molstar 2.3.3 → 2.3.5

package/lib/commonjs/mol-gl/renderer.d.ts

@@ -44,6 +44,7 @@ interface Renderer {
     setViewport: (x: number, y: number, width: number, height: number) => void;
     setTransparentBackground: (value: boolean) => void;
     setDrawingBufferSize: (width: number, height: number) => void;
+    setPixelRatio: (value: number) => void;
     dispose: () => void;
 }
 export declare const RendererParams: {
@@ -58,13 +59,13 @@ export declare const RendererParams: {
     selectStrength: PD.Numeric;
     markerPriority: PD.Select<number>;
     xrayEdgeFalloff: PD.Numeric;
-    style: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    style: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "flat"> | PD.NamedParams<PD.Normalize<unknown>, "metallic"> | PD.NamedParams<PD.Normalize<{
         lightIntensity: number;
         ambientIntensity: number;
         metalness: number;
         roughness: number;
         reflectivity: number;
-    }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "matte"> | PD.NamedParams<PD.Normalize<unknown>, "flat"> | PD.NamedParams<PD.Normalize<unknown>, "glossy"> | PD.NamedParams<PD.Normalize<unknown>, "metallic"> | PD.NamedParams<PD.Normalize<unknown>, "plastic">>;
+    }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "matte"> | PD.NamedParams<PD.Normalize<unknown>, "glossy"> | PD.NamedParams<PD.Normalize<unknown>, "plastic">>;
     clip: PD.Group<PD.Normalize<{
         variant: Clipping.Variant;
         objects: PD.Normalize<{

package/lib/commonjs/mol-gl/renderer.js

@@ -569,6 +569,9 @@ var Renderer;
                     mol_util_1.ValueCell.update(globalUniforms.uDrawingBufferSize, linear_algebra_1.Vec2.set(drawingBufferSize, width, height));
                 }
             },
+            setPixelRatio: function (value) {
+                mol_util_1.ValueCell.update(globalUniforms.uPixelRatio, value);
+            },
             props: p,
             get stats() {
                 return {

package/lib/commonjs/mol-gl/renderer.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-gl/shader/lines.vert.d.ts

