diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index e50ae25be452619e817f76e65107f94badc49a58..0614e84107ffc60182a213c6c27fcc01df209493 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -11,16 +11,15 @@ import { Database, Column } from 'mol-data/db'
import Schema = Column.Schema
const str = Schema.str;
-const int = Schema.int;
const float = Schema.float;
-// const coord = Schema.coord;
-
const Aliased = Schema.Aliased;
-// const Matrix = Schema.Matrix;
-// const Vector = Schema.Vector;
-// const List = Schema.List;
+const int = Schema.int;
export const BIRD_Schema = {
+ /**
+ * Data items in the PDBX_REFERENCE_MOLECULE category record
+ * reference information about small polymer molecules.
+ */
pdbx_reference_molecule: {
/**
* The value of _pdbx_reference_molecule.prd_id is the unique identifier
@@ -108,6 +107,10 @@ export const BIRD_Schema = {
*/
replaced_by: str,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_LIST category record
+ * the list of entities within each reference molecule.
+ */
pdbx_reference_entity_list: {
/**
* The value of _pdbx_reference_entity_list.prd_id is a reference
@@ -132,6 +135,10 @@ export const BIRD_Schema = {
*/
component_id: int,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_NONPOLY category record
+ * the list of entities within each reference molecule.
+ */
pdbx_reference_entity_nonpoly: {
/**
* The value of _pdbx_reference_entity_nonpoly.prd_id is a reference
@@ -153,6 +160,10 @@ export const BIRD_Schema = {
*/
chem_comp_id: str,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about
+ * the linkages between entities within reference molecules.
+ */
pdbx_reference_entity_link: {
/**
* The value of _pdbx_reference_entity_link.link_id uniquely identifies
@@ -248,6 +259,11 @@ export const BIRD_Schema = {
*/
link_class: Aliased<'PP' | 'PN' | 'NP' | 'NN'>(str),
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about
+ * polymer linkages including both standard and non-standard linkages between
+ * polymer componnents.
+ */
pdbx_reference_entity_poly_link: {
/**
* The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
@@ -317,6 +333,11 @@ export const BIRD_Schema = {
*/
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
},
+ /**
+ * Data items in the PDBX_REFERENCE_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.
+ */
pdbx_reference_entity_poly: {
/**
* The value of _pdbx_reference_entity_poly.prd_id is a reference
@@ -341,6 +362,10 @@ export const BIRD_Schema = {
*/
db_name: str,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence
+ * of monomers in a polymer.
+ */
pdbx_reference_entity_poly_seq: {
/**
* The value of _pdbx_reference_entity_poly_seq.prd_id is a reference
@@ -377,6 +402,9 @@ export const BIRD_Schema = {
*/
hetero: Aliased<'Y' | 'N'>(str),
},
+ /**
+ * Additional features associated with the reference entity.
+ */
pdbx_reference_entity_sequence: {
/**
* The value of _pdbx_reference_entity_sequence.prd_id is a reference
@@ -401,6 +429,10 @@ export const BIRD_Schema = {
*/
one_letter_codes: str,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record
+ * details of the source from which the entity was obtained.
+ */
pdbx_reference_entity_src_nat: {
/**
* The value of _pdbx_reference_entity_src_nat.prd_id is a reference
@@ -434,6 +466,10 @@ export const BIRD_Schema = {
*/
db_name: str,
},
+ /**
+ * Data items in the PDBX_PRD_AUDIT category records
+ * the status and tracking information for this molecule.
+ */
pdbx_prd_audit: {
/**
* This data item is a pointer to _pdbx_reference_molecule.prd_id in the
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index 0149ed58fa59be1b992e6eda99343fe3823b566d..3a5e0d2c0987fb983c92c8ae555634513e5a4fab 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -11,16 +11,22 @@ import { Database, Column } from 'mol-data/db'
import Schema = Column.Schema
const str = Schema.str;
-const int = Schema.int;
const float = Schema.float;
-const coord = Schema.coord;
-
-const Aliased = Schema.Aliased;
-// const Matrix = Schema.Matrix;
-// const Vector = Schema.Vector;
const List = Schema.List;
+const Aliased = Schema.Aliased;
+const int = Schema.int;
+const coord = Schema.coord;
export const CCD_Schema = {
+ /**
+ * Data items in the CHEM_COMP category give details about each
+ * of the chemical components from which the relevant chemical
+ * structures can be constructed, such as name, mass or charge.
