From 01a69004f45cf7fc2007bf6c941fa49e62846306 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 16 Aug 2018 14:35:27 -0700
Subject: [PATCH] added description from dictionary to mmcif schema
---
.../schema-generator/generate-typescript.ts | 39 -
.../schema-generator/schema-from-mmcif-dic.ts | 2 +-
src/apps/schema-generator/util/cif-dic.ts | 77 +-
src/apps/schema-generator/util/generate.ts | 69 +-
src/apps/schema-generator/util/json-schema.ts | 74 -
src/apps/schema-generator/util/schema.ts | 70 +
src/apps/schema-generator/util/validate.ts | 95 -
src/apps/schema-generator/validate-schema.ts | 29 -
src/mol-io/reader/cif/schema/mmcif.ts | 2594 ++++++++++++++++-
.../structure/model/formats/mmcif/atomic.ts | 2 +-
src/mol-util/index.ts | 5 +
11 files changed, 2744 insertions(+), 312 deletions(-)
delete mode 100644 src/apps/schema-generator/generate-typescript.ts
delete mode 100644 src/apps/schema-generator/util/json-schema.ts
create mode 100644 src/apps/schema-generator/util/schema.ts
delete mode 100644 src/apps/schema-generator/util/validate.ts
delete mode 100644 src/apps/schema-generator/validate-schema.ts
diff --git a/src/apps/schema-generator/generate-typescript.ts b/src/apps/schema-generator/generate-typescript.ts
deleted file mode 100644
index fc0a4bd97..000000000
--- a/src/apps/schema-generator/generate-typescript.ts
+++ /dev/null
@@ -1,39 +0,0 @@
-/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import * as argparse from 'argparse'
-import * as fs from 'fs'
-
-import { generate } from './util/generate'
-
-function generateSchema (name: string, path: string) {
- const str = fs.readFileSync(path, 'utf8')
- return generate(name, '', JSON.parse(str))
-}
-
-const parser = new argparse.ArgumentParser({
- addHelp: true,
- description: 'Argparse example'
-});
-parser.addArgument([ 'name' ], {
- help: 'schema name'
-});
-parser.addArgument([ 'path' ], {
- help: 'json schema file path'
-});
-parser.addArgument([ '--out', '-o' ], {
- help: 'generated typescript output path'
-});
-const args = parser.parseArgs();
-
-if (args.name && args.path) {
- const schema = generateSchema(args.name, args.path)
- if (args.out) {
- fs.writeFileSync(args.out, schema)
- } else {
- console.log(schema)
- }
-}
diff --git a/src/apps/schema-generator/schema-from-mmcif-dic.ts b/src/apps/schema-generator/schema-from-mmcif-dic.ts
index 3d6fc0e4b..72dd804af 100644
--- a/src/apps/schema-generator/schema-from-mmcif-dic.ts
+++ b/src/apps/schema-generator/schema-from-mmcif-dic.ts
@@ -13,7 +13,7 @@ import Csv from 'mol-io/reader/csv/parser'
import CIF, { CifFrame } from 'mol-io/reader/cif'
import { generateSchema } from './util/cif-dic'
import { generate } from './util/generate'
-import { Filter } from './util/json-schema'
+import { Filter } from './util/schema'
async function runGenerateSchema(name: string, fieldNamesPath?: string, typescript = false, out?: string) {
await ensureMmcifDicAvailable()
diff --git a/src/apps/schema-generator/util/cif-dic.ts b/src/apps/schema-generator/util/cif-dic.ts
index bd48670c4..6036c7c82 100644
--- a/src/apps/schema-generator/util/cif-dic.ts
+++ b/src/apps/schema-generator/util/cif-dic.ts
@@ -4,11 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Database, ValueColumn, ListColumn } from './json-schema'
+import { Database, Column, EnumCol, StrCol, IntCol, ListCol, FloatCol, CoordCol, MatrixCol, VectorCol } from './schema'
import * as Data from 'mol-io/reader/cif/data-model'
import { CifFrame } from 'mol-io/reader/cif/data-model';
-export function getFieldType (type: string, values?: string[]): ValueColumn|ListColumn {
+export function getFieldType (type: string, description: string, values?: string[]): Column {
switch (type) {
case 'code':
case 'ucode':
@@ -19,11 +19,7 @@ export function getFieldType (type: string, values?: string[]): ValueColumn|List
case 'uchar3':
case 'uchar1':
case 'boolean':
- if (values && values.length) {
- return { enum: [ 'str', values ] }
- } else {
- return 'str'
- }
+ return values && values.length ? EnumCol(values, 'str', description) : StrCol(description)
case 'aliasname':
case 'name':
case 'idname':
@@ -56,24 +52,20 @@ export function getFieldType (type: string, values?: string[]): ValueColumn|List
case 'date_dep':
case 'url':
case 'symop':
- return 'str'
+ return StrCol(description)
case 'int':
case 'non_negative_int':
case 'positive_int':
- if (values && values.length) {
- return { enum: [ 'int', values ] }
- } else {
- return 'int'
- }
+ return values && values.length ? EnumCol(values, 'int', description) : IntCol(description)
case 'float':
- return 'float'
+ return FloatCol(description)
case 'ec-type':
case 'ucode-alphanum-csv':
case 'id_list':
- return { list: [ 'str', ',' ] }
+ return ListCol('str', ',', description)
}
console.log(`unknown type '${type}'`)
- return 'str'
+ return StrCol(description)
}
type FrameCategories = { [category: string]: Data.CifFrame }
@@ -135,6 +127,19 @@ function getSubCategory (d: Data.CifFrame, ctx: FrameData): string|undefined {
}
}
+function getDescription (d: Data.CifFrame, ctx: FrameData): string|undefined {
+ const value = getField('item_description', 'description', d, ctx)
+ if (value) {
+ return value.str(0).trim()
+ .replace(/(\r\n|\r|\n)([ \t]+)/g, '\n')
+ .replace(/(\[[1-3]\])+ element/, 'elements')
+ .replace(/(\[[1-3]\])+/, '')
+ }
+}
+
+const reMatrixField = /\[[1-3]\]\[[1-3]\]/
+const reVectorField = /\[[1-3]\]/
+
const FORCE_INT_FIELDS = [
'_atom_site.id',
'_atom_site.auth_seq_id',
@@ -190,6 +195,7 @@ export function generateSchema (frames: CifFrame[]) {
const links: FrameLinks = {}
const ctx = { categories, links }
+ // build list of links between categories
frames.forEach(d => {
if (d.header[0] !== '_') return
categories[d.header] = d
@@ -213,12 +219,12 @@ export function generateSchema (frames: CifFrame[]) {
Object.keys(categories).forEach(fullName => {
const d = categories[fullName]
if (!d) {
- console.log('foo', fullName)
+ console.log(`${fullName} not found, moving on`)
return
}
const categoryName = d.header.substring(1, d.header.indexOf('.'))
const itemName = d.header.substring(d.header.indexOf('.') + 1)
- let fields
+ let fields: { [k: string]: Column }
if (categoryName in schema) {
fields = schema[categoryName]
} else {
@@ -226,38 +232,41 @@ export function generateSchema (frames: CifFrame[]) {
schema[categoryName] = fields
}
+ const description = getDescription(d, ctx) || ''
+
// need to use regex to check for matrix or vector items
// as sub_category assignment is missing for some entries
const subCategory = getSubCategory(d, ctx)
if (subCategory === 'cartesian_coordinate' || subCategory === 'fractional_coordinate') {
- fields[itemName] = 'coord'
+ fields[itemName] = CoordCol(description)
} else if (FORCE_INT_FIELDS.includes(d.header)) {
- fields[itemName] = 'int'
+ fields[itemName] = IntCol(description)
+ console.log(`forcing int: ${d.header}`)
} else if (subCategory === 'matrix') {
- fields[itemName.replace(/\[[1-3]\]\[[1-3]\]/, '')] = { 'matrix': [ 3, 3 ] }
+ fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description)
} else if (subCategory === 'vector') {
- fields[itemName.replace(/\[[1-3]\]/, '')] = { 'vector': [ 3 ] }
+ fields[itemName.replace(reVectorField, '')] = VectorCol(3, description)
} else {
- if (itemName.match(/\[[1-3]\]\[[1-3]\]/)) {
- fields[itemName.replace(/\[[1-3]\]\[[1-3]\]/, '')] = { 'matrix': [ 3, 3 ] }
+ if (itemName.match(reMatrixField)) {
+ fields[itemName.replace(reMatrixField, '')] = MatrixCol(3, 3, description)
console.log(`${d.header} should have 'matrix' _item_sub_category.id`)
- } else if (itemName.match(/\[[1-3]\]/)) {
- fields[itemName.replace(/\[[1-3]\]/, '')] = { 'vector': [ 3 ] }
+ } else if (itemName.match(reVectorField)) {
+ fields[itemName.replace(reVectorField, '')] = VectorCol(3, description)
console.log(`${d.header} should have 'vector' _item_sub_category.id`)
} else {
const code = getCode(d, ctx)
if (code) {
- let fieldType = getFieldType(code[0], code[1]);
- if (typeof fieldType === 'string') {
+ let fieldType = getFieldType(code[0], description, code[1]);
+ if (fieldType.type === 'str') {
if (COMMA_SEPARATED_LIST_FIELDS.includes(d.header)) {
- fieldType = { 'list': [ 'str', ',' ] };
- console.log(`comma separated: ${d.header}`)
+ fieldType = ListCol('str', ',', description)
+ console.log(`forcing comma separated: ${d.header}`)
} else if (SPACE_SEPARATED_LIST_FIELDS.includes(d.header)) {
- fieldType = { 'list': [ 'str', ' ' ] };
- console.log(`space separated: ${d.header}`)
+ fieldType = ListCol('str', ' ', description)
+ console.log(`forcing space separated: ${d.header}`)
} else if (SEMICOLON_SEPARATED_LIST_FIELDS.includes(d.header)) {
- fieldType = { 'list': [ 'str', ';' ] };
- console.log(`space separated: ${d.header}`)
+ fieldType = ListCol('str', ';', description)
+ console.log(`forcing space separated: ${d.header}`)
}
}
fields[itemName] = fieldType
diff --git a/src/apps/schema-generator/util/generate.ts b/src/apps/schema-generator/util/generate.ts
index 0f1c5d160..8b57095a8 100644
--- a/src/apps/schema-generator/util/generate.ts
+++ b/src/apps/schema-generator/util/generate.ts
@@ -4,8 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { validate } from './validate'
-import { Database, getTypeAndArgs, Filter } from './json-schema'
+import { Database, Filter, Column } from './schema'
+import { indentString } from 'mol-util';
function header (name: string, info: string, importDatabasePath = 'mol-data/db') {
return `/**
@@ -37,54 +37,47 @@ export type ${name}_Schema = typeof ${name}_Schema;
export interface ${name}_Database extends Database<${name}_Schema> {}`
}
-const value: { [k: string]: (...args: any[]) => string } = {
- enum: function (type: string, values: string[]) {
- return `Aliased<'${values.map(v => v.replace(/'/g, '\\\'')).join(`' | '`)}'>(${type})`
- },
- matrix: function (rows: number, cols: number) {
- return `Matrix(${rows}, ${cols})`
- },
- vector: function (dim: number) {
- return `Vector(${dim})`
- },
- list: function (type: 'str'|'int'|'float', separator: string) {
- if (type === 'int') {
- return `List('${separator}', x => parseInt(x, 10))`
- } else if (type === 'float') {
- return `List('${separator}', x => parseFloat(x))`
- } else {
- return `List('${separator}', x => x)`
- }
+function getTypeDef(c: Column): string {
+ switch (c.type) {
+ case 'str': return 'str'
+ case 'int': return 'int'
+ case 'float': return 'float'
+ case 'coord': return 'coord'
+ case 'enum':
+ return `Aliased<'${c.values.map(v => v.replace(/'/g, '\\\'')).join(`' | '`)}'>(${c.subType})`
+ case 'matrix':
+ return `Matrix(${c.rows}, ${c.columns})`
+ case 'vector':
+ return `Vector(${c.length})`
+ case 'list':
+ if (c.subType === 'int') {
+ return `List('${c.separator}', x => parseInt(x, 10))`
+ } else if (c.subType === 'float' || c.subType === 'coord') {
+ return `List('${c.separator}', x => parseFloat(x))`
+ } else {
+ return `List('${c.separator}', x => x)`
+ }
}
}
const reSafePropertyName = /^[a-zA-Z_$][0-9a-zA-Z_$]*$/
-function safePropertyString(name: string) {
- return name.match(reSafePropertyName) ? name : `'${name}'`
-}
+function safePropertyString(name: string) { return name.match(reSafePropertyName) ? name : `'${name}'` }
export function generate (name: string, info: string, schema: Database, fields?: Filter, importDatabasePath?: string) {
- const validationResult = validate(schema)
- if (validationResult !== true) {
- throw validationResult
- }
-
const codeLines: string[] = []
codeLines.push(`export const ${name}_Schema = {`)
Object.keys(schema).forEach(table => {
- if (fields && !fields[ table ]) return
+ if (fields && !fields[table]) return
codeLines.push(` ${safePropertyString(table)}: {`)
- const columns = schema[ table ]
+ const columns = schema[table]
Object.keys(columns).forEach(columnName => {
- if (fields && !fields[ table ][ columnName ]) return
- let typeDef
- const fieldType = columns[ columnName ]
- if (typeof fieldType === 'object') {
- const { type, args } = getTypeAndArgs(fieldType)
- typeDef = value[ type ](...args)
- } else {
- typeDef = fieldType
+ if (fields && !fields[table][columnName]) return
+ const typeDef = getTypeDef(columns[columnName])
+ if (columns[columnName].description) {
+ codeLines.push(` /**`)
+ codeLines.push(`${indentString(columns[columnName].description, 1, ' * ')}`)
+ codeLines.push(` */`)
}
codeLines.push(` ${safePropertyString(columnName)}: ${typeDef},`)
})
diff --git a/src/apps/schema-generator/util/json-schema.ts b/src/apps/schema-generator/util/json-schema.ts
deleted file mode 100644
index ed2e3139e..000000000
--- a/src/apps/schema-generator/util/json-schema.ts
+++ /dev/null
@@ -1,74 +0,0 @@
-/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-export interface Database {
- [ tableName: string ]: Table
-}
-
-export interface Table {
- [ columnName: string ]: Column
-}
-
-export type ValueColumn = IntCol | StrCol | FloatCol | CoordCol | EnumCol
-export type Column = ValueColumn | VectorCol | MatrixCol | ListColumn
-
-type IntCol = 'int'
-type StrCol = 'str'
-type FloatCol = 'float'
-type CoordCol = 'coord'
-
-interface ComplexColumn {
- [ fieldType: string ]: any[]
-}
-
-interface EnumCol extends ComplexColumn {
- enum: [ IntCol | StrCol, string[] ]
-}
-
-interface VectorCol extends ComplexColumn {
- vector: [ number ]
-}
-
-interface MatrixCol extends ComplexColumn {
- matrix: [ number, number ]
-}
-
-export interface ListColumn extends ComplexColumn {
- list: [ ValueColumn, string ]
-}
-
-export function getTypeAndArgs (column: ComplexColumn) {
- const type = Object.keys(column)[0] as string
- const args = column[ type ]
- return { type, args }
-}
-
-export type Filter = { [ table: string ]: { [ column: string ]: true } }
-
-export function mergeFilters (...filters: Filter[]) {
- const n = filters.length
- const mergedFilter: Filter = {}
- const fields: Map<string, number> = new Map()
- filters.forEach(filter => {
- Object.keys(filter).forEach(category => {
- Object.keys(filter[ category ]).forEach(field => {
- const key = `${category}.${field}`
- const value = fields.get(key) || 0
- fields.set(key, value + 1)
- })
- })
- })
- fields.forEach((v, k) => {
- if (v !== n) return
- const [categoryName, fieldName] = k.split('.')
