From 0f63ae0eacb7cd4ff6e3e413d32c01d5f6af47e2 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 11 Jul 2018 11:55:41 +0200
Subject: [PATCH] wip, strongly type model indexing
---
src/mol-data/int/segmentation.ts | 18 ++++++------
src/mol-model/structure/model.ts | 1 +
.../formats/mmcif/secondary-structure.ts | 5 ++--
src/mol-model/structure/model/indexing.ts | 10 +++++++
src/mol-model/structure/model/model.ts | 8 +----
.../model/properties/atomic/hierarchy.ts | 29 +++++++------------
.../structure/model/properties/common.ts | 3 +-
.../structure/model/properties/sequence.ts | 7 +++--
.../model/properties/utils/atomic-keys.ts | 17 ++++++-----
.../structure/structure/properties.ts | 6 ++--
src/mol-model/structure/structure/unit.ts | 5 ++--
11 files changed, 56 insertions(+), 53 deletions(-)
create mode 100644 src/mol-model/structure/model/indexing.ts
diff --git a/src/mol-data/int/segmentation.ts b/src/mol-data/int/segmentation.ts
index 6007a20c2..2afdd6a55 100644
--- a/src/mol-data/int/segmentation.ts
+++ b/src/mol-data/int/segmentation.ts
@@ -9,25 +9,25 @@ import OrderedSet from './ordered-set'
import * as Impl from './impl/segmentation'
namespace Segmentation {
- export interface Segment<T extends number = number> { index: number, start: T, end: T }
+ export interface Segment<T extends number = number, I extends number = number> { index: number, start: T, end: T }
- export const create: <T extends number = number>(segs: ArrayLike<T>) => Segmentation<T> = Impl.create as any;
- export const ofOffsets: <T extends number = number>(offsets: ArrayLike<T>, bounds: Interval) => Segmentation<T> = Impl.ofOffsets as any;
+ export const create: <T extends number = number, I extends number = number>(segs: ArrayLike<T>) => Segmentation<T, I> = Impl.create as any;
+ export const ofOffsets: <T extends number = number, I extends number = number>(offsets: ArrayLike<T>, bounds: Interval) => Segmentation<T, I> = Impl.ofOffsets as any;
- export const count: <T extends number = number>(segs: Segmentation<T>) => number = Impl.count as any;
- export const getSegment: <T extends number = number>(segs: Segmentation<T>, value: T) => number = Impl.getSegment as any;
- export const projectValue: <T extends number = number>(segs: Segmentation<T>, set: OrderedSet<T>, value: T) => Interval = Impl.projectValue as any;
+ export const count: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>) => number = Impl.count as any;
+ export const getSegment: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>, value: T) => number = Impl.getSegment as any;
+ export const projectValue: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>, set: OrderedSet<T>, value: T) => Interval = Impl.projectValue as any;
// Segment iterator that mutates a single segment object to mark all the segments.
- export const transientSegments: <T extends number = number>(segs: Segmentation<T>, set: OrderedSet<T>, segment?: Segment<T>) => Impl.SegmentIterator<T> = Impl.segments as any;
+ export const transientSegments: <T extends number = number, I extends number = number>(segs: Segmentation<T, I>, set: OrderedSet<T>, segment?: Segment<T>) => Impl.SegmentIterator<T> = Impl.segments as any;
}
-interface Segmentation<T extends number = number> {
+interface Segmentation<T extends number = number, I extends number = number> {
'@type': 'segmentation',
/** All segments are defined by offsets [offsets[i], offsets[i + 1]) for i \in [0, count - 1] */
readonly offsets: ArrayLike<T>,
/** Segment index of the i-th element */
- readonly index: ArrayLike<number>,
+ readonly index: ArrayLike<I>,
readonly count: number
}
diff --git a/src/mol-model/structure/model.ts b/src/mol-model/structure/model.ts
index af5b8c7bb..c208d036d 100644
--- a/src/mol-model/structure/model.ts
+++ b/src/mol-model/structure/model.ts
@@ -10,4 +10,5 @@ import Format from './model/format'
import { ModelSymmetry } from './model/properties/symmetry'
import StructureSequence from './model/properties/sequence'
+export * from './model/indexing'
export { Model, Types, Format, ModelSymmetry, StructureSequence }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
index 2e181f668..d871052c9 100644
