molstar 3.0.0 → 3.2.0

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

@@ -48,8 +48,8 @@ export declare namespace Cylinders {
         alpha: PD.Numeric;
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
-            metalness: number; /** Number of cylinders */
-            roughness: number;
+            metalness: number;
+            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/renderer.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,7 +37,7 @@ export declare const enum MarkingType {
 interface Renderer {
     readonly stats: RendererStats;
     readonly props: Readonly<RendererProps>;
-    clear: (toBackgroundColor: boolean) => void;
+    clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void;
     clearDepth: () => void;
     update: (camera: ICamera) => void;
     renderPick: (group: Scene.Group, camera: ICamera, variant: GraphicsRenderVariant, depthTexture: Texture | null, pickType: PickType) => void;

package/lib/mol-gl/renderer.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -379,12 +379,12 @@ var Renderer;
             }
         };
         return {
-            clear: function (toBackgroundColor) {
+            clear: function (toBackgroundColor, ignoreTransparentBackground) {
                 state.enable(gl.SCISSOR_TEST);
                 state.enable(gl.DEPTH_TEST);
                 state.colorMask(true, true, true, true);
                 state.depthMask(true);
-                if (transparentBackground) {
+                if (transparentBackground && !ignoreTransparentBackground) {
                     state.clearColor(0, 0, 0, 0);
                 }
                 else if (toBackgroundColor) {

package/lib/mol-gl/shader/chunks/apply-light-color.glsl.d.ts

@@ -1,9 +1,9 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
  * adapted from three.js (https://github.com/mrdoob/three.js/)
  * which under the MIT License, Copyright © 2010-2021 three.js authors
  */
-export declare const apply_light_color = "\n#ifdef bumpEnabled\n    if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {\n        vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);\n        #ifdef enabledFragDepth\n            if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {\n                normal = bumpNormal;\n            }\n        #else\n            normal = bumpNormal;\n        #endif\n    }\n#endif\n\nvec4 color = material;\n\nReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));\n\nPhysicalMaterial physicalMaterial;\nphysicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);\n#ifdef enabledFragDepth\n    physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);\n#else\n    vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));\n    float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);\n    physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);\n#endif\nphysicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);\nphysicalMaterial.specularF90 = 1.0;\n\nGeometricContext geometry;\ngeometry.position = -vViewPosition;\ngeometry.normal = normal;\ngeometry.viewDir = normalize(vViewPosition);\n\nIncidentLight directLight;\n#pragma unroll_loop_start\nfor (int i = 0; i < dLightCount; ++i) {\n    directLight.direction = uLightDirection[i];\n    directLight.color = uLightColor[i] * PI; // * PI for punctual light\n    RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);\n}\n#pragma unroll_loop_end\n\nvec3 irradiance = uAmbientColor * PI; // * PI for punctual light\nRE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);\n\n// indirect specular only metals\nvec3 radiance = uAmbientColor * metalness;\nvec3 iblIrradiance = uAmbientColor * metalness;\nvec3 clearcoatRadiance = vec3(0.0);\nRE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);\n\nvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;\n\ngl_FragColor = vec4(outgoingLight, color.a);\n\n#ifdef dXrayShaded\n    gl_FragColor.a *= 1.0 - pow(abs(dot(normal, vec3(0.0, 0.0, 1.0))), uXrayEdgeFalloff);\n#endif\n";
+export declare const apply_light_color = "\n#ifdef dIgnoreLight\n    gl_FragColor = material;\n#else\n    #ifdef bumpEnabled\n        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {\n            vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);\n            #ifdef enabledFragDepth\n                if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {\n                    normal = bumpNormal;\n                }\n            #else\n                normal = bumpNormal;\n            #endif\n        }\n    #endif\n\n    vec4 color = material;\n\n    ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));\n\n    PhysicalMaterial physicalMaterial;\n    physicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);\n    #ifdef enabledFragDepth\n        physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);\n    #else\n        vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));\n        float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);\n        physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);\n    #endif\n    physicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);\n    physicalMaterial.specularF90 = 1.0;\n\n    GeometricContext geometry;\n    geometry.position = -vViewPosition;\n    geometry.normal = normal;\n    geometry.viewDir = normalize(vViewPosition);\n\n    IncidentLight directLight;\n    #pragma unroll_loop_start\n    for (int i = 0; i < dLightCount; ++i) {\n        directLight.direction = uLightDirection[i];\n        directLight.color = uLightColor[i] * PI; // * PI for punctual light\n        RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);\n    }\n    #pragma unroll_loop_end\n\n    vec3 irradiance = uAmbientColor * PI; // * PI for punctual light\n    RE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);\n\n    // indirect specular only metals\n    vec3 radiance = uAmbientColor * metalness;\n    vec3 iblIrradiance = uAmbientColor * metalness;\n    vec3 clearcoatRadiance = vec3(0.0);\n    RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);\n\n    vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;\n\n    gl_FragColor = vec4(outgoingLight, color.a);\n#endif\n\n#ifdef dXrayShaded\n    gl_FragColor.a *= 1.0 - pow(abs(dot(normal, vec3(0.0, 0.0, 1.0))), uXrayEdgeFalloff);\n#endif\n";

