diff --git a/src/apps/docking-viewer/index.ts b/src/apps/docking-viewer/index.ts
index c288b158acc3927f496cb4a6fc8011857f83b519..1157b6a8efe3a601c5dab0ac37dafb78ff593884 100644
--- a/src/apps/docking-viewer/index.ts
+++ b/src/apps/docking-viewer/index.ts
@@ -69,9 +69,10 @@ class Viewer {
viewportShowSelectionMode: false,
viewportShowAnimation: false,
} };
+ const defaultSpec = DefaultPluginSpec();
const spec: PluginSpec = {
- actions: [...DefaultPluginSpec.actions],
+ actions: [...defaultSpec.actions],
behaviors: [
PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
@@ -81,8 +82,8 @@ class Viewer {
PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
],
- animations: [...DefaultPluginSpec.animations || []],
- customParamEditors: DefaultPluginSpec.customParamEditors,
+ animations: [...defaultSpec.animations || []],
+ customParamEditors: defaultSpec.customParamEditors,
layout: {
initial: {
isExpanded: o.layoutIsExpanded,
@@ -90,14 +91,14 @@ class Viewer {
controlsDisplay: o.layoutControlsDisplay,
},
controls: {
- ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+ ...defaultSpec.layout && defaultSpec.layout.controls,
top: o.layoutShowSequence ? undefined : 'none',
bottom: o.layoutShowLog ? undefined : 'none',
left: o.layoutShowLeftPanel ? undefined : 'none',
}
},
components: {
- ...DefaultPluginSpec.components,
+ ...defaultSpec.components,
remoteState: o.layoutShowRemoteState ? 'default' : 'none',
viewport: {
view: ViewportComponent
diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index 4c49970a98ccaa567b4e10c32d68030c2c52fbf4..4aa38dc519b7d92bf5777dcad3e33e2259651b7a 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -89,15 +89,16 @@ export class Viewer {
constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
const o = { ...DefaultViewerOptions, ...options };
+ const defaultSpec = DefaultPluginSpec();
const spec: PluginSpec = {
- actions: [...DefaultPluginSpec.actions],
+ actions: [...defaultSpec.actions],
behaviors: [
- ...DefaultPluginSpec.behaviors,
+ ...defaultSpec.behaviors,
...o.extensions.map(e => Extensions[e]),
],
- animations: [...DefaultPluginSpec.animations || []],
- customParamEditors: DefaultPluginSpec.customParamEditors,
+ animations: [...defaultSpec.animations || []],
+ customParamEditors: defaultSpec.customParamEditors,
customFormats: o?.customFormats,
layout: {
initial: {
@@ -106,14 +107,14 @@ export class Viewer {
controlsDisplay: o.layoutControlsDisplay,
},
controls: {
- ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+ ...defaultSpec.layout && defaultSpec.layout.controls,
top: o.layoutShowSequence ? undefined : 'none',
bottom: o.layoutShowLog ? undefined : 'none',
left: o.layoutShowLeftPanel ? undefined : 'none',
}
},
components: {
- ...DefaultPluginSpec.components,
+ ...defaultSpec.components,
remoteState: o.layoutShowRemoteState ? 'default' : 'none',
},
config: [
diff --git a/src/examples/alpha-orbitals/index.ts b/src/examples/alpha-orbitals/index.ts
index 612a835a06732b47f4d3df9257442fe0f8ab0294..efdc57abd3ac9e93168bc09b16bc1a4590e892a4 100644
--- a/src/examples/alpha-orbitals/index.ts
+++ b/src/examples/alpha-orbitals/index.ts
@@ -53,7 +53,7 @@ export class AlphaOrbitalsExample {
async init(target: string | HTMLElement) {
this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
+ ...DefaultPluginSpec(),
layout: {
initial: {
isExpanded: false,
diff --git a/src/examples/basic-wrapper/index.ts b/src/examples/basic-wrapper/index.ts
index f2dfbcefc92c0a9057f332d261e018bc049bd809..d8d1ed030a110aa6a739e4891ce81aee0080a6af 100644
--- a/src/examples/basic-wrapper/index.ts
+++ b/src/examples/basic-wrapper/index.ts
@@ -28,7 +28,7 @@ class BasicWrapper {
init(target: string | HTMLElement) {
this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
+ ...DefaultPluginSpec(),
layout: {
initial: {
isExpanded: false,
diff --git a/src/examples/lighting/index.ts b/src/examples/lighting/index.ts
index 95757a6215baf0d3737948d2cdf3065bb7f6a1f6..4305e6d925d69ec50b8537d291a760245265615c 100644
--- a/src/examples/lighting/index.ts
+++ b/src/examples/lighting/index.ts
@@ -67,7 +67,7 @@ class LightingDemo {
init(target: string | HTMLElement) {
this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
+ ...DefaultPluginSpec(),
layout: {
initial: {
isExpanded: false,
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index ebd4a00e5462fd51cb571c15ce1fb1dcc33236b3..233c1878a889620b3b9a6b5fcf9e809519960697 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -46,7 +46,7 @@ class MolStarProteopediaWrapper {
customColorList?: number[]
}) {
this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
- ...DefaultPluginSpec,
+ ...DefaultPluginSpec(),
animations: [
AnimateModelIndex
],
diff --git a/src/extensions/anvil/algorithm.ts b/src/extensions/anvil/algorithm.ts
index 726adb62dbe27444442fba1142d0e7d3ccc9c20e..8dbb5c72d7d67efeeaae5e253a2da46b8f24140c 100644
--- a/src/extensions/anvil/algorithm.ts
+++ b/src/extensions/anvil/algorithm.ts
@@ -54,13 +54,13 @@ export function computeANVIL(structure: Structure, props: ANVILProps) {
});
}
-const l = StructureElement.Location.create(void 0);
+
const centroidHelper = new CentroidHelper();
function initialize(structure: Structure, props: ANVILProps): ANVILContext {
+ const l = StructureElement.Location.create(structure);
const { label_atom_id, x, y, z } = StructureProperties.atom;
const elementCount = structure.polymerResidueCount;
centroidHelper.reset();
- l.structure = structure;
let offsets = new Int32Array(elementCount);
let exposed = new Array<boolean>(elementCount);
@@ -328,6 +328,7 @@ namespace HphobHphil {
const testPoint = Vec3();
export function filtered(ctx: ANVILContext, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil {
