molstar 2.3.2 → 2.3.7

package/lib/mol-repr/structure/visual/polymer-trace-mesh.js

@@ -22,8 +22,9 @@ import { Sphere3D } from '../../../mol-math/geometry';
 export var PolymerTraceMeshParams = {
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
     aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
-    arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }),
-    tubularHelices: PD.Boolean(false),
+    arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }),
+    tubularHelices: PD.Boolean(false, { description: 'Draw alpha helices as tubes' }),
+    helixProfile: PD.Select('elliptical', PD.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Protein and nucleic helix trace profile' }),
     detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo)
@@ -31,11 +32,10 @@ export var PolymerTraceMeshParams = {
 export var DefaultPolymerTraceMeshProps = PD.getDefaultValues(PolymerTraceMeshParams);
 var tmpV1 = Vec3();
 function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
-    var _a, _b, _c;
     var polymerElementCount = unit.polymerElements.length;
     if (!polymerElementCount)
         return Mesh.createEmpty(mesh);
-    var sizeFactor = props.sizeFactor, detail = props.detail, linearSegments = props.linearSegments, radialSegments = props.radialSegments, aspectRatio = props.aspectRatio, arrowFactor = props.arrowFactor, tubularHelices = props.tubularHelices;
+    var sizeFactor = props.sizeFactor, detail = props.detail, linearSegments = props.linearSegments, radialSegments = props.radialSegments, aspectRatio = props.aspectRatio, arrowFactor = props.arrowFactor, tubularHelices = props.tubularHelices, helixProfile = props.helixProfile;
     var vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2;
     var builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
     var isCoarse = Unit.isCoarse(unit);
@@ -118,9 +118,6 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
                 h0 = w0 * aspectRatio;
                 h1 = w1 * aspectRatio;
                 h2 = w2 * aspectRatio;
-                _a = [h0, w0], w0 = _a[0], h0 = _a[1];
-                _b = [h1, w1], w1 = _b[0], h1 = _b[1];
-                _c = [h2, w2], w2 = _c[0], h2 = _c[1];
             }
             else {
                 h0 = w0;
@@ -128,22 +125,31 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
                 h2 = w2;
             }
             interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift);
+            var _a = isNucleicType && !v.isCoarseBackbone ? [binormalVectors, normalVectors] : [normalVectors, binormalVectors], normals = _a[0], binormals = _a[1];
+            if (isNucleicType && !v.isCoarseBackbone) {
+                // TODO: find a cleaner way to swap normal and binormal for nucleic types
+                for (var i_1 = 0, il = normals.length; i_1 < il; i_1++)
+                    normals[i_1] *= -1;
+            }
             if (radialSegments === 2) {
                 if (isNucleicType && !v.isCoarseBackbone) {
-                    // TODO find a cleaner way to swap normal and binormal for nucleic types
-                    for (var i_1 = 0, il = binormalVectors.length; i_1 < il; i_1++)
-                        binormalVectors[i_1] *= -1;
-                    addRibbon(builderState, curvePoints, binormalVectors, normalVectors, segmentCount, heightValues, widthValues, 0);
+                    addRibbon(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0);
                 }
                 else {
-                    addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0);
+                    addRibbon(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0);
                 }
             }
             else if (radialSegments === 4) {
-                addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
+                addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
+            }
+            else if (h1 === w1) {
+                addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
+            }
+            else if (helixProfile === 'square') {
+                addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
             }
             else {
-                addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap);
+                addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, helixProfile);
             }
         }
         ++i;
@@ -168,7 +174,8 @@ export function PolymerTraceVisual(materialId) {
                 newProps.linearSegments !== currentProps.linearSegments ||
                 newProps.radialSegments !== currentProps.radialSegments ||
                 newProps.aspectRatio !== currentProps.aspectRatio ||
-                newProps.arrowFactor !== currentProps.arrowFactor);
+                newProps.arrowFactor !== currentProps.arrowFactor ||
+                newProps.helixProfile !== currentProps.helixProfile);
             var secondaryStructureHash = SecondaryStructureProvider.get(newStructureGroup.structure).version;
             if (state.info.secondaryStructureHash !== secondaryStructureHash) {
                 state.createGeometry = true;

package/lib/mol-repr/structure/visual/polymer-trace-mesh.js.map

@@ -1 +1 @@
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package/lib/mol-repr/structure/visual/polymer-tube-mesh.js

@@ -79,7 +79,7 @@ function createPolymerTubeMesh(ctx, unit, structure, theme, props, mesh) {
             addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
         }
         else {
-            addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap);
+            addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
         }
         ++i;
     }

package/lib/mol-repr/structure/visual/polymer-tube-mesh.js.map

@@ -1 +1 @@
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package/lib/mol-repr/structure/visual/util/bond.d.ts

