npm - molstar - Versions diffs - 3.44.0 → 3.45.0 - Mend

molstar 3.44.0 → 3.45.0

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Files changed (272) hide show

package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts CHANGED Viewed

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Structure } from '../../../mol-model/structure';
@@ -30,11 +31,12 @@ export declare const InterUnitBondCylinderParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     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;
@@ -83,11 +85,12 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     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;

package/lib/commonjs/mol-repr/structure/visual/bond-inter-unit-cylinder.js CHANGED Viewed

@@ -3,6 +3,7 @@
  * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.InterUnitBondCylinderMeshVisual = exports.InterUnitBondCylinderImpostorVisual = exports.InterUnitBondCylinderVisual = exports.InterUnitBondCylinderParams = void 0;
@@ -182,7 +183,7 @@ function InterUnitBondCylinderImpostorVisual(materialId) {
     return (0, complex_visual_1.ComplexCylindersVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitBondCylinderParams),
         createGeometry: createInterUnitBondCylinderImpostors,
-        createLocationIterator: bond_1.BondIterator.fromStructure,
+        createLocationIterator: function (structure, props) { return bond_1.BondIterator.fromStructure(structure, { includeLocation2: props.colorMode === 'interpolate' }); },
         getLoci: bond_1.getInterBondLoci,
         eachLocation: bond_1.eachInterBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
@@ -204,6 +205,11 @@ function InterUnitBondCylinderImpostorVisual(materialId) {
                 !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
                 newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
                 newProps.multipleBonds !== currentProps.multipleBonds);
+            if (newProps.colorMode !== currentProps.colorMode) {
+                state.createGeometry = true;
+                state.updateTransform = true;
+                state.updateColor = true;
+            }
             if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
                 state.createGeometry = true;
                 state.updateTransform = true;
@@ -221,7 +227,7 @@ function InterUnitBondCylinderMeshVisual(materialId) {
     return (0, complex_visual_1.ComplexMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitBondCylinderParams),
         createGeometry: createInterUnitBondCylinderMesh,
-        createLocationIterator: bond_1.BondIterator.fromStructure,
+        createLocationIterator: function (structure) { return bond_1.BondIterator.fromStructure(structure); },
         getLoci: bond_1.getInterBondLoci,
         eachLocation: bond_1.eachInterBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {

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

@@ -115,7 +115,7 @@ function InterUnitBondLineVisual(materialId) {
     return (0, complex_visual_1.ComplexLinesVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InterUnitBondLineParams),
         createGeometry: createInterUnitBondLines,
-        createLocationIterator: bond_1.BondIterator.fromStructure,
+        createLocationIterator: function (structure) { return bond_1.BondIterator.fromStructure(structure); },
         getLoci: bond_1.getInterBondLoci,
         eachLocation: bond_1.eachInterBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {

package/lib/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts CHANGED Viewed

@@ -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 { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Structure } from '../../../mol-model/structure';
@@ -31,11 +32,12 @@ export declare const IntraUnitBondCylinderParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     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;
@@ -84,11 +86,12 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     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;

