npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1829) hide show

package/lib/mol-repr/structure/visual/bond-intra-unit-line.js CHANGED Viewed

@@ -32,7 +32,9 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
     if (!edgeCount)
         return Lines.createEmpty(lines);
     var _order = edgeProps.order, _flags = edgeProps.flags;
-    var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
+    var sizeFactor = props.sizeFactor, aromaticBonds = props.aromaticBonds, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes, multipleBonds = props.multipleBonds;
+    var mbOff = multipleBonds === 'off';
+    var mbSymmetric = multipleBonds === 'symmetric';
     var include = BondType.fromNames(includeTypes);
     var exclude = BondType.fromNames(excludeTypes);
     var ignoreComputedAromatic = ignoreBondType(include, exclude, 32 /* Computed */);
@@ -82,7 +84,9 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
                 return 1 /* Dashed */;
             }
             else if (o === 3) {
-                return 3 /* Triple */;
+                return mbOff ? 0 /* Solid */ :
+                    mbSymmetric ? 4 /* Triple */ :
+                        5 /* OffsetTriple */;
             }
             else if (aromaticBonds) {
                 var aI = a[edgeIndex], bI = b[edgeIndex];
@@ -91,14 +95,16 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
                 var arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
                 if (isBondType(f, 16 /* Aromatic */) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
-                        return 6 /* MirroredAromatic */;
+                        return 8 /* MirroredAromatic */;
                     }
                     else {
-                        return 5 /* Aromatic */;
+                        return 7 /* Aromatic */;
                     }
                 }
             }
-            return o === 2 ? 2 /* Double */ : 0 /* Solid */;
+            return (o !== 2 || mbOff) ? 0 /* Solid */ :
+                mbSymmetric ? 2 /* Double */ :
+                    3 /* OffsetDouble */;
         },
         radius: function (edgeIndex) {
             location.element = elements[a[edgeIndex]];
@@ -126,11 +132,13 @@ export function IntraUnitBondLineVisual(materialId) {
             state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
+                newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
                 !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                 !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
-                newProps.aromaticBonds !== currentProps.aromaticBonds);
+                newProps.aromaticBonds !== currentProps.aromaticBonds ||
+                newProps.multipleBonds !== currentProps.multipleBonds);
             var newUnit = newStructureGroup.group.units[0];
             var currentUnit = currentStructureGroup.group.units[0];
             if (Unit.isAtomic(newUnit) && Unit.isAtomic(currentUnit)) {

package/lib/mol-repr/structure/visual/bond-intra-unit-line.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts CHANGED Viewed

@@ -10,12 +10,15 @@ export declare const CarbohydrateLinkParams: {
     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;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts CHANGED Viewed

@@ -8,7 +8,7 @@ import { ComplexVisual } from '../representation';
 export declare const CarbohydrateSymbolParams: {
     detail: PD.Numeric;
     sizeFactor: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts CHANGED Viewed

@@ -10,12 +10,15 @@ export declare const CarbohydrateTerminalLinkParams: {
     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;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/mol-repr/structure/visual/element-cross.d.ts ADDED Viewed

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsVisual } from '../units-visual';
+import { VisualContext } from '../../visual';
+import { Unit, Structure } from '../../../mol-model/structure';
+import { Theme } from '../../../mol-theme/theme';
+import { Lines } from '../../../mol-geo/geometry/lines/lines';
+export declare const ElementCrossParams: {
+    lineSizeAttenuation: PD.BooleanParam;
+    ignoreHydrogens: PD.BooleanParam;
+    traceOnly: PD.BooleanParam;
+    crosses: PD.Select<"all" | "lone">;
+    crossSize: PD.Numeric;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
+    includeParent: PD.BooleanParam;
+    sizeFactor: PD.Numeric;
+    alpha: PD.Numeric;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+};
+export declare type ElementCrossParams = typeof ElementCrossParams;
+export declare function createElementCross(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementCrossParams>, lines: Lines): Lines;
+export declare function ElementCrossVisual(materialId: number): UnitsVisual<ElementCrossParams>;

