molstar 3.44.0 → 3.45.0

package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts

@@ -17,10 +17,11 @@ export declare const PolymerBackboneCylinderParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
@@ -53,10 +54,11 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{

package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.js

@@ -44,8 +44,8 @@ function createPolymerBackboneCylinderImpostor(ctx, unit, structure, theme, prop
         var isNucleicType = isNucleic(moleculeType);
         var shift = isNucleicType ? NucleicShift : StandardShift;
         v3add(pM, pA, v3scale(pM, v3sub(pM, pB, pA), shift));
-        builder.add(pA[0], pA[1], pA[2], pM[0], pM[1], pM[2], 1, false, false, groupA);
-        builder.add(pM[0], pM[1], pM[2], pB[0], pB[1], pB[2], 1, false, false, groupB);
+        builder.add(pA[0], pA[1], pA[2], pM[0], pM[1], pM[2], 1, false, false, 2, groupA);
+        builder.add(pM[0], pM[1], pM[2], pB[0], pB[1], pB[2], 1, false, false, 2, groupB);
     };
     eachPolymerBackboneLink(unit, add);
     var c = builder.getCylinders();
@@ -57,7 +57,7 @@ export function PolymerBackboneCylinderImpostorVisual(materialId) {
     return UnitsCylindersVisual({
         defaultProps: PD.getDefaultValues(PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderImpostor,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) { },
@@ -103,7 +103,7 @@ export function PolymerBackboneCylinderMeshVisual(materialId) {
     return UnitsMeshVisual({
         defaultProps: PD.getDefaultValues(PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderMesh,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts

@@ -16,7 +16,7 @@ export declare const PolymerBackboneSphereParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     solidInterior: PD.BooleanParam;
     clipPrimitive: PD.BooleanParam;
     approximate: PD.BooleanParam;
@@ -54,7 +54,7 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     solidInterior: PD.BooleanParam;
     clipPrimitive: PD.BooleanParam;
     approximate: PD.BooleanParam;

package/lib/mol-repr/structure/visual/polymer-backbone-sphere.js

@@ -45,7 +45,7 @@ export function PolymerBackboneSphereImpostorVisual(materialId) {
     return UnitsSpheresVisual({
         defaultProps: PD.getDefaultValues(PolymerBackboneSphereParams),
         createGeometry: createPolymerBackboneSphereImpostor,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) { },
@@ -80,7 +80,7 @@ export function PolymerBackboneSphereMeshVisual(materialId) {
     return UnitsMeshVisual({
         defaultProps: PD.getDefaultValues(PolymerBackboneSphereParams),
         createGeometry: createPolymerBackboneSphereMesh,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts

@@ -21,7 +21,7 @@ export declare const PolymerDirectionParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-repr/structure/visual/polymer-direction-wedge.js

@@ -73,7 +73,7 @@ export function PolymerDirectionVisual(materialId) {
     return UnitsMeshVisual({
         defaultProps: PD.getDefaultValues(PolymerDirectionParams),
         createGeometry: createPolymerDirectionWedgeMesh,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts

@@ -25,7 +25,7 @@ export declare const PolymerGapParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -45,7 +45,7 @@ export declare const PolymerTraceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -166,7 +166,7 @@ export function PolymerTraceVisual(materialId) {
     return UnitsMeshVisual({
         defaultProps: PD.getDefaultValues(PolymerTraceParams),
         createGeometry: createPolymerTraceMesh,
-        createLocationIterator: function (sg) { return PolymerLocationIterator.fromGroup(sg, true); },
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup, { asSecondary: true }); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {

package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts

@@ -30,7 +30,7 @@ export declare const PolymerTubeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -93,7 +93,7 @@ export function PolymerTubeVisual(materialId) {
     return UnitsMeshVisual({
         defaultProps: PD.getDefaultValues(PolymerTubeParams),
         createGeometry: createPolymerTubeMesh,
-        createLocationIterator: function (sg) { return PolymerLocationIterator.fromGroup(sg, true); },
+        createLocationIterator: function (structureGroup) { return PolymerLocationIterator.fromGroup(structureGroup, { asSecondary: true }); },
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