+ *
+ * The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND,
+ * CHEM_COMP_ANGLE etc. describe the detailed geometry of these
+ * chemical components.
+ */
chem_comp: {
/**
* The formula for the chemical component. Formulae are written
@@ -167,6 +173,14 @@ export const CCD_Schema = {
*/
pdbx_processing_site: Aliased<'PDBE' | 'EBI' | 'PDBJ' | 'RCSB'>(str),
},
+ /**
+ * Data items in the CHEM_COMP_ATOM category record details about
+ * the atoms in a chemical component. Specifying the atomic
+ * coordinates for the components in this category is an
+ * alternative to specifying the structure of the component
+ * via bonds, angles, planes etc. in the appropriate
+ * CHEM_COMP subcategories.
+ */
chem_comp_atom: {
/**
* An alternative identifier for the atom. This data item would be
@@ -271,6 +285,12 @@ export const CCD_Schema = {
*/
pdbx_leaving_atom_flag: Aliased<'Y' | 'N'>(str),
},
+ /**
+ * Data items in the CHEM_COMP_BOND category record details about
+ * the bonds between atoms in a chemical component. Target values
+ * may be specified as bond orders, as a distance between the two
+ * atoms, or both.
+ */
chem_comp_bond: {
/**
* The ID of the first of the two atoms that define the bond.
@@ -310,6 +330,10 @@ export const CCD_Schema = {
*/
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
+ /**
+ * Data items in the CHEM_COMP_DESCRIPTOR category provide
+ * string descriptors of component chemical structure.
+ */
pdbx_chem_comp_descriptor: {
/**
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
@@ -336,6 +360,10 @@ export const CCD_Schema = {
*/
program_version: str,
},
+ /**
+ * Data items in the CHEM_COMP_IDENTIFIER category provide
+ * identifiers for chemical components.
+ */
pdbx_chem_comp_identifier: {
/**
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index f395639e8ab4e68823fdd37087f4195dbd56aac0..526cb248bf6d32e7953eb55055e8673db48d9931 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -14,13 +14,22 @@ const str = Schema.str;
const int = Schema.int;
const float = Schema.float;
const coord = Schema.coord;
-
const Aliased = Schema.Aliased;
const Matrix = Schema.Matrix;
const Vector = Schema.Vector;
const List = Schema.List;
export const mmCIF_Schema = {
+ /**
+ * Data items in the ATOM_SITE category record details about
+ * the atom sites in a macromolecular crystal structure, such as
+ * the positional coordinates, atomic displacement parameters,
+ * magnetic moments and directions.
+ *
+ * The data items for describing anisotropic atomic
+ * displacement factors are only used if the corresponding items
+ * are not given in the ATOM_SITE_ANISOTROP category.
+ */
atom_site: {
/**
* An alternative identifier for _atom_site.label_asym_id that
@@ -204,6 +213,11 @@ export const mmCIF_Schema = {
*/
ihm_model_id: int,
},
+ /**
+ * Data items in the ATOM_SITES category record details about
+ * the crystallographic cell and cell transformations, which are
+ * common to all atom sites.
+ */
atom_sites: {
/**
* This data item is a pointer to _entry.id in the ENTRY category.
@@ -236,6 +250,10 @@ export const mmCIF_Schema = {
*/
fract_transf_vector: Vector(3),
},
+ /**
+ * Data items in the CELL category record details about the
+ * crystallographic cell parameters.
+ */
cell: {
/**
* Unit-cell angle alpha of the reported structure in degrees.
@@ -283,6 +301,15 @@ export const mmCIF_Schema = {
*/
pdbx_unique_axis: str,
},
+ /**
+ * Data items in the CHEM_COMP category give details about each
+ * of the chemical components from which the relevant chemical
+ * structures can be constructed, such as name, mass or charge.
+ *
+ * The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND,
+ * CHEM_COMP_ANGLE etc. describe the detailed geometry of these
+ * chemical components.
+ */
chem_comp: {
/**
* The formula for the chemical component. Formulae are written
@@ -344,6 +371,12 @@ export const mmCIF_Schema = {
*/
pdbx_synonyms: List(';', x => x),
},
+ /**
+ * Data items in the CHEM_COMP_BOND category record details about
+ * the bonds between atoms in a chemical component. Target values
+ * may be specified as bond orders, as a distance between the two
+ * atoms, or both.
+ */
chem_comp_bond: {
/**
* The ID of the first of the two atoms that define the bond.