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

@@ -4,6 +4,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.IntraUnitBondCylinderMeshVisual = exports.IntraUnitBondCylinderImpostorVisual = exports.IntraUnitBondCylinderVisual = exports.IntraUnitBondCylinderParams = void 0;
@@ -203,7 +204,7 @@ function IntraUnitBondCylinderImpostorVisual(materialId) {
     return (0, units_visual_1.UnitsCylindersVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitBondCylinderParams),
         createGeometry: createIntraUnitBondCylinderImpostors,
-        createLocationIterator: bond_1.BondIterator.fromGroup,
+        createLocationIterator: function (structureGroup, props) { return bond_1.BondIterator.fromGroup(structureGroup, { includeLocation2: props.colorMode === 'interpolate' }); },
         getLoci: bond_1.getIntraBondLoci,
         eachLocation: bond_1.eachIntraBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {
@@ -226,6 +227,11 @@ function IntraUnitBondCylinderImpostorVisual(materialId) {
                 newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
                 newProps.aromaticBonds !== currentProps.aromaticBonds ||
                 newProps.multipleBonds !== currentProps.multipleBonds);
+            if (newProps.colorMode !== currentProps.colorMode) {
+                state.createGeometry = true;
+                state.updateTransform = true;
+                state.updateColor = true;
+            }
             var newUnit = newStructureGroup.group.units[0];
             var currentUnit = currentStructureGroup.group.units[0];
             if (structure_1.Unit.isAtomic(newUnit) && structure_1.Unit.isAtomic(currentUnit)) {
@@ -247,7 +253,7 @@ function IntraUnitBondCylinderMeshVisual(materialId) {
     return (0, units_visual_1.UnitsMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitBondCylinderParams),
         createGeometry: createIntraUnitBondCylinderMesh,
-        createLocationIterator: bond_1.BondIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return bond_1.BondIterator.fromGroup(structureGroup); },
         getLoci: bond_1.getIntraBondLoci,
         eachLocation: bond_1.eachIntraBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {

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

@@ -137,7 +137,7 @@ function IntraUnitBondLineVisual(materialId) {
     return (0, units_visual_1.UnitsLinesVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IntraUnitBondLineParams),
         createGeometry: createIntraUnitBondLines,
-        createLocationIterator: bond_1.BondIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return bond_1.BondIterator.fromGroup(structureGroup); },
         getLoci: bond_1.getIntraBondLoci,
         eachLocation: bond_1.eachIntraBond,
         setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructureGroup, currentStructureGroup) {

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

@@ -18,6 +18,7 @@ export declare const CarbohydrateLinkParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -25,7 +26,7 @@ export declare const CarbohydrateLinkParams: {
     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/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.d.ts CHANGED Viewed

@@ -15,7 +15,7 @@ export declare const CarbohydrateSymbolParams: {
     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/commonjs/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.d.ts CHANGED Viewed

@@ -18,6 +18,7 @@ export declare const CarbohydrateTerminalLinkParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -25,7 +26,7 @@ export declare const CarbohydrateTerminalLinkParams: {
     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/commonjs/mol-repr/structure/visual/element-sphere.d.ts CHANGED Viewed

@@ -31,7 +31,7 @@ export declare const ElementSphereParams: {
     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;
@@ -73,7 +73,7 @@ export declare function ElementSphereVisual(materialId: number, structure: Struc
     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;
@@ -116,7 +116,7 @@ export declare const StructureElementSphereParams: {
     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;
@@ -158,7 +158,7 @@ export declare function StructureElementSphereVisual(materialId: number, structu
     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/commonjs/mol-repr/structure/visual/ellipsoid-mesh.d.ts CHANGED Viewed

@@ -20,7 +20,7 @@ export declare const EllipsoidMeshParams: {
     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/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.d.ts CHANGED Viewed

@@ -27,7 +27,7 @@ export declare const GaussianSurfaceMeshParams: {
     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;
@@ -69,7 +69,7 @@ export declare const StructureGaussianSurfaceMeshParams: {
     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;
@@ -111,7 +111,7 @@ export declare function GaussianSurfaceVisual(materialId: number, structure: Str
     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;
@@ -152,7 +152,7 @@ export declare function StructureGaussianSurfaceVisual(materialId: number, struc
     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/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts CHANGED Viewed

@@ -24,7 +24,7 @@ export declare const MolecularSurfaceMeshParams: {
     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/commonjs/mol-repr/structure/visual/nucleotide-atomic-bond.d.ts CHANGED Viewed

@@ -18,10 +18,11 @@ export declare const NucleotideAtomicBondParams: {
     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<{
@@ -54,10 +55,11 @@ export declare function NucleotideAtomicBondVisual(materialId: number, structure
     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/commonjs/mol-repr/structure/visual/nucleotide-atomic-bond.js CHANGED Viewed

