diff --git a/src/mol-data/int/_spec/ordered-set.spec.ts b/src/mol-data/int/_spec/ordered-set.spec.ts
index 04ca406f4aa38c26ab4acf1d9522f15cdedc77cd..4bd7fbdc0f13167d17c8b3880e2b72823b6e1f2d 100644
--- a/src/mol-data/int/_spec/ordered-set.spec.ts
+++ b/src/mol-data/int/_spec/ordered-set.spec.ts
@@ -1,12 +1,11 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import OrderedSet from '../ordered-set'
import Interval from '../interval'
-//import SortedArray from '../sorted-array';
describe('ordered set', () => {
function ordSetToArray(set: OrderedSet) {
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index 8f6d7f8eb03a35ad45a89b6f6480daf7ba19c510..74c0f1345e6d3ec13d628092d96564e2c27032e4 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -200,13 +200,30 @@ export namespace Loci {
return false;
}
- export function extendToWholeResidues(loci: Loci): Loci {
+ /** Check if second loci is a subset of the first */
+ export function isSubset(xs: Loci, ys: Loci): boolean {
+ if (Loci.isEmpty(xs)) return Loci.isEmpty(ys);
+
+ const map = new Map<number, OrderedSet<UnitIndex>>();
+
+ for (const e of xs.elements) map.set(e.unit.id, e.indices);
+ for (const e of ys.elements) {
+ if (!map.has(e.unit.id)) continue;
+ if (!OrderedSet.isSubset(map.get(e.unit.id)!, e.indices)) return false;
+ }
+
+ return true;
+ }
+
+ export function extendToWholeResidues(loci: Loci, restrictToConformation?: boolean): Loci {
const elements: Loci['elements'][0][] = [];
+ const residueAltIds = new Set<string>()
for (const lociElement of loci.elements) {
if (lociElement.unit.kind === Unit.Kind.Atomic) {
const unitElements = lociElement.unit.elements;
const h = lociElement.unit.model.atomicHierarchy;
+ const { label_alt_id } = lociElement.unit.model.atomicHierarchy.atoms;
const { index: residueIndex, offsets: residueOffsets } = h.residueAtomSegments;
@@ -214,15 +231,26 @@ export namespace Loci {
const indices = lociElement.indices, len = OrderedSet.size(indices);
let i = 0;
while (i < len) {
- const rI = residueIndex[unitElements[OrderedSet.getAt(indices, i)]];
+ residueAltIds.clear()
+ const eI = unitElements[OrderedSet.getAt(indices, i)]
+ const rI = residueIndex[eI];
+ residueAltIds.add(label_alt_id.value(eI))
i++;
- while (i < len && residueIndex[unitElements[OrderedSet.getAt(indices, i)]] === rI) {
+ while (i < len) {
+ const eI = unitElements[OrderedSet.getAt(indices, i)]
+ if (residueIndex[eI] !== rI) break;
+ residueAltIds.add(label_alt_id.value(eI))
i++;
}
-
+ const hasSharedAltId = residueAltIds.has('')
for (let j = residueOffsets[rI], _j = residueOffsets[rI + 1]; j < _j; j++) {
const idx = OrderedSet.indexOf(unitElements, j);
- if (idx >= 0) newIndices[newIndices.length] = idx as UnitIndex;
+ if (idx >= 0) {
+ const altId = label_alt_id.value(j)
+ if (!restrictToConformation || hasSharedAltId || !altId || residueAltIds.has(altId)) {
+ newIndices[newIndices.length] = idx as UnitIndex;
+ }
+ }
}
}
@@ -244,6 +272,7 @@ export namespace Loci {
}
}
+ // take chainGroupId into account
export function extendToWholeChains(loci: Loci): Loci {
const elements: Loci['elements'][0][] = [];
diff --git a/src/mol-model/structure/structure/element/stats.ts b/src/mol-model/structure/structure/element/stats.ts
index 805df216c1cb7eaa7aada59254b7f340e0a4f742..447cd7364d2a837a650d09bbb999d33162af2e52 100644
--- a/src/mol-model/structure/structure/element/stats.ts
+++ b/src/mol-model/structure/structure/element/stats.ts
@@ -9,13 +9,14 @@ import Unit from '../unit';
import { Loci } from './loci';
import { Location } from './location';
-
export interface Stats {
elementCount: number
+ conformationCount: number
residueCount: number
unitCount: number
firstElementLoc: Location
+ firstConformationLoc: Location
firstResidueLoc: Location
firstUnitLoc: Location
}
@@ -24,10 +25,12 @@ export namespace Stats {
export function create(): Stats {
return {
elementCount: 0,