@@ -383,6 +416,37 @@ export const mmCIF_Schema = {
*/
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
+ /**
+ * Data items in the ENTITY category record details (such as
+ * chemical composition, name and source) about the molecular
+ * entities that are present in the crystallographic structure.
+ *
+ * Items in the various ENTITY subcategories provide a full
+ * chemical description of these molecular entities.
+ *
+ * Entities are of three types: polymer, non-polymer and water.
+ * Note that the water category includes only water; ordered
+ * solvent such as sulfate ion or acetone would be described as
+ * individual non-polymer entities.
+ *
+ * The ENTITY category is specific to macromolecular CIF
+ * applications and replaces the function of the CHEMICAL category
+ * in the CIF core.
+ *
+ * It is important to remember that the ENTITY data are not the
+ * result of the crystallographic experiment; those results are
+ * represented by the ATOM_SITE data items. ENTITY data items
+ * describe the chemistry of the molecules under investigation
+ * and can most usefully be thought of as the ideal groups to which
+ * the structure is restrained or constrained during refinement.
+ *
+ * It is also important to remember that entities do not correspond
+ * directly to the enumeration of the contents of the asymmetric
+ * unit. Entities are described only once, even in those structures
+ * that contain multiple observations of an entity. The
+ * STRUCT_ASYM data items, which reference the entity list,
+ * describe and label the contents of the asymmetric unit.
+ */
entity: {
/**
* A description of special aspects of the entity.
@@ -446,6 +510,11 @@ export const mmCIF_Schema = {
*/
pdbx_ec: List(',', x => x),
},
+ /**
+ * Data items in the ENTITY_POLY category record details about the
+ * polymer, such as the type of the polymer, the number of
+ * monomers and whether it has nonstandard features.
+ */
entity_poly: {
/**
* This data item is a pointer to _entity.id in the ENTITY category.
@@ -511,6 +580,14 @@ export const mmCIF_Schema = {
*/
pdbx_target_identifier: str,
},
+ /**
+ * Data items in the ENTITY_POLY_SEQ category specify the sequence
+ * of monomers in a polymer. Allowance is made for the possibility
+ * of microheterogeneity in a sample by allowing a given sequence
+ * number to be correlated with more than one monomer ID. The
+ * corresponding ATOM_SITE entries should reflect this
+ * heterogeneity.
+ */
entity_poly_seq: {
/**
* This data item is a pointer to _entity.id in the ENTITY category.
@@ -535,6 +612,12 @@ export const mmCIF_Schema = {
*/
num: int,
},
+ /**
+ * There is only one item in the ENTRY category, _entry.id. This
+ * data item gives a name to this entry and is indirectly a key to
+ * the categories (such as CELL, GEOM, EXPTL) that describe
+ * information pertinent to the entire data block.
+ */
entry: {
/**
* The value of _entry.id identifies the data block.
@@ -544,6 +627,11 @@ export const mmCIF_Schema = {
*/
id: str,
},
+ /**
+ * Data items in the EXPTL category record details about the
+ * experimental work prior to the intensity measurements and
+ * details about the absorption-correction technique employed.
+ */
exptl: {
/**
* This data item is a pointer to _entry.id in the ENTRY category.
@@ -554,6 +642,10 @@ export const mmCIF_Schema = {
*/
method: Aliased<'X-RAY DIFFRACTION' | 'NEUTRON DIFFRACTION' | 'FIBER DIFFRACTION' | 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'SOLUTION NMR' | 'SOLID-STATE NMR' | 'SOLUTION SCATTERING' | 'POWDER DIFFRACTION' | 'INFRARED SPECTROSCOPY' | 'EPR' | 'FLUORESCENCE TRANSFER' | 'THEORETICAL MODEL'>(str),
},
+ /**
+ * Data items in the STRUCT category record details about the
+ * description of the crystallographic structure.
+ */
struct: {
/**
* This data item is a pointer to _entry.id in the ENTRY category.
@@ -566,6 +658,10 @@ export const mmCIF_Schema = {
*/
title: str,
},
+ /**
+ * Data items in the STRUCT_ASYM category record details about the
+ * structural elements in the asymmetric unit.
+ */
struct_asym: {
/**
* A description of special aspects of this portion of the contents
@@ -594,6 +690,13 @@ export const mmCIF_Schema = {
*/
pdbx_blank_PDB_chainid_flag: Aliased<'Y' | 'N'>(str),
},
+ /**
+ * Data items in the STRUCT_CONF category record details about
+ * the backbone conformation of a segment of polymer.
