model being deposited.
A decsriptive name for the model.
The type of model.
A unique identifier for the model / model group combination.
Data items in the MA_QA_METRIC category record the details of the metrics use to assess model quality.
An identifier for the QA metric.
The mode of calculation of the QA metric.
Name of the QA metric.
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.
The type of QA metric.
Data items in the MA_QA_METRIC_GLOBAL category captures the details of the global QA metrics, calculated at the model-level.
The identifier for the QA metric. This data item is a pointer to _ma_qa_metric.id in the MA_QA_METRIC category.
The value of the global QA metric.
The identifier for the structural model, for which global QA metric is provided. This data item is a pointer to _ma_model_list.model_id in the MA_MODEL_LIST category.
A unique identifier for the category.
Data items in the MA_QA_METRIC_LOCAL category captures the details of the local QA metrics, calculated at the residue-level.
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.
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.
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.
The identifier for the QA metric. This data item is a pointer to _ma_qa_metric.id in the MA_QA_METRIC category.
The value of the local QA metric.
The identifier for the structural model, for which local QA metric is provided. This data item is a pointer to _ma_model_list.model_id in the MA_MODEL_LIST category.
A unique identifier for the category.
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.
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.
A unique identifier for the category.
The identifier for the software. This data item is a pointer to _software.pdbx_ordinal in the SOFTWARE category.
Data items in the MA_TARGET_ENTITY category record details about the target entities. The details are provided for each entity being modeled.
The data_id identifier. This data item is a pointer to _ma_data.id in the MA_DATA category.
A unique identifier for the distinct molecular entity of the target. This data item is a pointer to _entity.id in the ENTITY category.
The origin of the target entity.
Data items in the MA_TARGET_ENTITY_INSTANCE category record details about the instances of target entities modeled.
A unique identifier for the instance of the entity.
Additional details about the entity instance.
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.
Data items in the MA_TARGET_REF_DB_DETAILS category record details about the reference databases for the target sequences.
Accession code assigned by the reference database.
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.
The name of the database containing reference information about this entity or biological unit.
Taxonomy identifier provided by NCBI.
Scientific name of the organism.
Beginning index in the chemical sequence from the reference database.
Ending index in the chemical sequence from the reference database.
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.
An identifier for the target entity.
The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities.
Pointer to _atom_site.label_asym_id.
This data item is a pointer to _atom_site.pdbx_auth_asym_id in the ATOM_SITE category.
This data item is a pointer to _atom_site.pdbx_auth_comp_id in the ATOM_SITE category.
This data item is a pointer to _atom_site.pdbx_auth_seq_id in the ATOM_SITE category.
This data item is a pointer to _entity.id in the ENTITY category.
A flag to indicate whether this monomer in the entity is heterogeneous in sequence.
This data item is a pointer to _atom_site.label_comp_id in the PDBX_ENTITY_BRANCH_LIST category.
This data item is a pointer to _pdbx_entity_branch_list.num in the PDBX_ENTITY_BRANCH_LIST category.
This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Data items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components.
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
This data item contains the identifier value for this component.
This data item contains the name of the program or library used to compute the identifier.
This data item contains the version of the program or library used to compute the identifier.
This data item contains the identifier type.
PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
The chemical component for which this relationship applies.
Describes the type of relationship
The related chemical component for which this chemical component is based.
Describes the type of relationship
PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
The chemical component for which this synonym applies.
The synonym of this particular chemical component.
The provenance of this synonym.
Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry.
The identifying content type of the related entry.
The identifying code in the related database.
The name of the database containing the related entry.
A description of the related entry.
These are internal RCSB records to keep track of data processing and status of the entry.
This code indicates whether the entry belongs to Structural Genomics Project.
The site where the file was deposited.
The value of _pdbx_database_status.entry_id identifies the data block.
The methods development category in which this entry has been placed.
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.
The site where the file was deposited.
The date of initial deposition. (The first message for deposition has been received.)
Code for status of file.
Code for status of chemical shift data file.
Code for status of NMR constraints file.
Code for status of structure factor file.
Data items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type.
The entity id for this branched entity.
This data item is a pointer to _entity.id
The type of this branched oligosaccharide.
Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide string descriptors of entity chemical structure.
This data item contains the descriptor value for this entity.