@@ -5,4 +5,4 @@
  *
  * heavily based on code by WestLangley from https://github.com/WestLangley/three.js/blob/af28b2fb706ac109771ecad0a7447fad90ab3210/examples/js/lines/LineMaterial.js
  */
-export declare const lines_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec2 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\n\nvoid trimSegment(const in vec4 start, inout vec4 end) {\n    // trim end segment so it terminates between the camera plane and the near plane\n    // conservative estimate of the near plane\n    float a = uProjection[2][2];  // 3rd entry in 3rd column\n    float b = uProjection[3][2];  // 3rd entry in 4th column\n    float nearEstimate = -0.5 * b / a;\n    float alpha = (nearEstimate - start.z) / (end.z - start.z);\n    end.xyz = mix(start.xyz, end.xyz, alpha);\n}\n\nvoid main(){\n    float aspect = uViewport.z / uViewport.w;\n\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 modelView = uView * uModel * aTransform;\n\n    // camera space\n    vec4 start = modelView * vec4(aStart, 1.0);\n    vec4 end = modelView * vec4(aEnd, 1.0);\n\n    // assign position\n    vec4 position4 = vec4((aMapping.y < 0.5) ? aStart : aEnd, 1.0);\n    vec4 mvPosition = modelView * position4;\n    vViewPosition = mvPosition.xyz;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    // special case for perspective projection, and segments that terminate either in, or behind, the camera plane\n    // clearly the gpu firmware has a way of addressing this issue when projecting into ndc space\n    // but we need to perform ndc-space calculations in the shader, so we must address this issue directly\n    // perhaps there is a more elegant solution -- WestLangley\n    bool perspective = (uProjection[2][3] == -1.0); // 4th entry in the 3rd column\n    if (perspective) {\n        if (start.z < 0.0 && end.z >= 0.0) {\n            trimSegment(start, end);\n        } else if (end.z < 0.0 && start.z >= 0.0) {\n            trimSegment(end, start);\n        }\n    }\n\n    // clip space\n    vec4 clipStart = uProjection * start;\n    vec4 clipEnd = uProjection * end;\n\n    // ndc space\n    vec2 ndcStart = clipStart.xy / clipStart.w;\n    vec2 ndcEnd = clipEnd.xy / clipEnd.w;\n\n    // direction\n    vec2 dir = ndcEnd - ndcStart;\n\n    // account for clip-space aspect ratio\n    dir.x *= aspect;\n    dir = normalize(dir);\n\n    // perpendicular to dir\n    vec2 offset = vec2(dir.y, - dir.x);\n\n    // undo aspect ratio adjustment\n    dir.x /= aspect;\n    offset.x /= aspect;\n\n    // sign flip\n    if (aMapping.x < 0.0) offset *= -1.0;\n\n    // calculate linewidth\n    float linewidth;\n    #ifdef dLineSizeAttenuation\n        linewidth = size * uPixelRatio * ((uViewport.w / 2.0) / -start.z) * 5.0;\n    #else\n        linewidth = size * uPixelRatio;\n    #endif\n\n    // adjust for linewidth\n    offset *= linewidth;\n\n    // adjust for clip-space to screen-space conversion\n    offset /= uViewport.w;\n\n    // select end\n    vec4 clip = (aMapping.y < 0.5) ? clipStart : clipEnd;\n\n    // back to clip space\n    offset *= clip.w;\n    clip.xy += offset;\n    gl_Position = clip;\n\n    #include clip_instance\n}\n";
+export declare const lines_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec2 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\n\nvoid trimSegment(const in vec4 start, inout vec4 end) {\n    // trim end segment so it terminates between the camera plane and the near plane\n    // conservative estimate of the near plane\n    float a = uProjection[2][2];  // 3rd entry in 3rd column\n    float b = uProjection[3][2];  // 3rd entry in 4th column\n    float nearEstimate = -0.5 * b / a;\n    float alpha = (nearEstimate - start.z) / (end.z - start.z);\n    end.xyz = mix(start.xyz, end.xyz, alpha);\n}\n\nvoid main(){\n    float aspect = uViewport.z / uViewport.w;\n\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 modelView = uView * uModel * aTransform;\n\n    // camera space\n    vec4 start = modelView * vec4(aStart, 1.0);\n    vec4 end = modelView * vec4(aEnd, 1.0);\n\n    // assign position\n    vec4 position4 = vec4((aMapping.y < 0.5) ? aStart : aEnd, 1.0);\n    vec4 mvPosition = modelView * position4;\n    vViewPosition = mvPosition.xyz;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    // special case for perspective projection, and segments that terminate either in, or behind, the camera plane\n    // clearly the gpu firmware has a way of addressing this issue when projecting into ndc space\n    // but we need to perform ndc-space calculations in the shader, so we must address this issue directly\n    // perhaps there is a more elegant solution -- WestLangley\n    bool perspective = (uProjection[2][3] == -1.0); // 4th entry in the 3rd column\n    if (perspective) {\n        if (start.z < 0.0 && end.z >= 0.0) {\n            trimSegment(start, end);\n        } else if (end.z < 0.0 && start.z >= 0.0) {\n            trimSegment(end, start);\n        }\n    }\n\n    // clip space\n    vec4 clipStart = uProjection * start;\n    vec4 clipEnd = uProjection * end;\n\n    // ndc space\n    vec2 ndcStart = clipStart.xy / clipStart.w;\n    vec2 ndcEnd = clipEnd.xy / clipEnd.w;\n\n    // direction\n    vec2 dir = ndcEnd - ndcStart;\n\n    // account for clip-space aspect ratio\n    dir.x *= aspect;\n    dir = normalize(dir);\n\n    // perpendicular to dir\n    vec2 offset = vec2(dir.y, - dir.x);\n\n    // undo aspect ratio adjustment\n    dir.x /= aspect;\n    offset.x /= aspect;\n\n    // sign flip\n    if (aMapping.x < 0.0) offset *= -1.0;\n\n    // calculate linewidth\n    float linewidth;\n    #ifdef dLineSizeAttenuation\n        linewidth = size * uPixelRatio * ((uViewport.w / 2.0) / -start.z) * 5.0;\n    #else\n        linewidth = size * uPixelRatio;\n    #endif\n    linewidth = max(1.0, linewidth);\n\n    // adjust for linewidth\n    offset *= linewidth;\n\n    // adjust for clip-space to screen-space conversion\n    offset /= uViewport.w;\n\n    // select end\n    vec4 clip = (aMapping.y < 0.5) ? clipStart : clipEnd;\n\n    // back to clip space\n    offset *= clip.w;\n    clip.xy += offset;\n    gl_Position = clip;\n\n    #include clip_instance\n}\n";