+ conformationCount: 0,
residueCount: 0,
unitCount: 0,
firstElementLoc: Location.create(),
+ firstConformationLoc: Location.create(),
firstResidueLoc: Location.create(),
firstUnitLoc: Location.create(),
}
@@ -38,6 +41,13 @@ export namespace Stats {
const { elements } = unit
const size = OrderedSet.size(indices)
+ const lociResidueAltIdCounts = new Map<string, number>()
+ const residueAltIdCounts = new Map<string, number>()
+ const addCount = (map: Map<string, number>, altId: string) => {
+ const count = map.get(altId) || 0
+ map.set(altId, count + 1)
+ }
+
if (size > 0) {
Location.set(stats.firstElementLoc, unit, elements[OrderedSet.start(indices)])
}
@@ -55,12 +65,20 @@ export namespace Stats {
} else {
if (Unit.isAtomic(unit)) {
const { index, offsets } = unit.model.atomicHierarchy.residueAtomSegments
+ const { label_alt_id } = unit.model.atomicHierarchy.atoms;
let i = 0
while (i < size) {
+ lociResidueAltIdCounts.clear()
let j = 0
const eI = elements[OrderedSet.getAt(indices, i)]
const rI = index[eI]
- while (i < size && index[elements[OrderedSet.getAt(indices, i)]] === rI) {
+ addCount(lociResidueAltIdCounts, label_alt_id.value(eI))
+ ++i
+ ++j
+ while (i < size) {
+ const eI = elements[OrderedSet.getAt(indices, i)]
+ if (index[eI] !== rI) break
+ addCount(lociResidueAltIdCounts, label_alt_id.value(eI))
++i
++j
}
@@ -69,10 +87,32 @@ export namespace Stats {
// full residue
stats.residueCount += 1
if (stats.residueCount === 1) {
- Location.set(stats.firstResidueLoc, unit, elements[OrderedSet.start(indices)])
+ Location.set(stats.firstResidueLoc, unit, elements[offsets[rI]])
}
} else {
// partial residue
+ residueAltIdCounts.clear()
+ for (let l = offsets[rI], _l = offsets[rI + 1]; l < _l; ++l) {
+ addCount(residueAltIdCounts, label_alt_id.value(l))
+ }
+ // check if shared atom count match
+ if (residueAltIdCounts.get('') === lociResidueAltIdCounts.get('')) {
+ lociResidueAltIdCounts.forEach((v, k) => {
+ if (residueAltIdCounts.get(k) !== v) return
+ if (k !== '') {
+ stats.conformationCount += 1
+ if (stats.conformationCount === 1) {
+ for (let l = offsets[rI], _l = offsets[rI + 1]; l < _l; ++l) {
+ if (k === label_alt_id.value(l)) {
+ Location.set(stats.firstConformationLoc, unit, l)
+ break
+ }
+ }
+ }
+ }
+ j -= v
+ })
+ }
stats.elementCount += j
}
}
@@ -93,6 +133,7 @@ export namespace Stats {
return stats
}
+ /** Adds counts of two Stats objects together, assumes they describe different structures */
export function add(out: Stats, a: Stats, b: Stats) {
if (a.elementCount === 1 && b.elementCount === 0) {
Location.copy(out.firstElementLoc, a.firstElementLoc)
@@ -100,6 +141,12 @@ export namespace Stats {
Location.copy(out.firstElementLoc, b.firstElementLoc)
}
+ if (a.conformationCount === 1 && b.conformationCount === 0) {
+ Location.copy(out.firstConformationLoc, a.firstConformationLoc)
+ } else if (a.conformationCount === 0 && b.conformationCount === 1) {
+ Location.copy(out.firstConformationLoc, b.firstConformationLoc)
+ }
+
if (a.residueCount === 1 && b.residueCount === 0) {
Location.copy(out.firstResidueLoc, a.firstResidueLoc)
} else if (a.residueCount === 0 && b.residueCount === 1) {
@@ -113,6 +160,7 @@ export namespace Stats {
}
out.elementCount = a.elementCount + b.elementCount
+ out.conformationCount = a.conformationCount + b.conformationCount
out.residueCount = a.residueCount + b.residueCount
out.unitCount = a.unitCount + b.unitCount
return out
diff --git a/src/mol-plugin/ui/sequence.tsx b/src/mol-plugin/ui/sequence.tsx
index 7fd4d3e210f69df38a43e7e60cbc6e43aa3a44c8..5ce88829d905c1bdae9746e23ea4b596daff8006 100644
--- a/src/mol-plugin/ui/sequence.tsx
+++ b/src/mol-plugin/ui/sequence.tsx
@@ -21,7 +21,6 @@ import { State, StateSelection } from '../../mol-state';
import { ChainSequenceWrapper } from './sequence/chain';
import { ElementSequenceWrapper } from './sequence/element';
import { elementLabel } from '../../mol-theme/label';