This data item is a pointer to _entity_poly.entity_id in the ENTITY category.
Ordinal index for this category.
This data item contains the name of the program or library used to compute the descriptor.
This data item contains the version of the program or library used to compute the descriptor.
This data item contains the descriptor type.
Data items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity.
The atom identifier/name for the first atom making the linkage.
The atom identifier/name for the second atom making the linkage.
The chiral configuration of the first atom making the linkage.
The chiral configuration of the second atom making the linkage.
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.
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.
A description of special aspects of this linkage.
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.
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.
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.
The leaving atom identifier/name bonded to the first atom making the linkage.
The leaving atom identifier/name bonded to the second atom making the linkage.
The value of _pdbx_entity_branch_link.link_id uniquely identifies linkages within the branched entity.
The bond order target for the chemical linkage.
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.
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
This data item is a pointer to _entity.id in the ENTITY category.
A flag to indicate whether this monomer in the entity is heterogeneous in sequence.
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.
Data items in the pdbx_entity_instance_feature category records special features of selected entity instances.
Instance identifier for this entity.
Author instance identifier (formerly PDB Chain ID)
The author provided chemical component identifier
Author provided residue number.
Chemical component identifier
Special structural details about this entity instance.
A feature type associated with entity instance.
An ordinal index for this category
Position in the sequence.
The PDBX_ENTITY_NONPOLY category provides a mapping between entity and the nonpolymer component
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
This data item is a pointer to _entity.id in the ENTITY category.
A name for the non-polymer entity
The data items in category PDBX_ENTITY_SRC_SYN record the source details about chemically synthesized molecules.
This data item is a pointer to _entity.id in the ENTITY category.
The scientific name of the organism from which the sequence of the synthetic entity was derived.
The beginning polymer sequence position for the polymer section corresponding to this source.
A reference to the sequence position in the entity_poly category.
The ending polymer sequence position for the polymer section corresponding to this source.
A reference to the sequence position in the entity_poly category.
This data item is an ordinal identifier for pdbx_entity_src_syn data records.
Data items in the PDBX_MOLECULE category identify reference molecules within a PDB entry.
A reference to _struct_asym.id in the STRUCT_ASYM category.
The value of _pdbx_molecule.instance_id is identifies a particular molecule in the molecule list.
The value of _pdbx_molecule.prd_id is the PDB accession code for this reference molecule.
Data items in the PDBX_MOLECULE_FEATURES category record features of molecules within a PDB entry.
Broadly defines the function of the molecule.
Additional details describing the molecule.
A name of the molecule.
The value of _pdbx_molecule_features.prd_id is the accession code for this reference molecule.
Defines the structural classification of the molecule.
The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities.
Pointer to _atom_site.label_asym_id.
Author provided residue identifier. This value may differ from the PDB residue identifier and may not correspond to residue identification within the coordinate records.
Author provided residue numbering. This value may differ from the PDB residue number and may not correspond to residue numbering within the coordinate records.
Pointer to _atom_site.label_entity_id.
Pointer to _atom_site.label_comp_id.
NDB/RCSB residue number.
PDB insertion code.
PDB residue identifier.
PDB residue number.
PDB strand/chain id.
Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about the linkages between entities within reference molecules.
The atom identifier/name in the first of the two entities containing the linkage.
The atom identifier/name in the second of the two entities containing the linkage.
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.
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.
The entity component identifier for the first of two entities containing the linkage.
The entity component identifier for the second of two entities containing the linkage.
A description of special aspects of a linkage between chemical components in the structure.
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.
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.
A code indicating the entity types involved in the linkage.
The value of _pdbx_reference_entity_link.link_id uniquely identifies linkages between entities with a molecule.
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.
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.
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.
The bond order target for the chemical linkage.
Data items in the PDBX_REFERENCE_ENTITY_LIST category record the list of entities within each reference molecule.
The component number of this entity within the molecule.
Additional details about this entity.
The value of _pdbx_reference_entity_list.prd_id is a reference _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier the a constituent entity within this reference molecule.
Defines the polymer characteristic of the entity.
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.
The atom identifier/name in the first of the two components making the linkage.
The atom identifier/name in the second of the two components making the linkage.
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.
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.
The entity component identifier entity containing the linkage.
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.
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.
The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies a linkage within a polymer entity.
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.
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.