package/lib/commonjs/mol-gl/shader/lines.vert.js

@@ -8,5 +8,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.lines_vert = void 0;
-exports.lines_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec2 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\n\nvoid trimSegment(const in vec4 start, inout vec4 end) {\n    // trim end segment so it terminates between the camera plane and the near plane\n    // conservative estimate of the near plane\n    float a = uProjection[2][2];  // 3rd entry in 3rd column\n    float b = uProjection[3][2];  // 3rd entry in 4th column\n    float nearEstimate = -0.5 * b / a;\n    float alpha = (nearEstimate - start.z) / (end.z - start.z);\n    end.xyz = mix(start.xyz, end.xyz, alpha);\n}\n\nvoid main(){\n    float aspect = uViewport.z / uViewport.w;\n\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 modelView = uView * uModel * aTransform;\n\n    // camera space\n    vec4 start = modelView * vec4(aStart, 1.0);\n    vec4 end = modelView * vec4(aEnd, 1.0);\n\n    // assign position\n    vec4 position4 = vec4((aMapping.y < 0.5) ? aStart : aEnd, 1.0);\n    vec4 mvPosition = modelView * position4;\n    vViewPosition = mvPosition.xyz;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    // special case for perspective projection, and segments that terminate either in, or behind, the camera plane\n    // clearly the gpu firmware has a way of addressing this issue when projecting into ndc space\n    // but we need to perform ndc-space calculations in the shader, so we must address this issue directly\n    // perhaps there is a more elegant solution -- WestLangley\n    bool perspective = (uProjection[2][3] == -1.0); // 4th entry in the 3rd column\n    if (perspective) {\n        if (start.z < 0.0 && end.z >= 0.0) {\n            trimSegment(start, end);\n        } else if (end.z < 0.0 && start.z >= 0.0) {\n            trimSegment(end, start);\n        }\n    }\n\n    // clip space\n    vec4 clipStart = uProjection * start;\n    vec4 clipEnd = uProjection * end;\n\n    // ndc space\n    vec2 ndcStart = clipStart.xy / clipStart.w;\n    vec2 ndcEnd = clipEnd.xy / clipEnd.w;\n\n    // direction\n    vec2 dir = ndcEnd - ndcStart;\n\n    // account for clip-space aspect ratio\n    dir.x *= aspect;\n    dir = normalize(dir);\n\n    // perpendicular to dir\n    vec2 offset = vec2(dir.y, - dir.x);\n\n    // undo aspect ratio adjustment\n    dir.x /= aspect;\n    offset.x /= aspect;\n\n    // sign flip\n    if (aMapping.x < 0.0) offset *= -1.0;\n\n    // calculate linewidth\n    float linewidth;\n    #ifdef dLineSizeAttenuation\n        linewidth = size * uPixelRatio * ((uViewport.w / 2.0) / -start.z) * 5.0;\n    #else\n        linewidth = size * uPixelRatio;\n    #endif\n\n    // adjust for linewidth\n    offset *= linewidth;\n\n    // adjust for clip-space to screen-space conversion\n    offset /= uViewport.w;\n\n    // select end\n    vec4 clip = (aMapping.y < 0.5) ? clipStart : clipEnd;\n\n    // back to clip space\n    offset *= clip.w;\n    clip.xy += offset;\n    gl_Position = clip;\n\n    #include clip_instance\n}\n";
+exports.lines_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\n\nattribute vec2 aMapping;\nattribute vec3 aStart;\nattribute vec3 aEnd;\n\nvoid trimSegment(const in vec4 start, inout vec4 end) {\n    // trim end segment so it terminates between the camera plane and the near plane\n    // conservative estimate of the near plane\n    float a = uProjection[2][2];  // 3rd entry in 3rd column\n    float b = uProjection[3][2];  // 3rd entry in 4th column\n    float nearEstimate = -0.5 * b / a;\n    float alpha = (nearEstimate - start.z) / (end.z - start.z);\n    end.xyz = mix(start.xyz, end.xyz, alpha);\n}\n\nvoid main(){\n    float aspect = uViewport.z / uViewport.w;\n\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 modelView = uView * uModel * aTransform;\n\n    // camera space\n    vec4 start = modelView * vec4(aStart, 1.0);\n    vec4 end = modelView * vec4(aEnd, 1.0);\n\n    // assign position\n    vec4 position4 = vec4((aMapping.y < 0.5) ? aStart : aEnd, 1.0);\n    vec4 mvPosition = modelView * position4;\n    vViewPosition = mvPosition.xyz;\n\n    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader\n\n    // special case for perspective projection, and segments that terminate either in, or behind, the camera plane\n    // clearly the gpu firmware has a way of addressing this issue when projecting into ndc space\n    // but we need to perform ndc-space calculations in the shader, so we must address this issue directly\n    // perhaps there is a more elegant solution -- WestLangley\n    bool perspective = (uProjection[2][3] == -1.0); // 4th entry in the 3rd column\n    if (perspective) {\n        if (start.z < 0.0 && end.z >= 0.0) {\n            trimSegment(start, end);\n        } else if (end.z < 0.0 && start.z >= 0.0) {\n            trimSegment(end, start);\n        }\n    }\n\n    // clip space\n    vec4 clipStart = uProjection * start;\n    vec4 clipEnd = uProjection * end;\n\n    // ndc space\n    vec2 ndcStart = clipStart.xy / clipStart.w;\n    vec2 ndcEnd = clipEnd.xy / clipEnd.w;\n\n    // direction\n    vec2 dir = ndcEnd - ndcStart;\n\n    // account for clip-space aspect ratio\n    dir.x *= aspect;\n    dir = normalize(dir);\n\n    // perpendicular to dir\n    vec2 offset = vec2(dir.y, - dir.x);\n\n    // undo aspect ratio adjustment\n    dir.x /= aspect;\n    offset.x /= aspect;\n\n    // sign flip\n    if (aMapping.x < 0.0) offset *= -1.0;\n\n    // calculate linewidth\n    float linewidth;\n    #ifdef dLineSizeAttenuation\n        linewidth = size * uPixelRatio * ((uViewport.w / 2.0) / -start.z) * 5.0;\n    #else\n        linewidth = size * uPixelRatio;\n    #endif\n    linewidth = max(1.0, linewidth);\n\n    // adjust for linewidth\n    offset *= linewidth;\n\n    // adjust for clip-space to screen-space conversion\n    offset /= uViewport.w;\n\n    // select end\n    vec4 clip = (aMapping.y < 0.5) ? clipStart : clipEnd;\n\n    // back to clip space\n    offset *= clip.w;\n    clip.xy += offset;\n    gl_Position = clip;\n\n    #include clip_instance\n}\n";
 //# sourceMappingURL=lines.vert.js.map