const { offsets, exposed, structure } = ctx;
+ const l = StructureElement.Location.create(structure);
const { x, y, z } = StructureProperties.atom;
let hphob = 0;
let hphil = 0;
diff --git a/src/mol-math/geometry/boundary-helper.ts b/src/mol-math/geometry/boundary-helper.ts
index b1cc0ec6bf5dad1e481fef4cf166e3f76db6e5ac..3d719a15e248d1dae934cd384ecf31d0affc386e 100644
--- a/src/mol-math/geometry/boundary-helper.ts
+++ b/src/mol-math/geometry/boundary-helper.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Vec3 } from '../linear-algebra/3d';
+import { Vec3 } from '../linear-algebra/3d/vec3';
import { CentroidHelper } from './centroid-helper';
import { Sphere3D } from '../geometry';
import { Box3D } from './primitives/box3d';
diff --git a/src/mol-math/geometry/centroid-helper.ts b/src/mol-math/geometry/centroid-helper.ts
index 0398cfe68bb74d128f9f36eea050cc58da0baee1..32c67e8665a815898780218c2865e821195da3b2 100644
--- a/src/mol-math/geometry/centroid-helper.ts
+++ b/src/mol-math/geometry/centroid-helper.ts
@@ -5,7 +5,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Vec3 } from '../../mol-math/linear-algebra/3d';
+import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
import { Sphere3D } from './primitives/sphere3d';
export { CentroidHelper };
diff --git a/src/mol-math/geometry/molecular-surface.ts b/src/mol-math/geometry/molecular-surface.ts
index 5e864332182c97d3f3542a54f5ada7ad6e74cf98..c9532f808a8f11024ae54c4d1abd0b0782de430f 100644
--- a/src/mol-math/geometry/molecular-surface.ts
+++ b/src/mol-math/geometry/molecular-surface.ts
@@ -12,7 +12,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { RuntimeContext } from '../../mol-task';
import { OrderedSet } from '../../mol-data/int';
import { PositionData } from './common';
-import { Mat4 } from '../../mol-math/linear-algebra/3d';
+import { Mat4 } from '../../mol-math/linear-algebra/3d/mat4';
import { Box3D, GridLookup3D, fillGridDim } from '../../mol-math/geometry';
import { BaseGeometry } from '../../mol-geo/geometry/base';
import { Boundary } from './boundary';
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 00c14df63a6098fa59a2b14ebd467e4b605e2f60..d1257fc923ca36c09cd2d8ef687d2b0bcbb3e3cb 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -4,9 +4,12 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Vec3, Mat4, Mat3, Quat } from '../linear-algebra/3d';
import { lerp as scalar_lerp } from '../../mol-math/interpolate';
import { defaults } from '../../mol-util';
+import { Mat3 } from '../linear-algebra/3d/mat3';
+import { Mat4 } from '../linear-algebra/3d/mat4';
+import { Quat } from '../linear-algebra/3d/quat';
+import { Vec3 } from '../linear-algebra/3d/vec3';
interface SymmetryOperator {
readonly name: string,
@@ -51,13 +54,13 @@ namespace SymmetryOperator {
export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number }
export function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator {
let { assembly, ncsId, hkl, spgrOp } = info || { };
- const _hkl = hkl ? Vec3.clone(hkl) : Vec3.zero();
+ const _hkl = hkl ? Vec3.clone(hkl) : Vec3();
spgrOp = defaults(spgrOp, -1);
ncsId = ncsId || -1;
const suffix = getSuffix(info);
if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) throw new Error(`Symmetry operator (${name}) must be a composition of rotation and translation.`);
- return { name, assembly, matrix, inverse: Mat4.invert(Mat4.zero(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId, suffix };
+ return { name, assembly, matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId, suffix };
}
function getSuffix(info?: CreateInfo) {
@@ -101,7 +104,7 @@ namespace SymmetryOperator {
return create(name, t, { ncsId });
}
- const _q1 = Quat.identity(), _q2 = Quat.zero(), _q3 = Quat.zero(), _axis = Vec3.zero();
+ const _q1 = Quat.identity(), _q2 = Quat(), _q3 = Quat(), _axis = Vec3();
export function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4 {
const m = op.inverse;
if (op.isIdentity) return Mat4.copy(out, m);
@@ -145,7 +148,7 @@ namespace SymmetryOperator {
* Keep `name`, `assembly`, `ncsId`, `hkl` and `spgrOpId` properties from second.
*/
export function compose(first: SymmetryOperator, second: SymmetryOperator) {
- const matrix = Mat4.mul(Mat4.zero(), second.matrix, first.matrix);
+ const matrix = Mat4.mul(Mat4(), second.matrix, first.matrix);
return create(second.name, matrix, second);
}
diff --git a/src/mol-math/linear-algebra/3d/mat3.ts b/src/mol-math/linear-algebra/3d/mat3.ts
index 6d05361fde38ef418b98692ac0ba0ebb1d441657..28072161503aef6725a13e34e1309a40081a4213 100644
--- a/src/mol-math/linear-algebra/3d/mat3.ts
+++ b/src/mol-math/linear-algebra/3d/mat3.ts
@@ -134,7 +134,7 @@ namespace Mat3 {
* Creates a new Mat3 initialized with values from an existing matrix
*/
export function clone(a: Mat3) {
- return Mat3.copy(Mat3.zero(), a);
+ return copy(zero(), a);
}
export function areEqual(a: Mat3, b: Mat3, eps: number) {
@@ -372,7 +372,7 @@ namespace Mat3 {
}
const piThird = Math.PI / 3;
- const tmpB = Mat3();
+ const tmpB = zero();
/**
* Given a real symmetric 3x3 matrix A, compute the eigenvalues
*
@@ -447,9 +447,9 @@ namespace Mat3 {
* Get matrix to transform directions, e.g. normals
*/
export function directionTransform(out: Mat3, t: Mat4) {
- Mat3.fromMat4(out, t);
- Mat3.invert(out, out);
- Mat3.transpose(out, out);
+ fromMat4(out, t);
+ invert(out, out);
+ transpose(out, out);
return out;
}
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index 1370593934e2a4bdb0bbdf487fe36e79cfc190a2..f57fc231c922fb441a10f85fed0355f40354471c 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -165,17 +165,17 @@ namespace Mat4 {
}
export function fromBasis(a: Mat4, x: Vec3, y: Vec3, z: Vec3) {