@@ -16,12 +16,14 @@ export declare const BondParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
 };
 export declare const DefaultBondProps: PD.Values<{
     includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
 }>;
 export declare type BondProps = typeof DefaultBondProps;
 export declare const BondCylinderParams: {
@@ -30,9 +32,13 @@ export declare const BondCylinderParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -45,9 +51,13 @@ export declare const DefaultBondCylinderProps: PD.Values<{
     excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -60,8 +70,10 @@ export declare const BondLineParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 };
 export declare const DefaultBondLineProps: PD.Values<{
@@ -69,8 +81,10 @@ export declare const DefaultBondLineProps: PD.Values<{
     excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 }>;
 export declare type BondLineProps = typeof DefaultBondLineProps;
@@ -81,11 +95,11 @@ export declare namespace BondIterator {
     function fromGroup(structureGroup: StructureGroup): LocationIterator;
     function fromStructure(structure: Structure): LocationIterator;
 }
-export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
+export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
     kind: "empty-loci";
-} | Bond.Loci;
+};
 export declare function eachIntraBond(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;
-export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): {
+export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): Bond.Loci | {
     kind: "empty-loci";
-} | Bond.Loci;
+};
 export declare function eachInterBond(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;

package/lib/mol-repr/structure/visual/util/bond.js

@@ -18,9 +18,10 @@ export var BondParams = {
     excludeTypes: PD.MultiSelect([], PD.objectToOptions(BondType.Names)),
     ignoreHydrogens: PD.Boolean(false),
     aromaticBonds: PD.Boolean(false, { description: 'Display aromatic bonds with dashes' }),
+    multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'])),
 };
 export var DefaultBondProps = PD.getDefaultValues(BondParams);
-export var BondCylinderParams = __assign(__assign(__assign({}, LinkCylinderParams), BondParams), { adjustCylinderLength: PD.Boolean(true, { description: 'Shorten cylinders to reduce overlap with spheres.' }) });
+export var BondCylinderParams = __assign(__assign(__assign({}, LinkCylinderParams), BondParams), { adjustCylinderLength: PD.Boolean(false, { description: 'Shorten cylinders to reduce overlap with spheres. Useful for for transparent bonds. Not working well with aromatic bonds.' }) });
 export var DefaultBondCylinderProps = PD.getDefaultValues(BondCylinderParams);
 export var BondLineParams = __assign(__assign({}, LinkLineParams), BondParams);
 export var DefaultBondLineProps = PD.getDefaultValues(BondLineParams);

package/lib/mol-repr/structure/visual/util/bond.js.map

@@ -1 +1 @@
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package/lib/mol-repr/structure/visual/util/color.d.ts

@@ -10,10 +10,10 @@ import { Texture } from '../../../../mol-gl/webgl/texture';
 import { Theme } from '../../../../mol-theme/theme';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 export declare const ColorSmoothingParams: {
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
 };
 export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
 export declare function getColorSmoothingProps(props: PD.Values<ColorSmoothingParams>, theme: Theme, resolution?: number): {

package/lib/mol-repr/structure/visual/util/element.d.ts

@@ -29,13 +29,13 @@ export declare type ElementSphereImpostorProps = {
 } & ElementProps;
 export declare function createElementSphereImpostor(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereImpostorProps, spheres?: Spheres): Spheres;
 export declare function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;
-export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
+export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): StructureElement.Loci | {
     kind: "empty-loci";
-} | StructureElement.Loci;
+};
 export declare function eachSerialElement(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean;
-export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): {
+export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): StructureElement.Loci | {
     kind: "empty-loci";
-} | StructureElement.Loci;
+};
 export declare namespace ElementIterator {
     function fromGroup(structureGroup: StructureGroup): LocationIterator;
     function fromStructure(structure: Structure): LocationIterator;

package/lib/mol-repr/structure/visual/util/link.d.ts

@@ -13,6 +13,9 @@ export declare const LinkCylinderParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -23,6 +26,9 @@ export declare const DefaultLinkCylinderProps: PD.Values<{
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -33,11 +39,13 @@ export declare type LinkCylinderProps = typeof DefaultLinkCylinderProps;
 export declare const LinkLineParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 };
 export declare const DefaultLinkLineProps: PD.Values<{
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 }>;
 export declare type LinkLineProps = typeof DefaultLinkLineProps;
@@ -56,10 +64,12 @@ export declare const enum LinkStyle {
     Solid = 0,
     Dashed = 1,
     Double = 2,
-    Triple = 3,
-    Disk = 4,
-    Aromatic = 5,
-    MirroredAromatic = 6
+    OffsetDouble = 3,
+    Triple = 4,
+    OffsetTriple = 5,
+    Disk = 6,
+    Aromatic = 7,
+    MirroredAromatic = 8
 }
 /**
  * Each edge is included twice to allow for coloring/picking