package/lib/mol-repr/structure/visual/element-cross.js ADDED Viewed

@@ -0,0 +1,72 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __assign } from "tslib";
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
+import { Unit } from '../../../mol-model/structure';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ElementIterator, getElementLoci, eachElement, makeElementIgnoreTest } from './util/element';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { Lines } from '../../../mol-geo/geometry/lines/lines';
+import { LinesBuilder } from '../../../mol-geo/geometry/lines/lines-builder';
+import { bondCount } from '../../../mol-model-props/computed/chemistry/util';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+var v3scaleAndAdd = Vec3.scaleAndAdd;
+var v3unitX = Vec3.unitX;
+var v3unitY = Vec3.unitY;
+var v3unitZ = Vec3.unitZ;
+export var ElementCrossParams = __assign(__assign({}, UnitsLinesParams), { lineSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), traceOnly: PD.Boolean(false), crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'])), crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
+export function createElementCross(ctx, unit, structure, theme, props, lines) {
+    var child = structure.child;
+    if (child && !child.unitMap.get(unit.id))
+        return Lines.createEmpty(lines);
+    var elements = unit.elements;
+    var n = elements.length;
+    var builder = LinesBuilder.create(n, n / 10, lines);
+    var p = Vec3();
+    var s = Vec3();
+    var e = Vec3();
+    var pos = unit.conformation.invariantPosition;
+    var ignore = makeElementIgnoreTest(structure, unit, props);
+    var r = props.crossSize / 2;
+    var lone = props.crosses === 'lone';
+    for (var i = 0; i < n; ++i) {
+        if (ignore && ignore(elements[i]))
+            continue;
+        if (lone && Unit.isAtomic(unit) && bondCount(structure, unit, i) !== 0)
+            continue;
+        pos(elements[i], p);
+        v3scaleAndAdd(s, p, v3unitX, r);
+        v3scaleAndAdd(e, p, v3unitX, -r);
+        builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
+        v3scaleAndAdd(s, p, v3unitY, r);
+        v3scaleAndAdd(e, p, v3unitY, -r);
+        builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
+        v3scaleAndAdd(s, p, v3unitZ, r);
+        v3scaleAndAdd(e, p, v3unitZ, -r);
+        builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
+    }
+    var l = builder.getLines();
+    var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    l.setBoundingSphere(sphere);
+    return l;
+}
+export function ElementCrossVisual(materialId) {
+    return UnitsLinesVisual({
+        defaultProps: PD.getDefaultValues(ElementCrossParams),
+        createGeometry: createElementCross,
+        createLocationIterator: ElementIterator.fromGroup,
+        getLoci: getElementLoci,
+        eachLocation: eachElement,
+        setUpdateState: function (state, newProps, currentProps) {
+            state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.traceOnly !== currentProps.traceOnly ||
+                newProps.crosses !== currentProps.crosses ||
+                newProps.crossSize !== currentProps.crossSize);
+        }
+    }, materialId);
+}
+//# sourceMappingURL=element-cross.js.map