package/lib/commonjs/mol-gl/shader/lines.vert.js.map

@@ -1 +1 @@
-{"version":3,"file":"lines.vert.js","sourceRoot":"","sources":["../../../../src/mol-gl/shader/lines.vert.ts"],"names":[],"mappings":";AAAA;;;;;;GAMG;;;AAEU,QAAA,UAAU,GAAG,61GAoHzB,CAAC"}
+{"version":3,"file":"lines.vert.js","sourceRoot":"","sources":["../../../../src/mol-gl/shader/lines.vert.ts"],"names":[],"mappings":";AAAA;;;;;;GAMG;;;AAEU,QAAA,UAAU,GAAG,m4GAqHzB,CAAC"}

package/lib/commonjs/mol-gl/shader/points.vert.d.ts

@@ -3,4 +3,4 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const points_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute vec3 aPosition;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\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_position\n    #include assign_size\n\n    #ifdef dPointSizeAttenuation\n        gl_PointSize = size * uPixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 5.0;\n    #else\n        gl_PointSize = size * uPixelRatio;\n    #endif\n\n    gl_Position = uProjection * mvPosition;\n\n    #include clip_instance\n}\n";
+export declare const points_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute vec3 aPosition;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\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_position\n    #include assign_size\n\n    #ifdef dPointSizeAttenuation\n        gl_PointSize = size * uPixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 5.0;\n    #else\n        gl_PointSize = size * uPixelRatio;\n    #endif\n    gl_PointSize = max(1.0, gl_PointSize);\n\n    gl_Position = uProjection * mvPosition;\n\n    #include clip_instance\n}\n";

