molstar 3.31.2 → 3.31.4

package/lib/extensions/meshes/mesh-extension.d.ts

@@ -40,18 +40,20 @@ declare const MeshlistStateObject_base: {
         description?: string | undefined;
     } | undefined): {
         id: import("../../mol-util/uuid").UUID;
-        /** Data type for `MeshlistStateObject` - list of meshes */
         type: PluginStateObject.TypeInfo;
+        /** Data type for `MeshlistStateObject` - list of meshes */
         label: string;
+        /** Data type for `MeshlistStateObject` - list of meshes */
         description?: string | undefined;
         data: MeshlistData;
     };
     type: PluginStateObject.TypeInfo;
     is(obj?: import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../mol-util/uuid").UUID;
-        /** Data type for `MeshlistStateObject` - list of meshes */
         type: PluginStateObject.TypeInfo;
+        /** Data type for `MeshlistStateObject` - list of meshes */
         label: string;
+        /** Data type for `MeshlistStateObject` - list of meshes */
         description?: string | undefined;
         data: MeshlistData;
     };

package/lib/extensions/meshes/mesh-streaming/behavior.d.ts

@@ -20,6 +20,7 @@ declare const MeshStreaming_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
+        /** Segments whose bounding box volume is above this value (relative to the overall bounding box) are considered as background segments */
         id: UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
@@ -28,6 +29,7 @@ declare const MeshStreaming_base: {
     };
     type: PluginStateObject.TypeInfo;
     is(obj?: import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
+        /** Segments whose bounding box volume is above this value (relative to the overall bounding box) are considered as background segments */
         id: UUID;
         type: PluginStateObject.TypeInfo;
         label: string;

package/lib/mol-canvas3d/canvas3d.js

@@ -59,7 +59,7 @@ export var Canvas3DParams = {
     cameraClipping: PD.Group({
         radius: PD.Numeric(100, { min: 0, max: 99, step: 1 }, { label: 'Clipping', description: 'How much of the scene to show.' }),
         far: PD.Boolean(true, { description: 'Hide scene in the distance' }),
-        minNear: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }, { description: 'Note, may cause performance issues rendering impostors when set too small and cause issues with outline rendering when too close to 0.' }),
+        minNear: PD.Numeric(5, { min: 0.1, max: 100, step: 0.1 }, { description: 'Note, may cause performance issues rendering impostors when set too small and cause issues with outline rendering when too close to 0.' }),
     }, { pivot: 'radius' }),
     viewport: PD.MappedStatic('canvas', {
         canvas: PD.Group({}),
@@ -777,6 +777,7 @@ var Canvas3D;
             },
             dispose: function () {
                 contextRestoredSub.unsubscribe();
+                cancelAnimationFrame(animationFrameHandle);
                 markBuffer = [];
                 scene.clear();
                 helper.debug.clear();

package/lib/mol-geo/geometry/cylinders/cylinders.d.ts

@@ -51,8 +51,8 @@ export declare namespace Cylinders {
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
-            /** Number of cylinders */
             roughness: number;
+            /** Number of cylinders */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/mol-geo/geometry/lines/lines.d.ts

@@ -44,7 +44,6 @@ export declare namespace Lines {
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
-            /** Number of lines */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/mol-geo/geometry/points/points.d.ts

@@ -43,7 +43,7 @@ export declare namespace Points {
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
-            roughness: number;
+            roughness: number; /** Number of vertices in the point cloud */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/mol-gl/shader/cylinders.vert.d.ts