- if (categoryName in mergedFilter) {
- mergedFilter[categoryName][fieldName] = true
- } else {
- mergedFilter[categoryName] = { fieldName: true }
- }
- })
- return mergedFilter
-}
diff --git a/src/apps/schema-generator/util/schema.ts b/src/apps/schema-generator/util/schema.ts
new file mode 100644
index 000000000..3cc2026e7
--- /dev/null
+++ b/src/apps/schema-generator/util/schema.ts
@@ -0,0 +1,70 @@
+/**
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export interface Database { [ tableName: string ]: Table }
+export interface Table { [ columnName: string ]: Column }
+export type Column = IntCol | StrCol | FloatCol | CoordCol | EnumCol | VectorCol | MatrixCol | ListCol
+
+type BaseCol = { description: string }
+
+export type IntCol = { type: 'int' } & BaseCol
+export function IntCol(description: string): IntCol { return { type: 'int', description } }
+
+export type StrCol = { type: 'str' } & BaseCol
+export function StrCol(description: string): StrCol { return { type: 'str', description } }
+
+export type FloatCol = { type: 'float' } & BaseCol
+export function FloatCol(description: string): FloatCol { return { type: 'float', description } }
+
+export type CoordCol = { type: 'coord' } & BaseCol
+export function CoordCol(description: string): CoordCol { return { type: 'coord', description } }
+
+export type EnumCol = { type: 'enum', subType: 'int' | 'str', values: string[] } & BaseCol
+export function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol {
+ return { type: 'enum', description, values, subType }
+}
+
+export type VectorCol = { type: 'vector', length: number } & BaseCol
+export function VectorCol(length: number, description: string): VectorCol {
+ return { type: 'vector', description, length }
+}
+
+export type MatrixCol = { type: 'matrix', rows: number, columns: number } & BaseCol
+export function MatrixCol(columns: number, rows: number, description: string): MatrixCol {
+ return { type: 'matrix', description, columns, rows }
+}
+
+export type ListCol = { type: 'list', subType: 'int' | 'str' | 'float' | 'coord', separator: string } & BaseCol
+export function ListCol(subType: 'int' | 'str' | 'float' | 'coord', separator: string, description: string): ListCol {
+ return { type: 'list', description, separator, subType }
+}
+
+export type Filter = { [ table: string ]: { [ column: string ]: true } }
+
+export function mergeFilters (...filters: Filter[]) {
+ const n = filters.length
+ const mergedFilter: Filter = {}
+ const fields: Map<string, number> = new Map()
+ filters.forEach(filter => {
+ Object.keys(filter).forEach(category => {
+ Object.keys(filter[ category ]).forEach(field => {
+ const key = `${category}.${field}`
+ const value = fields.get(key) || 0
+ fields.set(key, value + 1)
+ })
+ })
+ })
+ fields.forEach((v, k) => {
+ if (v !== n) return
+ const [categoryName, fieldName] = k.split('.')
+ if (categoryName in mergedFilter) {
+ mergedFilter[categoryName][fieldName] = true
+ } else {
+ mergedFilter[categoryName] = { fieldName: true }
+ }
+ })
+ return mergedFilter
+}
diff --git a/src/apps/schema-generator/util/validate.ts b/src/apps/schema-generator/util/validate.ts
deleted file mode 100644
index cda7677ed..000000000
--- a/src/apps/schema-generator/util/validate.ts
+++ /dev/null
@@ -1,95 +0,0 @@
-/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Database, Table, Column } from './json-schema'
-
-const SimpleColumnTypes = [ 'str', 'int', 'float', 'coord' ]
-const ComplexColumnTypes = [ 'enum', 'vector', 'matrix', 'list' ]
-
-function allTrue<T> (list: T[], fn: (e: T) => boolean) {
- return list.reduce((a, v) => a && fn(v), true)
-}
-
-function allString (list: string[]) {
- return list.reduce((a, v) => a && typeof v === 'string', true)
-}
-
-function validateColumn (column: Column): true|Error {
- if (typeof column === 'string') {
- if (!SimpleColumnTypes.includes(column)) {
- return new Error(`simple column types must be one of '${SimpleColumnTypes.join(', ')}' not '${column}'`)
- }
- return true
- } else if (typeof column === 'object') {
- const keys = Object.keys(column)
- if (keys.length !== 1) {
- return new Error(`complex column object must have a single key`)
- }
- const type = keys[0]
- const args = column[ type ]
- if (!Array.isArray(args)) {
- return new Error(`complex column args must be an array`)
- }
- switch (type) {
- case 'enum':
- if (args.length !== 2 && (!allString(args[1]) && !allTrue(args[1], Number.isInteger))) {
- return new Error(`enum column must have all string or all integer args ${args}`)
- }
- break;
- case 'vector':
- if (args.length !== 1 || !allTrue(args, Number.isInteger)) {
- return new Error(`vector column must have one integer arg`)
- }
- break;
- case 'matrix':
- if (args.length !== 2 || !allTrue(args, Number.isInteger)) {
- return new Error(`matrix column must have two integer args`)
- }
- break;
- case 'list':
- if (args.length !== 2 || !allString(args)) {
- return new Error(`list column must have two string args`)
- }
- break;
- default:
- return new Error(`complex column types must be one of '${ComplexColumnTypes.join(', ')}' not '${type}'`)
- }
- return true
- }
- return new Error(`columns must be of type 'object' or 'string' not '${typeof column}'`)
-}
-
-function validateTable (table: Table): true|Error {
- if (typeof table !== 'object') {
- return new Error(`table must be of type 'object' not '${typeof table}'`)
- }
- for (const columnName in table) {
- // could check columnName with regex
- const r = validateColumn(table[columnName])
- if (r !== true) {
- return new Error(`[${columnName}] ${r.message}`)
- }
- }
- return true
-}
-
-function validateDatabase (database: Database): true|Error {
- if (typeof database !== 'object') {
- return new Error(`database must be of type 'object' not '${typeof database}'`)
- }
- for (const tableName in database) {
- // could check tableName with regex
- const r = validateTable(database[tableName])
- if (r !== true) {
- return new Error(`[${tableName}] ${r.message}`)
- }
- }
- return true
-}
-
-export function validate (schema: any): true|Error {
- return validateDatabase(schema)
-}
diff --git a/src/apps/schema-generator/validate-schema.ts b/src/apps/schema-generator/validate-schema.ts
deleted file mode 100644
index 698090c99..000000000
--- a/src/apps/schema-generator/validate-schema.ts
+++ /dev/null
@@ -1,29 +0,0 @@
-/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import * as argparse from 'argparse'
-import * as fs from 'fs'
-
-import { validate } from './util/validate'
-
-function runValidateSchema (path: string) {
- const str = fs.readFileSync(path, 'utf8')
- const result = validate(JSON.parse(str))
- console.log(result === true ? 'valid json schema' : `invalid json schema: "${result}"`)
-}
-
-const parser = new argparse.ArgumentParser({
- addHelp: true,
- description: 'Validate json schema'
-});
-parser.addArgument([ 'path' ], {
- help: 'path to json schema'
-});
-const args = parser.parseArgs();
-
-if (args.path) {
- runValidateSchema(args.path)
-}
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 4e664e087..f395639e8 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.296, IHM 0.132.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -22,686 +22,3278 @@ const List = Schema.List;
export const mmCIF_Schema = {
atom_site: {
+ /**
+ * An alternative identifier for _atom_site.label_asym_id that
+ * may be provided by an author in order to match the identification
+ * used in the publication that describes the structure.
+ */
auth_asym_id: str,
+ /**
+ * An alternative identifier for _atom_site.label_atom_id that
+ * may be provided by an author in order to match the identification
+ * used in the publication that describes the structure.
+ */
auth_atom_id: str,
+ /**
+ * An alternative identifier for _atom_site.label_comp_id that
+ * may be provided by an author in order to match the identification
+ * used in the publication that describes the structure.
+ */
auth_comp_id: str,
+ /**
+ * An alternative identifier for _atom_site.label_seq_id that
+ * may be provided by an author in order to match the identification
+ * used in the publication that describes the structure.
+ *
+ * Note that this is not necessarily a number, that the values do
+ * not have to be positive, and that the value does not have to
+ * correspond to the value of _atom_site.label_seq_id. The value
+ * of _atom_site.label_seq_id is required to be a sequential list
+ * of positive integers.
+ *
+ * The author may assign values to _atom_site.auth_seq_id in any
+ * desired way. For instance, the values may be used to relate
+ * this structure to a numbering scheme in a homologous structure,
+ * including sequence gaps or insertion codes. Alternatively, a
+ * scheme may be used for a truncated polymer that maintains the
+ * numbering scheme of the full length polymer. In all cases, the
+ * scheme used here must match the scheme used in the publication
+ * that describes the structure.
+ */
auth_seq_id: int,
+ /**
+ * Isotropic atomic displacement parameter, or equivalent isotropic
+ * atomic displacement parameter, B~eq~, calculated from the
+ * anisotropic displacement parameters.
+ *
+ * B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)]
+ *
+ * A = the real space cell lengths
+ * a* = the reciprocal space cell lengths
+ * B^ij^ = 8 pi^2^ U^ij^
+ *
+ * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
+ * 775-776.
+ *
+ * The IUCr Commission on Nomenclature recommends against the use
+ * of B for reporting atomic displacement parameters. U, being
+ * directly proportional to B, is preferred.
+ *
+ * Note -
+ *
+ * The particular type of ADP stored in this item is qualified
+ * by item _refine.pdbx_adp_type.
+ */
B_iso_or_equiv: float,
+ /**
+ * The x atom-site coordinate in angstroms specified according to
+ * a set of orthogonal Cartesian axes related to the cell axes as
+ * specified by the description given in
+ * _atom_sites.Cartn_transform_axes.
+ */
Cartn_x: coord,
+ /**
+ * The y atom-site coordinate in angstroms specified according to
+ * a set of orthogonal Cartesian axes related to the cell axes as
+ * specified by the description given in
+ * _atom_sites.Cartn_transform_axes.
+ */
Cartn_y: coord,
+ /**
+ * The z atom-site coordinate in angstroms specified according to
+ * a set of orthogonal Cartesian axes related to the cell axes as
+ * specified by the description given in
+ * _atom_sites.Cartn_transform_axes.
+ */
Cartn_z: coord,
+ /**
+ * The group of atoms to which the atom site belongs. This data
+ * item is provided for compatibility with the original Protein
+ * Data Bank format, and only for that purpose.