package/lib/commonjs/mol-gl/shader/points.vert.js

@@ -6,5 +6,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.points_vert = void 0;
-exports.points_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute vec3 aPosition;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\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_position\n    #include assign_size\n\n    #ifdef dPointSizeAttenuation\n        gl_PointSize = size * uPixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 5.0;\n    #else\n        gl_PointSize = size * uPixelRatio;\n    #endif\n\n    gl_Position = uProjection * mvPosition;\n\n    #include clip_instance\n}\n";
+exports.points_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 float uPixelRatio;\nuniform vec4 uViewport;\n\nattribute vec3 aPosition;\nattribute mat4 aTransform;\nattribute float aInstance;\nattribute float aGroup;\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_position\n    #include assign_size\n\n    #ifdef dPointSizeAttenuation\n        gl_PointSize = size * uPixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 5.0;\n    #else\n        gl_PointSize = size * uPixelRatio;\n    #endif\n    gl_PointSize = max(1.0, gl_PointSize);\n\n    gl_Position = uProjection * mvPosition;\n\n    #include clip_instance\n}\n";
 //# sourceMappingURL=points.vert.js.map

package/lib/commonjs/mol-gl/shader/points.vert.js.map

@@ -1 +1 @@
-{"version":3,"file":"points.vert.js","sourceRoot":"","sources":["../../../../src/mol-gl/shader/points.vert.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAEU,QAAA,WAAW,GAAG,i1BAqC1B,CAAC"}
+{"version":3,"file":"points.vert.js","sourceRoot":"","sources":["../../../../src/mol-gl/shader/points.vert.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAEU,QAAA,WAAW,GAAG,63BAsC1B,CAAC"}

package/lib/commonjs/mol-gl/webgl/context.d.ts

@@ -17,7 +17,7 @@ import { ComputeRenderable } from '../renderable';
 export declare function getGLContext(canvas: HTMLCanvasElement, attribs?: WebGLContextAttributes & {
     preferWebGl1?: boolean;
 }): GLRenderingContext | null;
-export declare function getErrorDescription(gl: GLRenderingContext, error: number): "no error" | "invalid enum" | "invalid value" | "invalid operation" | "invalid framebuffer operation" | "out of memory" | "context lost" | "unknown error";
+export declare function getErrorDescription(gl: GLRenderingContext, error: number): "context lost" | "no error" | "invalid enum" | "invalid value" | "invalid operation" | "invalid framebuffer operation" | "out of memory" | "unknown error";
 export declare function checkError(gl: GLRenderingContext): void;
 export declare function readPixels(gl: GLRenderingContext, x: number, y: number, width: number, height: number, buffer: Uint8Array | Float32Array | Int32Array): void;
 declare function createStats(): {

package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts

@@ -121,7 +121,7 @@ export declare const BIRD_Schema: {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Schema.Aliased<"polymer" | "branched" | "non-polymer" | "polymer-like">;
+        type: Schema.Aliased<"non-polymer" | "polymer" | "branched" | "polymer-like">;
         /**
          * Additional details about this entity.
          */
@@ -241,7 +241,7 @@ export declare const BIRD_Schema: {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -327,7 +327,7 @@ export declare const BIRD_Schema: {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     };
     /**
      * Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about
@@ -348,7 +348,7 @@ export declare const BIRD_Schema: {
         /**
          * The type of the polymer.
          */
-        type: Schema.Aliased<"oligosaccharide" | "peptide-like" | "nucleic-acid-like" | "polysaccharide-like">;
+        type: Schema.Aliased<"peptide-like" | "oligosaccharide" | "nucleic-acid-like" | "polysaccharide-like">;
         /**
          * The database code for this source information
          */
@@ -479,7 +479,7 @@ export declare const BIRD_Schema: {
         /**
          * An identifier for the wwPDB site creating or modifying the molecule.
          */
-        processing_site: Schema.Aliased<"PDBe" | "RCSB" | "BMRB" | "PDBJ" | "PDBC">;
+        processing_site: Schema.Aliased<"RCSB" | "BMRB" | "PDBJ" | "PDBC" | "PDBe">;
         /**
          * The action associated with this audit record.
          */

package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts

@@ -93,7 +93,7 @@ export declare const CCD_Schema: {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other">;
         /**
          * Synonym list for the component.
          */
@@ -310,7 +310,7 @@ export declare const CCD_Schema: {
          * bond associated with the specified atoms, expressed as a bond
          * order.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         /**
          * Ordinal index for the component bond list.
          */