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const cylinders_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec3 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\nattribute float aScale;\nattribute float aCap;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform float uIsOrtho;\nuniform vec3 uCameraDir;\n\nvoid main() {\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    mat4 modelTransform = uModel * aTransform;\n\n    vTransform = aTransform;\n    vStart = (modelTransform * vec4(aStart, 1.0)).xyz;\n    vEnd = (modelTransform * vec4(aEnd, 1.0)).xyz;\n    vSize = size * aScale;\n    vCap = aCap;\n\n    vModelPosition = (vStart + vEnd) * 0.5;\n    vec3 camDir = -mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 dir = vEnd - vStart;\n    // ensure cylinder 'dir' is pointing towards the camera\n    if(dot(camDir, dir) < 0.0) {\n        dir = -dir;\n    }\n\n    vec3 left = cross(camDir, dir);\n    vec3 up = cross(left, dir);\n    left = vSize * normalize(left);\n    up = vSize * normalize(up);\n\n    // move vertex in object-space from center to corner\n    vModelPosition += aMapping.x * dir + aMapping.y * left + aMapping.z * up;\n\n    vec4 mvPosition = uView * vec4(vModelPosition, 1.0);\n    vViewPosition = mvPosition.xyz;\n    gl_Position = uProjection * mvPosition;\n\n    mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping\n    gl_Position.z = (uProjection * mvPosition).z;\n\n    #include clip_instance\n}\n";
+export declare const cylinders_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec3 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\nattribute float aScale;\nattribute float aCap;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform float uIsOrtho;\nuniform vec3 uCameraDir;\n\nvoid main() {\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    mat4 modelTransform = uModel * aTransform;\n\n    vTransform = aTransform;\n    vStart = (modelTransform * vec4(aStart, 1.0)).xyz;\n    vEnd = (modelTransform * vec4(aEnd, 1.0)).xyz;\n    vSize = size * aScale;\n    vCap = aCap;\n\n    vModelPosition = (vStart + vEnd) * 0.5;\n    vec3 camDir = -mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 dir = vEnd - vStart;\n    // ensure cylinder 'dir' is pointing towards the camera\n    if(dot(camDir, dir) < 0.0) {\n        dir = -dir;\n    }\n\n    vec3 left = cross(camDir, dir);\n    vec3 up = cross(left, dir);\n    left = vSize * normalize(left);\n    up = vSize * normalize(up);\n\n    // move vertex in object-space from center to corner\n    vModelPosition += aMapping.x * dir + aMapping.y * left + aMapping.z * up;\n\n    vec4 mvPosition = uView * vec4(vModelPosition, 1.0);\n    vViewPosition = mvPosition.xyz;\n    gl_Position = uProjection * mvPosition;\n\n    if (gl_Position.z < -gl_Position.w) {\n        mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping\n        gl_Position.z = (uProjection * mvPosition).z;\n    }\n\n    #include clip_instance\n}\n";