The bond order target for the non-standard linkage.
Data items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies.
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.
The value of _pdbx_struct_assembly.id must uniquely identify a record in the PDBX_STRUCT_ASSEMBLY list.
Provides details of the method used to determine or compute the assembly.
The number of polymer molecules in the assembly.
Provides the details of the oligomeric state of the assembly.
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.
This data item is a pointer to _pdbx_struct_assembly.id in the PDBX_STRUCT_ASSEMBLY category.
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.
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)
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.
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.
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.
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.
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.
Details of the modification for this polymer component.
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.
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.
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.
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.
The parent component identifier for this modified polymer component.
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.
This identifier code must uniquely identify a record in the PDBX_STRUCT_OPER_LIST list.
The elements of the 3x3 matrix component of the transformation operation.
A descriptive name for the transformation operation.
The symmetry operation corresponding to the transformation operation.
A code to indicate the type of operator.
The elements of the three-element vector component of the transformation operation.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
The value of occupancy flag indicates whether the residue is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
The value of polymer flag indicates whether the unobserved or zero occupancy residue is part of a polymer chain or not
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.
The classification of the program according to its major function.
The date the software was released.
Description of the software.
The name of the software.
An ordinal index for this category
The classification of the software according to the most common types.
The version of the software.
Data items in the STRUCT category record details about the description of the crystallographic structure.
This data item is a pointer to _entry.id in the ENTRY category.
An automatically generated descriptor for an NDB structure or the unstructured content of the PDB COMPND record.
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.
Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit.
A description of special aspects of this portion of the contents of the asymmetric unit.
This data item is a pointer to _entity.id in the ENTITY category.
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.
A flag indicating that this entity was originally labeled with a blank PDB chain id.
This data item indicates whether the structural elements are modified.
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.
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.
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.
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.
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.
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.
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.
This data item is a pointer to _struct_conf_type.id in the STRUCT_CONF_TYPE category.
A description of special aspects of the conformation assignment.
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.
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.
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.
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.
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.
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.
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.
This item is a place holder for the helix class used in the PDB HELIX record.
A placeholder for the helix identifier of the PDB HELIX record.
A placeholder for the lengths of the helix of the PDB HELIX record.
A component of the identifier for the residue at which the conformation segment starts.
A component of the identifier for the residue at which the conformation segment ends.
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.
This data item is a pointer to _struct_conn_type.id in the STRUCT_CONN_TYPE category.
A description of special aspects of the connection.
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.
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.
Distance value for this contact.
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.
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.
A placeholder for the standard residue name found in the MODRES record of a PDB file.
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.
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.
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.
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.
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.
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.
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.
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.
The chemical bond order associated with the specified atoms in this contact.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure.
The criteria used to define the interaction.
The chemical or structural type of the interaction.
A reference that specifies the criteria used to define the interaction.
Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry.
This data item is a pointer to _entry.id in the ENTRY category.
Terms characterizing the macromolecular structure.
Keywords describing this structure.
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.
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').
A description of special aspects of the noncrystallographic symmetry operator.
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.
The elements of the 3x3 matrix component of a noncrystallographic symmetry operation.
The elements of the three-element vector component of a noncrystallographic symmetry operation.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
A component of the identifier for the residue at which the beta sheet range begins. Insertion code.
A component of the identifier for the residue at which the beta sheet range ends. Insertion code.
This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category.
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).
A description of special aspects of the site.
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.
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.
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.
PDB insertion code for the ligand in the site.
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.
Source of evidence supporting the assignment of this site.
Number of residues in the site.
Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites.
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.
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.
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.
A description of special aspects of the symmetry generation of this portion of the structural site.
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.
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.
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.
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.
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.
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.
PDB insertion code.
Number of residues in the site.
This data item is a pointer to _struct_site.id in the STRUCT_SITE category.
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.
Data items in the SYMMETRY category record details about the space-group symmetry.
Space-group number from International Tables for Crystallography Vol. A (2002).
The cell settings for this space-group symmetry.
This data item is a pointer to _entry.id in the ENTRY category.
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 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.
Has type extended with 'ION' and 'LIPID'
Creates a Collection.
The type of Collection created is based on the input.
Collection, that same Collection.Collection.Indexed.Collection.Indexed.Collection.Keyed.This methods forces the conversion of Objects and Strings to Collections.