package/lib/mol-repr/structure/visual/element-cross.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"element-cross.js","sourceRoot":"","sources":["../../../../src/mol-repr/structure/visual/element-cross.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAEH,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,oCAAoC,CAAC;AAC3E,OAAO,EAAe,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AAElF,OAAO,EAAE,IAAI,EAA+B,MAAM,8BAA8B,CAAC;AAEjF,OAAO,EAAE,IAAI,EAAE,MAAM,kCAAkC,CAAC;AACxD,OAAO,EAAE,eAAe,EAAE,cAAc,EAAE,WAAW,EAAE,qBAAqB,EAAE,MAAM,gBAAgB,CAAC;AAErG,OAAO,EAAE,QAAQ,EAAE,MAAM,4BAA4B,CAAC;AACtD,OAAO,EAAE,KAAK,EAAE,MAAM,uCAAuC,CAAC;AAC9D,OAAO,EAAE,YAAY,EAAE,MAAM,+CAA+C,CAAC;AAC7E,OAAO,EAAE,SAAS,EAAE,MAAM,kDAAkD,CAAC;AAE7E,sEAAsE;AACtE,IAAM,aAAa,GAAG,IAAI,CAAC,WAAW,CAAC;AACvC,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC;AAC3B,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC;AAC3B,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC;AAE3B,MAAM,CAAC,IAAM,kBAAkB,yBACxB,gBAAgB,KACnB,mBAAmB,EAAE,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EACtC,eAAe,EAAE,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAClC,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,EAC5B,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,CAAC,cAAc,CAAC,CAAC,MAAM,EAAE,KAAK,CAAU,CAAC,CAAC,EACvE,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,GAC9D,CAAC;AAGF,MAAM,UAAU,kBAAkB,CAAC,GAAkB,EAAE,IAAU,EAAE,SAAoB,EAAE,KAAY,EAAE,KAAoC,EAAE,KAAY;IAC7I,IAAA,KAAK,GAAK,SAAS,MAAd,CAAe;IAC5B,IAAI,KAAK,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;QAAE,OAAO,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC;IAE1E,IAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;IAC/B,IAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC;IAC1B,IAAM,OAAO,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,CAAC;IAEtD,IAAM,CAAC,GAAG,IAAI,EAAE,CAAC;IACjB,IAAM,CAAC,GAAG,IAAI,EAAE,CAAC;IACjB,IAAM,CAAC,GAAG,IAAI,EAAE,CAAC;IAEjB,IAAM,GAAG,GAAG,IAAI,CAAC,YAAY,CAAC,iBAAiB,CAAC;IAChD,IAAM,MAAM,GAAG,qBAAqB,CAAC,SAAS,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC;IAE7D,IAAM,CAAC,GAAG,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC;IAC9B,IAAM,IAAI,GAAG,KAAK,CAAC,OAAO,KAAK,MAAM,CAAC;IAEtC,KAAK,IAAI,CAAC,GAAG,CAA+B,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;QACtD,IAAI,MAAM,IAAI,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;YAAE,SAAS;QAC5C,IAAI,IAAI,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,SAAS,CAAC,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC;YAAE,SAAS;QAEjF,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;QACpB,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC;QAChC,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC;QACjC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;QACnD,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC;QAChC,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC;QACjC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;QACnD,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC;QAChC,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC;QACjC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;KACtD;IAED,IAAM,CAAC,GAAG,OAAO,CAAC,QAAQ,EAAE,CAAC;IAE7B,IAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;IACvF,CAAC,CAAC,iBAAiB,CAAC,MAAM,CAAC,CAAC;IAE5B,OAAO,CAAC,CAAC;AACb,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,UAAkB;IACjD,OAAO,gBAAgB,CAAqB;QACxC,YAAY,EAAE,EAAE,CAAC,gBAAgB,CAAC,kBAAkB,CAAC;QACrD,cAAc,EAAE,kBAAkB;QAClC,sBAAsB,EAAE,eAAe,CAAC,SAAS;QACjD,OAAO,EAAE,cAAc;QACvB,YAAY,EAAE,WAAW;QACzB,cAAc,EAAE,UAAC,KAAwB,EAAE,QAAuC,EAAE,YAA2C;YAC3H,KAAK,CAAC,cAAc,GAAG,CACnB,QAAQ,CAAC,eAAe,KAAK,YAAY,CAAC,eAAe;gBACzD,QAAQ,CAAC,SAAS,KAAK,YAAY,CAAC,SAAS;gBAC7C,QAAQ,CAAC,OAAO,KAAK,YAAY,CAAC,OAAO;gBACzC,QAAQ,CAAC,SAAS,KAAK,YAAY,CAAC,SAAS,CAChD,CAAC;QACN,CAAC;KACJ,EAAE,UAAU,CAAC,CAAC;AACnB,CAAC"}

package/lib/mol-repr/structure/visual/element-point.d.ts CHANGED Viewed

@@ -13,10 +13,10 @@ export declare const ElementPointParams: {
     pointSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
-    pointStyle: PD.Select<"square" | "circle" | "fuzzy">;
+    pointStyle: PD.Select<"fuzzy" | "square" | "circle">;
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
 };

package/lib/mol-repr/structure/visual/element-sphere.d.ts CHANGED Viewed

@@ -14,7 +14,7 @@ export declare const ElementSphereParams: {
     ignoreHydrogens: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
@@ -31,7 +31,7 @@ export declare function ElementSphereVisual(materialId: number, structure: Struc
     ignoreHydrogens: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;

package/lib/mol-repr/structure/visual/ellipsoid-mesh.d.ts CHANGED Viewed

@@ -13,7 +13,7 @@ export declare const EllipsoidMeshParams: {
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/mol-repr/structure/visual/gaussian-density-volume.d.ts CHANGED Viewed