+ *
+ * Data items in the STRUCT_CONF_TYPE category define the
+ * criteria used to identify the backbone conformations.
+ */
struct_conf: {
/**
* A component of the identifier for the residue at which the
@@ -734,6 +837,14 @@ export const mmCIF_Schema = {
*/
pdbx_PDB_helix_id: str,
},
+ /**
+ * Data items in the STRUCT_CONN category record details about
+ * the connections between portions of the structure. These can be
+ * hydrogen bonds, salt bridges, disulfide bridges and so on.
+ *
+ * The STRUCT_CONN_TYPE records define the criteria used to
+ * identify these connections.
+ */
struct_conn: {
/**
* This data item is a pointer to _struct_conn_type.id in the
@@ -961,6 +1072,11 @@ export const mmCIF_Schema = {
*/
pdbx_value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad'>(str),
},
+ /**
+ * Data items in the STRUCT_CONN_TYPE category record details
+ * about the criteria used to identify interactions between
+ * portions of the structure.
+ */
struct_conn_type: {
/**
* The criteria used to define the interaction.
@@ -976,6 +1092,10 @@ export const mmCIF_Schema = {
*/
reference: str,
},
+ /**
+ * Data items in the STRUCT_KEYWORDS category specify keywords
+ * that describe the chemical structure in this entry.
+ */
struct_keywords: {
/**
* This data item is a pointer to _entry.id in the ENTRY category.
@@ -990,6 +1110,14 @@ export const mmCIF_Schema = {
*/
pdbx_keywords: str,
},
+ /**
+ * Data items in the STRUCT_NCS_OPER category describe the
+ * noncrystallographic symmetry operations.
+ *
+ * Each operator is specified as a matrix and a subsequent
+ * translation vector. Operators need not represent proper
+ * rotations.
+ */
struct_ncs_oper: {
/**
* A code to indicate whether this operator describes a
@@ -1024,6 +1152,13 @@ export const mmCIF_Schema = {
*/
vector: Vector(3),
},
+ /**
+ * Data items in the STRUCT_SHEET_RANGE category record details
+ * about the residue ranges that form a beta-sheet. Residues are
+ * included in a range if they made beta-sheet-type hydrogen-bonding
+ * interactions with at least one adjacent strand and if there are
+ * at least two residues in the range.
+ */
struct_sheet_range: {
/**
* A component of the identifier for the residue at which the
@@ -1145,6 +1280,12 @@ export const mmCIF_Schema = {
*/
pdbx_end_PDB_ins_code: str,
},
+ /**
+ * Data items in the STRUCT_SITE category record details about
+ * portions of the structure that contribute to structurally
+ * relevant sites (e.g. active sites, substrate-binding subsites,
+ * metal-coordination sites).
+ */
struct_site: {
/**
* A description of special aspects of the site.
@@ -1192,6 +1333,11 @@ export const mmCIF_Schema = {
*/
pdbx_auth_ins_code: str,
},
+ /**
+ * Data items in the STRUCT_SITE_GEN category record details about
+ * the generation of portions of the structure that contribute to
+ * structurally relevant sites.
+ */
struct_site_gen: {
/**
* A description of special aspects of the symmetry generation of
@@ -1282,6 +1428,10 @@ export const mmCIF_Schema = {
*/
pdbx_num_res: int,
},
+ /**
+ * Data items in the SYMMETRY category record details about the
+ * space-group symmetry.
+ */
symmetry: {
/**
* This data item is a pointer to _entry.id in the ENTRY category.
@@ -1320,30 +1470,11 @@ export const mmCIF_Schema = {
*/
'space_group_name_H-M': str,
},
- pdbx_struct_assembly: {
- /**
- * Provides details of the method used to determine or
- * compute the assembly.
- */
- method_details: str,
- /**
- * Provides the details of the oligomeric state of the assembly.
- */
- oligomeric_details: str,
- /**
- * The number of polymer molecules in the assembly.
- */
- oligomeric_count: int,
- /**
- * A description of special aspects of the macromolecular assembly.
- */
- details: str,
- /**
- * The value of _pdbx_struct_assembly.id must uniquely identify a record in
- * the PDBX_STRUCT_ASSEMBLY list.