package/lib/mol-gl/shader/cylinders.vert.js

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var cylinders_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec3 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\nattribute float aScale;\nattribute float aCap;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform float uIsOrtho;\nuniform vec3 uCameraDir;\n\nvoid main() {\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    mat4 modelTransform = uModel * aTransform;\n\n    vTransform = aTransform;\n    vStart = (modelTransform * vec4(aStart, 1.0)).xyz;\n    vEnd = (modelTransform * vec4(aEnd, 1.0)).xyz;\n    vSize = size * aScale;\n    vCap = aCap;\n\n    vModelPosition = (vStart + vEnd) * 0.5;\n    vec3 camDir = -mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 dir = vEnd - vStart;\n    // ensure cylinder 'dir' is pointing towards the camera\n    if(dot(camDir, dir) < 0.0) {\n        dir = -dir;\n    }\n\n    vec3 left = cross(camDir, dir);\n    vec3 up = cross(left, dir);\n    left = vSize * normalize(left);\n    up = vSize * normalize(up);\n\n    // move vertex in object-space from center to corner\n    vModelPosition += aMapping.x * dir + aMapping.y * left + aMapping.z * up;\n\n    vec4 mvPosition = uView * vec4(vModelPosition, 1.0);\n    vViewPosition = mvPosition.xyz;\n    gl_Position = uProjection * mvPosition;\n\n    mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping\n    gl_Position.z = (uProjection * mvPosition).z;\n\n    #include clip_instance\n}\n";
+export var cylinders_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec3 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\nattribute float aScale;\nattribute float aCap;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform float uIsOrtho;\nuniform vec3 uCameraDir;\n\nvoid main() {\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    mat4 modelTransform = uModel * aTransform;\n\n    vTransform = aTransform;\n    vStart = (modelTransform * vec4(aStart, 1.0)).xyz;\n    vEnd = (modelTransform * vec4(aEnd, 1.0)).xyz;\n    vSize = size * aScale;\n    vCap = aCap;\n\n    vModelPosition = (vStart + vEnd) * 0.5;\n    vec3 camDir = -mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 dir = vEnd - vStart;\n    // ensure cylinder 'dir' is pointing towards the camera\n    if(dot(camDir, dir) < 0.0) {\n        dir = -dir;\n    }\n\n    vec3 left = cross(camDir, dir);\n    vec3 up = cross(left, dir);\n    left = vSize * normalize(left);\n    up = vSize * normalize(up);\n\n    // move vertex in object-space from center to corner\n    vModelPosition += aMapping.x * dir + aMapping.y * left + aMapping.z * up;\n\n    vec4 mvPosition = uView * vec4(vModelPosition, 1.0);\n    vViewPosition = mvPosition.xyz;\n    gl_Position = uProjection * mvPosition;\n\n    if (gl_Position.z < -gl_Position.w) {\n        mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping\n        gl_Position.z = (uProjection * mvPosition).z;\n    }\n\n    #include clip_instance\n}\n";