- Mat4.setZero(a);
- Mat4.setValue(a, 0, 0, x[0]);
- Mat4.setValue(a, 1, 0, x[1]);
- Mat4.setValue(a, 2, 0, x[2]);
- Mat4.setValue(a, 0, 1, y[0]);
- Mat4.setValue(a, 1, 1, y[1]);
- Mat4.setValue(a, 2, 1, y[2]);
- Mat4.setValue(a, 0, 2, z[0]);
- Mat4.setValue(a, 1, 2, z[1]);
- Mat4.setValue(a, 2, 2, z[2]);
- Mat4.setValue(a, 3, 3, 1);
+ setZero(a);
+ setValue(a, 0, 0, x[0]);
+ setValue(a, 1, 0, x[1]);
+ setValue(a, 2, 0, x[2]);
+ setValue(a, 0, 1, y[0]);
+ setValue(a, 1, 1, y[1]);
+ setValue(a, 2, 1, y[2]);
+ setValue(a, 0, 2, z[0]);
+ setValue(a, 1, 2, z[1]);
+ setValue(a, 2, 2, z[2]);
+ setValue(a, 3, 3, 1);
return a;
}
@@ -200,7 +200,7 @@ namespace Mat4 {
}
export function clone(a: Mat4) {
- return Mat4.copy(Mat4.zero(), a);
+ return copy(zero(), a);
}
/**
@@ -541,7 +541,7 @@ namespace Mat4 {
b20, b21, b22;
if (Math.abs(len) < EPSILON) {
- return Mat4.identity();
+ return identity();
}
len = 1 / len;
@@ -1075,29 +1075,29 @@ namespace Mat4 {
const zAxis = Vec3.create(0, 0, 1);
/** Rotation matrix for 90deg around x-axis */
- export const rotX90: ReadonlyMat4 = fromRotation(Mat4(), degToRad(90), xAxis);
+ export const rotX90: ReadonlyMat4 = fromRotation(zero(), degToRad(90), xAxis);
/** Rotation matrix for 180deg around x-axis */
- export const rotX180: ReadonlyMat4 = fromRotation(Mat4(), degToRad(180), xAxis);
+ export const rotX180: ReadonlyMat4 = fromRotation(zero(), degToRad(180), xAxis);
/** Rotation matrix for 90deg around y-axis */
- export const rotY90: ReadonlyMat4 = fromRotation(Mat4(), degToRad(90), yAxis);
+ export const rotY90: ReadonlyMat4 = fromRotation(zero(), degToRad(90), yAxis);
/** Rotation matrix for 180deg around y-axis */
- export const rotY180: ReadonlyMat4 = fromRotation(Mat4(), degToRad(180), yAxis);
+ export const rotY180: ReadonlyMat4 = fromRotation(zero(), degToRad(180), yAxis);
/** Rotation matrix for 270deg around y-axis */
- export const rotY270: ReadonlyMat4 = fromRotation(Mat4(), degToRad(270), yAxis);
+ export const rotY270: ReadonlyMat4 = fromRotation(zero(), degToRad(270), yAxis);
/** Rotation matrix for 90deg around z-axis */
- export const rotZ90: ReadonlyMat4 = fromRotation(Mat4(), degToRad(90), zAxis);
+ export const rotZ90: ReadonlyMat4 = fromRotation(zero(), degToRad(90), zAxis);
/** Rotation matrix for 180deg around z-axis */
- export const rotZ180: ReadonlyMat4 = fromRotation(Mat4(), degToRad(180), zAxis);
+ export const rotZ180: ReadonlyMat4 = fromRotation(zero(), degToRad(180), zAxis);
/** Rotation matrix for 90deg around first x-axis and then y-axis */
- export const rotXY90: ReadonlyMat4 = mul(Mat4(), rotX90, rotY90);
+ export const rotXY90: ReadonlyMat4 = mul(zero(), rotX90, rotY90);
/** Rotation matrix for 90deg around first z-axis and then y-axis */
- export const rotZY90: ReadonlyMat4 = mul(Mat4(), rotZ90, rotY90);
+ export const rotZY90: ReadonlyMat4 = mul(zero(), rotZ90, rotY90);
/** Rotation matrix for 90deg around first z-axis and then y-axis and then z-axis */
- export const rotZYZ90: ReadonlyMat4 = mul(Mat4(), rotZY90, rotZ90);
+ export const rotZYZ90: ReadonlyMat4 = mul(zero(), rotZY90, rotZ90);
/** Rotation matrix for 90deg around first z-axis and then 180deg around x-axis */
- export const rotZ90X180: ReadonlyMat4 = mul(Mat4(), rotZ90, rotX180);
+ export const rotZ90X180: ReadonlyMat4 = mul(zero(), rotZ90, rotX180);
/** Rotation matrix for 90deg around first y-axis and then 180deg around z-axis */
- export const rotY90Z180: ReadonlyMat4 = mul(Mat4(), rotY90, rotZ180);
+ export const rotY90Z180: ReadonlyMat4 = mul(zero(), rotY90, rotZ180);
/** Identity matrix */
export const id: ReadonlyMat4 = identity();
diff --git a/src/mol-math/linear-algebra/3d/quat.ts b/src/mol-math/linear-algebra/3d/quat.ts
index 717052692f942b1b2c4589bff55ae8a5eab6e1ea..2f9872490cf78312a5408999668741e5e8f1c467 100644
--- a/src/mol-math/linear-algebra/3d/quat.ts
+++ b/src/mol-math/linear-algebra/3d/quat.ts
@@ -407,8 +407,8 @@ namespace Quat {
/**
* Performs a spherical linear interpolation with two control points
*/
- let sqlerpTemp1 = Quat();
- let sqlerpTemp2 = Quat();
+ let sqlerpTemp1 = zero();
+ let sqlerpTemp2 = zero();
export function sqlerp(out: Quat, a: Quat, b: Quat, c: Quat, d: Quat, t: number) {
slerp(sqlerpTemp1, a, d, t);
slerp(sqlerpTemp2, b, c, t);
@@ -435,7 +435,7 @@ namespace Quat {
axesTmpMat[5] = -view[1];
axesTmpMat[8] = -view[2];
- return normalize(out, Quat.fromMat3(out, axesTmpMat));
+ return normalize(out, fromMat3(out, axesTmpMat));
}
export function toString(a: Quat, precision?: number) {
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index 13a6973419f764ae2079a1b6651dc8e1b0cced01..4e0cd46cf29e8f6ae9bf3d82b14f8c1287451795 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -18,9 +18,11 @@
*/
import { Mat4 } from './mat4';
-import { Quat, Mat3, EPSILON } from '../3d';
import { spline as _spline, quadraticBezier as _quadraticBezier, clamp } from '../../interpolate';
import { NumberArray } from '../../../mol-util/type-helpers';
+import { Mat3 } from './mat3';
+import { Quat } from './quat';
+import { EPSILON } from './common';
export { ReadonlyVec3 };
@@ -273,7 +275,7 @@ namespace Vec3 {
}
export function setMagnitude(out: Vec3, a: Vec3, l: number) {
- return Vec3.scale(out, Vec3.normalize(out, a), l);
+ return scale(out, normalize(out, a), l);
}
/**
@@ -339,11 +341,11 @@ namespace Vec3 {
const slerpRelVec = zero();
export function slerp(out: Vec3, a: Vec3, b: Vec3, t: number) {
- const dot = clamp(Vec3.dot(a, b), -1, 1);
- const theta = Math.acos(dot) * t;
- Vec3.scaleAndAdd(slerpRelVec, b, a, -dot);
- Vec3.normalize(slerpRelVec, slerpRelVec);
- return Vec3.add(out, Vec3.scale(out, a, Math.cos(theta)), Vec3.scale(slerpRelVec, slerpRelVec, Math.sin(theta)));