@@ -59,6 +59,7 @@ function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props,
     var chainIt = int_1.Segmentation.transientSegments(chainAtomSegments, elements);
     var residueIt = int_1.Segmentation.transientSegments(residueAtomSegments, elements);
     var i = 0;
+    var colorModeFlag = 2.0;
     while (chainIt.hasNext) {
         residueIt.setSegment(chainIt.move());
         while (residueIt.hasNext) {
@@ -74,13 +75,13 @@ function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props,
                     pos(idx.O4_1, pO4_1);
                     // trace cylinder
                     pos(idx.trace, pTrace);
-                    builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, i);
+                    builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
                     // sugar ring
-                    builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pC4_1[0], pC4_1[1], pC4_1[2], 1, true, true, i);
-                    builder.add(pC4_1[0], pC4_1[1], pC4_1[2], pO4_1[0], pO4_1[1], pO4_1[2], 1, true, true, i);
-                    builder.add(pO4_1[0], pO4_1[1], pO4_1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, i);
-                    builder.add(pC1_1[0], pC1_1[1], pC1_1[2], pC2_1[0], pC2_1[1], pC2_1[2], 1, true, true, i);
-                    builder.add(pC2_1[0], pC2_1[1], pC2_1[2], pC3_1[0], pC3_1[1], pC3_1[2], 1, true, true, i);
+                    builder.add(pC3_1[0], pC3_1[1], pC3_1[2], pC4_1[0], pC4_1[1], pC4_1[2], 1, true, true, colorModeFlag, i);
+                    builder.add(pC4_1[0], pC4_1[1], pC4_1[2], pO4_1[0], pO4_1[1], pO4_1[2], 1, true, true, colorModeFlag, i);
+                    builder.add(pO4_1[0], pO4_1[1], pO4_1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
+                    builder.add(pC1_1[0], pC1_1[1], pC1_1[2], pC2_1[0], pC2_1[1], pC2_1[2], 1, true, true, colorModeFlag, i);
+                    builder.add(pC2_1[0], pC2_1[1], pC2_1[2], pC3_1[0], pC3_1[1], pC3_1[2], 1, true, true, colorModeFlag, i);
                 }
                 var _b = (0, nucleotide_1.getNucleotideBaseType)(unit, residueIndex), isPurine = _b.isPurine, isPyrimidine = _b.isPyrimidine;
                 if (isPurine) {
@@ -88,12 +89,12 @@ function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props,
                     if (idx.C1_1 !== -1 && idx.N9 !== -1) {
                         pos(idx.C1_1, pC1_1);
                         pos(idx.N9, pN9);
-                        builder.add(pN9[0], pN9[1], pN9[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, i);
+                        builder.add(pN9[0], pN9[1], pN9[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
                     }
                     else if (idx.N9 !== -1 && idx.trace !== -1) {
                         pos(idx.N9, pN9);
                         pos(idx.trace, pTrace);
-                        builder.add(pN9[0], pN9[1], pN9[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, i);
+                        builder.add(pN9[0], pN9[1], pN9[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
                     }
                     if ((0, nucleotide_1.hasPurinIndices)(idx)) {
                         pos(idx.N1, pN1);
@@ -106,16 +107,16 @@ function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props,
                         pos(idx.C8, pC8);
                         pos(idx.N9, pN9);
                         // base ring
-                        builder.add(pN9[0], pN9[1], pN9[2], pC8[0], pC8[1], pC8[2], 1, true, true, i);
-                        builder.add(pC8[0], pC8[1], pC8[2], pN7[0], pN7[1], pN7[2], 1, true, true, i);
-                        builder.add(pN7[0], pN7[1], pN7[2], pC5[0], pC5[1], pC5[2], 1, true, true, i);
-                        builder.add(pC5[0], pC5[1], pC5[2], pC6[0], pC6[1], pC6[2], 1, true, true, i);
-                        builder.add(pC6[0], pC6[1], pC6[2], pN1[0], pN1[1], pN1[2], 1, true, true, i);
-                        builder.add(pN1[0], pN1[1], pN1[2], pC2[0], pC2[1], pC2[2], 1, true, true, i);