package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts

@@ -10,12 +10,12 @@ export declare const DensityServer_Header_Schema: {
         server_version: Schema.Str;
         datetime_utc: Schema.Str;
         guid: Schema.Str;
-        is_empty: Schema.Aliased<"y" | "no" | "n" | "yes">;
-        has_error: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        is_empty: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        has_error: Schema.Aliased<"no" | "n" | "yes" | "y">;
         error: Schema.Str;
         query_source_id: Schema.Str;
-        query_type: Schema.Aliased<"box" | "cell">;
-        query_box_type: Schema.Aliased<"cartesian" | "fractional">;
+        query_type: Schema.Aliased<"cell" | "box">;
+        query_box_type: Schema.Aliased<"fractional" | "cartesian">;
         query_box_a: Schema.Tensor;
         query_box_b: Schema.Tensor;
     };

package/lib/commonjs/mol-io/reader/cif/schema/mmcif-extras.d.ts

@@ -21,18 +21,18 @@ export declare const mmCIF_chemCompBond_schema: {
     atom_id_1: Column.Schema.Str;
     atom_id_2: Column.Schema.Str;
     comp_id: Column.Schema.Str;
-    value_order: Column.Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+    value_order: Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     pdbx_ordinal: Column.Schema.Int;
     pdbx_stereo_config: Column.Schema.Aliased<"E" | "Z" | "N">;
     pdbx_aromatic_flag: Column.Schema.Aliased<"N" | "Y">;
 };
 /** Has `type` extended with 'Ion' and 'Lipid' */
 export declare const mmCIF_chemComp_schema: {
-    type: Column.Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+    type: Column.Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
     formula: Column.Schema.Str;
     formula_weight: Column.Schema.Float;
     id: Column.Schema.Str;
-    mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+    mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
     name: Column.Schema.Str;
     pdbx_synonyms: Column.Schema.List<string>;
 };