--- a/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
+++ b/src/mol-model/structure/model/formats/mmcif/secondary-structure.ts
@@ -10,6 +10,7 @@ import { SecondaryStructureType } from '../../types';
import { AtomicHierarchy } from '../../properties/atomic';
import { SecondaryStructure } from '../../properties/seconday-structure';
import { Column } from 'mol-data/db';
+import { ChainIndex, ResidueIndex } from '../../indexing';
export function getSecondaryStructureMmCif(data: mmCIF_Database, hierarchy: AtomicHierarchy): SecondaryStructure {
const map: SecondaryStructureMap = new Map();
@@ -130,7 +131,7 @@ function addSheets(cat: mmCIF['struct_sheet_range'], map: SecondaryStructureMap,
return;
}
-function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: SecondaryStructureEntry, resStart: number, resEnd: number, data: SecondaryStructureData) {
+function assignSecondaryStructureEntry(hierarchy: AtomicHierarchy, entry: SecondaryStructureEntry, resStart: ResidueIndex, resEnd: ResidueIndex, data: SecondaryStructureData) {
const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
const { endSeqNumber, endInsCode, key, type } = entry;
@@ -154,7 +155,7 @@ function assignSecondaryStructureRanges(hierarchy: AtomicHierarchy, map: Seconda
const { label_asym_id } = hierarchy.chains;
const { label_seq_id, pdbx_PDB_ins_code } = hierarchy.residues;
- for (let cI = 0; cI < chainCount; cI++) {
+ for (let cI = 0 as ChainIndex; cI < chainCount; cI++) {
const resStart = AtomicHierarchy.chainStartResidueIndex(hierarchy, cI), resEnd = AtomicHierarchy.chainEndResidueIndexExcl(hierarchy, cI);
const asymId = label_asym_id.value(cI);
if (map.has(asymId)) {
diff --git a/src/mol-model/structure/model/indexing.ts b/src/mol-model/structure/model/indexing.ts
new file mode 100644
index 000000000..65dfce091
--- /dev/null
+++ b/src/mol-model/structure/model/indexing.ts
@@ -0,0 +1,10 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export type ElementIndex = { readonly '@type': 'element-index' } & number
+export type ResidueIndex = { readonly '@type': 'residue-index' } & number
+export type ChainIndex = { readonly '@type': 'chain-index' } & number
+export type EntityIndex = { readonly '@type': 'entity-index' } & number
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 412531f73..4ffd21aac 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -71,10 +71,4 @@ export namespace Model {
case 'mmCIF': return from_mmCIF(format);
}
}
-}
-
-
-export type ElementIndex = { readonly '@type': 'element-index' } & number
-export type ResidueIndex = { readonly '@type': 'residue-index' } & number
-export type ChainIndex = { readonly '@type': 'chain-index' } & number
-export type EntityIndex = { readonly '@type': 'entity-index' } & number
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index a4aeaacad..0a924c80d 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -9,6 +9,7 @@ import { Segmentation } from 'mol-data/int'
import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol } from '../../types'
import { Element } from '../../../structure'
+import { ChainIndex, EntityIndex, ResidueIndex } from '../../indexing';
export const AtomsSchema = {
type_symbol: Column.Schema.Aliased<ElementSymbol>(mmCIF.atom_site.type_symbol),
@@ -49,7 +50,7 @@ export interface AtomicData {
export interface AtomicSegments {
/** Maps residueIndex to a range of atoms [segments[rI], segments[rI + 1]) */
- residueAtomSegments: Segmentation<Element>,
+ residueAtomSegments: Segmentation<Element, ResidueIndex>,
/**
* Maps chainIndex to a range of atoms [segments[cI], segments[cI + 1]),
*
@@ -58,7 +59,7 @@ export interface AtomicSegments {
* const start = rI[offsets[i]], const end = rI[offsets[i + 1] - 1] + 1;
* for (let j = start; j < end; i++) { }
*/
- chainAtomSegments: Segmentation<Element>,
+ chainAtomSegments: Segmentation<Element, ChainIndex>,
/**
* bonded/connected stretches of polymer chains, i.e. a chain will be
* broken into multiple polymer segments if there are missing residues
@@ -69,27 +70,19 @@ export interface AtomicSegments {
}
export interface AtomicKeys {
- // TODO: since Atoms must be sorted now, get rid of keys
// TODO: include (lazily computed) "entity/chain/residue" indices?