-                        builder.add(pC2[0], pC2[1], pC2[2], pN3[0], pN3[1], pN3[2], 1, true, true, i);
-                        builder.add(pN3[0], pN3[1], pN3[2], pC4[0], pC4[1], pC4[2], 1, true, true, i);
-                        builder.add(pC4[0], pC4[1], pC4[2], pC5[0], pC5[1], pC5[2], 1, true, true, i);
-                        builder.add(pC4[0], pC4[1], pC4[2], pN9[0], pN9[1], pN9[2], 1, true, true, i);
+                        builder.add(pN9[0], pN9[1], pN9[2], pC8[0], pC8[1], pC8[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC8[0], pC8[1], pC8[2], pN7[0], pN7[1], pN7[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pN7[0], pN7[1], pN7[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC5[0], pC5[1], pC5[2], pC6[0], pC6[1], pC6[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC6[0], pC6[1], pC6[2], pN1[0], pN1[1], pN1[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pN1[0], pN1[1], pN1[2], pC2[0], pC2[1], pC2[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC2[0], pC2[1], pC2[2], pN3[0], pN3[1], pN3[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pN3[0], pN3[1], pN3[2], pC4[0], pC4[1], pC4[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC4[0], pC4[1], pC4[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC4[0], pC4[1], pC4[2], pN9[0], pN9[1], pN9[2], 1, true, true, colorModeFlag, i);
                     }
                 }
                 else if (isPyrimidine) {
@@ -123,12 +124,12 @@ function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props,
                     if (idx.C1_1 !== -1 && idx.N1 !== -1) {
                         pos(idx.N1, pN1);
                         pos(idx.C1_1, pC1_1);
-                        builder.add(pN1[0], pN1[1], pN1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, i);
+                        builder.add(pN1[0], pN1[1], pN1[2], pC1_1[0], pC1_1[1], pC1_1[2], 1, true, true, colorModeFlag, i);
                     }
                     else if (idx.N1 !== -1 && idx.trace !== -1) {
                         pos(idx.N1, pN1);
                         pos(idx.trace, pTrace);
-                        builder.add(pN1[0], pN1[1], pN1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, i);
+                        builder.add(pN1[0], pN1[1], pN1[2], pTrace[0], pTrace[1], pTrace[2], 1, true, true, colorModeFlag, i);
                     }
                     if ((0, nucleotide_1.hasPyrimidineIndices)(idx)) {
                         pos(idx.N1, pN1);
@@ -138,12 +139,12 @@ function createNucleotideAtomicBondImpostor(ctx, unit, structure, theme, props,
                         pos(idx.C5, pC5);
                         pos(idx.C6, pC6);
                         // base ring
-                        builder.add(pN1[0], pN1[1], pN1[2], pC6[0], pC6[1], pC6[2], 1, true, true, i);
-                        builder.add(pC6[0], pC6[1], pC6[2], pC5[0], pC5[1], pC5[2], 1, true, true, i);
-                        builder.add(pC5[0], pC5[1], pC5[2], pC4[0], pC4[1], pC4[2], 1, true, true, i);
-                        builder.add(pC4[0], pC4[1], pC4[2], pN3[0], pN3[1], pN3[2], 1, true, true, i);
-                        builder.add(pN3[0], pN3[1], pN3[2], pC2[0], pC2[1], pC2[2], 1, true, true, i);
-                        builder.add(pC2[0], pC2[1], pC2[2], pN1[0], pN1[1], pN1[2], 1, true, true, i);
+                        builder.add(pN1[0], pN1[1], pN1[2], pC6[0], pC6[1], pC6[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC6[0], pC6[1], pC6[2], pC5[0], pC5[1], pC5[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC5[0], pC5[1], pC5[2], pC4[0], pC4[1], pC4[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC4[0], pC4[1], pC4[2], pN3[0], pN3[1], pN3[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pN3[0], pN3[1], pN3[2], pC2[0], pC2[1], pC2[2], 1, true, true, colorModeFlag, i);
+                        builder.add(pC2[0], pC2[1], pC2[2], pN1[0], pN1[1], pN1[2], 1, true, true, colorModeFlag, i);
                     }
                 }
                 ++i;