@@ -13,7 +13,7 @@ export declare const GaussianDensityVolumeParams: {
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -22,7 +22,7 @@ export declare const GaussianDensityVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -49,7 +49,7 @@ export declare const UnitsGaussianDensityVolumeParams: {
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -58,7 +58,7 @@ export declare const UnitsGaussianDensityVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts CHANGED Viewed

@@ -12,15 +12,15 @@ export declare const GaussianSurfaceMeshParams: {
     ignoreHydrogens: PD.BooleanParam;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
-    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>, "off"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -34,15 +34,15 @@ export declare const StructureGaussianSurfaceMeshParams: {
     ignoreHydrogens: PD.BooleanParam;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
-    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>, "off"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -56,15 +56,15 @@ export declare function GaussianSurfaceVisual(materialId: number, structure: Str
     ignoreHydrogens: PD.BooleanParam;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
-    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>, "off"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -77,15 +77,15 @@ export declare function StructureGaussianSurfaceVisual(materialId: number, struc
     ignoreHydrogens: PD.BooleanParam;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
-    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>, "off"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;

package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts CHANGED Viewed

@@ -14,7 +14,7 @@ export declare const GaussianWireframeParams: {
     resolution: PD.Numeric;
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
 };

package/lib/mol-repr/structure/visual/label-text.d.ts CHANGED Viewed

@@ -15,7 +15,7 @@ export declare const LabelTextParams: {
     chainScale: PD.Numeric;
     residueScale: PD.Numeric;
     elementScale: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     borderWidth: PD.Numeric;

package/lib/mol-repr/structure/visual/label-text.js CHANGED Viewed

@@ -56,7 +56,7 @@ function createChainText(ctx, structure, theme, props, text) {
         Vec3.transformMat4(tmpVec, center, unit.conformation.operator.matrix);
         var authId = auth_asym_id(l);
         var labelId = label_asym_id(l);
-        var text_1 = authId === labelId ? labelId : labelId + " [" + authId + "]";
+        var text_1 = authId === labelId ? labelId : "".concat(labelId, " [").concat(authId, "]");
         builder.add(text_1, tmpVec[0], tmpVec[1], tmpVec[2], radius, chainScale, cumulativeUnitElementCount[i]);
     }
     return builder.getText();
@@ -99,7 +99,7 @@ function createResidueText(ctx, structure, theme, props, text) {
             var _a = boundaryHelper.getSphere(), center = _a.center, radius = _a.radius;
             var authSeqId = auth_seq_id(l);
             var compId = label_comp_id(l);
-            var text_2 = compId + " " + authSeqId;
+            var text_2 = "".concat(compId, " ").concat(authSeqId);
             builder.add(text_2, center[0], center[1], center[2], radius, residueScale, groupOffset + start);
         }
     }
@@ -125,7 +125,7 @@ function createElementText(ctx, structure, theme, props, text) {
             pos(l.element, tmpVec);
             var atomId = label_atom_id(l);
             var altId = label_alt_id(l);
-            var text_3 = altId ? atomId + "%" + altId : atomId;
+            var text_3 = altId ? "".concat(atomId, "%").concat(altId) : atomId;
             builder.add(text_3, tmpVec[0], tmpVec[1], tmpVec[2], sizeTheme.size(l), elementScale, groupOffset + j);
         }
     }

package/lib/mol-repr/structure/visual/label-text.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-repr/structure/visual/molecular-surface-mesh.d.ts CHANGED Viewed