+ */
group_PDB: Aliased<'ATOM' | 'HETATM'>(str),
+ /**
+ * The value of _atom_site.id must uniquely identify a record in the
+ * ATOM_SITE list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ *
+ * This data item was introduced to provide compatibility between
+ * small-molecule and macromolecular CIFs. In a small-molecule
+ * CIF, _atom_site_label is the identifier for the atom. In a
+ * macromolecular CIF, the atom identifier is the aggregate of
+ * _atom_site.label_alt_id, _atom_site.label_asym_id,
+ * _atom_site.label_atom_id, _atom_site.label_comp_id and
+ * _atom_site.label_seq_id. For the two types of files to be
+ * compatible, a formal identifier for the category had to be
+ * introduced that was independent of the different modes of
+ * identifying the atoms. For compatibility with older CIFs,
+ * _atom_site_label is aliased to _atom_site.id.
+ */
id: int,
+ /**
+ * A component of the identifier for this atom site.
+ * For further details, see the definition of the ATOM_SITE_ALT
+ * category.
+ *
+ * This data item is a pointer to _atom_sites_alt.id in the
+ * ATOM_SITES_ALT category.
+ */
label_alt_id: str,
+ /**
+ * A component of the identifier for this atom site.
+ * For further details, see the definition of the STRUCT_ASYM
+ * category.
+ *
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
label_asym_id: str,
+ /**
+ * A component of the identifier for this atom site.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
label_atom_id: str,
+ /**
+ * A component of the identifier for this atom site.
+ *
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
label_comp_id: str,
+ /**
+ * This data item is a pointer to _entity.id in the ENTITY category.
+ */
label_entity_id: str,
+ /**
+ * This data item is a pointer to _entity_poly_seq.num in the
+ * ENTITY_POLY_SEQ category.
+ */
label_seq_id: int,
+ /**
+ * The fraction of the atom type present at this site.
+ * The sum of the occupancies of all the atom types at this site
+ * may not significantly exceed 1.0 unless it is a dummy site.
+ */
occupancy: float,
+ /**
+ * This data item is a pointer to _atom_type.symbol in the
+ * ATOM_TYPE category.
+ */
type_symbol: str,
+ /**
+ * PDB insertion code.
+ */
pdbx_PDB_ins_code: str,
+ /**
+ * PDB model number.
+ */
pdbx_PDB_model_num: int,
+ /**
+ * The net integer charge assigned to this atom. This is the
+ * formal charge assignment normally found in chemical diagrams.
+ */
pdbx_formal_charge: int,
+ /**
+ * The model id corresponding to the atom site.
+ * This data item is a pointer to _ihm_model_list.model_id
+ * in the IHM_MODEL_LIST category.
+ */
ihm_model_id: int,
},
atom_sites: {
+ /**
+ * This data item is a pointer to _entry.id in the ENTRY category.
+ */
entry_id: str,
+ /**
+ * The elements of the 3x3 matrix used to transform Cartesian
+ * coordinates in the ATOM_SITE category to fractional coordinates
+ * in the same category. The axial alignments of this
+ * transformation are described in _atom_sites.Cartn_transform_axes.
+ * The 3x1 translation is defined in
+ * _atom_sites.fract_transf_vector[].
+ *
+ * |x'| |11 12 13| |x| |1|
+ * |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
+ * |z'| |31 32 33| |z| |3|
+ */
fract_transf_matrix: Matrix(3, 3),
+ /**
+ * The elements of the three-element vector used to transform
+ * Cartesian coordinates in the ATOM_SITE category to fractional
+ * coordinates in the same category. The axial alignments of this
+ * transformation are described in _atom_sites.Cartn_transform_axes.
+ * The 3x3 rotation is defined in
+ * _atom_sites.fract_transf_matrix[][].
+ *
+ * |x'| |11 12 13| |x| |1|
+ * |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
+ * |z'| |31 32 33| |z| |3|
+ */
fract_transf_vector: Vector(3),
},
cell: {
+ /**
+ * Unit-cell angle alpha of the reported structure in degrees.
+ */
angle_alpha: float,
+ /**
+ * Unit-cell angle beta of the reported structure in degrees.
+ */
angle_beta: float,
+ /**
+ * Unit-cell angle gamma of the reported structure in degrees.
+ */
angle_gamma: float,
+ /**
+ * This data item is a pointer to _entry.id in the ENTRY category.
+ */
entry_id: str,
+ /**
+ * Unit-cell length a corresponding to the structure reported in
+ * angstroms.
+ */
length_a: float,
+ /**
+ * Unit-cell length b corresponding to the structure reported in
+ * angstroms.
+ */
length_b: float,
+ /**
+ * Unit-cell length c corresponding to the structure reported in
+ * angstroms.
+ */
length_c: float,
+ /**
+ * The number of the polymeric chains in a unit cell. In the case
+ * of heteropolymers, Z is the number of occurrences of the most
+ * populous chain.
+ *
+ * This data item is provided for compatibility with the original
+ * Protein Data Bank format, and only for that purpose.
+ */
Z_PDB: int,
+ /**
+ * To further identify unique axis if necessary. E.g., P 21 with
+ * an unique C axis will have 'C' in this field.
+ */
pdbx_unique_axis: str,
},
chem_comp: {
+ /**
+ * The formula for the chemical component. Formulae are written
+ * according to the following rules:
+ *
+ * (1) Only recognized element symbols may be used.
+ *
+ * (2) Each element symbol is followed by a 'count' number. A count
+ * of '1' may be omitted.
+ *
+ * (3) A space or parenthesis must separate each cluster of
+ * (element symbol + count), but in general parentheses are
+ * not used.
+ *
+ * (4) The order of elements depends on whether carbon is
+ * present or not. If carbon is present, the order should be:
+ * C, then H, then the other elements in alphabetical order
+ * of their symbol. If carbon is not present, the elements
+ * are listed purely in alphabetic order of their symbol. This
+ * is the 'Hill' system used by Chemical Abstracts.
+ */
formula: str,
+ /**
+ * Formula mass in daltons of the chemical component.
+ */
formula_weight: float,
+ /**
+ * The value of _chem_comp.id must uniquely identify each item in
+ * the CHEM_COMP list.
+ *
+ * For protein polymer entities, this is the three-letter code for
+ * the amino acid.
+ *
+ * For nucleic acid polymer entities, this is the one-letter code
+ * for the base.
+ */
id: str,
+ /**
+ * 'yes' indicates that this is a 'standard' monomer, 'no'
+ * indicates that it is 'nonstandard'. Nonstandard monomers
+ * should be described in more detail using the
+ * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
+ * _chem_comp.mon_nstd_details data items.
+ */
mon_nstd_flag: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+ /**
+ * The full name of the component.
+ */
name: str,
+ /**
+ * For standard polymer components, the type of the monomer.
+ * Note that monomers that will form polymers are of three types:
+ * linking monomers, monomers with some type of N-terminal (or 5')
+ * cap and monomers with some type of C-terminal (or 3') cap.
+ */
type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
+ /**
+ * Synonym list for the component.
+ */
pdbx_synonyms: List(';', x => x),
},
chem_comp_bond: {
+ /**
+ * The ID of the first of the two atoms that define the bond.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_1: str,
+ /**
+ * The ID of the second of the two atoms that define the bond.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_2: str,
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
comp_id: str,
+ /**
+ * The value that should be taken as the target for the chemical
+ * bond associated with the specified atoms, expressed as a bond
+ * order.
+ */
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ /**
+ * Ordinal index for the component bond list.
+ */
pdbx_ordinal: int,
+ /**
+ * Stereochemical configuration across a double bond.
+ */
pdbx_stereo_config: Aliased<'E' | 'Z' | 'N'>(str),
+ /**
+ * A flag indicating an aromatic bond.
+ */
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
entity: {
+ /**
+ * A description of special aspects of the entity.
+ */
details: str,
+ /**
+ * Formula mass in daltons of the entity.
+ */
formula_weight: float,
+ /**
+ * The value of _entity.id must uniquely identify a record in the
+ * ENTITY list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * The method by which the sample for the entity was produced.
+ * Entities isolated directly from natural sources (tissues, soil
+ * samples etc.) are expected to have further information in the
+ * ENTITY_SRC_NAT category. Entities isolated from genetically
+ * manipulated sources are expected to have further information in
+ * the ENTITY_SRC_GEN category.
+ */
src_method: Aliased<'nat' | 'man' | 'syn'>(str),
+ /**
+ * Defines the type of the entity.
+ *
+ * Polymer entities are expected to have corresponding
+ * ENTITY_POLY and associated entries.
+ *
+ * Non-polymer entities are expected to have corresponding
+ * CHEM_COMP and associated entries.
+ *
+ * Water entities are not expected to have corresponding
+ * entries in the ENTITY category.
+ */
type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
+ /**
+ * A description of the entity.
+ *
+ * Corresponds to the compound name in the PDB format.
+ */
pdbx_description: str,
+ /**
+ * A place holder for the number of molecules of the entity in
+ * the entry.
+ */
pdbx_number_of_molecules: float,
+ /**
+ * Details about any entity mutation(s).
+ */
pdbx_mutation: str,
+ /**
+ * Entity fragment description(s).
+ */
pdbx_fragment: str,
+ /**
+ * Enzyme Commission (EC) number(s)
+ */
pdbx_ec: List(',', x => x),
},
entity_poly: {
+ /**
+ * This data item is a pointer to _entity.id in the ENTITY category.
+ */
entity_id: str,
+ /**
+ * A flag to indicate whether the polymer contains at least
+ * one monomer-to-monomer link different from that implied by
+ * _entity_poly.type.
+ */
nstd_linkage: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+ /**
+ * A flag to indicate whether the polymer contains at least
+ * one monomer that is not considered standard.
+ */
nstd_monomer: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+ /**
+ * The type of the polymer.
+ */
type: Aliased<'polypeptide(D)' | 'polypeptide(L)' | 'polydeoxyribonucleotide' | 'polyribonucleotide' | 'polysaccharide(D)' | 'polysaccharide(L)' | 'polydeoxyribonucleotide/polyribonucleotide hybrid' | 'cyclic-pseudo-peptide' | 'peptide nucleic acid' | 'other'>(str),
+ /**
+ * The PDB strand/chain id(s) corresponding to this polymer entity.
+ */
pdbx_strand_id: List(',', x => x),
+ /**
+ * Chemical sequence expressed as string of one-letter
+ * amino acid codes. Modifications and non-standard
+ * amino acids are coded as X.
+ */
pdbx_seq_one_letter_code: str,
+ /**
+ * Cannonical chemical sequence expressed as string of
+ * one-letter amino acid codes. Modifications are coded
+ * as the parent amino acid where possible.
+ *
+ * A for alanine or adenine
+ * B for ambiguous asparagine/aspartic-acid
+ * R for arginine
+ * N for asparagine
+ * D for aspartic-acid
+ * C for cysteine or cystine or cytosine
+ * Q for glutamine
+ * E for glutamic-acid
+ * Z for ambiguous glutamine/glutamic acid
+ * G for glycine or guanine
+ * H for histidine
+ * I for isoleucine
+ * L for leucine
+ * K for lysine
+ * M for methionine
+ * F for phenylalanine
+ * P for proline
+ * S for serine
+ * T for threonine or thymine
+ * W for tryptophan
+ * Y for tyrosine
+ * V for valine
+ * U for uracil
+ */
pdbx_seq_one_letter_code_can: str,
+ /**
+ * For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.
+ */
pdbx_target_identifier: str,
},
entity_poly_seq: {
+ /**
+ * This data item is a pointer to _entity.id in the ENTITY category.
+ */
entity_id: str,
+ /**
+ * A flag to indicate whether this monomer in the polymer is
+ * heterogeneous in sequence.
+ */
hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
mon_id: str,
+ /**
+ * The value of _entity_poly_seq.num must uniquely and sequentially
+ * identify a record in the ENTITY_POLY_SEQ list.
+ *
+ * Note that this item must be a number and that the sequence
+ * numbers must progress in increasing numerical order.
+ */
num: int,
},
entry: {
+ /**
+ * The value of _entry.id identifies the data block.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
},
exptl: {
+ /**
+ * This data item is a pointer to _entry.id in the ENTRY category.
+ */
entry_id: str,
+ /**
+ * The method used in the experiment.
+ */
method: Aliased<'X-RAY DIFFRACTION' | 'NEUTRON DIFFRACTION' | 'FIBER DIFFRACTION' | 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'SOLUTION NMR' | 'SOLID-STATE NMR' | 'SOLUTION SCATTERING' | 'POWDER DIFFRACTION' | 'INFRARED SPECTROSCOPY' | 'EPR' | 'FLUORESCENCE TRANSFER' | 'THEORETICAL MODEL'>(str),
},
struct: {
+ /**
+ * This data item is a pointer to _entry.id in the ENTRY category.
+ */
entry_id: str,
+ /**
+ * A title for the data block. The author should attempt to convey
+ * the essence of the structure archived in the CIF in the title,
+ * and to distinguish this structural result from others.
+ */
title: str,
},
struct_asym: {
+ /**
+ * A description of special aspects of this portion of the contents
+ * of the asymmetric unit.
+ */
details: str,
+ /**
+ * This data item is a pointer to _entity.id in the ENTITY category.
+ */
entity_id: str,
+ /**
+ * The value of _struct_asym.id must uniquely identify a record in
+ * the STRUCT_ASYM list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * This data item indicates whether the structural elements are modified.
+ */
pdbx_modified: str,
+ /**
+ * A flag indicating that this entity was originally labeled
+ * with a blank PDB chain id.
+ */
pdbx_blank_PDB_chainid_flag: Aliased<'Y' | 'N'>(str),
},
struct_conf: {
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment begins.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
beg_label_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment begins.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in
+ * the ATOM_SITE category.