+ const d = clamp(dot(a, b), -1, 1);
+ const theta = Math.acos(d) * t;
+ scaleAndAdd(slerpRelVec, b, a, -d);
+ normalize(slerpRelVec, slerpRelVec);
+ return add(out, scale(out, a, Math.cos(theta)), scale(slerpRelVec, slerpRelVec, Math.sin(theta)));
}
/**
@@ -562,8 +564,8 @@ namespace Vec3 {
* i.e. where the dot product is > 0
*/
export function matchDirection(out: Vec3, a: Vec3, b: Vec3) {
- if (Vec3.dot(a, b) > 0) Vec3.copy(out, a);
- else Vec3.negate(out, Vec3.copy(out, a));
+ if (dot(a, b) > 0) copy(out, a);
+ else negate(out, copy(out, a));
return out;
}
@@ -580,14 +582,14 @@ namespace Vec3 {
return `[${a[0].toPrecision(precision)} ${a[1].toPrecision(precision)} ${a[2].toPrecision(precision)}]`;
}
- export const origin: ReadonlyVec3 = Vec3.create(0, 0, 0);
+ export const origin: ReadonlyVec3 = create(0, 0, 0);
- export const unit: ReadonlyVec3 = Vec3.create(1, 1, 1);
- export const negUnit: ReadonlyVec3 = Vec3.create(-1, -1, -1);
+ export const unit: ReadonlyVec3 = create(1, 1, 1);
+ export const negUnit: ReadonlyVec3 = create(-1, -1, -1);
- export const unitX: ReadonlyVec3 = Vec3.create(1, 0, 0);
- export const unitY: ReadonlyVec3 = Vec3.create(0, 1, 0);
- export const unitZ: ReadonlyVec3 = Vec3.create(0, 0, 1);
+ export const unitX: ReadonlyVec3 = create(1, 0, 0);
+ export const unitY: ReadonlyVec3 = create(0, 1, 0);
+ export const unitZ: ReadonlyVec3 = create(0, 0, 1);
}
export { Vec3 };
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/vec4.ts b/src/mol-math/linear-algebra/3d/vec4.ts
index 09437726d911797c4176f94b9cb6cd0d1bb8bc33..7f724c9735cbe240612fb56987c28d052d971930 100644
--- a/src/mol-math/linear-algebra/3d/vec4.ts
+++ b/src/mol-math/linear-algebra/3d/vec4.ts
@@ -18,9 +18,9 @@
*/
import { Mat4 } from './mat4';
-import { EPSILON } from '../3d';
import { NumberArray } from '../../../mol-util/type-helpers';
import { Sphere3D } from '../../geometry/primitives/sphere3d';
+import { EPSILON } from './common';
interface Vec4 extends Array<number> { [d: number]: number, '@type': 'vec4', length: 4 }
diff --git a/src/mol-math/linear-algebra/_spec/mat3.spec.ts b/src/mol-math/linear-algebra/_spec/mat3.spec.ts
index d1007d8b2e87c708eca74609b1122c177058d094..171acc1e14aa5c90e72ee08779945e233a7a3ece 100644
--- a/src/mol-math/linear-algebra/_spec/mat3.spec.ts
+++ b/src/mol-math/linear-algebra/_spec/mat3.spec.ts
@@ -4,7 +4,8 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Mat3, Vec3 } from '../3d';
+import { Mat3 } from '../3d/mat3';
+import { Vec3 } from '../3d/vec3';
describe('Mat3', () => {
it('symmetricEigenvalues', () => {
diff --git a/src/mol-math/linear-algebra/_spec/mat4.spec.ts b/src/mol-math/linear-algebra/_spec/mat4.spec.ts
index df801e27bf592b513112d201a5ecd761eaa53d90..97ff10e2057d4dfd53ead65d294015e152c5b835 100644
--- a/src/mol-math/linear-algebra/_spec/mat4.spec.ts
+++ b/src/mol-math/linear-algebra/_spec/mat4.spec.ts
@@ -4,21 +4,22 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Mat4, Vec3 } from '../3d';
+import { Mat4 } from '../3d/mat4';
+import { Vec3 } from '../3d/vec3';
describe('Mat4', () => {
it('permutation', () => {
- expect(Mat4.areEqual(Mat4.fromPermutation(Mat4.zero(), [0, 1, 2, 3]), Mat4.identity(), 1e-6)).toBe(true);
+ expect(Mat4.areEqual(Mat4.fromPermutation(Mat4(), [0, 1, 2, 3]), Mat4.identity(), 1e-6)).toBe(true);
- expect(Mat4.areEqual(Mat4.fromPermutation(Mat4.zero(), [1, 0, 2, 3]), Mat4.ofRows([
+ expect(Mat4.areEqual(Mat4.fromPermutation(Mat4(), [1, 0, 2, 3]), Mat4.ofRows([
[0, 1, 0, 0],
[1, 0, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1],
]), 1e-6)).toBe(true);
- const perm = Mat4.fromPermutation(Mat4.zero(), [1, 2, 0, 3]);
+ const perm = Mat4.fromPermutation(Mat4(), [1, 2, 0, 3]);
- expect(Vec3.transformMat4(Vec3.zero(), Vec3.create(1, 2, 3), perm)).toEqual(Vec3.create(2, 3, 1));
+ expect(Vec3.transformMat4(Vec3(), Vec3.create(1, 2, 3), perm)).toEqual(Vec3.create(2, 3, 1));
});
});
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/_spec/tensor.spec.ts b/src/mol-math/linear-algebra/_spec/tensor.spec.ts
index d36522c3a8e6f2afdb7605cdc18ec46fc3288a00..923e6455e4369ad8a006563d0d052326e3924c6d 100644
--- a/src/mol-math/linear-algebra/_spec/tensor.spec.ts
+++ b/src/mol-math/linear-algebra/_spec/tensor.spec.ts
@@ -5,7 +5,7 @@
*/
import { Tensor as T } from '../tensor';
-import { Mat4 } from '../3d';
+import { Mat4 } from '../3d/mat4';
describe('tensor', () => {
it('vector', () => {
diff --git a/src/mol-math/linear-algebra/_spec/vec3.spec.ts b/src/mol-math/linear-algebra/_spec/vec3.spec.ts
index 38909706a44b00afc45b86bb2cb33ea273748c43..36bdd88d5a114e8ad55f31143b81d5b7814aed2d 100644
--- a/src/mol-math/linear-algebra/_spec/vec3.spec.ts
+++ b/src/mol-math/linear-algebra/_spec/vec3.spec.ts
@@ -1,4 +1,10 @@
-import { Vec3 } from '../3d';
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { Vec3 } from '../3d/vec3';
describe('vec3', () => {
const vec1 = [ 1, 2, 3 ] as Vec3;
diff --git a/src/mol-math/linear-algebra/matrix/principal-axes.ts b/src/mol-math/linear-algebra/matrix/principal-axes.ts
index db338445538e8ec4576d8714f425a6fa7a2f112a..2f28473a06a85a72cbf6136c789c007a758a6126 100644
--- a/src/mol-math/linear-algebra/matrix/principal-axes.ts
+++ b/src/mol-math/linear-algebra/matrix/principal-axes.ts
@@ -5,7 +5,7 @@
*/
import { Matrix } from './matrix';
-import { Vec3 } from '../3d';
+import { Vec3 } from '../3d/vec3';
import { svd } from './svd';
import { NumberArray } from '../../../mol-util/type-helpers';
import { Axes3D } from '../../geometry';
diff --git a/src/mol-math/linear-algebra/tensor.ts b/src/mol-math/linear-algebra/tensor.ts
index 824b772bad1283823a5465dce37cf96c76b6c173..2632e9eb25528f9c2bcd1e4da3eec2b039e7b5d9 100644
