diff --git a/CHANGELOG.md b/CHANGELOG.md
index f9dfd4beaa3ee2555fdf37ae0ea88529bddb638c..a0b3c1390c5c8aa6eeb43ba74a3e40a66a5bcb10 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,14 @@ Note that since we don't clearly distinguish between a public and private interf
- Add ``UnitResonance`` property with info about delocalized triplets
- Resolve marking in main renderer loop to improve overall performance
- Use ``throttleTime`` instead of ``debounceTime`` in sequence viewer for better responsiveness
+- Change line geometry default ``scaleFactor`` to 2 (3 is too big after fixing line rendering)
+- Trajectory animation performance improvements
+ - Reuse ``Model.CoarseGrained`` for coordinate trajectories
+ - Avoid calculating ``InterUnitBonds`` when ``Structure.parent`` ones are empty
+ - Reuse unit boundary if sphere has not changed too much
+ - Don't show 'inter-bond' and 'element-cross' visuals in line representations of polymerAndLigand preset
+- Fix additional mononucleotides detected as polymer components
+- Fix and improve ``canRemap`` handling in ``IntraUnitBonds``
- Reuse occlusion for secondary passes during multi-sampling
- Check if marking passes are needed before doing them
- Add ``scaleFactor`` parameter to adjust resolution of occlusion calculation
diff --git a/src/mol-geo/geometry/lines/lines.ts b/src/mol-geo/geometry/lines/lines.ts
index d8e4051fe11931dffcbea168227d021f70471d84..5452ac7611d4698522c1cf08c31ccddd1272f2c3 100644
--- a/src/mol-geo/geometry/lines/lines.ts
+++ b/src/mol-geo/geometry/lines/lines.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -165,7 +165,7 @@ export namespace Lines {
export const Params = {
...BaseGeometry.Params,
- sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
+ sizeFactor: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }),
lineSizeAttenuation: PD.Boolean(false),
};
export type Params = typeof Params
diff --git a/src/mol-model-formats/structure/common/component.ts b/src/mol-model-formats/structure/common/component.ts
index cdacb28722b658ff42e32c6e50d737b31a540868..11c5249757daa3fa1ed98acd53e4f81b791bd435 100644
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -30,7 +30,7 @@ const DnaAtomIdsList = [
/** Used to reduce false positives for atom name-based type guessing */
const NonPolymerNames = new Set([
- 'FMN', 'NCN', 'FNS', 'FMA' // Mononucleotides
+ 'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
]);
const StandardComponents = (function () {
@@ -156,7 +156,7 @@ export class ComponentBuilder {
this.set(StandardComponents.get(compId)!);
} else if (WaterNames.has(compId)) {
this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
- } else if (NonPolymerNames.has(compId)) {
+ } else if (NonPolymerNames.has(compId.toUpperCase())) {
this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
} else {
const atomIds = this.getAtomIds(index);
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index a78df048811350138596ef5a2be48d6189118d0c..1e8b9fc4306313c64827770f5b0cf1908b5b5e46 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -98,6 +98,7 @@ export namespace Model {
const srcIndex = model.atomicHierarchy.atomSourceIndex;
const isIdentity = Column.isIdentity(srcIndex);
const srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
+ const coarseGrained = isCoarseGrained(model);
for (let i = 0, il = frames.length; i < il; ++i) {
const f = frames[i];
@@ -119,6 +120,7 @@ export namespace Model {
}
TrajectoryInfo.set(m, { index: i, size: frames.length });
+ CoarseGrained.set(m, coarseGrained);
trajectory.push(m);
}
@@ -138,11 +140,13 @@ export namespace Model {
const bondData = { pairs: topology.bonds, count: model.atomicHierarchy.atoms._rowCount };
const indexPairBonds = IndexPairBonds.fromData(bondData);
+ const coarseGrained = isCoarseGrained(model);
let index = 0;
for (const m of trajectory) {
IndexPairBonds.Provider.set(m, indexPairBonds);
TrajectoryInfo.set(m, { index: index++, size: trajectory.length });
+ CoarseGrained.set(m, coarseGrained);
}
return new ArrayTrajectory(trajectory);
});
@@ -225,35 +229,44 @@ export namespace Model {
};
const CoarseGrainedProp = '__CoarseGrained__';
+ export const CoarseGrained = {
+ get(model: Model): boolean | undefined {
+ return model._staticPropertyData[CoarseGrainedProp];
+ },
+ set(model: Model, coarseGrained: boolean) {
+ return model._staticPropertyData[CoarseGrainedProp] = coarseGrained;
+ }
+ };
/**
* Has typical coarse grained atom names (BB, SC1) or less than three times as many
* atoms as polymer residues (C-alpha only models).
