diff --git a/src/mol-plugin/state/actions/data-format.ts b/src/mol-plugin/state/actions/data-format.ts
index 7e4bbd656f0e3d47097f3c7d73f0960571a448b3..c8eff16e37cb84cb2d61fc5174cff5e74f55f7ab 100644
--- a/src/mol-plugin/state/actions/data-format.ts
+++ b/src/mol-plugin/state/actions/data-format.ts
@@ -13,6 +13,7 @@ import { ParamDefinition as PD } from 'mol-util/param-definition';
import { Ccp4Provider, Dsn6Provider, DscifProvider } from './volume';
import { StateTransforms } from '../transforms';
import { MmcifProvider, PdbProvider, GroProvider } from './structure';
+import msgpackDecode from 'mol-io/common/msgpack/decode'
export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> {
private _list: { name: string, provider: DataFormatProvider<D> }[] = []
@@ -139,4 +140,18 @@ export const OpenFile = StateAction.build({
const b = state.build().to(data.ref);
// need to await the 2nd update the so that the enclosing Task finishes after the update is done.
await provider.getDefaultBuilder(ctx, b, state).runInContext(taskCtx)
-}));
\ No newline at end of file
+}));
+
+//
+
+type cifVariants = 'dscif' | -1
+export function guessCifVariant(info: FileInfo, data: Uint8Array | string): cifVariants {
+ if (info.ext === 'bcif') {
+ try {
+ if (msgpackDecode(data as Uint8Array).encoder.startsWith('VolumeServer')) return 'dscif'
+ } catch { }
+ } else if (info.ext === 'cif') {
+ if ((data as string).startsWith('data_SERVER\n#\n_density_server_result')) return 'dscif'
+ }
+ return -1
+}
\ No newline at end of file
diff --git a/src/mol-plugin/state/actions/structure.ts b/src/mol-plugin/state/actions/structure.ts
index 714adecf217632e6c000e5e2344ff76866148005..b9b623d33ce48996797da7efe367930b6235cc22 100644
--- a/src/mol-plugin/state/actions/structure.ts
+++ b/src/mol-plugin/state/actions/structure.ts
@@ -13,7 +13,7 @@ import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { StructureRepresentation3DHelpers } from '../transforms/representation';
import { CustomModelProperties, StructureSelection } from '../transforms/model';
-import { DataFormatProvider } from './data-format';
+import { DataFormatProvider, guessCifVariant } from './data-format';
import { FileInfo } from 'mol-util/file-info';
import { Task } from 'mol-task';
import { StructureElement } from 'mol-model/structure';
@@ -24,7 +24,10 @@ export const MmcifProvider: DataFormatProvider<any> = {
stringExtensions: ['cif', 'mmcif', 'mcif'],
binaryExtensions: ['bcif'],
isApplicable: (info: FileInfo, data: Uint8Array | string) => {
- return info.ext === 'cif' || info.ext === 'mmcif' || info.ext === 'mcif' || info.ext === 'bcif'
+ if (info.ext === 'mmcif' || info.ext === 'mcif') return true
+ // assume cif/bcif files that are not DensityServer CIF are mmCIF
+ if (info.ext === 'cif' || info.ext === 'bcif') return guessCifVariant(info, data) !== 'dscif'
+ return false
},
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, state: State) => {
return Task.create('mmCIF default builder', async taskCtx => {
diff --git a/src/mol-plugin/state/actions/volume.ts b/src/mol-plugin/state/actions/volume.ts
index baf6e0ded64d08c380cf907bd4a671302cbeac5a..727114bf9f8b56ec9b7c619130b28e208d79ab06 100644
--- a/src/mol-plugin/state/actions/volume.ts
+++ b/src/mol-plugin/state/actions/volume.ts
@@ -16,7 +16,7 @@ import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { VolumeRepresentation3DHelpers } from '../transforms/representation';
-import { DataFormatProvider } from './data-format';
+import { DataFormatProvider, guessCifVariant } from './data-format';
export const Ccp4Provider: DataFormatProvider<any> = {
label: 'CCP4/MRC/BRIX',
@@ -59,10 +59,10 @@ export const DscifProvider: DataFormatProvider<any> = {
description: 'DensityServer CIF',
stringExtensions: ['cif'],
binaryExtensions: ['bcif'],
- isApplicable: (info: FileInfo, data: Uint8Array) => {
- return info.ext === 'cif' || info.ext === 'bcif'
+ isApplicable: (info: FileInfo, data: Uint8Array | string) => {
+ return guessCifVariant(info, data) === 'dscif' ? true : false
},
- getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary>, state: State) => {
+ getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, state: State) => {
return Task.create('DensityServer CIF default builder', async taskCtx => {
const cifBuilder = data.apply(StateTransforms.Data.ParseCif)
const cifStateObject = await state.updateTree(cifBuilder).runInContext(taskCtx)
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index 1e2f479d22e546a668aab603854caf7841db563f..cd0e2271a17f32e5821ebca489f0f935eb15c4a8 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -11,7 +11,7 @@ import { OrderedSet, SortedArray } from 'mol-data/int';
import { EmptyLoci, Loci } from 'mol-model/loci';
/** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
-export function getResidueLoci(structure: Structure, unit: Unit, elementIndex: ElementIndex): Loci {
+export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
const { elements, model } = unit
if (OrderedSet.indexOf(elements, elementIndex) !== -1) {
const { index, offsets } = model.atomicHierarchy.residueAtomSegments
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 71b987a3ea8b5ac3954524d393e59875b55b5733..bf0f536b8c15cbbd1f4f98788507fd9fa6807e4e 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -72,12 +72,25 @@ export function getPolymerElementLoci(pickingId: PickingId, structureGroup: Stru
if (id === objectId) {
const { structure, group } = structureGroup
const unit = group.units[instanceId]
- return getResidueLoci(structure, unit, unit.polymerElements[groupId])
+ if (Unit.isAtomic(unit)) {
+ return getResidueLoci(structure, unit, unit.polymerElements[groupId])
+ } else {
+ const { elements } = unit
+ const elementIndex = unit.polymerElements[groupId]
+ const unitIndex = OrderedSet.indexOf(elements, elementIndex) as StructureElement.UnitIndex | -1
+ if (unitIndex !== -1) {
+ const indices = OrderedSet.ofSingleton(unitIndex)
+ return StructureElement.Loci(structure, [{ unit, indices }])
+ }
+ }
}
return EmptyLoci
}
-/** Mark a polymer element (e.g. part of a cartoon trace) when all its residue's elements are in a loci. */
+/**
+ * Mark a polymer element (e.g. part of a cartoon trace)
+ * - for atomic units mark only when all its residue's elements are in a loci
+ */
export function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
let changed = false
if (!StructureElement.isLoci(loci)) return false
@@ -90,19 +103,32 @@ export function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, a
for (const e of loci.elements) {
const unitIdx = group.unitIndexMap.get(e.unit.id)
if (unitIdx !== undefined) {
- // TODO optimized implementation for intervals
- OrderedSet.forEach(e.indices, v => {
- const rI = index[elements[v]]
- const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
- const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
- const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
- if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
- const eI = traceElementIndex[rI]
- const idx = OrderedSet.indexOf(e.unit.polymerElements, eI)
- if (idx !== -1) {
- if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
+ if (Unit.isAtomic(e.unit)) {
+ // TODO optimized implementation for intervals
+ OrderedSet.forEach(e.indices, v => {
+ const rI = index[elements[v]]
+ const unitIndexMin = OrderedSet.findPredecessorIndex(elements, offsets[rI])
+ const unitIndexMax = OrderedSet.findPredecessorIndex(elements, offsets[rI + 1] - 1)
+ const unitIndexInterval = Interval.ofRange(unitIndexMin, unitIndexMax)
+ if (!OrderedSet.isSubset(e.indices, unitIndexInterval)) return
+ const eI = traceElementIndex[rI]
+ const idx = OrderedSet.indexOf(e.unit.polymerElements, eI)
+ if (idx !== -1) {
+ if (apply(Interval.ofSingleton(unitIdx * groupCount + idx))) changed = true
+ }
+ })
+ } else {
+ if (Interval.is(e.indices)) {
+ const start = unitIdx * groupCount + Interval.start(e.indices);
+ const end = unitIdx * groupCount + Interval.end(e.indices);
+ if (apply(Interval.ofBounds(start, end))) changed = true
+ } else {
+ for (let i = 0, _i = e.indices.length; i < _i; i++) {
+ const idx = unitIdx * groupCount + e.indices[i];
+ if (apply(Interval.ofSingleton(idx))) changed = true
+ }
}
- })
+ }
}
}
return changed