- */
- id: str,
- },
+ /**
+ * Data items in the PDBX_STRUCT_MOD_RESIDUE category list the
+ * modified polymer components in the entry and provide some
+ * details describing the nature of the modification.
+ */
pdbx_struct_mod_residue: {
/**
* The value of _pdbx_struct_mod_residue.id must uniquely identify
@@ -1410,6 +1541,11 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the PDBX_STRUCT_OPER_LIST category describe
+ * Cartesian rotation and translation operations required to
+ * generate or transform the coordinates deposited with this entry.
+ */
pdbx_struct_oper_list: {
/**
* This identifier code must uniquely identify a
@@ -1439,6 +1575,40 @@ export const mmCIF_Schema = {
*/
vector: Vector(3),
},
+ /**
+ * Data items in the PDBX_STRUCT_ASSEMBLY category record details about
+ * the structural elements that form macromolecular assemblies.
+ */
+ pdbx_struct_assembly: {
+ /**
+ * Provides details of the method used to determine or
+ * compute the assembly.
+ */
+ method_details: str,
+ /**
+ * Provides the details of the oligomeric state of the assembly.
+ */
+ oligomeric_details: str,
+ /**
+ * The number of polymer molecules in the assembly.
+ */
+ oligomeric_count: int,
+ /**
+ * A description of special aspects of the macromolecular assembly.
+ */
+ details: str,
+ /**
+ * The value of _pdbx_struct_assembly.id must uniquely identify a record in
+ * the PDBX_STRUCT_ASSEMBLY list.
+ */
+ id: str,
+ },
+ /**
+ * Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about
+ * the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN
+ * data items provide the specifications of the components that
+ * constitute that assembly in terms of cartesian transformations.
+ */
pdbx_struct_assembly_gen: {
/**
* This data item is a pointer to _struct_asym.id in
@@ -1468,6 +1638,10 @@ export const mmCIF_Schema = {
*/
oper_expression: str,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_LIST category record
+ * the list of entities within each reference molecule.
+ */
pdbx_reference_entity_list: {
/**
* The value of _pdbx_reference_entity_list.prd_id is a reference
@@ -1492,6 +1666,10 @@ export const mmCIF_Schema = {
*/
component_id: int,
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about
+ * the linkages between entities within reference molecules.
+ */
pdbx_reference_entity_link: {
/**
* The value of _pdbx_reference_entity_link.link_id uniquely identifies
@@ -1587,6 +1765,11 @@ export const mmCIF_Schema = {
*/
link_class: Aliased<'PP' | 'PN' | 'NP' | 'NN'>(str),
},
+ /**
+ * Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about
+ * polymer linkages including both standard and non-standard linkages between
+ * polymer componnents.
+ */
pdbx_reference_entity_poly_link: {
/**
* The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
@@ -1656,6 +1839,10 @@ export const mmCIF_Schema = {
*/
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
},
+ /**
+ * Data items in the PDBX_MOLECULE category identify reference molecules
+ * within a PDB entry.
+ */
pdbx_molecule: {
/**
* The value of _pdbx_molecule.prd_id is the PDB accession code for this
@@ -1672,6 +1859,10 @@ export const mmCIF_Schema = {
*/
asym_id: str,
},
+ /**
+ * Data items in the PDBX_MOLECULE_FEATURES category record features of molecules
+ * within a PDB entry.
+ */
pdbx_molecule_features: {
/**
* The value of _pdbx_molecule_features.prd_id is the PDB accession code for this
@@ -1695,6 +1886,11 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the IHM_STARTING_MODEL_DETAILS category records the
+ * details about structural models used as starting inputs in
+ * the integrative model building process.
+ */
ihm_starting_model_details: {
/**
* A unique identifier for the starting structural model.
@@ -1750,6 +1946,11 @@ export const mmCIF_Schema = {
*/
dataset_list_id: int,
},
+ /**
+ * Data items in the IHM_STARTING_COMPARATIVE_MODELS category records
+ * additional details about comparative models used as starting inputs in
+ * the integrative model building process.
+ */
ihm_starting_comparative_models: {
/**
* A unique identifier for the starting comparative model.
@@ -1805,6 +2006,15 @@ export const mmCIF_Schema = {
*/
alignment_file_id: int,
},
+ /**
+ * Data items in the IHM_STARTING_MODEL_SEQ_DIF category provide a
+ * mechanism for indicating and annotating point differences
+ * between the sequence of the entity or biological unit described
+ * in the data block and the sequence of the starting model used in
+ * the integrative modeling referenced from a database. The point
+ * differences may be due to point mutations introduced in the
+ * starting model or the presence of modified amino acid residues.