If you want to ensure that a Collection of one item is returned, use
Seq.of.
Note: An Iterator itself will be treated as an object, becoming a Seq.Keyed,
which is usually not what you want. You should turn your Iterator Object into
an iterable object by defining a Symbol.iterator (or @@iterator) method which
returns this.
Note: Collection is a conversion function and not a class, and does not
use the new keyword during construction.
Creates a new Collection.Indexed.
Note: Collection.Indexed is a conversion function and not a class, and
does not use the new keyword during construction.
Always returns Seq.Indexed, discarding associated keys and supplying incrementing indices.
Note: Seq.Indexed is a conversion function and not a class, and does
not use the new keyword during construction.
Always returns a Seq.Keyed, if input is not keyed, expects an collection of [K, V] tuples.
Note: Seq.Keyed is a conversion function and not a class, and does not
use the new keyword during construction.
Create a new immutable List containing the values of the provided collection-like.
Note: List is a factory function and not a class, and does not use the
new keyword during construction.
const { List, Set } = require('immutable')
const emptyList = List()
// List []
const plainArray = [ 1, 2, 3, 4 ]
const listFromPlainArray = List(plainArray)
// List [ 1, 2, 3, 4 ]
const plainSet = Set([ 1, 2, 3, 4 ])
const listFromPlainSet = List(plainSet)
// List [ 1, 2, 3, 4 ]
const arrayIterator = plainArray[Symbol.iterator]()
const listFromCollectionArray = List(arrayIterator)
// List [ 1, 2, 3, 4 ]
listFromPlainArray.equals(listFromCollectionArray) // true
listFromPlainSet.equals(listFromCollectionArray) // true
listFromPlainSet.equals(listFromPlainArray) // true
Creates a new Immutable Map.
Created with the same key value pairs as the provided Collection.Keyed or JavaScript Object or expects a Collection of [K, V] tuple entries.
Note: Map is a factory function and not a class, and does not use the
new keyword during construction.
const { Map } = require('immutable')
Map({ key: "value" })
Map([ [ "key", "value" ] ])
Keep in mind, when using JS objects to construct Immutable Maps, that JavaScript Object properties are always strings, even if written in a quote-less shorthand, while Immutable Maps accept keys of any type.
let obj = { 1: "one" }
Object.keys(obj) // [ "1" ]
assert.equal(obj["1"], obj[1]) // "one" === "one"
let map = Map(obj)
assert.notEqual(map.get("1"), map.get(1)) // "one" !== undefined
Property access for JavaScript Objects first converts the key to a string,
but since Immutable Map keys can be of any type the argument to get() is
not altered.
Creates a new Immutable OrderedMap.
Created with the same key value pairs as the provided Collection.Keyed or JavaScript Object or expects a Collection of [K, V] tuple entries.
The iteration order of key-value pairs provided to this constructor will be preserved in the OrderedMap.
let newOrderedMap = OrderedMap({key: "value"})
let newOrderedMap = OrderedMap([["key", "value"]])
Note: OrderedMap is a factory function and not a class, and does not use
the new keyword during construction.
Create a new immutable OrderedSet containing the values of the provided collection-like.
Note: OrderedSet is a factory function and not a class, and does not use
the new keyword during construction.
Creates a Seq.
Returns a particular kind of Seq based on the input.
Seq, that same Seq.Collection, a Seq of the same kind (Keyed, Indexed, or Set).Seq.Indexed.Seq.Indexed.Seq.Keyed.Note: An Iterator itself will be treated as an object, becoming a Seq.Keyed,
which is usually not what you want. You should turn your Iterator Object into
an iterable object by defining a Symbol.iterator (or @@iterator) method which
returns this.
Note: Seq is a conversion function and not a class, and does not use the
new keyword during construction.
Create a new immutable Set containing the values of the provided collection-like.
Note: Set is a factory function and not a class, and does not use the
new keyword during construction.
Always returns a Seq.Set, discarding associated indices or keys.
Note: Seq.Set is a conversion function and not a class, and does not
use the new keyword during construction.
Create a new immutable Stack containing the values of the provided collection-like.
The iteration order of the provided collection is preserved in the
resulting Stack.
Note: Stack is a factory function and not a class, and does not use the
new keyword during construction.
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David Sehnal david.sehnal@gmail.com