package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-element.d.ts CHANGED Viewed

@@ -17,7 +17,7 @@ export declare const NucleotideAtomicElementParams: {
     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;
@@ -55,7 +55,7 @@ export declare function NucleotideAtomicElementVisual(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;
     clipPrimitive: PD.BooleanParam;
     approximate: PD.BooleanParam;

package/lib/commonjs/mol-repr/structure/visual/nucleotide-atomic-ring-fill.d.ts CHANGED Viewed

@@ -25,7 +25,7 @@ export declare const NucleotideAtomicRingFillParams: {
     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/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts CHANGED Viewed

@@ -27,7 +27,7 @@ export declare const NucleotideBlockParams: {
     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/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts CHANGED Viewed

@@ -30,7 +30,7 @@ export declare const NucleotideRingParams: {
     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/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts CHANGED Viewed

@@ -19,7 +19,7 @@ export declare const OrientationEllipsoidMeshParams: {
     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/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts CHANGED Viewed

@@ -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/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.js CHANGED Viewed

@@ -48,8 +48,8 @@ function createPolymerBackboneCylinderImpostor(ctx, unit, structure, theme, prop
         var isNucleicType = (0, types_1.isNucleic)(moleculeType);
         var shift = isNucleicType ? polymer_1.NucleicShift : polymer_1.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);
     };
     (0, backbone_1.eachPolymerBackboneLink)(unit, add);
     var c = builder.getCylinders();
@@ -61,7 +61,7 @@ function PolymerBackboneCylinderImpostorVisual(materialId) {
     return (0, units_visual_1.UnitsCylindersVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderImpostor,
-        createLocationIterator: polymer_1.PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return polymer_1.PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: polymer_1.getPolymerElementLoci,
         eachLocation: polymer_1.eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) { },
@@ -108,7 +108,7 @@ function PolymerBackboneCylinderMeshVisual(materialId) {
     return (0, units_visual_1.UnitsMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderMesh,
-        createLocationIterator: polymer_1.PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return polymer_1.PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: polymer_1.getPolymerElementLoci,
         eachLocation: polymer_1.eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

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

@@ -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/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.js CHANGED Viewed

@@ -49,7 +49,7 @@ function PolymerBackboneSphereImpostorVisual(materialId) {
     return (0, units_visual_1.UnitsSpheresVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerBackboneSphereParams),
         createGeometry: createPolymerBackboneSphereImpostor,
-        createLocationIterator: polymer_1.PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return polymer_1.PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: polymer_1.getPolymerElementLoci,
         eachLocation: polymer_1.eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) { },
@@ -85,7 +85,7 @@ function PolymerBackboneSphereMeshVisual(materialId) {
     return (0, units_visual_1.UnitsMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerBackboneSphereParams),
         createGeometry: createPolymerBackboneSphereMesh,
-        createLocationIterator: polymer_1.PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return polymer_1.PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: polymer_1.getPolymerElementLoci,
         eachLocation: polymer_1.eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

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

@@ -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/commonjs/mol-repr/structure/visual/polymer-direction-wedge.js CHANGED Viewed

@@ -76,7 +76,7 @@ function PolymerDirectionVisual(materialId) {
     return (0, units_visual_1.UnitsMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerDirectionParams),
         createGeometry: createPolymerDirectionWedgeMesh,
-        createLocationIterator: polymer_1.PolymerLocationIterator.fromGroup,
+        createLocationIterator: function (structureGroup) { return polymer_1.PolymerLocationIterator.fromGroup(structureGroup); },
         getLoci: polymer_1.getPolymerElementLoci,
         eachLocation: polymer_1.eachPolymerElement,
         setUpdateState: function (state, newProps, currentProps) {

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

@@ -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;