package/lib/mol-gl/shader/spheres.vert.d.ts

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const spheres_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\nuniform mat4 uInvProjection;\n\nattribute vec3 aPosition;\nattribute vec2 aMapping;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\n#include matrix_scale\n\nconst mat4 D = mat4(\n    1.0, 0.0, 0.0, 0.0,\n    0.0, 1.0, 0.0, 0.0,\n    0.0, 0.0, 1.0, 0.0,\n    0.0, 0.0, 0.0, -1.0\n);\n\n/**\n * Compute point size and center using the technique described in:\n * \"GPU-Based Ray-Casting of Quadratic Surfaces\" http://dl.acm.org/citation.cfm?id=2386396\n * by Christian Sigg, Tim Weyrich, Mario Botsch, Markus Gross.\n */\nvoid quadraticProjection(const in float radius, const in vec3 position){\n    vec2 xbc, ybc;\n\n    mat4 T = mat4(\n        radius, 0.0, 0.0, 0.0,\n        0.0, radius, 0.0, 0.0,\n        0.0, 0.0, radius, 0.0,\n        position.x, position.y, position.z, 1.0\n    );\n\n    mat4 R = transpose4(uProjection * uModelView * aTransform * T);\n    float A = dot(R[3], D * R[3]);\n    float B = -2.0 * dot(R[0], D * R[3]);\n    float C = dot(R[0], D * R[0]);\n    xbc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    xbc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sx = abs(xbc[0] - xbc[1]) * 0.5;\n\n    A = dot(R[3], D * R[3]);\n    B = -2.0 * dot(R[1], D * R[3]);\n    C = dot(R[1], D * R[1]);\n    ybc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    ybc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sy = abs(ybc[0] - ybc[1]) * 0.5;\n\n    gl_Position.xy = vec2(0.5 * (xbc.x + xbc.y), 0.5 * (ybc.x + ybc.y));\n    gl_Position.xy -= aMapping * vec2(sx, sy);\n    gl_Position.xy *= gl_Position.w;\n}\n\n\nvoid main(void){\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    vRadius = size * matrixScale(uModelView);\n\n    vec4 position4 = vec4(aPosition, 1.0);\n    vec4 mvPosition = uModelView * aTransform * position4;\n\n    gl_Position = uProjection * vec4(mvPosition.xyz, 1.0);\n    quadraticProjection(size, aPosition);\n\n    vRadiusSq = vRadius * vRadius;\n    vec4 vPoint4 = uInvProjection * gl_Position;\n    vPoint = vPoint4.xyz / vPoint4.w;\n    vPointViewPosition = -mvPosition.xyz / mvPosition.w;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    mvPosition.z -= 2.0 * vRadius; // avoid clipping\n    gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;\n\n    #include clip_instance\n}\n";
+export declare const spheres_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\nuniform mat4 uInvProjection;\n\nattribute vec3 aPosition;\nattribute vec2 aMapping;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\n#include matrix_scale\n\nconst mat4 D = mat4(\n    1.0, 0.0, 0.0, 0.0,\n    0.0, 1.0, 0.0, 0.0,\n    0.0, 0.0, 1.0, 0.0,\n    0.0, 0.0, 0.0, -1.0\n);\n\n/**\n * Compute point size and center using the technique described in:\n * \"GPU-Based Ray-Casting of Quadratic Surfaces\" http://dl.acm.org/citation.cfm?id=2386396\n * by Christian Sigg, Tim Weyrich, Mario Botsch, Markus Gross.\n */\nvoid quadraticProjection(const in float radius, const in vec3 position){\n    vec2 xbc, ybc;\n\n    mat4 T = mat4(\n        radius, 0.0, 0.0, 0.0,\n        0.0, radius, 0.0, 0.0,\n        0.0, 0.0, radius, 0.0,\n        position.x, position.y, position.z, 1.0\n    );\n\n    mat4 R = transpose4(uProjection * uModelView * aTransform * T);\n    float A = dot(R[3], D * R[3]);\n    float B = -2.0 * dot(R[0], D * R[3]);\n    float C = dot(R[0], D * R[0]);\n    xbc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    xbc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sx = abs(xbc[0] - xbc[1]) * 0.5;\n\n    A = dot(R[3], D * R[3]);\n    B = -2.0 * dot(R[1], D * R[3]);\n    C = dot(R[1], D * R[1]);\n    ybc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    ybc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sy = abs(ybc[0] - ybc[1]) * 0.5;\n\n    gl_Position.xy = vec2(0.5 * (xbc.x + xbc.y), 0.5 * (ybc.x + ybc.y));\n    gl_Position.xy -= aMapping * vec2(sx, sy);\n    gl_Position.xy *= gl_Position.w;\n}\n\n\nvoid main(void){\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    vRadius = size * matrixScale(uModelView);\n\n    vec4 position4 = vec4(aPosition, 1.0);\n    vec4 mvPosition = uModelView * aTransform * position4;\n\n    gl_Position = uProjection * vec4(mvPosition.xyz, 1.0);\n    quadraticProjection(size, aPosition);\n\n    vRadiusSq = vRadius * vRadius;\n    vec4 vPoint4 = uInvProjection * gl_Position;\n    vPoint = vPoint4.xyz / vPoint4.w;\n    vPointViewPosition = -mvPosition.xyz / mvPosition.w;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    if (gl_Position.z < -gl_Position.w) {\n        mvPosition.z -= 2.0 * vRadius; // avoid clipping\n        gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;\n    }\n\n    #include clip_instance\n}\n";