- // assign a key to each residue index.
- residueKey: ArrayLike<number>,
- // assign a key to each chain index
- chainKey: ArrayLike<number>,
- // assigne a key to each chain index
- // also index to the Entities table.
- entityKey: ArrayLike<number>,
+ /** @returns index or -1 if not present. */
+ getEntityKey(cI: ChainIndex): EntityIndex,
- /**
- * @returns index or -1 if not present.
- */
- findChainKey(entityId: string, label_asym_id: string): number,
+ /** @returns index or -1 if not present. */
+ findChainKey(entityId: string, label_asym_id: string): ChainIndex,
/**
* Unique number for each of the residue. Also the index of the 1st occurence of this residue.
* @returns index or -1 if not present.
*/
- findResidueKey(entityId: string, label_asym_id: string, label_comp_id: string, auth_seq_id: number, pdbx_PDB_ins_code: string): number
+ findResidueKey(entityId: string, label_asym_id: string, label_comp_id: string, auth_seq_id: number, pdbx_PDB_ins_code: string): ResidueIndex
}
type _Hierarchy = AtomicData & AtomicSegments & AtomicKeys
@@ -97,12 +90,12 @@ export interface AtomicHierarchy extends _Hierarchy { }
export namespace AtomicHierarchy {
/** Start residue inclusive */
- export function chainStartResidueIndex(segs: AtomicSegments, cI: number) {
+ export function chainStartResidueIndex(segs: AtomicSegments, cI: ChainIndex) {
return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI]];
}
/** End residue exclusive */
- export function chainEndResidueIndexExcl(segs: AtomicSegments, cI: number) {
- return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI + 1] - 1] + 1;
+ export function chainEndResidueIndexExcl(segs: AtomicSegments, cI: ChainIndex) {
+ return segs.residueAtomSegments.index[segs.chainAtomSegments.offsets[cI + 1] - 1] + 1 as ResidueIndex;
}
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/common.ts b/src/mol-model/structure/model/properties/common.ts
index 35d9143ae..c1b7af14d 100644
--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -5,8 +5,9 @@
*/
import { mmCIF_Database as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
+import { EntityIndex } from '../indexing';
export interface Entities {
data: mmCIF['entity'],
- getEntityIndex(id: string): import('../model').EntityIndex
+ getEntityIndex(id: string): EntityIndex
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/sequence.ts b/src/mol-model/structure/model/properties/sequence.ts
index ec7b5da76..b29ead3f5 100644
--- a/src/mol-model/structure/model/properties/sequence.ts
+++ b/src/mol-model/structure/model/properties/sequence.ts
@@ -8,6 +8,7 @@ import { Column } from 'mol-data/db'
import { AtomicHierarchy } from './atomic/hierarchy';
import { Entities } from './common';
import { Sequence } from '../../../sequence';
+import { ChainIndex } from '../indexing';
interface StructureSequence {
readonly sequences: ReadonlyArray<StructureSequence.Entity>,
@@ -30,14 +31,14 @@ namespace StructureSequence {
const byEntityKey: StructureSequence['byEntityKey'] = { };
const sequences: StructureSequence.Entity[] = [];
- for (let cI = 0, _cI = hierarchy.chains._rowCount; cI < _cI; cI++) {
- const entityKey = hierarchy.entityKey[cI];
+ for (let cI = 0 as ChainIndex, _cI = hierarchy.chains._rowCount; cI < _cI; cI++) {
+ const entityKey = hierarchy.getEntityKey(cI);
// Only for polymers, trying to mirror _entity_poly_seq
if (byEntityKey[entityKey] !== void 0 || entities.data.type.value(entityKey) !== 'polymer') continue;
let start = cI;
cI++;
- while (cI < _cI && entityKey === hierarchy.entityKey[cI] && entities.data.type.value(entityKey) !== 'polymer') {
+ while (cI < _cI && entityKey === hierarchy.getEntityKey(cI) && entities.data.type.value(entityKey) !== 'polymer') {
cI++;
}
cI--;
diff --git a/src/mol-model/structure/model/properties/utils/atomic-keys.ts b/src/mol-model/structure/model/properties/utils/atomic-keys.ts
index 0fdf1c8e5..de4029984 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-keys.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-keys.ts