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

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { Unit, Structure, Bond } from '../../../../mol-model/structure';
@@ -48,6 +49,7 @@ export declare const BondCylinderParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
 };
 export declare const DefaultBondCylinderProps: PD.Values<{
     adjustCylinderLength: PD.BooleanParam;
@@ -68,6 +70,7 @@ export declare const DefaultBondCylinderProps: PD.Values<{
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
 }>;
 export type BondCylinderProps = typeof DefaultBondCylinderProps;
 export declare const BondLineParams: {
@@ -99,8 +102,12 @@ export declare function ignoreBondType(include: BondType.Flag, exclude: BondType
 export declare function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic, props: BondProps): undefined | ((edgeIndex: number) => boolean);
 export declare function makeInterBondIgnoreTest(structure: Structure, props: BondProps): undefined | ((edgeIndex: number) => boolean);
 export declare namespace BondIterator {
-    function fromGroup(structureGroup: StructureGroup): LocationIterator;
-    function fromStructure(structure: Structure): LocationIterator;
+    function fromGroup(structureGroup: StructureGroup, props?: {
+        includeLocation2?: boolean;
+    }): LocationIterator;
+    function fromStructure(structure: Structure, props?: {
+        includeLocation2?: boolean;
+    }): LocationIterator;
 }
 export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
     kind: "empty-loci";

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

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { __assign } from "tslib";
 import { BondType } from '../../../../mol-model/structure/model/types';
@@ -98,7 +99,7 @@ export function makeInterBondIgnoreTest(structure, props) {
 }
 export var BondIterator;
 (function (BondIterator) {
-    function fromGroup(structureGroup) {
+    function fromGroup(structureGroup, props) {
         var group = structureGroup.group, structure = structureGroup.structure;
         var unit = group.units[0];
         var groupCount = Unit.isAtomic(unit) ? unit.bonds.edgeCount * 2 : 0;
@@ -112,10 +113,22 @@ export var BondIterator;
             location.bIndex = unit.bonds.b[groupIndex];
             return location;
         };
+        if (props === null || props === void 0 ? void 0 : props.includeLocation2) {
+            var location2_1 = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
+            var getLocation2 = function (groupIndex, instanceIndex) {
+                var unit = group.units[instanceIndex];
+                location2_1.aUnit = unit;
+                location2_1.bUnit = unit;
+                location2_1.aIndex = unit.bonds.b[groupIndex];
+                location2_1.bIndex = unit.bonds.a[groupIndex];
+                return location2_1;
+            };
+            return LocationIterator(groupCount, instanceCount, 1, getLocation, false, function () { return false; }, getLocation2);
+        }
         return LocationIterator(groupCount, instanceCount, 1, getLocation);
     }
     BondIterator.fromGroup = fromGroup;
-    function fromStructure(structure) {
+    function fromStructure(structure, props) {
         var groupCount = structure.interUnitBonds.edgeCount;
         var instanceCount = 1;
         var location = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
@@ -127,6 +140,19 @@ export var BondIterator;
             location.bIndex = bond.indexB;
             return location;
         };
+        if (props === null || props === void 0 ? void 0 : props.includeLocation2) {
+            var location2_2 = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
+            var getLocation2 = function (groupIndex) {
+                var bond = structure.interUnitBonds.edges[groupIndex];
+                location2_2.aUnit = structure.unitMap.get(bond.unitB);
+                location2_2.aIndex = bond.indexB;
+                location2_2.bUnit = structure.unitMap.get(bond.unitA);
+                location2_2.bIndex = bond.indexA;
+                return location2_2;
+            };
+            return LocationIterator(groupCount, instanceCount, 1, getLocation, true, function () { return false; }, getLocation2);
+        }
+        ;
         return LocationIterator(groupCount, instanceCount, 1, getLocation, true);
     }
     BondIterator.fromStructure = fromStructure;

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

@@ -25,6 +25,7 @@ export declare const LinkCylinderParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
 };
 export declare const DefaultLinkCylinderProps: PD.Values<{
     linkScale: PD.Numeric;
@@ -38,6 +39,7 @@ export declare const DefaultLinkCylinderProps: PD.Values<{
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
 }>;
 export type LinkCylinderProps = typeof DefaultLinkCylinderProps;
 export declare const LinkLineParams: {