package/lib/mol-gl/shader/spheres.vert.js

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var spheres_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\nuniform mat4 uInvProjection;\n\nattribute vec3 aPosition;\nattribute vec2 aMapping;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\n#include matrix_scale\n\nconst mat4 D = mat4(\n    1.0, 0.0, 0.0, 0.0,\n    0.0, 1.0, 0.0, 0.0,\n    0.0, 0.0, 1.0, 0.0,\n    0.0, 0.0, 0.0, -1.0\n);\n\n/**\n * Compute point size and center using the technique described in:\n * \"GPU-Based Ray-Casting of Quadratic Surfaces\" http://dl.acm.org/citation.cfm?id=2386396\n * by Christian Sigg, Tim Weyrich, Mario Botsch, Markus Gross.\n */\nvoid quadraticProjection(const in float radius, const in vec3 position){\n    vec2 xbc, ybc;\n\n    mat4 T = mat4(\n        radius, 0.0, 0.0, 0.0,\n        0.0, radius, 0.0, 0.0,\n        0.0, 0.0, radius, 0.0,\n        position.x, position.y, position.z, 1.0\n    );\n\n    mat4 R = transpose4(uProjection * uModelView * aTransform * T);\n    float A = dot(R[3], D * R[3]);\n    float B = -2.0 * dot(R[0], D * R[3]);\n    float C = dot(R[0], D * R[0]);\n    xbc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    xbc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sx = abs(xbc[0] - xbc[1]) * 0.5;\n\n    A = dot(R[3], D * R[3]);\n    B = -2.0 * dot(R[1], D * R[3]);\n    C = dot(R[1], D * R[1]);\n    ybc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    ybc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sy = abs(ybc[0] - ybc[1]) * 0.5;\n\n    gl_Position.xy = vec2(0.5 * (xbc.x + xbc.y), 0.5 * (ybc.x + ybc.y));\n    gl_Position.xy -= aMapping * vec2(sx, sy);\n    gl_Position.xy *= gl_Position.w;\n}\n\n\nvoid main(void){\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    vRadius = size * matrixScale(uModelView);\n\n    vec4 position4 = vec4(aPosition, 1.0);\n    vec4 mvPosition = uModelView * aTransform * position4;\n\n    gl_Position = uProjection * vec4(mvPosition.xyz, 1.0);\n    quadraticProjection(size, aPosition);\n\n    vRadiusSq = vRadius * vRadius;\n    vec4 vPoint4 = uInvProjection * gl_Position;\n    vPoint = vPoint4.xyz / vPoint4.w;\n    vPointViewPosition = -mvPosition.xyz / mvPosition.w;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    mvPosition.z -= 2.0 * vRadius; // avoid clipping\n    gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;\n\n    #include clip_instance\n}\n";
+export var spheres_vert = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include size_vert_params\n#include common_clip\n\nuniform mat4 uModelView;\nuniform mat4 uInvProjection;\n\nattribute vec3 aPosition;\nattribute vec2 aMapping;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\n#include matrix_scale\n\nconst mat4 D = mat4(\n    1.0, 0.0, 0.0, 0.0,\n    0.0, 1.0, 0.0, 0.0,\n    0.0, 0.0, 1.0, 0.0,\n    0.0, 0.0, 0.0, -1.0\n);\n\n/**\n * Compute point size and center using the technique described in:\n * \"GPU-Based Ray-Casting of Quadratic Surfaces\" http://dl.acm.org/citation.cfm?id=2386396\n * by Christian Sigg, Tim Weyrich, Mario Botsch, Markus Gross.\n */\nvoid quadraticProjection(const in float radius, const in vec3 position){\n    vec2 xbc, ybc;\n\n    mat4 T = mat4(\n        radius, 0.0, 0.0, 0.0,\n        0.0, radius, 0.0, 0.0,\n        0.0, 0.0, radius, 0.0,\n        position.x, position.y, position.z, 1.0\n    );\n\n    mat4 R = transpose4(uProjection * uModelView * aTransform * T);\n    float A = dot(R[3], D * R[3]);\n    float B = -2.0 * dot(R[0], D * R[3]);\n    float C = dot(R[0], D * R[0]);\n    xbc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    xbc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sx = abs(xbc[0] - xbc[1]) * 0.5;\n\n    A = dot(R[3], D * R[3]);\n    B = -2.0 * dot(R[1], D * R[3]);\n    C = dot(R[1], D * R[1]);\n    ybc[0] = (-B - sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    ybc[1] = (-B + sqrt(B * B - 4.0 * A * C)) / (2.0 * A);\n    float sy = abs(ybc[0] - ybc[1]) * 0.5;\n\n    gl_Position.xy = vec2(0.5 * (xbc.x + xbc.y), 0.5 * (ybc.x + ybc.y));\n    gl_Position.xy -= aMapping * vec2(sx, sy);\n    gl_Position.xy *= gl_Position.w;\n}\n\n\nvoid main(void){\n    #include assign_group\n    #include assign_color_varying\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_size\n\n    vRadius = size * matrixScale(uModelView);\n\n    vec4 position4 = vec4(aPosition, 1.0);\n    vec4 mvPosition = uModelView * aTransform * position4;\n\n    gl_Position = uProjection * vec4(mvPosition.xyz, 1.0);\n    quadraticProjection(size, aPosition);\n\n    vRadiusSq = vRadius * vRadius;\n    vec4 vPoint4 = uInvProjection * gl_Position;\n    vPoint = vPoint4.xyz / vPoint4.w;\n    vPointViewPosition = -mvPosition.xyz / mvPosition.w;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    if (gl_Position.z < -gl_Position.w) {\n        mvPosition.z -= 2.0 * vRadius; // avoid clipping\n        gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;\n    }\n\n    #include clip_instance\n}\n";