@@ -7,6 +7,7 @@
import { AtomicData, AtomicSegments, AtomicKeys } from '../atomic'
import { Interval, Segmentation } from 'mol-data/int'
import { Entities } from '../common'
+import { ChainIndex, ResidueIndex, EntityIndex } from '../../indexing';
function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
return `${comp_id} ${seq_id} ${ins_code}`;
@@ -30,20 +31,20 @@ function createLookUp(entities: Entities, chain: Map<number, Map<string, number>
const getEntKey = entities.getEntityIndex;
const findChainKey: AtomicKeys['findChainKey'] = (e, c) => {
let eKey = getEntKey(e);
- if (eKey < 0) return -1;
+ if (eKey < 0) return -1 as ChainIndex;
const cm = chain.get(eKey)!;
- if (!cm.has(c)) return -1;
- return cm.get(c)!;
+ if (!cm.has(c)) return -1 as ChainIndex;
+ return cm.get(c)! as ChainIndex;
}
const findResidueKey: AtomicKeys['findResidueKey'] = (e, c, name, seq, ins) => {
let eKey = getEntKey(e);
- if (eKey < 0) return -1;
+ if (eKey < 0) return -1 as ResidueIndex;
const cm = chain.get(eKey)!;
- if (!cm.has(c)) return -1;
+ if (!cm.has(c)) return -1 as ResidueIndex;
const rm = residue.get(cm.get(c)!)!
const id = getResidueId(name, seq, ins);
- if (!rm.has(id)) return -1;
- return rm.get(id)!;
+ if (!rm.has(id)) return -1 as ResidueIndex;
+ return rm.get(id)! as ResidueIndex;
}
return { findChainKey, findResidueKey };
}
@@ -92,5 +93,5 @@ export function getAtomicKeys(data: AtomicData, entities: Entities, segments: At
const { findChainKey, findResidueKey } = createLookUp(entities, chainMaps, residueMaps);
- return { residueKey, chainKey, entityKey, findChainKey, findResidueKey };
+ return { getEntityKey: cI => entityKey[cI] as EntityIndex, findChainKey, findResidueKey };
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index d13f5ddd8..181e8b6b7 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -48,7 +48,7 @@ const atom = {
}
const residue = {
- key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residueKey[l.unit.residueIndex[l.element]]),
+ key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.residueIndex[l.element]),
group_PDB: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.group_PDB.value(l.unit.residueIndex[l.element])),
label_comp_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])),
@@ -63,7 +63,7 @@ const residue = {
}
const chain = {
- key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chainKey[l.unit.chainIndex[l.element]]),
+ key: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.chainIndex[l.element]),
label_asym_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chains.label_asym_id.value(l.unit.chainIndex[l.element])),
auth_asym_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.chains.auth_asym_id.value(l.unit.chainIndex[l.element])),
@@ -92,7 +92,7 @@ const coarse = {
function eK(l: Element.Location) {
switch (l.unit.kind) {
case Unit.Kind.Atomic:
- return l.unit.model.atomicHierarchy.entityKey[l.unit.chainIndex[l.element]]
+ return l.unit.model.atomicHierarchy.getEntityKey(l.unit.chainIndex[l.element])
case Unit.Kind.Spheres:
return l.unit.model.coarseHierarchy.spheres.entityKey[l.element]
case Unit.Kind.Gaussians:
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 14d0fc818..f5b9f1c4c 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -13,6 +13,7 @@ import { CoarseElements, CoarseSphereConformation, CoarseGaussianConformation }
import { ValueRef } from 'mol-util';
import { UnitRings } from './unit/rings';
import Element from './element'
+import { ChainIndex, ResidueIndex } from '../model/indexing';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -82,8 +83,8 @@ namespace Unit {
readonly conformation: SymmetryOperator.ArrayMapping;
// Reference some commonly accessed things for faster access.
- readonly residueIndex: ArrayLike<number>;
- readonly chainIndex: ArrayLike<number>;
+ readonly residueIndex: ArrayLike<ResidueIndex>;
+ readonly chainIndex: ArrayLike<ChainIndex>;
private props: AtomicProperties;
--
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