--- a/src/mol-math/linear-algebra/tensor.ts
+++ b/src/mol-math/linear-algebra/tensor.ts
@@ -1,3 +1,4 @@
+import { Mat3 } from './3d/mat3';
/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
@@ -5,7 +6,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Mat4, Vec3, Vec4, Mat3 } from './3d';
+import { Mat4 } from './3d/mat4';
+import { Vec3 } from './3d/vec3';
+import { Vec4 } from './3d/vec4';
export interface Tensor { data: Tensor.Data, space: Tensor.Space }
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts
index 7c01e6f6d928a08d7d506628ce4420cb90fe599a..d2f6a7846baf942f8989db0de4da24349908130e 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts
+++ b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.ts
@@ -31,8 +31,6 @@ export async function computeArea(runtime: RuntimeContext, ctx: ShrakeRupleyCont
const aPos = Vec3();
const bPos = Vec3();
const testPoint = Vec3();
-const aLoc = StructureElement.Location.create(void 0 as any);
-const bLoc = StructureElement.Location.create(void 0 as any);
function setLocation(l: StructureElement.Location, structure: Structure, serialIndex: number) {
l.structure = structure;
@@ -43,6 +41,8 @@ function setLocation(l: StructureElement.Location, structure: Structure, serialI
function computeRange(ctx: ShrakeRupleyContext, begin: number, end: number) {
const { structure, atomRadiusType, serialResidueIndex, area, spherePoints, scalingConstant, maxLookupRadius, probeSize } = ctx;
+ const aLoc = StructureElement.Location.create(structure);
+ const bLoc = StructureElement.Location.create(structure);
const { x, y, z } = StructureProperties.atom;
const { lookup3d, serialMapping, unitIndexMap } = structure;
const { cumulativeUnitElementCount } = serialMapping;
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
index 7c74846e741f7474d6d1858f214eb22f5cb7cc27..3b469df371058495ac765f06bc41f6ae032a5d03 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
+++ b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
@@ -12,12 +12,11 @@ import { VdwRadius } from '../../../../mol-model/structure/model/properties/atom
import { StructureElement, StructureProperties } from '../../../../mol-model/structure/structure';
import { getElementMoleculeType } from '../../../../mol-model/structure/util';
-const l = StructureElement.Location.create(void 0);
-
export function assignRadiusForHeavyAtoms(ctx: ShrakeRupleyContext) {
const { key } = StructureProperties.residue;
const { type_symbol, label_atom_id, label_comp_id } = StructureProperties.atom;
const { structure, atomRadiusType, serialResidueIndex } = ctx;
+ const l = StructureElement.Location.create(structure);
let prevResidueIdx = 0;
let residueIdx = 0;
diff --git a/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts b/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
index 086b3ebd381c0926d8cc9a3de9b551ca7be6ce58..1bcf555c877bfa1b9c10dc4ca12cbeefd8864854 100644
--- a/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
+++ b/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
@@ -23,11 +23,10 @@ import { InteractionFlag } from '../interactions/common';
import { Unit } from '../../../mol-model/structure/structure';
import { Sphere3D } from '../../../mol-math/geometry';
-const tmpLoc = StructureElement.Location.create(void 0);
-
function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InteractionsInterUnitParams>, mesh?: Mesh) {
if (!structure.hasAtomic) return Mesh.createEmpty(mesh);
+ const l = StructureElement.Location.create(structure);
const interactions = InteractionsProvider.get(structure).value!;
const { contacts, unitsFeatures } = interactions;
@@ -55,14 +54,13 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
radius: (edgeIndex: number) => {
const b = edges[edgeIndex];
const fA = unitsFeatures.get(b.unitA);
- tmpLoc.structure = structure;
- tmpLoc.unit = structure.unitMap.get(b.unitA);
- tmpLoc.element = tmpLoc.unit.elements[fA.members[fA.offsets[b.indexA]]];
- const sizeA = theme.size.size(tmpLoc);
+ l.unit = structure.unitMap.get(b.unitA);
+ l.element = l.unit.elements[fA.members[fA.offsets[b.indexA]]];
+ const sizeA = theme.size.size(l);
const fB = unitsFeatures.get(b.unitB);
- tmpLoc.unit = structure.unitMap.get(b.unitB);
- tmpLoc.element = tmpLoc.unit.elements[fB.members[fB.offsets[b.indexB]]];
- const sizeB = theme.size.size(tmpLoc);
+ l.unit = structure.unitMap.get(b.unitB);
+ l.element = l.unit.elements[fB.members[fB.offsets[b.indexB]]];
+ const sizeB = theme.size.size(l);
return Math.min(sizeA, sizeB) * sizeFactor;
},
ignore: (edgeIndex: number) => edges[edgeIndex].props.flag === InteractionFlag.Filtered
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index 98ab02958a7658f08c13d58f823cb96cbef72911..404783aef18831e7d0de8d01bd18a5152b256824 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/src/mol-model/structure/export/categories/atom_site.ts
@@ -12,23 +12,21 @@ import CifField = CifWriter.Field
import CifCategory = CifWriter.Category
import E = CifWriter.Encodings
-const _label_asym_id = P.chain.label_asym_id;
function atom_site_label_asym_id(e: StructureElement.Location) {
- const l = _label_asym_id(e);
+ const l = P.chain.label_asym_id(e);
const suffix = e.unit.conformation.operator.suffix;
if (!suffix) return l;
return l + suffix;
}
-const _auth_asym_id = P.chain.auth_asym_id;
function atom_site_auth_asym_id(e: StructureElement.Location) {
- const l = _auth_asym_id(e);
+ const l = P.chain.auth_asym_id(e);
const suffix = e.unit.conformation.operator.suffix;
if (!suffix) return l;
return l + suffix;
}
-const atom_site_fields = CifWriter.fields<StructureElement.Location, Structure>()