+ */
ihm_starting_model_seq_dif: {
/**
* A unique identifier for the entry.
@@ -1857,6 +2067,12 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the IHM_MODEL_REPRESENTATION category records the
+ * details about the architecture and representation of structural
+ * models created by the integrative model building tasks. This
+ * category handles the multi-scale model representation, if employed.
+ */
ihm_model_representation: {
/**
* A unique identifier for the model details record.
@@ -1918,6 +2134,11 @@ export const mmCIF_Schema = {
*/
model_object_count: int,
},
+ /**
+ * Data items in the IHM_STRUCT_ASSEMBLY category records the
+ * details of the structural assemblies and used in the
+ * IHM modeling.
+ */
ihm_struct_assembly: {
/**
* A unique identifier for the structural assembly description.
@@ -1968,6 +2189,10 @@ export const mmCIF_Schema = {
*/
seq_id_end: int,
},
+ /**
+ * Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides
+ * additional details regarding the structure assembly.
+ */
ihm_struct_assembly_details: {
/**
* A unique identifier for the structural assembly.
@@ -1982,6 +2207,10 @@ export const mmCIF_Schema = {
*/
assembly_description: str,
},
+ /**
+ * Data items in the IHM_MODELING_PROTOCOL category records the
+ * step-wise details of the integrative modeling workflow.
+ */
ihm_modeling_protocol: {
/**
* A unique identifier for the modeling protocol/step combination.
@@ -2049,6 +2278,10 @@ export const mmCIF_Schema = {
*/
ordered_flag: Aliased<'YES' | 'NO'>(str),
},
+ /**
+ * Data items in the IHM_MULTI_STATE_MODELING category records the
+ * details of the multi-state modeling protocol, if applicable.
+ */
ihm_multi_state_modeling: {
/**
* A unique identifier for the multiple states being described.
@@ -2094,6 +2327,11 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the IHM_MODELING_POST_PROCESS category records
+ * the details of the post processing of the models/results of
+ * the modeling protocol.
+ */
ihm_modeling_post_process: {
/**
* A unique identifier for the post modeling analysis/step combination.
@@ -2133,6 +2371,11 @@ export const mmCIF_Schema = {
*/
num_models_end: int,
},
+ /**
+ * Data items in the IHM_ENSEMBLE_INFO category records the
+ * details of the model clusters or ensembles obtained after
+ * sampling.
+ */
ihm_ensemble_info: {
/**
* A unique id for the ensemble.
@@ -2193,6 +2436,10 @@ export const mmCIF_Schema = {
*/
ensemble_file_id: int,
},
+ /**
+ * Data items in the IHM_MODEL_LIST category record the
+ * details of the models being deposited.
+ */
ihm_model_list: {
/**
* A unique identifier for the model / model group combination.
@@ -2246,6 +2493,10 @@ export const mmCIF_Schema = {
*/
representation_id: int,
},
+ /**
+ * Data items in the IHM_MODEL_REPRESENTATIVE category record the
+ * details of the representative model in an ensemble or cluster.
+ */
ihm_model_representative: {
/**
* A unique identifier for the representative of the model group.
@@ -2268,6 +2519,15 @@ export const mmCIF_Schema = {
*/
selection_criteria: Aliased<'medoid' | 'closest to the average' | 'lowest energy' | 'target function' | 'fewest violations' | 'minimized average structure' | 'best scoring model' | 'centroid' | 'other selction criteria'>(str),
},
+ /**
+ * Category holds the list of all datasets used in the IHM modeling.
+ * These can be datasets archived in other related databases such as
+ * BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc., or can be hosted in other
+ * places such as the authors website, github etc. These datasets are
+ * elaborated in detail in the IHM_DATASET_RELATED_DB_REFERENCE and/or
+ * the IHM_DATASET_EXTERNAL_REFERENCE categories. This category
+ * holds the list of all datasets used.
+ */
ihm_dataset_list: {
/**
* A unique identifier for the dataset.
@@ -2283,6 +2543,9 @@ export const mmCIF_Schema = {
*/
database_hosted: Aliased<'YES' | 'NO'>(str),
},
+ /**
+ * Category provides a mechanism to group datasets.
+ */
ihm_dataset_group: {
/**
* A unique identifier for the entry.