*/
export function isCoarseGrained(model: Model): boolean {
- if (model._staticPropertyData[CoarseGrainedProp] !== undefined) return model._staticPropertyData[CoarseGrainedProp];
+ let coarseGrained = CoarseGrained.get(model);
+ if (coarseGrained === undefined) {
+ let polymerResidueCount = 0;
+ const { polymerType } = model.atomicHierarchy.derived.residue;
+ for (let i = 0; i < polymerType.length; ++i) {
+ if (polymerType[i] !== PolymerType.NA) polymerResidueCount += 1;
+ }
- let polymerResidueCount = 0;
- const { polymerType } = model.atomicHierarchy.derived.residue;
- for (let i = 0; i < polymerType.length; ++i) {
- if (polymerType[i] !== PolymerType.NA) polymerResidueCount += 1;
- }
+ // check for coarse grained atom names
+ let hasBB = false, hasSC1 = false;
+ const { label_atom_id, _rowCount: atomCount } = model.atomicHierarchy.atoms;
+ for (let i = 0; i < atomCount; ++i) {
+ const atomName = label_atom_id.value(i);
+ if (!hasBB && atomName === 'BB') hasBB = true;
+ if (!hasSC1 && atomName === 'SC1') hasSC1 = true;
+ if (hasBB && hasSC1) break;
+ }
- // check for coarse grained atom names
- let hasBB = false, hasSC1 = false;
- const { label_atom_id, _rowCount: atomCount } = model.atomicHierarchy.atoms;
- for (let i = 0; i < atomCount; ++i) {
- const atomName = label_atom_id.value(i);
- if (!hasBB && atomName === 'BB') hasBB = true;
- if (!hasSC1 && atomName === 'SC1') hasSC1 = true;
- if (hasBB && hasSC1) break;
+ coarseGrained = (hasBB && hasSC1) || (
+ polymerResidueCount && atomCount
+ ? atomCount / polymerResidueCount < 3
+ : false
+ );
+ CoarseGrained.set(model, coarseGrained);
}
-
- const coarseGrained = (hasBB && hasSC1) || (
- polymerResidueCount && atomCount
- ? atomCount / polymerResidueCount < 3
- : false
- );
- model._staticPropertyData[CoarseGrainedProp] = coarseGrained;
return coarseGrained;
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index f962ee68207d5ea93d2b7fa605c9a78aae1b6ec1..a2d8e86805c87cf1552709c0ca217902c42c2770 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -232,7 +232,14 @@ class Structure {
get interUnitBonds() {
if (this.state.interUnitBonds) return this.state.interUnitBonds;
- this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+ if (this.parent && this.state.dynamicBonds === this.parent.state.dynamicBonds &&
+ this.parent.state.interUnitBonds && this.parent.state.interUnitBonds.edgeCount === 0
+ ) {
+ // no need to compute InterUnitBonds if parent's ones are empty
+ this.state.interUnitBonds = new InterUnitBonds(new Map());
+ } else {
+ this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+ }
return this.state.interUnitBonds;
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 79cb163989a99cde662b300efba80b25fedc0f23..4c4f0e30975ce1a23fe2c4f97504621d079d814c 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -27,6 +27,9 @@ import { ElementSetIntraBondCache } from './unit/bonds/element-set-intra-bond-ca
import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
import { getResonance, UnitResonance } from './unit/resonance';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3add = Vec3.add;
+
/**
* A building block of a structure that corresponds to an atomic or
* a coarse grained representation 'conveniently grouped together'.