+ */
beg_label_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment begins.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
beg_label_seq_id: int,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment begins.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
beg_auth_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment begins.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in
+ * the ATOM_SITE category.
+ */
beg_auth_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment begins.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
beg_auth_seq_id: int,
+ /**
+ * This data item is a pointer to _struct_conf_type.id in the
+ * STRUCT_CONF_TYPE category.
+ */
conf_type_id: Aliased<'HELX_P' | 'HELX_OT_P' | 'HELX_RH_P' | 'HELX_RH_OT_P' | 'HELX_RH_AL_P' | 'HELX_RH_GA_P' | 'HELX_RH_OM_P' | 'HELX_RH_PI_P' | 'HELX_RH_27_P' | 'HELX_RH_3T_P' | 'HELX_RH_PP_P' | 'HELX_LH_P' | 'HELX_LH_OT_P' | 'HELX_LH_AL_P' | 'HELX_LH_GA_P' | 'HELX_LH_OM_P' | 'HELX_LH_PI_P' | 'HELX_LH_27_P' | 'HELX_LH_3T_P' | 'HELX_LH_PP_P' | 'HELX_N' | 'HELX_OT_N' | 'HELX_RH_N' | 'HELX_RH_OT_N' | 'HELX_RH_A_N' | 'HELX_RH_B_N' | 'HELX_RH_Z_N' | 'HELX_LH_N' | 'HELX_LH_OT_N' | 'HELX_LH_A_N' | 'HELX_LH_B_N' | 'HELX_LH_Z_N' | 'TURN_P' | 'TURN_OT_P' | 'TURN_TY1_P' | 'TURN_TY1P_P' | 'TURN_TY2_P' | 'TURN_TY2P_P' | 'TURN_TY3_P' | 'TURN_TY3P_P' | 'STRN'>(str),
+ /**
+ * A description of special aspects of the conformation assignment.
+ */
details: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
end_label_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
end_label_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
end_label_seq_id: int,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
end_auth_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
end_auth_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
end_auth_seq_id: int,
+ /**
+ * The value of _struct_conf.id must uniquely identify a record in
+ * the STRUCT_CONF list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment starts.
+ */
pdbx_beg_PDB_ins_code: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * conformation segment ends.
+ */
pdbx_end_PDB_ins_code: str,
+ /**
+ * This item is a place holder for the helix class used in the PDB
+ * HELIX record.
+ */
pdbx_PDB_helix_class: str,
+ /**
+ * A placeholder for the lengths of the helix of the PDB
+ * HELIX record.
+ */
pdbx_PDB_helix_length: int,
+ /**
+ * A placeholder for the helix identifier of the PDB
+ * HELIX record.
+ */
pdbx_PDB_helix_id: str,
},
struct_conn: {
+ /**
+ * This data item is a pointer to _struct_conn_type.id in the
+ * STRUCT_CONN_TYPE category.
+ */
conn_type_id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
+ /**
+ * A description of special aspects of the connection.
+ */
details: str,
+ /**
+ * The value of _struct_conn.id must uniquely identify a record in
+ * the STRUCT_CONN list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
ptnr1_label_asym_id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
ptnr1_label_atom_id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
ptnr1_label_comp_id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
ptnr1_label_seq_id: int,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
ptnr1_auth_asym_id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
ptnr1_auth_comp_id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
ptnr1_auth_seq_id: int,
+ /**
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _struct_conn.ptnr1_label* to generate the
+ * first partner in the structure connection.
+ */
ptnr1_symmetry: str,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
ptnr2_label_asym_id: str,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
ptnr2_label_atom_id: str,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
ptnr2_label_comp_id: str,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
ptnr2_label_seq_id: int,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
ptnr2_auth_asym_id: str,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
ptnr2_auth_comp_id: str,
+ /**
+ * A component of the identifier for partner 2 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
ptnr2_auth_seq_id: int,
+ /**
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _struct_conn.ptnr2_label* to generate the
+ * second partner in the structure connection.
+ */
ptnr2_symmetry: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
+ * ATOM_SITE category.
+ */
pdbx_ptnr1_PDB_ins_code: str,
+ /**
+ * A component of the identifier for partner 1 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_alt_id in the ATOM_SITE category.
+ */
pdbx_ptnr1_label_alt_id: str,
+ /**
+ * A placeholder for the standard residue name found in
+ * the MODRES record of a PDB file.
+ */
pdbx_ptnr1_standard_comp_id: str,
+ /**
+ * A component of the identifier for partner 1 of the structure
+ * connection.
+ *
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
+ * ATOM_SITE category.
+ */
pdbx_ptnr2_PDB_ins_code: str,
+ /**
+ * A component of the identifier for partner 2 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_alt_id in the ATOM_SITE category.
+ */
pdbx_ptnr2_label_alt_id: str,
+ /**
+ * A component of the identifier for partner 3 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
+ */
pdbx_ptnr3_PDB_ins_code: str,
+ /**
+ * A component of the identifier for partner 3 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_alt_id in the ATOM_SITE category.
+ */
pdbx_ptnr3_label_alt_id: str,
+ /**
+ * A component of the identifier for partner 3 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_asym_id in the ATOM_SITE category.
+ */
pdbx_ptnr3_label_asym_id: str,
+ /**
+ * A component of the identifier for partner 3 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_atom_id in the ATOM_SITE category.
+ */
pdbx_ptnr3_label_atom_id: str,
+ /**
+ * A component of the identifier for partner 3 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_comp_id in the ATOM_SITE category.
+ */
pdbx_ptnr3_label_comp_id: str,
+ /**
+ * A component of the identifier for partner 1 of the
+ * structure connection. This data item is a pointer to
+ * _atom_site.label_seq_id in the ATOM_SITE category.
+ */
pdbx_ptnr3_label_seq_id: int,
+ /**
+ * A placeholder for the PDB id in the case the category
+ * is used to hold the information of the MODRES record of
+ * a PDB file.
+ */
pdbx_PDB_id: str,
+ /**
+ * Distance value for this contact.
+ */
pdbx_dist_value: float,
+ /**
+ * The chemical bond order associated with the specified atoms in
+ * this contact.
+ */
pdbx_value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad'>(str),
},
struct_conn_type: {
+ /**
+ * The criteria used to define the interaction.
+ */
criteria: str,
+ /**
+ * The chemical or structural type of the interaction.
+ */
id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
+ /**
+ * A reference that specifies the criteria used to define the
+ * interaction.
+ */
reference: str,
},
struct_keywords: {
+ /**
+ * This data item is a pointer to _entry.id in the ENTRY category.
+ */
entry_id: str,
+ /**
+ * Keywords describing this structure.
+ */
text: List(',', x => x),
+ /**
+ * Terms characterizing the macromolecular structure.
+ */
pdbx_keywords: str,
},
struct_ncs_oper: {
+ /**
+ * A code to indicate whether this operator describes a
+ * relationship between coordinates all of which are given in the
+ * data block (in which case the value of code is 'given'), or
+ * whether the operator is used to generate new coordinates from
+ * those that are given in the data block (in which case the value
+ * of code is 'generate').
+ */
code: Aliased<'given' | 'generate'>(str),
+ /**
+ * A description of special aspects of the noncrystallographic
+ * symmetry operator.
+ */
details: str,
+ /**
+ * The value of _struct_ncs_oper.id must uniquely identify a
+ * record in the STRUCT_NCS_OPER list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * The elements of the 3x3 matrix component of a
+ * noncrystallographic symmetry operation.
+ */
matrix: Matrix(3, 3),
+ /**
+ * The elements of the three-element vector component of a
+ * noncrystallographic symmetry operation.
+ */
vector: Vector(3),
},
struct_sheet_range: {
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range begins.
+ *
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
beg_label_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range begins.
+ *
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
beg_label_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range begins.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
beg_label_seq_id: int,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range ends.
+ *
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
end_label_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range ends.
+ *
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
end_label_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range ends.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
end_label_seq_id: int,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range begins.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
beg_auth_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range begins.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in
+ * the ATOM_SITE category.
+ */
beg_auth_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range begins.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
beg_auth_seq_id: int,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range ends.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
end_auth_asym_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range ends.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
end_auth_comp_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta-sheet range ends.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
end_auth_seq_id: int,
+ /**
+ * The value of _struct_sheet_range.id must uniquely identify a
+ * range in a given sheet in the STRUCT_SHEET_RANGE list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * This data item is a pointer to _struct_sheet.id in the
+ * STRUCT_SHEET category.
+ */
sheet_id: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta sheet range begins. Insertion code.
+ */
pdbx_beg_PDB_ins_code: str,
+ /**
+ * A component of the identifier for the residue at which the
+ * beta sheet range ends. Insertion code.
+ */
pdbx_end_PDB_ins_code: str,
},
struct_site: {
+ /**
+ * A description of special aspects of the site.
+ */
details: str,
+ /**
+ * The value of _struct_site.id must uniquely identify a record in
+ * the STRUCT_SITE list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * Number of residues in the site.
+ */
pdbx_num_residues: int,
+ /**
+ * Source of evidence supporting the assignment of this site.
+ */
pdbx_evidence_code: str,
+ /**
+ * A component of the identifier for the ligand in the site.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
pdbx_auth_asym_id: str,
+ /**
+ * A component of the identifier for the ligand in the site.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
pdbx_auth_comp_id: str,
+ /**
+ * A component of the identifier for the ligand in the site.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
pdbx_auth_seq_id: str,
+ /**
+ * PDB insertion code for the ligand in the site.
+ */
pdbx_auth_ins_code: str,
},
struct_site_gen: {
+ /**
+ * A description of special aspects of the symmetry generation of
+ * this portion of the structural site.
+ */
details: str,
+ /**
+ * The value of _struct_site_gen.id must uniquely identify a record
+ * in the STRUCT_SITE_GEN list.
+ *
+ * Note that this item need not be a number; it can be any unique
+ * identifier.
+ */
id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_sites_alt.id in the
+ * ATOM_SITES_ALT category.
+ */
label_alt_id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
label_asym_id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
label_atom_id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
label_comp_id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
label_seq_id: int,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
auth_asym_id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
auth_comp_id: str,
+ /**
+ * A component of the identifier for participants in the site.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
auth_seq_id: str,
+ /**
+ * This data item is a pointer to _struct_site.id in the STRUCT_SITE
+ * category.
+ */
site_id: str,
+ /**
+ * Describes the symmetry operation that should be applied to the
+ * atom set specified by _struct_site_gen.label* to generate a
+ * portion of the site.
+ */
symmetry: str,
+ /**
+ * PDB insertion code.
+ */
pdbx_auth_ins_code: str,
+ /**
+ * Number of residues in the site.
+ */
pdbx_num_res: int,
},
symmetry: {
+ /**
+ * This data item is a pointer to _entry.id in the ENTRY category.
+ */
entry_id: str,
+ /**
+ * The cell settings for this space-group symmetry.
+ */
cell_setting: Aliased<'triclinic' | 'monoclinic' | 'orthorhombic' | 'tetragonal' | 'rhombohedral' | 'trigonal' | 'hexagonal' | 'cubic'>(str),
+ /**
+ * Space-group number from International Tables for Crystallography
+ * Vol. A (2002).
+ */
Int_Tables_number: int,
+ /**
+ * Space-group symbol as described by Hall (1981). This symbol
+ * gives the space-group setting explicitly. Leave spaces between
+ * the separate components of the symbol.
+ *
+ * Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
+ * (1981) A37, 921.
+ */
space_group_name_Hall: str,
+ /**
+ * Hermann-Mauguin space-group symbol. Note that the
+ * Hermann-Mauguin symbol does not necessarily contain complete
+ * information about the symmetry and the space-group origin. If
+ * used, always supply the FULL symbol from International Tables
+ * for Crystallography Vol. A (2002) and indicate the origin and
+ * the setting if it is not implicit. If there is any doubt that
+ * the equivalent positions can be uniquely deduced from this
+ * symbol, specify the _symmetry_equiv.pos_as_xyz or
+ * _symmetry.space_group_name_Hall data items as well. Leave
+ * spaces between symbols referring to
+ * different axes.
+ */
'space_group_name_H-M': str,
},
pdbx_struct_assembly: {
+ /**
+ * Provides details of the method used to determine or
+ * compute the assembly.
+ */
method_details: str,
+ /**
+ * Provides the details of the oligomeric state of the assembly.
+ */
oligomeric_details: str,
+ /**
+ * The number of polymer molecules in the assembly.
+ */
oligomeric_count: int,
+ /**
+ * A description of special aspects of the macromolecular assembly.
+ */
details: str,
+ /**
+ * The value of _pdbx_struct_assembly.id must uniquely identify a record in
+ * the PDBX_STRUCT_ASSEMBLY list.
+ */
id: str,
},
pdbx_struct_mod_residue: {
+ /**
+ * The value of _pdbx_struct_mod_residue.id must uniquely identify
+ * each item in the PDBX_STRUCT_MOD_RESIDUE list.
+ *
+ * This is an integer serial number.
+ */
id: int,
+ /**
+ * Part of the identifier for the modified polymer component.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
auth_asym_id: str,
+ /**
+ * Part of the identifier for the modified polymer component.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
auth_comp_id: str,
+ /**
+ * Part of the identifier for the modified polymer component.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
auth_seq_id: int,
+ /**
+ * Part of the identifier for the modified polymer component.