package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts

@@ -478,7 +478,7 @@ export declare const mmCIF_Schema: {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * The full name of the component.
          */
@@ -489,7 +489,7 @@ export declare const mmCIF_Schema: {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other">;
         /**
          * Synonym list for the component.
          */
@@ -526,7 +526,7 @@ export declare const mmCIF_Schema: {
          * bond associated with the specified atoms, expressed as a bond
          * order.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         /**
          * Ordinal index for the component bond list.
          */
@@ -670,7 +670,7 @@ export declare const mmCIF_Schema: {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Schema.Aliased<"EMDB" | "PDB" | "CAS" | "CSD" | "ICSD" | "MDF" | "NDB" | "NBS" | "PDF" | "RCSB" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
+        database_id: Schema.Aliased<"CAS" | "CSD" | "EMDB" | "ICSD" | "MDF" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -746,7 +746,7 @@ export declare const mmCIF_Schema: {
          * Water entities are not expected to have corresponding
          * entries in the ENTITY category.
          */
-        type: Schema.Aliased<"polymer" | "water" | "branched" | "non-polymer" | "macrolide">;
+        type: Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         /**
          * A description of the entity.
          *
@@ -786,12 +786,12 @@ export declare const mmCIF_Schema: {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_linkage: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_monomer: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * The type of the polymer.
          */
@@ -885,7 +885,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -1420,7 +1420,7 @@ export declare const mmCIF_Schema: {
          * those that are given in the data block (in which case the value
          * of code is 'generate').
          */
-        code: Schema.Aliased<"generate" | "given">;
+        code: Schema.Aliased<"given" | "generate">;
         /**
          * A description of special aspects of the noncrystallographic
          * symmetry operator.
@@ -1886,7 +1886,7 @@ export declare const mmCIF_Schema: {
         /**
          * The identifying content type of the related entry.
          */
-        content_type: Schema.Aliased<"split" | "other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "re-refinement" | "complete structure" | "unspecified">;
+        content_type: Schema.Aliased<"other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "split" | "re-refinement" | "complete structure" | "unspecified">;
     };
     /**
      * The PDBX_ENTITY_NONPOLY category provides a mapping between
@@ -2218,7 +2218,7 @@ export declare const mmCIF_Schema: {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Schema.Aliased<"polymer" | "branched" | "non-polymer" | "polymer-like">;
+        type: Schema.Aliased<"non-polymer" | "polymer" | "branched" | "polymer-like">;
         /**
          * Additional details about this entity.
          */
@@ -2313,7 +2313,7 @@ export declare const mmCIF_Schema: {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -2399,7 +2399,7 @@ export declare const mmCIF_Schema: {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     };
     /**
      * Data items in the PDBX_MOLECULE category identify reference molecules
@@ -2660,7 +2660,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2748,7 +2748,7 @@ export declare const mmCIF_Schema: {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     };
     /**
      * Data items in the PDBX_ENTITY_BRANCH category specify the list
@@ -2779,7 +2779,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3083,7 +3083,7 @@ export declare const mmCIF_Schema: {
         /**
          * The primitive object used to model this segment.
          */
-        model_object_primitive: Schema.Aliased<"sphere" | "gaussian" | "other" | "atomistic">;
+        model_object_primitive: Schema.Aliased<"other" | "atomistic" | "sphere" | "gaussian">;
         /**
          * The identifier for the starting structural model.
          * This data item is a pointer to _ihm_starting_model_details.starting_model_id
@@ -3343,11 +3343,11 @@ export declare const mmCIF_Schema: {
         /**
          * The type of post modeling analysis being carried out.
          */
-        type: Schema.Aliased<"none" | "other" | "filter" | "cluster" | "rescore" | "validation">;
+        type: Schema.Aliased<"filter" | "other" | "cluster" | "rescore" | "validation" | "none">;
         /**
          * The parameter/feature used in the post modeling analysis.
          */
-        feature: Schema.Aliased<"none" | "other" | "energy/score" | "RMSD" | "dRMSD">;
+        feature: Schema.Aliased<"other" | "none" | "energy/score" | "RMSD" | "dRMSD">;
         /**
          * The number of models at the beginning of the post processing step.
          */
@@ -3566,7 +3566,7 @@ export declare const mmCIF_Schema: {
         /**
          * The application / utilization of the dataset group in modeling.
          */
-        application: Schema.Aliased<"representation" | "other" | "filter" | "validation" | "restraint" | "sampling">;
+        application: Schema.Aliased<"filter" | "other" | "validation" | "restraint" | "representation" | "sampling">;
         /**
          * Additional details regarding the dataset group.
          */
@@ -4591,11 +4591,11 @@ export declare const mmCIF_Schema: {
         /**
          * The type of feature.
          */
-        feature_type: Schema.Aliased<"ligand" | "residue" | "atom" | "residue range" | "pseudo site">;
+        feature_type: Schema.Aliased<"atom" | "residue" | "residue range" | "ligand" | "pseudo site">;
         /**
          * The type of entity.
          */
-        entity_type: Schema.Aliased<"polymer" | "water" | "non-polymer" | "other">;
+        entity_type: Schema.Aliased<"non-polymer" | "other" | "polymer" | "water">;
     };
     /**
      * Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions

package/lib/commonjs/mol-io/reader/ply/schema.d.ts

@@ -24,7 +24,7 @@ export declare const PlyTypeByteLength: {
 };
 export declare type PlyType = keyof typeof PlyTypeByteLength;
 export declare const PlyTypes: Set<string>;
-export declare function PlyType(str: string): "uint8" | "float32" | "ushort" | "float" | "int" | "int32" | "uint32" | "uint16" | "char" | "double" | "int8" | "int16" | "uchar" | "short" | "uint" | "float64";
+export declare function PlyType(str: string): "int" | "float" | "ushort" | "float32" | "int32" | "uint32" | "uint16" | "char" | "uchar" | "short" | "uint" | "double" | "int8" | "uint8" | "int16" | "float64";
 export interface PlyFile {
     readonly comments: ReadonlyArray<string>;
     readonly elementNames: ReadonlyArray<string>;

package/lib/commonjs/mol-math/linear-algebra/3d/vec3.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -150,6 +150,8 @@ declare namespace Vec3 {
     function isZero(v: Vec3): boolean;
     /** Project `point` onto `vector` starting from `origin` */
     function projectPointOnVector(out: Vec3, point: Vec3, vector: Vec3, origin: Vec3): Vec3;
+    /** Project `point` onto `plane` defined by `normal` starting from `origin` */
+    function projectPointOnPlane(out: Vec3, point: Vec3, normal: Vec3, origin: Vec3): Vec3;
     function projectOnVector(out: Vec3, p: Vec3, vector: Vec3): Vec3;
     function projectOnPlane(out: Vec3, p: Vec3, normal: Vec3): Vec3;
     /** Get a vector that is similar to `b` but orthogonal to `a` */