+const atom_site_fields = () => CifWriter.fields<StructureElement.Location, Structure>()
.str('group_PDB', P.residue.group_PDB)
.index('id')
.str('type_symbol', P.atom.type_symbol as any)
@@ -73,7 +71,7 @@ export const _atom_site: CifCategory<CifExportContext> = {
name: 'atom_site',
instance({ structures }: CifExportContext) {
return {
- fields: atom_site_fields,
+ fields: atom_site_fields(),
source: structures.map(s => ({
data: s,
rowCount: s.elementCount,
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index 1f1458a4f44b299434547fbab489f3e889079d9a..a8288e4213d79945e8cfb07c0d16b2f24ab85857 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -20,7 +20,7 @@ export const _struct_conf: CifCategory<CifExportContext> = {
instance(ctx) {
const elements = findElements(ctx, 'helix');
return {
- fields: struct_conf_fields,
+ fields: struct_conf_fields(),
source: [{ data: elements, rowCount: elements.length }]
};
}
@@ -31,7 +31,7 @@ export const _struct_sheet_range: CifCategory<CifExportContext> = {
instance(ctx) {
const elements = (findElements(ctx, 'sheet') as SSElement<SecondaryStructure.Sheet>[]).sort(compare_ssr);
return {
- fields: struct_sheet_range_fields,
+ fields: struct_sheet_range_fields(),
source: [{ data: elements, rowCount: elements.length }]
};
}
@@ -42,7 +42,7 @@ function compare_ssr(x: SSElement<SecondaryStructure.Sheet>, y: SSElement<Second
return a.sheet_id < b.sheet_id ? -1 : a.sheet_id === b.sheet_id ? x.start.element - y.start.element : 1;
};
-const struct_conf_fields: CifField[] = [
+const struct_conf_fields = (): CifField[] => [
CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('conf_type_id', (i, data) => data[i].element.type_id),
CifField.str<number, SSElement<SecondaryStructure.Helix>[]>('id', (i, data, idx) => `${data[i].element.type_id}${idx + 1}`),
...residueIdFields<number, SSElement<SecondaryStructure.Helix>[]>((i, e) => e[i].start, { prefix: 'beg' }),
@@ -54,7 +54,7 @@ const struct_conf_fields: CifField[] = [
CifField.int<number, SSElement<SecondaryStructure.Helix>[]>('pdbx_PDB_helix_length', (i, data) => data[i].length)
];
-const struct_sheet_range_fields: CifField[] = [
+const struct_sheet_range_fields = (): CifField[] => [
CifField.str<number, SSElement<SecondaryStructure.Sheet>[]>('sheet_id', (i, data) => data[i].element.sheet_id),
CifField.index('id'),
...residueIdFields<number, SSElement<SecondaryStructure.Sheet>[]>((i, e) => e[i].start, { prefix: 'beg' }),
diff --git a/src/mol-plugin-state/animation/built-in/camera-spin.ts b/src/mol-plugin-state/animation/built-in/camera-spin.ts
index bcf2c8c52151f0484fe46cdc40906c7b5ab2884e..d0e3a4a49580f52579a838acaebc8b1279408bd5 100644
--- a/src/mol-plugin-state/animation/built-in/camera-spin.ts
+++ b/src/mol-plugin-state/animation/built-in/camera-spin.ts
@@ -6,7 +6,8 @@
import { Camera } from '../../../mol-canvas3d/camera';
import { clamp } from '../../../mol-math/interpolate';
-import { Quat, Vec3 } from '../../../mol-math/linear-algebra/3d';
+import { Quat } from '../../../mol-math/linear-algebra/3d/quat';
+import { Vec3 } from '../../../mol-math/linear-algebra/3d/vec3';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { PluginStateAnimation } from '../model';
diff --git a/src/mol-plugin-state/helpers/structure-component.ts b/src/mol-plugin-state/helpers/structure-component.ts
index 0f9dc09c9c9f5ba1377ae9af42672b7227fbd1a5..06226bafa6f4b2352e2361fdffc1d18f7df63d18 100644
--- a/src/mol-plugin-state/helpers/structure-component.ts
+++ b/src/mol-plugin-state/helpers/structure-component.ts
@@ -34,7 +34,7 @@ export const StaticStructureComponentTypes = [
export type StaticStructureComponentType = (typeof StaticStructureComponentTypes)[number]
-export const StructureComponentParams = {
+export const StructureComponentParams = () => ({
type: PD.MappedStatic('static', {
static: PD.Text<StaticStructureComponentType>('polymer'),
expression: PD.Value<Expression>(MolScriptBuilder.struct.generator.all),
@@ -43,8 +43,8 @@ export const StructureComponentParams = {
}, { isHidden: true }),
nullIfEmpty: PD.Optional(PD.Boolean(true, { isHidden: true })),
label: PD.Text('', { isHidden: true })
-};
-export type StructureComponentParams = PD.ValuesFor<typeof StructureComponentParams>
+});
+export type StructureComponentParams = PD.ValuesFor<ReturnType<typeof StructureComponentParams>>
export function createStructureComponent(a: Structure, params: StructureComponentParams, cache: { source: Structure, entry?: StructureQueryHelper.CacheEntry }) {
cache.source = a;
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index 0fe48aa93cfcb1ae891f80518cf99a2d12ef5a11..c8bfcf78c90dd142729c6570fa83ef59415f9ea3 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -486,10 +486,10 @@ const StructureSelectionFromExpression = PluginStateTransform.BuiltIn({
display: { name: 'Selection', description: 'Create a molecular structure from the specified expression.' },
from: SO.Molecule.Structure,
to: SO.Molecule.Structure,
- params: {
+ params: () => ({
expression: PD.Value<Expression>(MolScriptBuilder.struct.generator.all, { isHidden: true }),
label: PD.Optional(PD.Text('', { isHidden: true }))
- }
+ })
})({
apply({ a, params, cache }) {
const { selection, entry } = StructureQueryHelper.createAndRun(a.data, params.expression);
@@ -526,7 +526,7 @@ const MultiStructureSelectionFromExpression = PluginStateTransform.BuiltIn({
display: { name: 'Multi-structure Measurement Selection', description: 'Create selection object from multiple structures.' },
from: SO.Root,
to: SO.Molecule.Structure.Selections,
- params: {
+ params: () => ({
selections: PD.ObjectList({
key: PD.Text(void 0, { description: 'A unique key.' }),
ref: PD.Text(),
@@ -535,7 +535,7 @@ const MultiStructureSelectionFromExpression = PluginStateTransform.BuiltIn({