+ *
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
+ * ATOM_SITE category.
+ */
PDB_ins_code: str,
+ /**
+ * Part of the identifier for the modified polymer component.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
label_asym_id: str,
+ /**
+ * Part of the identifier for the modified polymer component.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
label_comp_id: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
label_seq_id: int,
+ /**
+ * The parent component identifier for this modified polymer component.
+ */
parent_comp_id: str,
+ /**
+ * Details of the modification for this polymer component.
+ */
details: str,
},
pdbx_struct_oper_list: {
+ /**
+ * This identifier code must uniquely identify a
+ * record in the PDBX_STRUCT_OPER_LIST list.
+ */
id: str,
+ /**
+ * A code to indicate the type of operator.
+ */
type: Aliased<'identity operation' | 'point symmetry operation' | 'helical symmetry operation' | 'crystal symmetry operation' | '3D crystal symmetry operation' | '2D crystal symmetry operation' | 'transform to point frame' | 'transform to helical frame' | 'transform to crystal frame' | 'transform to 2D crystal frame' | 'transform to 3D crystal frame' | 'build point asymmetric unit' | 'build helical asymmetric unit' | 'build 2D crystal asymmetric unit' | 'build 3D crystal asymmetric unit'>(str),
+ /**
+ * A descriptive name for the transformation operation.
+ */
name: str,
+ /**
+ * The symmetry operation corresponding to the transformation operation.
+ */
symmetry_operation: str,
+ /**
+ * The elements of the 3x3 matrix component of the
+ * transformation operation.
+ */
matrix: Matrix(3, 3),
+ /**
+ * The elements of the three-element vector component of the
+ * transformation operation.
+ */
vector: Vector(3),
},
pdbx_struct_assembly_gen: {
+ /**
+ * This data item is a pointer to _struct_asym.id in
+ * the STRUCT_ASYM category.
+ *
+ * This item may be expressed as a comma separated list of identifiers.
+ */
asym_id_list: List(',', x => x),
+ /**
+ * This data item is a pointer to _pdbx_struct_assembly.id in the
+ * PDBX_STRUCT_ASSEMBLY category.
+ */
assembly_id: str,
+ /**
+ * Identifies the operation of collection of operations
+ * from category PDBX_STRUCT_OPER_LIST.
+ *
+ * Operation expressions may have the forms:
+ *
+ * (1) the single operation 1
+ * (1,2,5) the operations 1, 2, 5
+ * (1-4) the operations 1,2,3 and 4
+ * (1,2)(3,4) the combinations of operations
+ * 3 and 4 followed by 1 and 2 (i.e.
+ * the cartesian product of parenthetical
+ * groups applied from right to left)
+ */
oper_expression: str,
},
pdbx_reference_entity_list: {
+ /**
+ * The value of _pdbx_reference_entity_list.prd_id is a reference
+ * _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier
+ * the a constituent entity within this reference molecule.
+ */
ref_entity_id: str,
+ /**
+ * Defines the polymer characteristic of the entity.
+ */
type: str,
+ /**
+ * Additional details about this entity.
+ */
details: str,
+ /**
+ * The component number of this entity within the molecule.
+ */
component_id: int,
},
pdbx_reference_entity_link: {
+ /**
+ * The value of _pdbx_reference_entity_link.link_id uniquely identifies
+ * linkages between entities with a molecule.
+ */
link_id: int,
+ /**
+ * The value of _pdbx_reference_entity_link.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
prd_id: str,
+ /**
+ * A description of special aspects of a linkage between
+ * chemical components in the structure.
+ */
details: str,
+ /**
+ * The reference entity id of the first of the two entities joined by the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id_1: str,
+ /**
+ * The reference entity id of the second of the two entities joined by the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_list.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_LIST category.
+ */
ref_entity_id_2: str,
+ /**
+ * For a polymer entity, the sequence number in the first of
+ * the two entities containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_1: int,
+ /**
+ * For a polymer entity, the sequence number in the second of
+ * the two entities containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_2: int,
+ /**
+ * The component identifier in the first of the two entities containing the linkage.
+ *
+ * For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ *
+ * For non-polymer entities, this data item is a pointer to
+ * _pdbx_reference_entity_nonpoly.chem_comp_id in the
+ * PDBX_REFERENCE_ENTITY_NONPOLY category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier in the second of the two entities containing the linkage.
+ *
+ * For polymer entities, this data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ *
+ * For non-polymer entities, this data item is a pointer to
+ * _pdbx_reference_entity_nonpoly.chem_comp_id in the
+ * PDBX_REFERENCE_ENTITY_NONPOLY category.
+ */
comp_id_2: str,
+ /**
+ * The atom identifier/name in the first of the two entities containing the linkage.
+ */
atom_id_1: str,
+ /**
+ * The atom identifier/name in the second of the two entities containing the linkage.
+ */
atom_id_2: str,
+ /**
+ * The bond order target for the chemical linkage.
+ */
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ /**
+ * The entity component identifier for the first of two entities containing the linkage.
+ */
component_1: int,
+ /**
+ * The entity component identifier for the second of two entities containing the linkage.
+ */
component_2: int,
+ /**
+ * A code indicating the entity types involved in the linkage.
+ */
link_class: Aliased<'PP' | 'PN' | 'NP' | 'NN'>(str),
},
pdbx_reference_entity_poly_link: {
+ /**
+ * The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies
+ * a linkage within a polymer entity.
+ */
link_id: int,
+ /**
+ * The value of _pdbx_reference_entity_poly_link.prd_id is a reference
+ * _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
prd_id: str,
+ /**
+ * The reference entity id of the polymer entity containing the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id
+ * in the PDBX_REFERENCE_ENTITY_POLY category.
+ */
ref_entity_id: str,
+ /**
+ * The entity component identifier entity containing the linkage.
+ */
component_id: int,
+ /**
+ * For a polymer entity, the sequence number in the first of
+ * the two components making the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_1: int,
+ /**
+ * For a polymer entity, the sequence number in the second of
+ * the two components making the linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.num
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
entity_seq_num_2: int,
+ /**
+ * The component identifier in the first of the two components making the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier in the second of the two components making the
+ * linkage.
+ *
+ * This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id
+ * in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.
+ */
comp_id_2: str,
+ /**
+ * The atom identifier/name in the first of the two components making
+ * the linkage.
+ */
atom_id_1: str,
+ /**
+ * The atom identifier/name in the second of the two components making
+ * the linkage.
+ */
atom_id_2: str,
+ /**
+ * The bond order target for the non-standard linkage.
+ */
value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
},
pdbx_molecule: {
+ /**
+ * The value of _pdbx_molecule.prd_id is the PDB accession code for this
+ * reference molecule.
+ */
prd_id: str,
+ /**
+ * The value of _pdbx_molecule.instance_id is identifies a particular molecule
+ * in the molecule list.
+ */
instance_id: int,
+ /**
+ * A reference to _struct_asym.id in the STRUCT_ASYM category.
+ */
asym_id: str,
},
pdbx_molecule_features: {
+ /**
+ * The value of _pdbx_molecule_features.prd_id is the PDB accession code for this
+ * reference molecule.
+ */
prd_id: str,
+ /**
+ * Broadly defines the function of the molecule.
+ */
class: Aliased<'Antagonist' | 'Antibiotic' | 'Anticancer' | 'Anticoagulant' | 'Antifungal' | 'Antiinflammatory' | 'Antimicrobial' | 'Antineoplastic' | 'Antiparasitic' | 'Antiretroviral' | 'Anthelmintic' | 'Antithrombotic' | 'Antitumor' | 'Antiviral' | 'CASPASE inhibitor' | 'Chaperone binding' | 'Enzyme inhibitor' | 'Growth factor' | 'Immunosuppressant' | 'Inhibitor' | 'Lantibiotic' | 'Metabolism' | 'Metal transport' | 'Oxidation-reduction' | 'Receptor' | 'Thrombin inhibitor' | 'Trypsin inhibitor' | 'Toxin' | 'Transport activator' | 'Unknown' | 'Anticoagulant, Antithrombotic' | 'Antibiotic, Antimicrobial' | 'Antibiotic, Anthelmintic' | 'Antibiotic, Antineoplastic' | 'Antimicrobial, Antiretroviral' | 'Antimicrobial, Antitumor' | 'Antimicrobial, Antiparasitic, Antibiotic' | 'Thrombin inhibitor, Trypsin inhibitor'>(str),
+ /**
+ * Defines the structural classification of the molecule.
+ */
type: Aliased<'Amino acid' | 'Aminoglycoside' | 'Anthracycline' | 'Anthraquinone' | 'Ansamycin' | 'Chalkophore' | 'Chromophore' | 'Glycopeptide' | 'Cyclic depsipeptide' | 'Cyclic lipopeptide' | 'Cyclic peptide' | 'Heterocyclic' | 'Imino sugar' | 'Keto acid' | 'Lipoglycopeptide' | 'Lipopeptide' | 'Macrolide' | 'Non-polymer' | 'Nucleoside' | 'Oligopeptide' | 'Oligosaccharide' | 'Peptaibol' | 'Peptide-like' | 'Polycyclic' | 'Polypeptide' | 'Polysaccharide' | 'Quinolone' | 'Thiolactone' | 'Thiopeptide' | 'Siderophore' | 'Unknown' | 'Chalkophore, Polypeptide'>(str),
+ /**
+ * A name of the molecule.
+ */
name: str,
+ /**
+ * Additional details describing the molecule.
+ */
details: str,
},
ihm_starting_model_details: {
+ /**
+ * A unique identifier for the starting structural model.
+ */
starting_model_id: str,
+ /**
+ * A unique identifier for the distinct molecular entities.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * A text description of the molecular entity
+ */
entity_description: str,
+ /**
+ * An asym/strand identifier for the entity molecule.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The leading residue index for the sequence segment modeled using this starting model.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_begin: int,
+ /**
+ * The trailing residue index for the sequence segment modeled using this starting model.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_end: int,
+ /**
+ * The source of the starting model.
+ */
starting_model_source: Aliased<'comparative model' | 'experimental model' | 'integrative model' | 'ab initio model' | 'other'>(str),
+ /**
+ * The author assigned chainId/auth_asym_id corresponding to this starting model.
+ * This corresponds to the chainId/auth_asym_id of the experimental models in the
+ * PDB or comparative models in the Model Archive or the starting models referenced
+ * via a DOI. If starting models are included in IHM_STARTING_MODEL_COORD, then
+ * this will be the same as _ihm_starting_model_details.asym_id.
+ */
starting_model_auth_asym_id: str,
+ /**
+ * The offset in residue numbering between the starting model and the deposited I/H model, if applicable.
+ * I/H model residue number = Starting model residue number + offset
+ */
starting_model_sequence_offset: int,
+ /**
+ * Identifier to the starting model (comparative, experimental or integrative)
+ * used as input in the integrative modeling.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
},
ihm_starting_comparative_models: {
+ /**
+ * A unique identifier for the starting comparative model.
+ */
ordinal_id: int,
+ /**
+ * The identifier for the starting structural model.
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id
+ * in the IHM_STARTING_MODEL_DETAILS category.
+ */
starting_model_id: str,
+ /**
+ * The chainId/auth_asym_id corresponding to the starting model.
+ */
starting_model_auth_asym_id: str,
+ /**
+ * The starting residue index of the starting model.
+ */
starting_model_seq_id_begin: int,
+ /**
+ * The ending residue index of the starting model.
+ */
starting_model_seq_id_end: int,
+ /**
+ * The chainId/auth_asym_id corresponding to the template.
+ */
template_auth_asym_id: str,
+ /**
+ * The starting residue index of the template.
+ */
template_seq_id_begin: int,
+ /**
+ * The ending residue index of the template.
+ */
template_seq_id_end: int,
+ /**
+ * The percentage sequence identity between the template sequence and the comparative model sequence.
+ */
template_sequence_identity: float,
+ /**
+ * The denominator used while calculating the sequence identity provided in
+ * _ihm_starting_comparative_models.template_sequence_identity.
+ */
template_sequence_identity_denominator: Aliased<'1' | '2' | '3' | '4' | '5'>(int),
+ /**
+ * The dataset list id corresponding to the template used to obtain the comparative model.
+ * This data item is a pointer to _ihm_dataset_list.id in the IHM_DATASET_LIST category.
+ */
template_dataset_list_id: int,
+ /**
+ * The file id corresponding to the sequence alignment of the template sequence and the comparative model sequence.
+ * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
+ */
alignment_file_id: int,
},
ihm_starting_model_seq_dif: {
+ /**
+ * A unique identifier for the entry.
+ */
ordinal_id: int,
+ /**
+ * A unique identifier for the distinct molecular entities.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * An asym/strand identifier for the entity molecule.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The residue index.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id: int,
+ /**
+ * The component identifier for the residue.
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id: str,
+ /**
+ * Unique identifier for the starting model record.
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id in the
+ * IHM_STARTING_MODEL_DETAILS category.
+ */
starting_model_id: str,
+ /**
+ * The asym/strand identifier for the entity molecule of the database starting model.
+ */
db_asym_id: str,
+ /**
+ * The corresponding residue index of the database starting model.
+ */
db_seq_id: int,
+ /**
+ * The correspinding component identifier for the residue in the database starting model.