@@ -2298,6 +2561,9 @@ export const mmCIF_Schema = {
*/
dataset_list_id: int,
},
+ /**
+ * Category holds information about related datasets, where one is derived from the other.
+ */
ihm_related_datasets: {
/**
* A unique identifier for the entry.
@@ -2316,6 +2582,11 @@ export const mmCIF_Schema = {
*/
dataset_list_id_primary: int,
},
+ /**
+ * Category holds information related to data sources for the entry.
+ * These can be datasets archived in other related databases such as
+ * BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc.
+ */
ihm_dataset_related_db_reference: {
/**
* A unique identifier for the related database entry.
@@ -2344,6 +2615,18 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Category holds links to other external data sources for the I/H model entry.
+ * Input datasets held in other databases such as EMDB, BMRB, SASBDB etc.
+ * are referenced in the IHM_DATASET_RELATED_DB_REFERENCE category.
+ * This data category, along with IHM_EXTERNAL_FILES category, holds information
+ * regarding other non-database external data sources, such as DOIs (digital
+ * object identifiers) or supplementary files stored locally. The DOIs can either
+ * lead to the external data file(s) directly (as in case of DOIs provided by the PDB)
+ * or might lead to an HTML landing page (as provided by Zenodo). In the latter case,
+ * additional URL (Uniform Resource Locator) information is required to retrieve
+ * the external data file(s).
+ */
ihm_external_reference_info: {
/**
* A unique identifier for the external reference.
@@ -2376,6 +2659,12 @@ export const mmCIF_Schema = {
*/
associated_url: str,
},
+ /**
+ * Category provides details regarding external files. The IHM_EXTERNAL_REFERENCE_INFO
+ * category captures the top-level details regarding external data sources.
+ * This category captures the specific details regarding externally stored files
+ * related to the particular I/H model entry.
+ */
ihm_external_files: {
/**
* A unique identifier for each external file.
@@ -2409,6 +2698,10 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Category provides additional details regarding input data hosted externally
+ * at other resources.
+ */
ihm_dataset_external_reference: {
/**
* A unique identifier for the external data.
@@ -2427,6 +2720,13 @@ export const mmCIF_Schema = {
*/
file_id: int,
},
+ /**
+ * Data items in the IHM_LOCALIZATION_DENSITY_FILES category records the
+ * details of files that provide information regarding localization densities
+ * of ensembles. These may be stored externally as local files or linked via
+ * DOI and can be in any accepted format that provides volume information
+ * (CCP4, MRC, etc.).
+ */
ihm_localization_density_files: {
/**
* A unique identifier.
@@ -2464,6 +2764,14 @@ export const mmCIF_Schema = {
*/
asym_id: str,
},
+ /**
+ * Data items in the IHM_PREDICTED_CONTACT_RESTRAINT category records the
+ * list of predicted contacts used in the integrative modeling experiment.
+ * This has been adapted from the widely used CASP RR format
+ * (http://www.predictioncenter.org/casp8/index.cgi?page=format#RR).
+ * These contacts may be derived from various computational tools.
+ * The software information can be provided in the SOFTWARE category.
+ */
ihm_predicted_contact_restraint: {
/**
* A unique identifier for the predicted contact restraint.
@@ -2563,6 +2871,11 @@ export const mmCIF_Schema = {
*/
software_id: int,
},
+ /**
+ * Data items in the IHM_CROSS_LINK_LIST category records the
+ * list of spatial restraints derived from chemical crosslinking
+ * experiment.
+ */
ihm_cross_link_list: {
/**
* A unique identifier for the cross link restraint.
@@ -2628,6 +2941,12 @@ export const mmCIF_Schema = {
*/
dataset_list_id: int,
},
+ /**
+ * Data items in the IHM_CROSS_LINK_RESTRAINT category enumerates the
+ * implementation details of the chemical crosslinking restraints in
+ * the integrative modeling. This category holds the details of how
+ * the experimentally derived crosslinks are applied in the modeling.
+ */
ihm_cross_link_restraint: {
/**
* A unique identifier for the cross link record.
@@ -2740,6 +3059,10 @@ export const mmCIF_Schema = {
*/
sigma_2: float,
},
+ /**
+ * Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the
+ * results of the crosslinking restraint parameters in the IHM modeling.
+ */
ihm_cross_link_result_parameters: {
/**
* A unique identifier for the restraint/model combination.