package/lib/mol-math/linear-algebra/matrix/principal-axes.js

@@ -19,7 +19,7 @@ var PrincipalAxes;
     PrincipalAxes.ofPositions = ofPositions;
     function calculateMomentsAxes(positions) {
         if (positions.length === 3) {
-            return Axes3D.create(Vec3.fromArray(Vec3(), positions, 0), Vec3.create(1, 0, 0), Vec3.create(0, 1, 0), Vec3.create(0, 1, 0));
+            return Axes3D.create(Vec3.fromArray(Vec3(), positions, 0), Vec3.create(1, 0, 0), Vec3.create(0, 1, 0), Vec3.create(0, 0, 1));
         }
         var points = Matrix.fromArray(positions, 3, positions.length / 3);
         var n = points.rows;

package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        label: string; /** Precision data the server can show. */
+        /** Precision data the server can show. */
+        label: string;
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,7 +23,6 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

package/lib/mol-plugin/context.js

@@ -355,6 +355,7 @@ var PluginContext = /** @class */ (function () {
             s.unsubscribe();
         }
         this.subs = [];
+        this.animationLoop.stop();
         this.commands.dispose();
         (_a = this.canvas3d) === null || _a === void 0 ? void 0 : _a.dispose();
         (_b = this.canvas3dContext) === null || _b === void 0 ? void 0 : _b.dispose(options);

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.31.2';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1676222248403);
+export var PLUGIN_VERSION = '3.31.4';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1677240729517);

package/lib/mol-plugin-ui/skin/base/base.scss

@@ -1,33 +1,33 @@
-
-@mixin user-select($select) {
-  -webkit-user-select: $select;
-     -moz-user-select: $select;
-      -ms-user-select: $select; // IE10+
-          user-select: $select;
-}
-
-.msp-plugin {
-    font-family: "Helvetica Neue", "Segoe UI", Helvetica, "Source Sans Pro", Arial, sans-serif;
-    font-size: 14px;
-    line-height: 1.42857143;
-
-    position: absolute;
-    left: 0;
-    top: 0;
-    right: 0;
-    bottom: 0;
-
-    @import 'variables';
-
-    @import "normalize";
-
-    @import 'layout';
-    @import 'ui';
-    @import 'logo';
-
-    .msp-plugin-content {
-        color: $font-color;
-    }
-
-    background: $default-background;
+
+@mixin user-select($select) {
+  -webkit-user-select: $select;
+     -moz-user-select: $select;
+      -ms-user-select: $select; // IE10+
+          user-select: $select;
+}
+
+.msp-plugin {
+    font-family: "Helvetica Neue", "Segoe UI", Helvetica, "Source Sans Pro", Arial, sans-serif;
+    font-size: 14px;
+    line-height: 1.42857143;
+
+    position: absolute;
+    left: 0;
+    top: 0;
+    right: 0;
+    bottom: 0;
+
+    @import 'variables';
+
+    @import "normalize";
+
+    @import 'layout';
+    @import 'ui';
+    @import 'logo';
+
+    .msp-plugin-content {
+        color: $font-color;
+    }
+
+    background: $default-background;
 }