+ */
db_comp_id: str,
+ /**
+ * A description of special aspects of the point differences
+ * between the sequence of the entity or biological unit described
+ * in the data block and that in the starting model referenced
+ * from a database.
+ */
details: str,
},
ihm_model_representation: {
+ /**
+ * A unique identifier for the model details record.
+ */
ordinal_id: int,
+ /**
+ * An identifier that collects or groups together a set of representations.
+ * This data item may be used to identify a complete model representation.
+ */
representation_id: int,
+ /**
+ * An identifier for the residue range segment within the structural model.
+ */
segment_id: int,
+ /**
+ * A unique identifier distinct molecular entities.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the
+ * ENTITY_POLY_SEQ category.
+ */
entity_id: str,
+ /**
+ * A text description of the molecular entity
+ */
entity_description: str,
+ /**
+ * An asym/strand identifier for the entity molecule.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
entity_asym_id: str,
+ /**
+ * The leading residue index for the sequence segment modeled using this starting model.
+ */
seq_id_begin: int,
+ /**
+ * The trailing residue index for the sequence segment modeled using this starting model.
+ */
seq_id_end: int,
+ /**
+ * The primitive object used to model this segment.
+ */
model_object_primitive: Aliased<'atomistic' | 'sphere' | 'gaussian' | 'other'>(str),
+ /**
+ * The identifier for the starting structural model.
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id
+ * in the IHM_STARTING_MODEL_DETAILS category.
+ */
starting_model_id: str,
+ /**
+ * The manner in which the segment is modeled.
+ */
model_mode: Aliased<'rigid' | 'flexible'>(str),
+ /**
+ * The level of detail at which model primitive objects are applied to the structure.
+ */
model_granularity: Aliased<'by-atom' | 'by-residue' | 'multi-residue' | 'by-feature'>(str),
+ /**
+ * The number of primitive objects used to model a feature in the case of 'by-feature' granularity.
+ */
model_object_count: int,
},
ihm_struct_assembly: {
+ /**
+ * A unique identifier for the structural assembly description.
+ */
ordinal_id: int,
+ /**
+ * An identifier for the structural assembly.
+ * This data item will remain the same for all components
+ * of an assembly.
+ */
assembly_id: int,
+ /**
+ * The parent of this assembly in a hierarchy.
+ * This data item is an internal category pointer to
+ * _ihm_struct_assembly.assembly_id
+ * This data item should point to the assembly id of the immediate
+ * parent in a hierarchy.
+ * By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).
+ * In case of assemblies that do not conform to a hierarchy,
+ * _ihm_struct_assembly.parent_assembly_id is the same as
+ * _ihm_struct_assembly.assembly_id indicating a self-parent.
+ */
parent_assembly_id: int,
+ /**
+ * A text description of the molecular entity
+ */
entity_description: str,
+ /**
+ * A unique identifier for distinct molecular entities.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the
+ * ENTITY_POLY_SEQ category.
+ */
entity_id: str,
+ /**
+ * An asym/strand identifier for the component in the assembly.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The starting residue index for the sequence segment of the entity instance
+ * that is part of the assembly.
+ */
seq_id_begin: int,
+ /**
+ * The ending residue index for the sequence segment of the entity instance
+ * that is part of the assembly.
+ */
seq_id_end: int,
},
ihm_struct_assembly_details: {
+ /**
+ * A unique identifier for the structural assembly.
+ */
assembly_id: int,
+ /**
+ * A name for the structural assembly.
+ */
assembly_name: str,
+ /**
+ * Description of the structural assembly.
+ */
assembly_description: str,
},
ihm_modeling_protocol: {
+ /**
+ * A unique identifier for the modeling protocol/step combination.
+ */
ordinal_id: int,
+ /**
+ * An index for the modeling protocol carried out.
+ */
protocol_id: int,
+ /**
+ * An index for a particular step within the modeling protocol.
+ */
step_id: int,
+ /**
+ * An index for the structural assembly being modeled.
+ * This is an indicator to whether the whole assembly is modeled
+ * or if only a subset of the structural assembly is modeled.
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
+ * details regarding the different structural assemblies used in the modeling.
+ * The default value for this data item is "1", indicating that the entire
+ * assembly is being modeled.
+ */
struct_assembly_id: int,
+ /**
+ * An index for the dataset group being used in the modeling protocol.
+ * This data item is a pointer to the _ihm_dataset_group.group_id in the
+ * IHM_DATASET_GROUP category.
+ */
dataset_group_id: int,
+ /**
+ * A textual description of the structural assembly being modeled.
+ */
struct_assembly_description: str,
+ /**
+ * The name for the modeling protocol.
+ */
protocol_name: str,
+ /**
+ * The name or type of the modeling step.
+ */
step_name: str,
+ /**
+ * Description of the method involved in the modeling step.
+ */
step_method: str,
+ /**
+ * The number of models in the beginning of the step.
+ */
num_models_begin: int,
+ /**
+ * The number of models at the end of the step.
+ */
num_models_end: int,
+ /**
+ * A flag to indicate if the modeling is multi scale.
+ */
multi_scale_flag: Aliased<'YES' | 'NO'>(str),
+ /**
+ * A flag to indicate if the modeling is multi state.
+ */
multi_state_flag: Aliased<'YES' | 'NO'>(str),
+ /**
+ * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
+ */
ordered_flag: Aliased<'YES' | 'NO'>(str),
},
ihm_multi_state_modeling: {
+ /**
+ * A unique identifier for the multiple states being described.
+ */
ordinal_id: int,
+ /**
+ * An identifier for the particular state in the multi-state modeling.
+ */
state_id: int,
+ /**
+ * An identifier for a collections of states in the multi-state modeling.
+ * If the states do not need to be grouped into collections, then
+ * _ihm_multi_state_modeling.state_group_id is the same as
+ * _ihm_multi_state_modeling.state_id.
+ */
state_group_id: int,
+ /**
+ * A fraction representing the population of the particular state.
+ */
population_fraction: float,
+ /**
+ * The type that the multiple states being modeled belong to.
+ */
state_type: str,
+ /**
+ * A descriptive name for the state.
+ */
state_name: str,
+ /**
+ * The model group id corresponding to the particular state in the multi-state model.
+ * This data item is a pointer to _ihm_model_list.model_group_id in the
+ * IHM_MODEL_LIST category.
+ * If there is only a single model corresponding to a particular state, then the
+ * _ihm_model_list.model_group_id is the same as the _ihm_model_list.model_id.
+ */
model_group_id: int,
+ /**
+ * The type of multi-state modeling experiment carried out.
+ */
experiment_type: Aliased<'Fraction of bulk' | 'Single molecule'>(str),
+ /**
+ * Additional textual details of the multi-state modeling, if required.
+ */
details: str,
},
ihm_modeling_post_process: {
+ /**
+ * A unique identifier for the post modeling analysis/step combination.
+ */
id: int,
+ /**
+ * An identifier for the modeling protocol, whose post modeling analysis
+ * is being carried out.
+ * This data item is a pointer to the _ihm_modeling_protocol.protocol_id
+ * in the IHM_MODELING_PROTOCOL category.
+ */
protocol_id: int,
+ /**
+ * An identifier for the post modeling analysis. This data item accounts for
+ * multiple post-modeling analyses that can be carried out.
+ */
analysis_id: int,
+ /**
+ * In a multi-step process, this identifier denotes the particular
+ * step in the post modeling analysis.
+ */
step_id: int,
+ /**
+ * The type of post modeling analysis being carried out.
+ */
type: Aliased<'filter' | 'cluster' | 'rescore' | 'validation' | 'other' | 'none'>(str),
+ /**
+ * The parameter/feature used in the post modeling analysis.
+ */
feature: Aliased<'energy/score' | 'RMSD' | 'dRMSD' | 'other' | 'none'>(str),
+ /**
+ * The number of models at the beginning of the post processing step.
+ */
num_models_begin: int,
+ /**
+ * The number of models the the end of the post processing step.
+ */
num_models_end: int,
},
ihm_ensemble_info: {
+ /**
+ * A unique id for the ensemble.
+ */
ensemble_id: int,
+ /**
+ * An optional name for the cluster or ensemble for better description.
+ */
ensemble_name: str,
+ /**
+ * An identifier for the post modeling analyses carried out.
+ * This data item is a pointer to _ihm_modeling_post_process.id in
+ * the IHM_MODELING_POST_PROCESS category.
+ */
post_process_id: int,
+ /**
+ * An identifier for the cluster or group of models being deposited.
+ * This data item is a pointer to the _ihm_model_list.model_group_id
+ * in the IHM_MODEL_LIST category.
+ */
model_group_id: int,
+ /**
+ * The clustering method used to obtain the ensemble, if applicable.
+ */
ensemble_clustering_method: Aliased<'Hierarchical' | 'Partitioning (k-means)' | 'Other'>(str),
+ /**
+ * The parameter/feature used for clustering the models, if applicable.
+ */
ensemble_clustering_feature: Aliased<'RMSD' | 'dRMSD' | 'other'>(str),
+ /**
+ * The number of models in the current ensemble being described.
+ */
num_ensemble_models: int,
+ /**
+ * The number of models from the current ensemble that is deposited.
+ */
num_ensemble_models_deposited: int,
+ /**
+ * The precision of each cluster or ensemble is calculated as dRMSD, which
+ * is the average C-alpha distance root mean square deviation (dRMSD)
+ * between the individual models in the cluster and the cluster centroid.
+ * The cluster centroid is defined as the model with the minimal sum of
+ * dRMSDs to the other models in the cluster or ensemble.
+ */
ensemble_precision_value: float,
+ /**
+ * A reference to the external file containing the structural models
+ * in the ensemble. The number of models in the external file should
+ * correspond to the number of models in the ensemble. This data item
+ * is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES
+ * category.
+ * It is recommended that the large ensemble files be stored as separate
+ * zip files within the same DOI. It is also recommended that large sphere
+ * model ensembles be in binary format, which facilitates faster access.
+ * Currently, a binary dump of co-ordinates in dcd format is suggested.
+ * The topology can be inferred from the IHM_SPHERE_OBJ_SITE and the
+ * ATOM_SITE categories in the corresponding mmCIF file.
+ */
ensemble_file_id: int,
},
ihm_model_list: {
+ /**
+ * A unique identifier for the model / model group combination.
+ */
ordinal_id: int,
+ /**
+ * A unique identifier for the structural model being deposited.
+ */
model_id: int,
+ /**
+ * An identifier to group structural models into collections or sets.
+ * This data item can be used to group models into structural clusters
+ * or using other criteria based on experimental data or other
+ * relationships such as those belonging to the same state or time stamp.
+ * An ensemble of models and its representative can either be grouped together
+ * or can be separate groups in the ihm_model_list table. The choice between
+ * the two options should be decided based on how the modeling was carried out
+ * and how the representative was chosen. If the representative is a member of
+ * the ensemble (i.e., best scoring model), then it is recommended that the
+ * representative and the ensemble belong to the same model group. If the
+ * representative is calculated from the ensemble (i.e., centroid), then it is
+ * recommended that the representative be separated into a different group.
+ * If the models do not need to be grouped into collections, then the
+ * _ihm_model_list.model_group_id is the same as _ihm_model_list.model_id.
+ */
model_group_id: int,
+ /**
+ * A decsriptive name for the model.
+ */
model_name: str,
+ /**
+ * A decsriptive name for the model group.
+ */
model_group_name: str,
+ /**
+ * An identifier to the structure assembly corresponding to the model.
+ * This data item is a pointer to the _ihm_struct_assembly.assembly_id
+ * in the IHM_STRUCT_ASSEMBLY category.
+ */
assembly_id: int,
+ /**
+ * An identifier to the modeling protocol that produced the model.
+ * This data item is a pointer to the _ihm_modeling_protocol.protocol_id
+ * in the IHM_MODELING_PROTOCOL category.
+ */
protocol_id: int,
+ /**
+ * An identifier to the multi-scale model representation id of the model.
+ * This data item is a pointer to the _ihm_model_representation.representation_id
+ * in the IHM_MODEL_REPRESENTATION category.
+ */
representation_id: int,
},
ihm_model_representative: {
+ /**
+ * A unique identifier for the representative of the model group.
+ */
id: int,
+ /**
+ * The model group identifier corresponding to the representative model.
+ * This data item is a pointer to _ihm_model_list.model_group_id in the
+ * IHM_MODEL_LIST category.
+ */
model_group_id: int,
+ /**
+ * The model identifier corresponding to the representative model.
+ * This data item is a pointer to _ihm_model_list.model_id in the
+ * IHM_MODEL_LIST category.
+ */
model_id: int,
+ /**
+ * The selection criteria based on which the representative is chosen.
+ */
selection_criteria: Aliased<'medoid' | 'closest to the average' | 'lowest energy' | 'target function' | 'fewest violations' | 'minimized average structure' | 'best scoring model' | 'centroid' | 'other selction criteria'>(str),
},
ihm_dataset_list: {
+ /**
+ * A unique identifier for the dataset.
+ */
id: int,
+ /**
+ * The type of data held in the dataset.
+ */
data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Yeast two-hybrid screening data' | 'Other'>(str),
+ /**
+ * A flag that indicates whether the dataset is archived in
+ * an IHM related database or elsewhere.
+ */
database_hosted: Aliased<'YES' | 'NO'>(str),
},
ihm_dataset_group: {
+ /**
+ * A unique identifier for the entry.
+ */
ordinal_id: int,
+ /**
+ * An identifier for the dataset group.