}, e => e.ref, { isHidden: true }),
isTransitive: PD.Optional(PD.Boolean(false, { isHidden: true, description: 'Remap the selections from the original structure if structurally equivalent.' })),
label: PD.Optional(PD.Text('', { isHidden: true }))
- }
+ })
})({
apply({ params, cache, dependencies }) {
const entries = new Map<string, StructureQueryHelper.CacheEntry>();
@@ -651,10 +651,10 @@ const StructureSelectionFromScript = PluginStateTransform.BuiltIn({
display: { name: 'Selection', description: 'Create a molecular structure from the specified script.' },
from: SO.Molecule.Structure,
to: SO.Molecule.Structure,
- params: {
+ params: () => ({
script: PD.Script({ language: 'mol-script', expression: '(sel.atom.atom-groups :residue-test (= atom.resname ALA))' }),
label: PD.Optional(PD.Text(''))
- }
+ })
})({
apply({ a, params, cache }) {
const { selection, entry } = StructureQueryHelper.createAndRun(a.data, params.script);
@@ -690,10 +690,10 @@ const StructureSelectionFromBundle = PluginStateTransform.BuiltIn({
display: { name: 'Selection', description: 'Create a molecular structure from the specified structure-element bundle.' },
from: SO.Molecule.Structure,
to: SO.Molecule.Structure,
- params: {
+ params: () => ({
bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty, { isHidden: true }),
label: PD.Optional(PD.Text('', { isHidden: true }))
- }
+ })
})({
apply({ a, params, cache }) {
if (params.bundle.hash !== a.data.hashCode) {
diff --git a/src/mol-plugin-state/transforms/representation.ts b/src/mol-plugin-state/transforms/representation.ts
index 78b03cc56ef665f906da13bccd869dadf0d1ccd5..eb1077fea8e7747929854aef29f0f05bfd02aa3a 100644
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -258,7 +258,7 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
display: 'Overpaint 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
- params: {
+ params: () => ({
layers: PD.ObjectList({
script: PD.Script(Script('(sel.atom.all)', 'mol-script')),
color: PD.Color(ColorNames.blueviolet),
@@ -270,7 +270,7 @@ const OverpaintStructureRepresentation3DFromScript = PluginStateTransform.BuiltI
clear: false
}]
}),
- }
+ })
})({
canAutoUpdate() {
return true;
@@ -309,7 +309,7 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
display: 'Overpaint 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
- params: {
+ params: () => ({
layers: PD.ObjectList({
bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty),
color: PD.Color(ColorNames.blueviolet),
@@ -322,7 +322,7 @@ const OverpaintStructureRepresentation3DFromBundle = PluginStateTransform.BuiltI
}],
isHidden: true
}),
- }
+ })
})({
canAutoUpdate() {
return true;
@@ -361,7 +361,7 @@ const TransparencyStructureRepresentation3DFromScript = PluginStateTransform.Bui
display: 'Transparency 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
- params: {
+ params: () => ({
layers: PD.ObjectList({
script: PD.Script(Script('(sel.atom.all)', 'mol-script')),
value: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }, { label: 'Transparency' }),
@@ -371,7 +371,7 @@ const TransparencyStructureRepresentation3DFromScript = PluginStateTransform.Bui
value: 0.5,
}]
})
- }
+ })
})({
canAutoUpdate() {
return true;
@@ -409,7 +409,7 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
display: 'Transparency 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
- params: {
+ params: () => ({
layers: PD.ObjectList({
bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty),
value: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }, { label: 'Transparency' }),
@@ -420,7 +420,7 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
}],
isHidden: true
})
- }
+ })
})({
canAutoUpdate() {
return true;
@@ -458,7 +458,7 @@ const ClippingStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn
display: 'Clipping 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
- params: {
+ params: () => ({
layers: PD.ObjectList({
script: PD.Script(Script('(sel.atom.all)', 'mol-script')),
groups: PD.Converted((g: Clipping.Groups) => Clipping.Groups.toNames(g), n => Clipping.Groups.fromNames(n), PD.MultiSelect(ObjectKeys(Clipping.Groups.Names), PD.objectToOptions(Clipping.Groups.Names))),
@@ -468,7 +468,7 @@ const ClippingStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn
groups: Clipping.Groups.Flag.None,
}]
}),
- }
+ })
})({
canAutoUpdate() {
return true;
@@ -506,7 +506,7 @@ const ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn
display: 'Clipping 3D Representation',
from: SO.Molecule.Structure.Representation3D,
to: SO.Molecule.Structure.Representation3DState,
- params: {
+ params: () => ({
layers: PD.ObjectList({
bundle: PD.Value<StructureElement.Bundle>(StructureElement.Bundle.Empty),
groups: PD.Converted((g: Clipping.Groups) => Clipping.Groups.toNames(g), n => Clipping.Groups.fromNames(n), PD.MultiSelect(ObjectKeys(Clipping.Groups.Names), PD.objectToOptions(Clipping.Groups.Names))),
@@ -517,7 +517,7 @@ const ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn
}],
isHidden: true
}),
- }
+ })
})({
canAutoUpdate() {
return true;
@@ -705,9 +705,9 @@ const ModelUnitcell3D = PluginStateTransform.BuiltIn({
display: 'Model Unit Cell',
from: SO.Molecule.Model,
to: SO.Shape.Representation3D,
- params: {
+ params: () => ({
...UnitcellParams,
- }
+ })
})({
isApplicable: a => !!ModelSymmetry.Provider.get(a.data),
canAutoUpdate({ oldParams, newParams }) {
@@ -743,9 +743,9 @@ const StructureSelectionsDistance3D = PluginStateTransform.BuiltIn({
display: '3D Distance',
from: SO.Molecule.Structure.Selections,
to: SO.Shape.Representation3D,
- params: {
+ params: () => ({
...DistanceParams,
- }
+ })
})({
canAutoUpdate({ oldParams, newParams }) {