@@ -6,17 +6,17 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { UnitsVisual } from '../units-visual';
 export declare const MolecularSurfaceMeshParams: {
-    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>, "off"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
     ignoreHydrogens: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     probeRadius: PD.Numeric;
     resolution: PD.Numeric;
     probePositions: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;

package/lib/mol-repr/structure/visual/molecular-surface-wireframe.d.ts CHANGED Viewed

@@ -13,7 +13,7 @@ export declare const MolecularSurfaceWireframeParams: {
     probeRadius: PD.Numeric;
     resolution: PD.Numeric;
     probePositions: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     lineSizeAttenuation: PD.BooleanParam;
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;

package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts CHANGED Viewed

@@ -17,7 +17,7 @@ export declare type NucleotideBlockMeshProps = typeof DefaultNucleotideBlockMesh
 export declare const NucleotideBlockParams: {
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts CHANGED Viewed

@@ -20,7 +20,7 @@ export declare const NucleotideRingParams: {
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
     detail: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/mol-repr/structure/visual/orientation-axes-mesh.d.ts ADDED Viewed

@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsVisual } from '../units-visual';
+import { VisualContext } from '../../visual';
+import { Unit, Structure } from '../../../mol-model/structure';
+import { Theme } from '../../../mol-theme/theme';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+export declare const OrientationAxesMeshParams: {
+    sizeFactor: PD.Numeric;
+    axesScale: PD.Numeric;
+    radialSegments: PD.Numeric;
+    detail: PD.Numeric;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    includeParent: PD.BooleanParam;
+    doubleSided: PD.BooleanParam;
+    flipSided: PD.BooleanParam;
+    flatShaded: PD.BooleanParam;
+    ignoreLight: PD.BooleanParam;
+    xrayShaded: PD.BooleanParam;
+    alpha: PD.Numeric;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+};
+export declare type OrientationAxesMeshParams = typeof OrientationAxesMeshParams;
+export declare function OrientationAxesMeshVisual(materialId: number): UnitsVisual<OrientationAxesMeshParams>;
+export interface OrientationAxesMeshProps {
+    detail: number;
+    radialSegments: number;
+    sizeFactor: number;
+    axesScale: number;
+}
+export declare function createOrientationAxesMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: OrientationAxesMeshProps, mesh?: Mesh): Mesh;

package/lib/mol-repr/structure/visual/orientation-axes-mesh.js ADDED Viewed

@@ -0,0 +1,43 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __assign } from "tslib";
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsMeshParams, UnitsMeshVisual } from '../units-visual';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { addAxes } from '../../../mol-geo/geometry/mesh/builder/axes';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { eachUnit, getUnitLoci, isUnitApplicable, UnitIterator } from './util/orientation';
+export var OrientationAxesMeshParams = __assign(__assign({}, UnitsMeshParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 2, step: 0.1 }), axesScale: PD.Numeric(1, { min: 0, max: 20, step: 0.1 }), radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo) });
+export function OrientationAxesMeshVisual(materialId) {
+    return UnitsMeshVisual({
+        defaultProps: PD.getDefaultValues(OrientationAxesMeshParams),
+        createGeometry: createOrientationAxesMesh,
+        createLocationIterator: UnitIterator,
+        getLoci: getUnitLoci,
+        eachLocation: eachUnit,
+        setUpdateState: function (state, newProps, currentProps) {
+            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.detail !== currentProps.detail);
+        }
+    }, materialId);
+}
+export function createOrientationAxesMesh(ctx, unit, structure, theme, props, mesh) {
+    if (!isUnitApplicable(unit))
+        return Mesh.createEmpty(mesh);
+    var detail = props.detail, sizeFactor = props.sizeFactor, radialSegments = props.radialSegments, axesScale = props.axesScale;
+    var vertexCount = 256;
+    var builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
+    var axes = unit.principalAxes.momentsAxes;
+    builderState.currentGroup = 0;
+    addAxes(builderState, axes, axesScale, detail, radialSegments);
+    var m = MeshBuilder.getMesh(builderState);
+    var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    m.setBoundingSphere(sphere);
+    return m;
+}
+//# sourceMappingURL=orientation-axes-mesh.js.map