-import { stripTags } from '../../mol-util/string';
const MaxDisplaySequenceLength = 5000
@@ -125,7 +124,7 @@ function getUnitOptions(structure: Structure, modelEntityId: string) {
// TODO handle special cases
// - more than one chain in a unit
// - chain spread over multiple units
- let label = stripTags(elementLabel(l, 'chain', true))
+ let label = elementLabel(l, { granularity: 'chain', hidePrefix: true, htmlStyling: false })
if (SP.entity.type(l) === 'water') {
const count = water.get(label) || 1
water.set(label, count + 1)
diff --git a/src/mol-plugin/ui/structure/selection.tsx b/src/mol-plugin/ui/structure/selection.tsx
index 9d9d3b63a3acb8eef5cb9b05f19fad52c4be8fe1..5a7e591f1a69d17716c0dfc992770bd1ac4ef1b0 100644
--- a/src/mol-plugin/ui/structure/selection.tsx
+++ b/src/mol-plugin/ui/structure/selection.tsx
@@ -12,6 +12,7 @@ import { PluginCommands } from '../../command';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Interactivity } from '../../util/interactivity';
import { ParameterControls } from '../controls/parameters';
+import { stripTags } from '../../../mol-util/string';
const StructureSelectionParams = {
granularity: Interactivity.Params.granularity,
@@ -43,7 +44,7 @@ export class StructureSelectionControls<P, S extends StructureSelectionControlsS
if (stats.structureCount === 0 || stats.elementCount === 0) {
return 'Selected nothing'
} else {
- return `Selected ${stats.label}`
+ return `Selected ${stripTags(stats.label)}`
}
}
diff --git a/src/mol-plugin/util/interactivity.ts b/src/mol-plugin/util/interactivity.ts
index 11f147a49785697ec7281fec5c906753bdd91c28..b1832b9a80fd3074e5aad0fc92d54c0790b4b97d 100644
--- a/src/mol-plugin/util/interactivity.ts
+++ b/src/mol-plugin/util/interactivity.ts
@@ -54,7 +54,7 @@ namespace Interactivity {
const Granularity = {
'element': (loci: ModelLoci) => loci,
- 'residue': (loci: ModelLoci) => SE.Loci.is(loci) ? SE.Loci.extendToWholeResidues(loci) : loci,
+ 'residue': (loci: ModelLoci) => SE.Loci.is(loci) ? SE.Loci.extendToWholeResidues(loci, true) : loci,
'chain': (loci: ModelLoci) => SE.Loci.is(loci) ? SE.Loci.extendToWholeChains(loci) : loci,
'structure': (loci: ModelLoci) => SE.Loci.is(loci) ? Structure.Loci(loci.structure) : loci
}
@@ -164,7 +164,7 @@ namespace Interactivity {
if (StructureElement.Loci.is(normalized.loci)) {
this.toggleSel(normalized);
} else {
- this.mark(normalized, MarkerAction.Toggle);
+ super.mark(normalized, MarkerAction.Toggle);
}
}
@@ -210,6 +210,18 @@ namespace Interactivity {
if (isEmptyLoci(current.loci)) this.deselectAll()
}
+ protected mark(current: Loci<ModelLoci>, action: MarkerAction.Select | MarkerAction.Deselect) {
+ const { loci } = current
+ if (StructureElement.Loci.is(loci)) {
+ // do a full deselect/select so visuals that are marked with
+ // granularity unequal to 'element' are handled properly
+ super.mark({ loci: EveryLoci }, MarkerAction.Deselect)
+ super.mark({ loci: this.sel.get(loci.structure) }, MarkerAction.Select)
+ } else {
+ super.mark(current, action)
+ }
+ }
+
private toggleSel(current: Loci<ModelLoci>) {
if (this.sel.has(current.loci)) {
this.sel.remove(current.loci);
diff --git a/src/mol-plugin/util/structure-element-selection.ts b/src/mol-plugin/util/structure-element-selection.ts
index 051929e0b6b2d8123fe0b952065e0d0609fbf883..e69d1f4d4850ed7c2f8a5e643ee864d0b60f7ed4 100644
--- a/src/mol-plugin/util/structure-element-selection.ts
+++ b/src/mol-plugin/util/structure-element-selection.ts
@@ -148,7 +148,7 @@ class StructureElementSelectionManager {
if (StructureElement.Loci.is(loci)) {
const entry = this.getEntry(loci.structure);
if (entry) {
- return StructureElement.Loci.areIntersecting(loci, entry.selection);
+ return StructureElement.Loci.isSubset(entry.selection, loci);
}
}
return false;