return true;
@@ -776,9 +776,9 @@ const StructureSelectionsAngle3D = PluginStateTransform.BuiltIn({
display: '3D Angle',
from: SO.Molecule.Structure.Selections,
to: SO.Shape.Representation3D,
- params: {
+ params: () => ({
...AngleParams,
- }
+ })
})({
canAutoUpdate({ oldParams, newParams }) {
return true;
@@ -809,9 +809,9 @@ const StructureSelectionsDihedral3D = PluginStateTransform.BuiltIn({
display: '3D Dihedral',
from: SO.Molecule.Structure.Selections,
to: SO.Shape.Representation3D,
- params: {
+ params: () => ({
...DihedralParams,
- }
+ })
})({
canAutoUpdate({ oldParams, newParams }) {
return true;
@@ -842,9 +842,9 @@ const StructureSelectionsLabel3D = PluginStateTransform.BuiltIn({
display: '3D Label',
from: SO.Molecule.Structure.Selections,
to: SO.Shape.Representation3D,
- params: {
+ params: () => ({
...LabelParams,
- }
+ })
})({
canAutoUpdate({ oldParams, newParams }) {
return true;
@@ -875,9 +875,9 @@ const StructureSelectionsOrientation3D = PluginStateTransform.BuiltIn({
display: '3D Orientation',
from: SO.Molecule.Structure.Selections,
to: SO.Shape.Representation3D,
- params: {
+ params: () => ({
...OrientationParams,
- }
+ })
})({
canAutoUpdate({ oldParams, newParams }) {
return true;
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts b/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts
index 99f51da2ffdf67229840e60df68048bd02d399ca..469fca3463ec3e26164cb77ffec055deb2c0510e 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/structure-info.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { PluginBehavior } from '../../../behavior';
+import { PluginBehavior } from '../../../behavior/behavior';
import { Structure, Model } from '../../../../mol-model/structure';
import { PluginStateObject } from '../../../../mol-plugin-state/objects';
import { StateSelection, StateObject } from '../../../../mol-state';
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 5556db6c76b39a5d2da480bd0f2896eb87caa8a5..019ead6aaa8e56193f4d16b662974f7ddbbb0694 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -22,7 +22,7 @@ import { AnimateAssemblyUnwind } from '../mol-plugin-state/animation/built-in/as
import { AnimateCameraSpin } from '../mol-plugin-state/animation/built-in/camera-spin';
import { AnimateStateSnapshots } from '../mol-plugin-state/animation/built-in/state-snapshots';
-export const DefaultPluginSpec: PluginSpec = {
+export const DefaultPluginSpec = (): PluginSpec => ({
actions: [
PluginSpec.Action(StateActions.Structure.DownloadStructure),
PluginSpec.Action(StateActions.Structure.AddTrajectory),
@@ -93,10 +93,10 @@ export const DefaultPluginSpec: PluginSpec = {
AnimateStateSnapshots,
AnimateAssemblyUnwind
]
-};
+});
export function createPlugin(target: HTMLElement, spec?: PluginSpec): PluginContext {
- const ctx = new PluginContext(spec || DefaultPluginSpec);
+ const ctx = new PluginContext(spec || DefaultPluginSpec());
ctx.init();
ReactDOM.render(React.createElement(Plugin, { plugin: ctx }), target);
return ctx;
@@ -104,7 +104,7 @@ export function createPlugin(target: HTMLElement, spec?: PluginSpec): PluginCont
/** Returns the instance of the plugin after all behaviors have been initialized */
export async function createPluginAsync(target: HTMLElement, spec?: PluginSpec) {
- const ctx = new PluginContext(spec || DefaultPluginSpec);
+ const ctx = new PluginContext(spec || DefaultPluginSpec());
const init = ctx.init();
ReactDOM.render(React.createElement(Plugin, { plugin: ctx }), target);
await init;
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-line.ts b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
index 946714ab1a1bcbdf17e6de81d3f20efb453542ad..45135f338339e4129d5493fbf9ce821bff2e7d3a 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -29,9 +29,6 @@ function setRefPosition(pos: Vec3, structure: Structure, unit: Unit.Atomic, inde
return null;
}
-const tmpRef = Vec3();
-const tmpLoc = StructureElement.Location.create(void 0);
-
function createInterUnitBondLines(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitBondLineParams>, lines?: Lines) {
const bonds = structure.interUnitBonds;
const { edgeCount, edges } = bonds;
@@ -39,6 +36,9 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
if (!edgeCount) return Lines.createEmpty(lines);
+ const ref = Vec3();
+ const loc = StructureElement.Location.create();
+
const builderProps = {
linkCount: edgeCount,
referencePosition: (edgeIndex: number) => {
@@ -58,7 +58,7 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
} else {
throw new Error('same units in createInterUnitBondLines');
}
- return setRefPosition(tmpRef, structure, unitA, indexA) || setRefPosition(tmpRef, structure, unitB, indexB);
+ return setRefPosition(ref, structure, unitA, indexA) || setRefPosition(ref, structure, unitB, indexB);
},
position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
const b = edges[edgeIndex];
@@ -83,13 +83,13 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
},
radius: (edgeIndex: number) => {
const b = edges[edgeIndex];
- tmpLoc.structure = structure;
- tmpLoc.unit = structure.unitMap.get(b.unitA);
- tmpLoc.element = tmpLoc.unit.elements[b.indexA];
- const sizeA = theme.size.size(tmpLoc);
- tmpLoc.unit = structure.unitMap.get(b.unitB);
- tmpLoc.element = tmpLoc.unit.elements[b.indexB];
- const sizeB = theme.size.size(tmpLoc);
+ loc.structure = structure;
+ loc.unit = structure.unitMap.get(b.unitA);
+ loc.element = loc.unit.elements[b.indexA];
+ const sizeA = theme.size.size(loc);
+ loc.unit = structure.unitMap.get(b.unitB);
+ loc.element = loc.unit.elements[b.indexB];
+ const sizeB = theme.size.size(loc);
return Math.min(sizeA, sizeB) * sizeFactor;
},
ignore: makeInterBondIgnoreTest(structure, props)