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

@@ -29,6 +29,7 @@ export var LinkCylinderParams = {
     dashCap: PD.Boolean(true),
     stubCap: PD.Boolean(true),
     radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
+    colorMode: PD.Select('default', PD.arrayToOptions(['default', 'interpolate']), BaseGeometry.ShadingCategory)
 };
 export var DefaultLinkCylinderProps = PD.getDefaultValues(LinkCylinderParams);
 export var LinkLineParams = {
@@ -209,7 +210,9 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
         return { cylinders: Cylinders.createEmpty(cylinders) };
-    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
+    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap, colorMode = props.colorMode;
+    var interpolate = colorMode === 'interpolate';
+    var colorModeFlag = interpolate === true ? 3 : 2;
     var cylindersCountEstimate = linkCount * 2;
     var builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
     var va = Vec3();
@@ -230,11 +233,11 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
         if (linkStyle === 0 /* LinkStyle.Solid */) {
             v3scale(vm, v3add(vm, va, vb), 0.5);
-            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, colorModeFlag, edgeIndex);
         }
         else if (linkStyle === 1 /* LinkStyle.Dashed */) {
             v3scale(vm, v3add(vm, va, vb), 0.5);
-            builder.addFixedCountDashes(va, vm, dashCount, dashScale, dashCap, dashCap, linkStub, edgeIndex);
+            builder.addFixedCountDashes(va, vm, dashCount, dashScale, dashCap, dashCap, linkStub, interpolate, edgeIndex);
         }
         else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
             var order = (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */) ? 2 :
@@ -244,44 +247,44 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
             v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
             if (linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
-                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, colorModeFlag, edgeIndex);
                 var aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
                 v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
                 v3add(va, va, tmpV12);
                 v3setMagnitude(vShift, vShift, aromaticOffset);
                 v3sub(va, va, vShift);
                 v3sub(vm, vm, vShift);
-                builder.addFixedCountDashes(va, vm, aromaticDashCount, aromaticScale, dashCap, dashCap, linkStub, edgeIndex);
+                builder.addFixedCountDashes(va, vm, aromaticDashCount, aromaticScale, dashCap, dashCap, linkStub, interpolate, edgeIndex);
                 if (linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                     v3setMagnitude(vShift, vShift, aromaticOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vm, vm, vShift);
-                    builder.addFixedCountDashes(va, vm, aromaticDashCount, aromaticScale, dashCap, dashCap, linkStub, edgeIndex);
+                    builder.addFixedCountDashes(va, vm, aromaticDashCount, aromaticScale, dashCap, dashCap, linkStub, interpolate, edgeIndex);
                 }
             }
             else if (linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 5 /* LinkStyle.OffsetTriple */) {
                 var multipleOffset = linkRadius + multiScale * linkRadius + linkScale * linkRadius * linkSpacing;
                 v3setMagnitude(vShift, vShift, multipleOffset);
-                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, colorModeFlag, edgeIndex);
                 v3setMagnitude(tmpV12, v3sub(tmpV12, va, vm), linkRadius / 1.5);
                 v3sub(va, va, tmpV12);
                 if (order === 3)
-                    builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
-                builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, dashCap, linkStub, edgeIndex);
+                    builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, colorModeFlag, edgeIndex);
+                builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, dashCap, linkStub, colorModeFlag, edgeIndex);
             }
             else {
                 v3setMagnitude(vShift, vShift, absOffset);
                 if (order === 3)
-                    builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, linkStub, edgeIndex);
-                builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
-                builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
+                    builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, linkStub, colorModeFlag, edgeIndex);
+                builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, colorModeFlag, edgeIndex);
+                builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, colorModeFlag, edgeIndex);
             }
         }
         else if (linkStyle === 6 /* LinkStyle.Disk */) {
             v3scale(tmpV12, v3sub(tmpV12, vm, va), 0.475);
             v3add(va, va, tmpV12);
             v3sub(vm, vm, tmpV12);
-            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+            builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, colorModeFlag, edgeIndex);
         }
     }
     var oldBoundingSphere = cylinders ? Sphere3D.clone(cylinders.boundingSphere) : undefined;

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

@@ -23,7 +23,9 @@ export declare const OverhangFactor = 2;
 export declare function getPolymerRanges(unit: Unit): SortedRanges<ElementIndex>;
 export declare function getGapRanges(unit: Unit): SortedRanges<ElementIndex>;
 export declare namespace PolymerLocationIterator {
-    function fromGroup(structureGroup: StructureGroup, asSecondary?: boolean): LocationIterator;
+    function fromGroup(structureGroup: StructureGroup, options?: {
+        asSecondary?: boolean;
+    }): LocationIterator;
 }
 export declare namespace PolymerGapLocationIterator {
     function fromGroup(structureGroup: StructureGroup): LocationIterator;