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index 4f8418f0e1e3541f6a9dd25e35caf80dd8d292ec..0863284304a9bf9b224cd63b3dabd57c9f461d4f 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -8,18 +8,9 @@
import { Unit, StructureElement, StructureProperties as Props, Link } from '../mol-model/structure';
import { Loci } from '../mol-model/loci';
import { OrderedSet } from '../mol-data/int';
-import { capitalize } from '../mol-util/string';
+import { capitalize, stripTags } from '../mol-util/string';
import { Column } from '../mol-data/db';
-// for `labelFirst`, don't create right away to avoid problems with circular dependencies/imports
-let elementLocA: StructureElement.Location
-let elementLocB: StructureElement.Location
-
-function setElementLocation(loc: StructureElement.Location, unit: Unit, index: StructureElement.UnitIndex) {
- loc.unit = unit
- loc.element = unit.elements[index]
-}
-
export function lociLabel(loci: Loci): string {
switch (loci.kind) {
case 'structure-loci':
@@ -47,8 +38,8 @@ function countLabel(count: number, label: string) {
return count === 1 ? `1 ${label}` : `${count} ${label}s`
}
-function otherLabel(count: number, location: StructureElement.Location, granularity: LabelGranularity, hidePrefix: boolean, altCount?: string) {
- return `${elementLabel(location, granularity, hidePrefix)} <small>[+ ${countLabel(count - 1, `other ${altCount || capitalize(granularity)}`)}]</small>`
+function otherLabel(count: number, location: StructureElement.Location, granularity: LabelGranularity, hidePrefix: boolean) {
+ return `${elementLabel(location, { granularity, hidePrefix })} <small>[+ ${countLabel(count - 1, `other ${capitalize(granularity)}`)}]</small>`
}
/** Gets residue count of the model chain segments the unit is a subset of */
@@ -61,47 +52,50 @@ function getResidueCount(unit: Unit.Atomic) {
}
export function structureElementStatsLabel(stats: StructureElement.Stats, countsOnly = false): string {
- const { unitCount, residueCount, elementCount } = stats
+ const { unitCount, residueCount, conformationCount, elementCount } = stats
if (!countsOnly && elementCount === 1 && residueCount === 0 && unitCount === 0) {
- return elementLabel(stats.firstElementLoc, 'element')
+ return elementLabel(stats.firstElementLoc, { granularity: 'element' })
} else if (!countsOnly && elementCount === 0 && residueCount === 1 && unitCount === 0) {
- return elementLabel(stats.firstResidueLoc, 'residue')
+ return elementLabel(stats.firstResidueLoc, { granularity: 'residue' })
} else if (!countsOnly && elementCount === 0 && residueCount === 0 && unitCount === 1) {
const { unit } = stats.firstUnitLoc
const granularity = (Unit.isAtomic(unit) && getResidueCount(unit) === 1) ? 'residue' : 'chain'
- return elementLabel(stats.firstUnitLoc, granularity)
+ return elementLabel(stats.firstUnitLoc, { granularity })
} else if (!countsOnly) {
const label: string[] = []
let hidePrefix = false;
if (unitCount > 0) {
- label.push(unitCount === 1 ? elementLabel(stats.firstUnitLoc, 'chain') : otherLabel(unitCount, stats.firstElementLoc, 'chain', false, 'Instance'))
+ label.push(unitCount === 1 ? elementLabel(stats.firstUnitLoc, { granularity: 'chain' }) : otherLabel(unitCount, stats.firstElementLoc, 'chain', false))
hidePrefix = true;
}
if (residueCount > 0) {
- label.push(residueCount === 1 ? elementLabel(stats.firstResidueLoc, 'residue', hidePrefix) : otherLabel(residueCount, stats.firstElementLoc, 'residue', hidePrefix))
+ label.push(residueCount === 1 ? elementLabel(stats.firstResidueLoc, { granularity: 'residue', hidePrefix }) : otherLabel(residueCount, stats.firstElementLoc, 'residue', hidePrefix))
+ hidePrefix = true;
+ }
+ if (conformationCount > 0) {
+ label.push(conformationCount === 1 ? elementLabel(stats.firstConformationLoc, { granularity: 'conformation', hidePrefix }) : otherLabel(conformationCount, stats.firstElementLoc, 'conformation', hidePrefix))
hidePrefix = true;
}
if (elementCount > 0) {