+ */
group_id: int,
+ /**
+ * An identifier to the dataset. This data item is a pointer to
+ * _ihm_dataset_list.id in the IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
},
ihm_related_datasets: {
+ /**
+ * A unique identifier for the entry.
+ */
ordinal_id: int,
+ /**
+ * The dataset list id corresponding to the derived dataset.
+ * This data item is a pointer to _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id_derived: int,
+ /**
+ * The primary dataset list id from which the corresponding derived dataset is obtained.
+ * This data item is a pointer to _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id_primary: int,
},
ihm_dataset_related_db_reference: {
+ /**
+ * A unique identifier for the related database entry.
+ */
id: int,
+ /**
+ * Identifier to the dataset list used in the IHM modeling.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
+ /**
+ * The name of the database containing the dataset entry.
+ */
db_name: Aliased<'PDB' | 'BMRB' | 'EMDB' | 'EMPIAR' | 'SASBDB' | 'PRIDE' | 'MODEL ARCHIVE' | 'MASSIVE' | 'BioGRID' | 'Other'>(str),
+ /**
+ * The accession code for the database entry.
+ */
accession_code: str,
+ /**
+ * Version of the database entry, if the database allows versioning.
+ */
version: str,
+ /**
+ * Details regarding the dataset entry.
+ */
details: str,
},
ihm_external_reference_info: {
+ /**
+ * A unique identifier for the external reference.
+ */
reference_id: int,
+ /**
+ * The name of the reference provider.
+ */
reference_provider: str,
+ /**
+ * The type of external reference.
+ * Currently, only Digital Object Identifiers (DOIs) and supplementary files
+ * stored locally are supported.
+ */
reference_type: Aliased<'DOI' | 'Supplementary Files'>(str),
+ /**
+ * The external reference or the Digital Object Identifier (DOI).
+ * This field is not relevant for local files.
+ */
reference: str,
+ /**
+ * The type of object that the external reference points to, usually
+ * a single file or an archive.
+ */
refers_to: Aliased<'File' | 'Archive' | 'Publication' | 'Other'>(str),
+ /**
+ * The Uniform Resource Locator (URL) corresponding to the external reference (DOI).
+ * This URL should link to the corresponding downloadable file or archive and is provided
+ * to enable automated software to download the referenced file or archive.
+ */
associated_url: str,
},
ihm_external_files: {
+ /**
+ * A unique identifier for each external file.
+ */
id: int,
+ /**
+ * A pointer to the source of the external file - either DOI or locally stored.
+ * This data item is a pointer to _ihm_external_reference_info.reference_id in the
+ * IHM_EXTERNAL_REFERENCE_INFO category.
+ */
reference_id: int,
+ /**
+ * The relative path (including filename) for each external file.
+ * Absolute paths (starting with "/") are not permitted.
+ * This is required for identifying individual files from within
+ * a tar-zipped archive file or for identifying supplementary local
+ * files organized within a directory structure.
+ * This data item assumes a POSIX-like directory structure or file path.
+ */
file_path: str,
+ /**
+ * The type of content in the file.
+ */
content_type: Aliased<'Input data or restraints' | 'Modeling or post-processing output' | 'Modeling workflow or script' | 'Visualization script' | 'Other'>(str),
+ /**
+ * Storage size of the external file in bytes.
+ */
file_size_bytes: float,
+ /**
+ * Textual description of what the external file is.
+ */
details: str,
},
ihm_dataset_external_reference: {
+ /**
+ * A unique identifier for the external data.
+ */
id: int,
+ /**
+ * Identifier to the dataset list used in the I/H modeling.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
+ /**
+ * The file id corresponding to this external data file.
+ * This data item is a pointer to _ihm_external_files.id
+ * in the IHM_EXTERNAL_FILES category.
+ */
file_id: int,
},
ihm_localization_density_files: {
+ /**
+ * A unique identifier.
+ */
id: int,
+ /**
+ * The file id for the externally stored localization density file.
+ * This data item is a pointer to _ihm_external_files.id
+ * in the IHM_EXTERNAL_FILES category.
+ */
file_id: int,
+ /**
+ * The ensemble identifier for the ensemble, for which the localization density is provided.
+ * This data item is a pointer to _ihm_ensemble_info.ensemble_id in the IHM_ENSEMBLE_INFO category.
+ */
ensemble_id: int,
+ /**
+ * The entity identifier corresponding to this localization density.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * The leading sequence index corresponding to this localization density.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_begin: int,
+ /**
+ * The trailing sequence index corresponding to this localization density.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_end: int,
+ /**
+ * An asym/strand identifier corresponding to this localization density.
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
+ */
asym_id: str,
},
ihm_predicted_contact_restraint: {
+ /**
+ * A unique identifier for the predicted contact restraint.
+ */
id: int,
+ /**
+ * An identifier to group the predicted contacts.
+ */
group_id: int,
+ /**
+ * The entity identifier for the first monomer partner in the predicted contact.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
+ */
entity_id_1: str,
+ /**
+ * The entity identifier for the second monomer partner in the predicted contact.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
+ */
entity_id_2: str,
+ /**
+ * An asym/strand identifier for the first monomer partner in the predicted contact.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id_1: str,
+ /**
+ * An asym/strand identifier for the second monomer partner in the predicted contact.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id_2: str,
+ /**
+ * The component identifier for the first monomer partner in the predicted contact.
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier for the second monomer partner in the predicted contact.
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id_2: str,
+ /**
+ * The sequence index for the first monomer partner in the predicted contact.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_1: int,
+ /**
+ * The sequence index for the second monomer partner in the predicted contact.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_2: int,
+ /**
+ * The atom id of the first partner in the predicted contact.
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_1: str,
+ /**
+ * The atom id of the second partner in the predicted contact.
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_2: str,
+ /**
+ * The lower limit to the distance threshold applied to this predicted contact restraint
+ * in the integrative modeling task.
+ */
distance_lower_limit: float,
+ /**
+ * The upper limit to the distance threshold applied to this predicted contact restraint
+ * in the integrative modeling task.
+ */
distance_upper_limit: float,
+ /**
+ * The real number that indicates the probability that the predicted distance restraint
+ * is correct. This number should fall between 0.0 and 1.0.
+ */
probability: float,
+ /**
+ * The type of distance restraint applied.
+ */
restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
+ /**
+ * The granularity of the predicted contact as applied to the multi-scale model.
+ */
model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
+ /**
+ * Identifier to the predicted contacts dataset.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
+ /**
+ * Identifier to the software used to obtain the predicted contacts dataset.
+ * This data item is a pointer to the _software.pdbx_ordinal in the
+ * SOFTWARE category.
+ */
software_id: int,
},
ihm_cross_link_list: {
+ /**
+ * A unique identifier for the cross link restraint.
+ */
id: int,
+ /**
+ * An identifier for a set of ambiguous crosslink restraints.
+ * Handles experimental uncertainties in the identities of
+ * crosslinked residues.
+ */
group_id: int,
+ /**
+ * A text description of molecular entity 1.
+ */
entity_description_1: str,
+ /**
+ * A text description of molecular entity 2.
+ */
entity_description_2: str,
+ /**
+ * The entity identifier for the first monomer partner in the cross link
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
+ */
entity_id_1: str,
+ /**
+ * The entity identifier for the second monomer partner in the cross link
+ *
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
+ */
entity_id_2: str,
+ /**
+ * The component identifier for the first monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier for the second monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id_2: str,
+ /**
+ * The sequence index for the first monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_1: int,
+ /**
+ * The sequence index for the second monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_2: int,
+ /**
+ * The type of crosslinker used.
+ */
linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'Other'>(str),
+ /**
+ * Identifier to the crosslinking dataset.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
},
ihm_cross_link_restraint: {
+ /**
+ * A unique identifier for the cross link record.
+ */
id: int,
+ /**
+ * An identifier for a set of ambiguous cross-links.
+ * Handles implementation uncertainties related to multiple copies of subunit.
+ * This data item is a pointer to _ihm_cross_link_list.id in the
+ * IHM_CROSS_LINK_LIST category.
+ */
group_id: int,
+ /**
+ * The entity identifier for the first monomer partner in the cross link
+ *
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category
+ * and the _ihm_cross_link_restraint.entity_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
+ */
entity_id_1: str,
+ /**
+ * The entity identifier for the second monomer partner in the cross link
+ *
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category
+ * and the _ihm_cross_link_restraint.entity_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
+ */
entity_id_2: str,
+ /**
+ * An asym/strand identifier for the first monomer partner in the cross-link.
+ *
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id_1: str,
+ /**
+ * An asym/strand identifier for the second monomer partner in the cross-link.
+ *
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id_2: str,
+ /**
+ * The component identifier for the first monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category
+ * and the _ihm_cross_link_restraint.comp_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
+ */
comp_id_1: str,
+ /**
+ * The component identifier for the second monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category
+ * and the _ihm_cross_link_restraint.comp_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
+ */
comp_id_2: str,
+ /**
+ * The sequence index for the first monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category
+ * and the _ihm_cross_link_restraint.seq_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
+ */
seq_id_1: int,
+ /**
+ * The sequence index for the second monomer partner in the cross link.
+ *
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category
+ * and the _ihm_cross_link_restraint.seq_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
+ */
seq_id_2: int,
+ /**
+ * The atom identifier for the first monomer partner in the cross link.
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_1: str,
+ /**
+ * The atom identifier for the second monomer partner in the cross link.
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id_2: str,
+ /**
+ * The type of the cross link restraint applied.
+ */
restraint_type: Aliased<'harmonic' | 'upper bound' | 'lower bound'>(str),
+ /**
+ * The cross link conditionality.
+ */
conditional_crosslink_flag: Aliased<'ALL' | 'ANY'>(str),
+ /**
+ * The coarse-graining information for the crosslink implementation.
+ */
model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
+ /**
+ * The distance threshold applied to this crosslink in the integrative modeling task.
+ */
distance_threshold: float,
+ /**
+ * The uncertainty in the crosslinking experimental data;
+ * may be approximated to the false positive rate.
+ */
psi: float,
+ /**
+ * The uncertainty in the position of residue 1 in the crosslink
+ * arising due to the multi-scale nature of the model represention.
+ */
sigma_1: float,
+ /**
+ * The uncertainty in the position of residue 2 in the crosslink
+ * arising due to the multi-scale nature of the model represention.
+ */
sigma_2: float,
},
ihm_cross_link_result_parameters: {
+ /**
+ * A unique identifier for the restraint/model combination.
+ */
ordinal_id: int,
+ /**
+ * An identifier for the crosslink restraint between a pair of residues.
+ * This data item is a pointer to _ihm_cross_link_restraint.id in the
+ * IHM_CROSS_LINK_RESTRAINT category.
+ */
restraint_id: int,
+ /**
+ * The model number corresponding to the cross link result presented.
+ * This data item is a pointer to _ihm_model_list.model_id in the
+ * IHM_MODEL_LIST category.
+ */
model_id: int,
+ /**
+ * The uncertainty in the crosslinking experimental data;
+ * May be approximated to the false positive rate.
+ */
psi: float,
+ /**
+ * The uncertainty in the position of residue 1 in the crosslink
+ * arising due to the multi-scale nature of the model represention.
+ */
sigma_1: float,
+ /**
+ * The uncertainty in the position of residue 2 in the crosslink
+ * arising due to the multi-scale nature of the model represention.
+ */
sigma_2: float,
},
ihm_2dem_class_average_restraint: {
+ /**
+ * A unique identifier for the 2dem class average.
+ */
id: int,
+ /**
+ * Identifier to the 2dem class average dataset.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
+ /**
+ * The number of raw micrographs used to obtain the class average.
+ */
number_raw_micrographs: int,
+ /**
+ * Pixel size width of the 2dem class average image.
+ * While fitting the model to the image, _ihm_2dem_class_average_restraint.pixel_size_width
+ * is used along with _ihm_2dem_class_average_restraint.pixel_size_height to scale the image.
+ */
pixel_size_width: float,
+ /**
+ * Pixel size height of the 2dem class average image.
+ * While fitting the model to the image, _ihm_2dem_class_average_restraint.pixel_size_height
+ * is used along with _ihm_2dem_class_average_restraint.pixel_size_width to scale the image.
+ */
pixel_size_height: float,
+ /**
+ * Resolution of the 2dem class average.
+ */
image_resolution: float,
+ /**
+ * A flag that indicates whether or not the 2DEM class average image is segmented i.e.,
+ * whether the whole image is used or only a portion of it is used (by masking
+ * or by other means) as restraint in the modeling.
+ */
image_segment_flag: Aliased<'YES' | 'NO'>(str),
+ /**
+ * Number of 2D projections of the model used in the fitting.
+ */
number_of_projections: int,
+ /**
+ * An indicator to whether the whole assembly that is modeled is fit into the image
+ * or if only a subset of the structural assembly is fit into the image.
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
+ * details regarding the different structural assemblies used in the modeling.
+ * The default value for this data item is "1" indicating that the entire assembly
+ * being modeled is fit into the EM data.
+ */
struct_assembly_id: int,
+ /**
+ * Details of how the 2DEM restraint is applied in the modeling algorithm.
+ */
details: str,
},
ihm_2dem_class_average_fitting: {
+ /**
+ * A unique identifier for the 2dem class average fitting data.