@@ -221,9 +224,32 @@ namespace Unit {
remapModel(model: Model, dynamicBonds: boolean, props?: AtomicProperties) {
if (!props) {
- props = { ...this.props, bonds: dynamicBonds ? undefined : tryRemapBonds(this, this.props.bonds, model) };
+ props = {
+ ...this.props,
+ bonds: dynamicBonds && !this.props.bonds?.props?.canRemap
+ ? undefined
+ : tryRemapBonds(this, this.props.bonds, model, dynamicBonds)
+ };
if (!Unit.isSameConformation(this, model)) {
- props.boundary = undefined;
+ const b = props.boundary;
+ if (b) {
+ const { elements } = this;
+ const pos = this.conformation.invariantPosition;
+ const v = Vec3();
+ const center = Vec3();
+
+ for (let i = 0, il = elements.length; i < il; i++) {
+ pos(elements[i], v);
+ v3add(center, center, v);
+ }
+ Vec3.scale(center, center, 1 / elements.length);
+
+ // only invalidate boundary if sphere has changed too much
+ if (Vec3.distance(center, b.sphere.center) / b.sphere.radius >= 1.0) {
+ props.boundary = undefined;
+ }
+ }
+
props.lookup3d = undefined;
props.principalAxes = undefined;
}
@@ -489,7 +515,7 @@ namespace Unit {
return isSameConformation(a, b.model);
}
- function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model) {
+ function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model, dynamicBonds: boolean) {
// TODO: should include additional checks?
if (!old) return void 0;
@@ -503,7 +529,7 @@ namespace Unit {
return void 0;
}
- if (old.props?.canRemap) {
+ if (old.props?.canRemap || !dynamicBonds) {
return old;
}
return isSameConformation(a, model) ? old : void 0;
diff --git a/src/mol-model/structure/structure/unit/bonds/data.ts b/src/mol-model/structure/structure/unit/bonds/data.ts
index 3f4692f2a4d1a6151fe213bae8fee51ab0389215..b05df8ed1d0e27a6a5e1c4720741bcc6ae11d356 100644
--- a/src/mol-model/structure/structure/unit/bonds/data.ts
+++ b/src/mol-model/structure/structure/unit/bonds/data.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -12,7 +12,13 @@ import { StructureElement } from '../../element';
import { Bond } from '../bonds';
import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
-type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, { readonly order: ArrayLike<number>, readonly flags: ArrayLike<BondType.Flag> }, { readonly canRemap?: boolean }>
+type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
+ readonly order: ArrayLike<number>,
+ readonly flags: ArrayLike<BondType.Flag>
+}, {
+ /** can remap even with dynamicBonds on, e.g., for water molecules */
+ readonly canRemap?: boolean
+}>
namespace IntraUnitBonds {
export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index f9eae7c0568aadfbfb37498123cd57b8ac0ebaa6..4792ca42fae30872316fab6846bacc7c0535b55b 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -141,7 +141,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
const aI = atoms[_aI];
const elemA = type_symbol.value(aI);
- if (isWatery && (elemA !== 'H' || elemA !== 'O')) isWatery = false;
+ if (isWatery && (elemA !== 'H' && elemA !== 'O')) isWatery = false;
const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
let hasStructConn = false;
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index bcccf0de5e0b9d2b590f5d63e3a75d6534927631..b581666d5548291d6082590eca1fadae460ccd94 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -185,9 +185,9 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
nonStandard: builder.buildRepresentation(update, components.nonStandard, { type: 'ball-and-stick', typeParams, color, colorParams: ballAndStickColor }, { tag: 'non-standard' }),
branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.3 }, color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color }, { tag: 'branched-snfg-3d' }),
- water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
+ water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ion' }),
- lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
+ lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'chain-id' }, { tag: 'coarse' })
};
diff --git a/src/mol-repr/structure/representation/line.ts b/src/mol-repr/structure/representation/line.ts
index c0936561151e29bc9222e7ac2c755c058d9344c7..65bed46df5ad924cac3592670349ded599e93492 100644
--- a/src/mol-repr/structure/representation/line.ts
+++ b/src/mol-repr/structure/representation/line.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -31,7 +31,7 @@ export const LineParams = {
...ElementCrossParams,
multipleBonds: PD.Select('offset', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
includeParent: PD.Boolean(false),
- sizeFactor: PD.Numeric(3, { min: 0.01, max: 10, step: 0.01 }),
+ sizeFactor: PD.Numeric(2, { min: 0.01, max: 10, step: 0.01 }),
unitKinds: getUnitKindsParam(['atomic']),
visuals: PD.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], PD.objectToOptions(LineVisuals))
};
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index 34ca57ffaf8d02daa31d2c1200c8cce4d513f6e5..a15721d5042997c7e62afc3062818020be3af39f 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -22,9 +22,6 @@ import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-bui
import { isTrace, isH, StructureGroup } from './common';
import { Sphere3D } from '../../../../mol-math/geometry';
-// avoiding namespace lookup improved performance in Chrome (Aug 2020)
-const v3add = Vec3.add;
-
type ElementProps = {
ignoreHydrogens: boolean,
traceOnly: boolean,
@@ -73,17 +70,13 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
const ignore = makeElementIgnoreTest(structure, unit, props);
const l = StructureElement.Location.create(structure, unit);
const themeSize = theme.size.size;
- const center = Vec3();
let maxSize = 0;
- let count = 0;
for (let i = 0; i < elementCount; i++) {
if (ignore && ignore(elements[i])) continue;
l.element = elements[i];
pos(elements[i], v);
- v3add(center, center, v);
- count += 1;
builderState.currentGroup = i;
const size = themeSize(l);
@@ -92,17 +85,8 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
addSphere(builderState, v, size * sizeFactor, detail);
}
- // re-use boundingSphere if it has not changed much
- let boundingSphere: Sphere3D;
- Vec3.scale(center, center, 1 / count);
- if (mesh && Vec3.distance(center, mesh.boundingSphere.center) / mesh.boundingSphere.radius < 1.0) {
- boundingSphere = Sphere3D.clone(mesh.boundingSphere);
- } else {
- boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * sizeFactor + 0.05);
- }
-
const m = MeshBuilder.getMesh(builderState);
- m.setBoundingSphere(boundingSphere);
+ m.setBoundingSphere(Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * sizeFactor + 0.05));
return m;
}
@@ -126,34 +110,21 @@ export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, stru
const l = StructureElement.Location.create(structure, unit);
const themeSize = theme.size.size;
- const center = Vec3();
let maxSize = 0;
- let count = 0;
for (let i = 0; i < elementCount; i++) {
if (ignore?.(elements[i])) continue;
pos(elements[i], v);
builder.add(v[0], v[1], v[2], i);
- v3add(center, center, v);
- count += 1;
l.element = elements[i];
const size = themeSize(l);
if (size > maxSize) maxSize = size;
}
- // re-use boundingSphere if it has not changed much
- let boundingSphere: Sphere3D;
- Vec3.scale(center, center, 1 / count);
- if (spheres && Vec3.distance(center, spheres.boundingSphere.center) / spheres.boundingSphere.radius < 1.0) {
- boundingSphere = Sphere3D.clone(spheres.boundingSphere);
- } else {
- boundingSphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * props.sizeFactor + 0.05);
- }
-
const s = builder.getSpheres();
- s.setBoundingSphere(boundingSphere);
+ s.setBoundingSphere(Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, maxSize * props.sizeFactor + 0.05));
return s;
}