- label.push(elementCount === 1 ? elementLabel(stats.firstElementLoc, 'element', hidePrefix) : otherLabel(elementCount, stats.firstElementLoc, 'element', hidePrefix))
+ label.push(elementCount === 1 ? elementLabel(stats.firstElementLoc, { granularity: 'element', hidePrefix }) : otherLabel(elementCount, stats.firstElementLoc, 'element', hidePrefix))
}
return label.join('<small> + </small>')
} else {
const label: string[] = []
- if (unitCount > 0) label.push(countLabel(unitCount, 'Instance'))
+ if (unitCount > 0) label.push(countLabel(unitCount, 'Chain'))
if (residueCount > 0) label.push(countLabel(residueCount, 'Residue'))
+ if (conformationCount > 0) label.push(countLabel(conformationCount, 'Conformation'))
if (elementCount > 0) label.push(countLabel(elementCount, 'Element'))
return label.join('<small> + </small>')
}
}
export function linkLabel(link: Link.Location): string {
- if (!elementLocA) elementLocA = StructureElement.Location.create()
- if (!elementLocB) elementLocB = StructureElement.Location.create()
- setElementLocation(elementLocA, link.aUnit, link.aIndex)
- setElementLocation(elementLocB, link.bUnit, link.bIndex)
- const labelA = _elementLabel(elementLocA)
- const labelB = _elementLabel(elementLocB)
+ const locA = StructureElement.Location.create(link.aUnit, link.aUnit.elements[link.aIndex])
+ const locB = StructureElement.Location.create(link.bUnit, link.bUnit.elements[link.bIndex])
+ const labelA = _elementLabel(locA)
+ const labelB = _elementLabel(locB)
let offset = 0
for (let i = 0, il = Math.min(labelA.length, labelB.length); i < il; ++i) {
if (labelA[i] === labelB[i]) offset += 1
@@ -110,10 +104,19 @@ export function linkLabel(link: Link.Location): string {
return `${labelA.join(' | ')} \u2014 ${labelB.slice(offset).join(' | ')}`
}
-export type LabelGranularity = 'element' | 'residue' | 'chain' | 'structure'
+export type LabelGranularity = 'element' | 'conformation' | 'residue' | 'chain' | 'structure'
+
+export const DefaultLabelOptions = {
+ granularity: 'element' as LabelGranularity,
+ hidePrefix: false,
+ htmlStyling: true,
+}
+export type LabelOptions = typeof DefaultLabelOptions
-export function elementLabel(location: StructureElement.Location, granularity: LabelGranularity = 'element', hidePrefix = false): string {
- return _elementLabel(location, granularity, hidePrefix).join(' | ')
+export function elementLabel(location: StructureElement.Location, options: Partial<LabelOptions>): string {
+ const o = { ...DefaultLabelOptions, ...options }
+ const label = _elementLabel(location, o.granularity, o.hidePrefix).join(' | ')
+ return o.htmlStyling ? label : stripTags(label)
}
function _elementLabel(location: StructureElement.Location, granularity: LabelGranularity = 'element', hidePrefix = false): string[] {
@@ -158,8 +161,12 @@ function _atomicElementLabel(location: StructureElement.Location<Unit.Atomic>, g
switch (granularity) {
case 'element':
label.push(`<b>${atom_id}</b>${alt_id ? `%${alt_id}` : ''}`)
+ case 'conformation':
+ if (granularity === 'conformation' && alt_id) {
+ label.push(`<small>Conformation</small> <b>${alt_id}</b>`)
+ }
case 'residue':
- label.push(`<b>${compId} ${has_label_seq_id ? label_seq_id : ''}</b>${label_seq_id !== auth_seq_id ? ` <small> [auth</small> <b>${auth_seq_id}</b><small>]</small>` : ''}<b>${ins_code ? ins_code : ''}</b>`)
+ label.push(`<b>${compId}${has_label_seq_id ? ` ${label_seq_id}` : ''}</b>${label_seq_id !== auth_seq_id ? ` <small>[auth</small> <b>${auth_seq_id}</b><small>]</small>` : ''}<b>${ins_code ? ins_code : ''}</b>`)
case 'chain':
if (label_asym_id === auth_asym_id) {
label.push(`<b>${label_asym_id}</b>`)
@@ -180,6 +187,7 @@ function _coarseElementLabel(location: StructureElement.Location<Unit.Spheres |
switch (granularity) {
case 'element':
+ case 'conformation':
case 'residue':
if (seq_id_begin === seq_id_end) {
const entityIndex = Props.coarse.entityKey(location)