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

@@ -34,8 +34,7 @@ export function getGapRanges(unit) {
 }
 export var PolymerLocationIterator;
 (function (PolymerLocationIterator) {
-    function fromGroup(structureGroup, asSecondary) {
-        if (asSecondary === void 0) { asSecondary = false; }
+    function fromGroup(structureGroup, options) {
         var group = structureGroup.group, structure = structureGroup.structure;
         var polymerElements = group.units[0].polymerElements;
         var groupCount = polymerElements.length;
@@ -47,6 +46,7 @@ export var PolymerLocationIterator;
             location.element = polymerElements[groupIndex];
             return location;
         };
+        var asSecondary = !!(options === null || options === void 0 ? void 0 : options.asSecondary);
         function isSecondary(elementIndex, instanceIndex) {
             return asSecondary;
         }

package/lib/mol-repr/volume/isosurface.d.ts

@@ -93,7 +93,7 @@ export declare function IsosurfaceVisual(materialId: number, volume: Volume, key
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -168,7 +168,7 @@ export declare const IsosurfaceMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -334,7 +334,7 @@ export declare const IsosurfaceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpAmplitude: PD.Numeric;
 };
 export type IsosurfaceParams = typeof IsosurfaceParams;
@@ -411,7 +411,7 @@ export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: V
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpAmplitude: PD.Numeric;
 };
 export type IsosurfaceRepresentation = VolumeRepresentation<IsosurfaceParams>;
@@ -489,6 +489,6 @@ export declare const IsosurfaceRepresentationProvider: VolumeRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpAmplitude: PD.Numeric;
 }, "isosurface">;

package/lib/mol-repr/volume/registry.d.ts

@@ -83,7 +83,7 @@ export declare namespace VolumeRepresentationRegistry {
             flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             xrayShaded: import("../../mol-util/param-definition").ParamDefinition.Select<boolean | "inverted">;
-            transparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.Select<string>;
+            transparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.Select<"on" | "off" | "opaque">;
             bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
         }, "isosurface">;
         slice: import("./representation").VolumeRepresentationProvider<{
@@ -232,7 +232,7 @@ export declare namespace VolumeRepresentationRegistry {
             flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             xrayShaded: import("../../mol-util/param-definition").ParamDefinition.Select<boolean | "inverted">;
-            transparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.Select<string>;
+            transparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.Select<"on" | "off" | "opaque">;
             bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             material: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{

package/lib/mol-repr/volume/segment.d.ts

@@ -49,7 +49,7 @@ export declare function SegmentVisual(materialId: number, volume: Volume, key: n
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -103,7 +103,7 @@ export declare const SegmentMeshParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -160,7 +160,7 @@ export declare const SegmentParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     material: PD.Group<PD.Normalize<{
@@ -214,7 +214,7 @@ export declare function getSegmentParams(ctx: ThemeRegistryContext, volume: Volu
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     material: PD.Group<PD.Normalize<{
@@ -269,7 +269,7 @@ export declare const SegmentRepresentationProvider: VolumeRepresentationProvider
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     material: PD.Group<PD.Normalize<{

package/lib/mol-util/param-definition.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -69,8 +69,15 @@ export declare namespace ParamDefinition {
     export function Boolean(defaultValue: boolean, info?: Info): BooleanParam;
     export interface Text<T extends string = string> extends Base<T> {
         type: 'text';
+        multiline?: boolean;
+        placeholder?: string;
+        disableInteractiveUpdates?: boolean;
     }
-    export function Text<T extends string = string>(defaultValue?: string, info?: Info): Text<T>;
+    export function Text<T extends string = string>(defaultValue?: string, info?: Info & {
+        multiline?: boolean;
+        placeholder?: string;
+        disableInteractiveUpdates?: boolean;
+    }): Text<T>;
     export interface Color extends Base<ColorData> {
         type: 'color';
         isExpanded?: boolean;

package/lib/mol-util/param-definition.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -69,7 +69,7 @@ export var ParamDefinition;
     ParamDefinition.Boolean = Boolean;
     function Text(defaultValue, info) {
         if (defaultValue === void 0) { defaultValue = ''; }
-        return setInfo({ type: 'text', defaultValue: defaultValue }, info);
+        return setInfo({ type: 'text', defaultValue: defaultValue, multiline: info === null || info === void 0 ? void 0 : info.multiline, placeholder: info === null || info === void 0 ? void 0 : info.placeholder, disableInteractiveUpdates: info === null || info === void 0 ? void 0 : info.disableInteractiveUpdates }, info);
     }
     ParamDefinition.Text = Text;
     function Color(defaultValue, info) {