+ */
ordinal_id: int,
+ /**
+ * Identifier to the 2dem class average restraint.
+ * This data item is a pointer to the _ihm_2dem_class_average_restraint.id in the
+ * IHM_2DEM_CLASS_AVERAGE_RESTRAINT category.
+ */
restraint_id: int,
+ /**
+ * The model number corresponding to the 2DEM fitting result presented.
+ * This data item is a pointer to _ihm_model_list.model_id in the
+ * IHM_MODEL_LIST category.
+ */
model_id: int,
+ /**
+ * The cross correlation coefficient corresponding to the model to image fitting.
+ */
cross_correlation_coefficient: float,
+ /**
+ * Data item of the rotation matrix used in the fitting of the model to the image.
+ */
rot_matrix: Matrix(3, 3),
+ /**
+ * Data item of the tranlation vector used in the fitting of the model to the image.
+ */
tr_vector: Vector(3),
},
ihm_3dem_restraint: {
+ /**
+ * A unique identifier for the 3DEM restraint description.
+ */
ordinal_id: int,
+ /**
+ * Identifier to the 3DEM map used.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
+ /**
+ * The model number corresponding to the 3DEM fitting result presented.
+ * This data item is a pointer to _ihm_model_list.model_id in the
+ * IHM_MODEL_LIST category.
+ */
model_id: int,
+ /**
+ * An indicator to whether the whole assembly that is modeled is fit into the 3DEM map
+ * or if only a subset of the structural assembly is fit into the map.
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
+ * details regarding the different structural assemblies used in the modeling.
+ * The default value for this data item is "1" indicating that the entire assembly
+ * being modeled is fit into the EM map.
+ */
struct_assembly_id: int,
+ /**
+ * Method used to fit the model to the 3DEM map.
+ */
fitting_method: str,
+ /**
+ * In case of Gaussian mixture models, the number of gaussians
+ * is a parameter used to covert the 3DEM maps and models into
+ * GMMs. This captures the level of granularity used in
+ * representing the maps and/or models as 3D Gaussians.
+ */
number_of_gaussians: int,
+ /**
+ * The cross correlation coefficient corresponding to the model to map fitting.
+ */
cross_correlation_coefficient: float,
},
ihm_sas_restraint: {
+ /**
+ * A unique identifier for the SAS restraint description.
+ */
ordinal_id: int,
+ /**
+ * Identifier to the SAS data used.
+ * This data item is a pointer to the _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
+ */
dataset_list_id: int,
+ /**
+ * The model number corresponding to the SAS fitting result presented.
+ * This data item is a pointer to _ihm_model_list.model_id in the
+ * IHM_MODEL_LIST category.
+ */
model_id: int,
+ /**
+ * An indicator to whether the whole assembly that is modeled is fit into the SAS data
+ * or if only a subset of the structural assembly is fit into the data.
+ * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
+ * details regarding the different structural assemblies used in the modeling.
+ * The default value for this data item is "1" indicating that the entire assembly
+ * being modeled is fit into the SAS data.
+ */
struct_assembly_id: int,
+ /**
+ * A flag that indicates whether or not the SAS profile is segmented i.e.,
+ * whether the whole SAS profile is used or only a portion of it is used
+ * (by masking or by other means) as restraint in the modeling.
+ */
profile_segment_flag: Aliased<'YES' | 'NO'>(str),
+ /**
+ * The type of atoms in the model fit to the SAS data.
+ */
fitting_atom_type: str,
+ /**
+ * The method used for fitting the model to the SAS data.
+ */
fitting_method: str,
+ /**
+ * An indicator to single or multiple state fitting.
+ */
fitting_state: Aliased<'Single' | 'Multiple'>(str),
+ /**
+ * Radius of gyration obtained from the SAS profile, if used as input restraint.
+ */
radius_of_gyration: float,
+ /**
+ * The chi value resulting from fitting the model to the SAS data.
+ */
chi_value: float,
+ /**
+ * Additional details regarding the SAS restraint used.
+ */
details: str,
},
ihm_starting_model_coord: {
+ /**
+ * A unique identifier for this coordinate position.
+ */
ordinal_id: int,
+ /**
+ * The identifier for the starting structural model.
+ * This data item is a pointer to _ihm_starting_model_details.starting_model_id
+ * in the IHM_STARTING_MODEL_DETAILS category.
+ */
starting_model_id: str,
+ /**
+ * The group of atoms to which the atom site in the starting model belongs. This data
+ * item is provided for compatibility with the original Protein Data Bank format,
+ * and only for that purpose.
+ */
group_PDB: Aliased<'ATOM' | 'HETATM'>(str),
+ /**
+ * The serial number for this coordinate position.
+ */
id: int,
+ /**
+ * The atom type symbol(element symbol) corresponding to this coordinate position.
+ */
type_symbol: str,
+ /**
+ * The entity identifier corresponding to this coordinate position.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * The atom identifier/name corresponding to this coordinate position.
+ * This data item is a pointer to _chem_comp_atom.atom_id in the
+ * CHEM_COMP_ATOM category.
+ */
atom_id: str,
+ /**
+ * The component identifier corresponding to this coordinate position.
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY category.
+ */
comp_id: str,
+ /**
+ * The sequence index corresponding this to coordinate position.
+ *
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id: int,
+ /**
+ * The asym/strand id corresponding to this coordinate position.
+ *
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The Cartesian X component corresponding to this coordinate position.
+ */
Cartn_x: float,
+ /**
+ * The Cartesian Y component corresponding to this coordinate position.
+ */
Cartn_y: float,
+ /**
+ * The Cartesian Z component corresponding to this coordinate position.
+ */
Cartn_z: float,
+ /**
+ * The isotropic temperature factor corresponding to this coordinate position.
+ */
B_iso_or_equiv: float,
},
ihm_sphere_obj_site: {
+ /**
+ * A unique identifier for this pseudo atom / sphere object.
+ */
ordinal_id: int,
+ /**
+ * The entity identifier corresponding to this sphere object.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * The leading sequence index corresponding to this sphere object.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_begin: int,
+ /**
+ * The trailing sequence index corresponding to this sphere object.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_end: int,
+ /**
+ * An asym/strand identifier corresponding to this sphere object.
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The Cartesian X component corresponding to this sphere object.
+ */
Cartn_x: float,
+ /**
+ * The Cartesian Y component corresponding to this sphere object.
+ */
Cartn_y: float,
+ /**
+ * The Cartesian Z component corresponding to this sphere object.
+ */
Cartn_z: float,
+ /**
+ * The radius associated with the primitive sphere object at this position.
+ */
object_radius: float,
+ /**
+ * The Root Mean Square Fluctuation (RMSF) observed in the primitive
+ * sphere object at this position.
+ */
rmsf: float,
+ /**
+ * The model id corresponding to the sphere object.
+ * This data item is a pointer to _ihm_model_list.model_id
+ * in the IHM_MODEL_LIST category.
+ */
model_id: int,
},
ihm_gaussian_obj_site: {
+ /**
+ * A unique identifier for this gaussian object in the model.
+ */
ordinal_id: int,
+ /**
+ * The entity identifier corresponding to this gaussian object.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * The leading sequence index corresponding to this gaussian object.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_begin: int,
+ /**
+ * The trailing sequence index corresponding to this gaussian object.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_end: int,
+ /**
+ * An asym/strand identifier corresponding to this gaussian object.
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The mean Cartesian X component corresponding to this gaussian object.
+ */
mean_Cartn_x: float,
+ /**
+ * The mean Cartesian Y component corresponding to this gaussian object.
+ */
mean_Cartn_y: float,
+ /**
+ * The mean Cartesian Z component corresponding to this gaussian object.
+ */
mean_Cartn_z: float,
+ /**
+ * The weight of the gaussian object.
+ */
weight: float,
+ /**
+ * Data item of the covariance matrix representing the Gaussian object.
+ */
covariance_matrix: Matrix(3, 3),
+ /**
+ * The model id corresponding to the gaussian object.
+ * This data item is a pointer to _ihm_model_list.model_id
+ * in the IHM_MODEL_LIST category.
+ */
model_id: int,
},
ihm_gaussian_obj_ensemble: {
+ /**
+ * A unique identifier for this gaussian object.
+ */
ordinal_id: int,
+ /**
+ * The entity identifier corresponding to this gaussian object.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
+ */
entity_id: str,
+ /**
+ * The leading sequence index corresponding to this gaussian object.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_begin: int,
+ /**
+ * The trailing sequence index corresponding to this gaussian object.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ */
seq_id_end: int,
+ /**
+ * An asym/strand identifier corresponding to this gaussian object.
+ * This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The mean Cartesian X component corresponding to this gaussian object.
+ */
mean_Cartn_x: float,
+ /**
+ * The mean Cartesian Y component corresponding to this gaussian object.
+ */
mean_Cartn_y: float,
+ /**
+ * The mean Cartesian Z component corresponding to this gaussian object.
+ */
mean_Cartn_z: float,
+ /**
+ * The weight of the gaussian object.
+ */
weight: float,
+ /**
+ * Data item of the covariance matrix representing the Gaussian object.
+ */
covariance_matrix: Matrix(3, 3),
+ /**
+ * The ensemble id corresponding to the gaussian object.
+ * This data item is a pointer to _ihm_ensemble_info.ensemble_id
+ * in the IHM_ENSEMBLE_INFO category.
+ */
ensemble_id: int,
},
ihm_feature_list: {
+ /**
+ * A unique identifier for the feature.
+ */
feature_id: int,
+ /**
+ * The type of feature.
+ */
feature_type: Aliased<'atom' | 'residue' | 'residue range'>(str),
+ /**
+ * The type of entity.
+ * This data item is a pointer to _entity.type in the ENTITY category.
+ */
entity_type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
},
ihm_poly_residue_feature: {
+ /**
+ * A unique identifier for the category.
+ */
ordinal_id: int,
+ /**
+ * An identifier for the selected residue / residue range feature.
+ * This data item is a pointer to _ihm_feature_list.feature_id in the
+ * IHM_FEATURE_LIST category.
+ */
feature_id: int,
+ /**
+ * The entity identifier for residue / residue range.
+ * This data item is a pointer to _entity_poly_seq.entity_id in the
+ * ENTITY_POLY_SEQ category.
+ */
entity_id: str,
+ /**
+ * An asym/strand identifier for the residue / residue range.
+ * This data item is a pointer to _struct_asym.id in the
+ * STRUCT_ASYM category.
+ */
asym_id: str,
+ /**
+ * The component identifier of the beginning residue / residue range.
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id_begin: str,
+ /**
+ * The component identifier of the ending residue / residue range.
+ * This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
+ */
comp_id_end: str,
+ /**
+ * The sequence index of the beginning residue / residue range.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_begin: int,
+ /**
+ * The sequence index of the ending residue / residue range.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ */
seq_id_end: int,
},
ihm_derived_distance_restraint: {
+ /**
+ * A unique identifier for the derived distance restraint.
+ */
id: int,
+ /**
+ * An identifier to group the distance restraints.
+ * This can be the same as the _ihm_derived_distance_restraint.id in case
+ * the some of the restraints are not grouped.
+ */
group_id: int,
+ /**
+ * The feature identifier for the first partner in the distance restraint.
+ * This data item is a pointer to _ihm_feature_list.feature_id in the
+ * IHM_FEATURE_LIST category.
+ */
feature_id_1: int,
+ /**
+ * The feature identifier for the second partner in the distance restraint.
+ * This data item is a pointer to _ihm_feature_list.feature_id in the
+ * IHM_FEATURE_LIST category.
+ */
feature_id_2: int,
+ /**
+ * If a group of atoms or residues are restrained, this data item defines
+ * the conditionality based on which the restraint is applied in the modeling.
+ */
group_conditionality: Aliased<'ALL' | 'ANY'>(str),
+ /**
+ * The fraction of randomly excluded distance restraints during modeling.
+ * In HADDOCK, this is used along with ambiguous interface restraints (AIRs)
+ * to account for uncertainties in AIRs.
+ */
random_exclusion_fraction: float,
+ /**
+ * The upper limit to the distance threshold applied to this distance restraint
+ * in the integrative modeling task.
+ */
distance_upper_limit: float,
+ /**
+ * The type of distance restraint applied.
+ */
restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
+ /**
+ * 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.
+ */
dataset_list_id: int,
},
}
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index 005dfc7ff..69327f011 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -73,7 +73,7 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
}
function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
- // need to cast because of how TS handles type resolution for interfaces https://github.com/Microsoft/TypeScript/issues/15300
+ // TODO need to cast because of how TS handles type resolution for interfaces https://github.com/Microsoft/TypeScript/issues/15300
return Table.areEqual(a.chains as Table<ChainsSchema>, b.chains as Table<ChainsSchema>)
&& Table.areEqual(a.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
diff --git a/src/mol-util/index.ts b/src/mol-util/index.ts
index 9c1aa24bf..b7c5b083f 100644
--- a/src/mol-util/index.ts
+++ b/src/mol-util/index.ts
@@ -183,4 +183,9 @@ export function formatProgress(p: Progress) {
if (tp.isIndeterminate) return tp.message;
const x = (100 * tp.current / tp.max).toFixed(2);
return `${tp.message} ${x}%`;
+}
+
+const reLine = /^/mg
+export function indentString(str: string, count: number, indent: string) {
+ return count === 0 ? str : str.replace(reLine, indent.repeat(count))
}
\ No newline at end of file
--
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