@@ -2773,6 +3096,10 @@ export const mmCIF_Schema = {
*/
sigma_2: float,
},
+ /**
+ * Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the
+ * details of the 2DEM class averages used in the IHM modeling.
+ */
ihm_2dem_class_average_restraint: {
/**
* A unique identifier for the 2dem class average.
@@ -2829,6 +3156,24 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the IHM_2DEM_CLASS_AVERAGE_FITTING category records the
+ * details of the fitting of the model to the 2DEM class averages
+ * used in the IHM modeling. The following conventions are recommended
+ * while generating the rotation matrix and translation vector for
+ * transformation.
+ *
+ * - The model is rotated and translated to fit to the 2DEM image.
+ * - The 2DEM image should be in the XY plane.
+ * - The lower left image corner (image pixel index 0,0) should be at x,y,z = (0,0,0).
+ * - The 2D image is scaled by the _ihm_2dem_class_average_restraint.pixel_size_width
+ * and _ihm_2dem_class_average_restraint.pixel_size_height from the
+ * IHM_2DEM_CLASS_AVERAGE_RESTRAINT table.
+ * - The transformation is applied after the scaling and hence the translation vector
+ * should account for the scaling.
+ * - There are no specifications for Z translations i.e., how far the image should be
+ * from the model while projecting. It may be set to zero.
+ */
ihm_2dem_class_average_fitting: {
/**
* A unique identifier for the 2dem class average fitting data.
@@ -2859,6 +3204,11 @@ export const mmCIF_Schema = {
*/
tr_vector: Vector(3),
},
+ /**
+ * Data items in the IHM_3DEM_RESTRAINT category records the
+ * details of the 3DEM maps used as restraints in the
+ * IHM modeling.
+ */
ihm_3dem_restraint: {
/**
* A unique identifier for the 3DEM restraint description.
@@ -2902,6 +3252,11 @@ export const mmCIF_Schema = {
*/
cross_correlation_coefficient: float,
},
+ /**
+ * Data items in the IHM_SAS_RESTRAINT category records the
+ * details of the SAS data used as restraints in the
+ * IHM modeling.
+ */
ihm_sas_restraint: {
/**
* A unique identifier for the SAS restraint description.
@@ -2960,6 +3315,11 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the IHM_STARTING_MODEL_COORD category records the coordinates
+ * for structural templates used as starting inputs in the integrative model
+ * building tasks.
+ */
ihm_starting_model_coord: {
/**
* A unique identifier for this coordinate position.
@@ -3030,6 +3390,10 @@ export const mmCIF_Schema = {
*/
B_iso_or_equiv: float,
},
+ /**
+ * Data items in the IHM_SPHERE_OBJ_SITE category records the details
+ * of the spherical objects modeled in the integrative structural model.
+ */
ihm_sphere_obj_site: {
/**
* A unique identifier for this pseudo atom / sphere object.
@@ -3083,6 +3447,10 @@ export const mmCIF_Schema = {
*/
model_id: int,
},
+ /**
+ * Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details
+ * of the gaussian objects modeled in the integrative structural model.
+ */
ihm_gaussian_obj_site: {
/**
* A unique identifier for this gaussian object in the model.
@@ -3135,6 +3503,10 @@ export const mmCIF_Schema = {
*/
model_id: int,
},
+ /**
+ * Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details
+ * of the gaussian objects representing an ensemble or cluster of models.
+ */
ihm_gaussian_obj_ensemble: {
/**
* A unique identifier for this gaussian object.
@@ -3187,6 +3559,10 @@ export const mmCIF_Schema = {
*/
ensemble_id: int,
},
+ /**
+ * IHM_FEATURE_LIST is the high level category that provides defintions
+ * to select atoms/residues from polymeric and non-polymeric entities.
+ */
ihm_feature_list: {
/**
* A unique identifier for the feature.
@@ -3202,6 +3578,11 @@ export const mmCIF_Schema = {
*/
entity_type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
},
+ /**
+ * Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions
+ * required to select a specific residue or a set of residues that may or may not be
+ * in a contiguous range.
+ */
ihm_poly_residue_feature: {
/**
* A unique identifier for the category.
@@ -3246,6 +3627,11 @@ export const mmCIF_Schema = {
*/
seq_id_end: int,
},
+ /**
+ * Data items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the
+ * list of distance restraints used in the integrative modeling experiment.
+ * These distance redistance restraints may be derived from various kinds of experiments.
+ */
ihm_derived_distance_restraint: {
/**
* A unique identifier for the derived distance restraint.