package/lib/mol-gl/shader/chunks/apply-light-color.glsl.js

@@ -1,10 +1,10 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
  * adapted from three.js (https://github.com/mrdoob/three.js/)
  * which under the MIT License, Copyright © 2010-2021 three.js authors
  */
-export var apply_light_color = "\n#ifdef bumpEnabled\n    if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {\n        vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);\n        #ifdef enabledFragDepth\n            if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {\n                normal = bumpNormal;\n            }\n        #else\n            normal = bumpNormal;\n        #endif\n    }\n#endif\n\nvec4 color = material;\n\nReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));\n\nPhysicalMaterial physicalMaterial;\nphysicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);\n#ifdef enabledFragDepth\n    physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);\n#else\n    vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));\n    float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);\n    physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);\n#endif\nphysicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);\nphysicalMaterial.specularF90 = 1.0;\n\nGeometricContext geometry;\ngeometry.position = -vViewPosition;\ngeometry.normal = normal;\ngeometry.viewDir = normalize(vViewPosition);\n\nIncidentLight directLight;\n#pragma unroll_loop_start\nfor (int i = 0; i < dLightCount; ++i) {\n    directLight.direction = uLightDirection[i];\n    directLight.color = uLightColor[i] * PI; // * PI for punctual light\n    RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);\n}\n#pragma unroll_loop_end\n\nvec3 irradiance = uAmbientColor * PI; // * PI for punctual light\nRE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);\n\n// indirect specular only metals\nvec3 radiance = uAmbientColor * metalness;\nvec3 iblIrradiance = uAmbientColor * metalness;\nvec3 clearcoatRadiance = vec3(0.0);\nRE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);\n\nvec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;\n\ngl_FragColor = vec4(outgoingLight, color.a);\n\n#ifdef dXrayShaded\n    gl_FragColor.a *= 1.0 - pow(abs(dot(normal, vec3(0.0, 0.0, 1.0))), uXrayEdgeFalloff);\n#endif\n";
+export var apply_light_color = "\n#ifdef dIgnoreLight\n    gl_FragColor = material;\n#else\n    #ifdef bumpEnabled\n        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {\n            vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);\n            #ifdef enabledFragDepth\n                if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {\n                    normal = bumpNormal;\n                }\n            #else\n                normal = bumpNormal;\n            #endif\n        }\n    #endif\n\n    vec4 color = material;\n\n    ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));\n\n    PhysicalMaterial physicalMaterial;\n    physicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);\n    #ifdef enabledFragDepth\n        physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);\n    #else\n        vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));\n        float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);\n        physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);\n    #endif\n    physicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);\n    physicalMaterial.specularF90 = 1.0;\n\n    GeometricContext geometry;\n    geometry.position = -vViewPosition;\n    geometry.normal = normal;\n    geometry.viewDir = normalize(vViewPosition);\n\n    IncidentLight directLight;\n    #pragma unroll_loop_start\n    for (int i = 0; i < dLightCount; ++i) {\n        directLight.direction = uLightDirection[i];\n        directLight.color = uLightColor[i] * PI; // * PI for punctual light\n        RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);\n    }\n    #pragma unroll_loop_end\n\n    vec3 irradiance = uAmbientColor * PI; // * PI for punctual light\n    RE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);\n\n    // indirect specular only metals\n    vec3 radiance = uAmbientColor * metalness;\n    vec3 iblIrradiance = uAmbientColor * metalness;\n    vec3 clearcoatRadiance = vec3(0.0);\n    RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);\n\n    vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;\n\n    gl_FragColor = vec4(outgoingLight, color.a);\n#endif\n\n#ifdef dXrayShaded\n    gl_FragColor.a *= 1.0 - pow(abs(dot(normal, vec3(0.0, 0.0, 1.0))), uXrayEdgeFalloff);\n#endif\n";
 //# sourceMappingURL=apply-light-color.glsl.js.map

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

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const cylinders_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\nuniform mat4 uView;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform vec3 uCameraDir;\nuniform vec3 uCameraPosition;\nuniform mat4 uInvView;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\n// adapted from https://www.shadertoy.com/view/4lcSRn\n// The MIT License, Copyright 2016 Inigo Quilez\nbool CylinderImpostor(\n    in vec3 rayOrigin, in vec3 rayDir,\n    in vec3 start, in vec3 end, in float radius,\n    out vec4 intersection, out bool interior\n){\n    vec3 ba = end - start;\n    vec3 oc = rayOrigin - start;\n\n    float baba = dot(ba, ba);\n    float bard = dot(ba, rayDir);\n    float baoc = dot(ba, oc);\n\n    float k2 = baba - bard*bard;\n    float k1 = baba * dot(oc, rayDir) - baoc * bard;\n    float k0 = baba * dot(oc, oc) - baoc * baoc - radius * radius * baba;\n\n    float h = k1 * k1 - k2 * k0;\n    if (h < 0.0) return false;\n\n    bool topCap = (vCap > 0.9 && vCap < 1.1) || vCap >= 2.9;\n    bool bottomCap = (vCap > 1.9 && vCap < 2.1) || vCap >= 2.9;\n\n    // body outside\n    h = sqrt(h);\n    float t = (-k1 - h) / k2;\n    float y = baoc + t * bard;\n    if (y > 0.0 && y < baba) {\n        interior = false;\n        intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n        return true;\n    }\n\n    if (topCap && y < 0.0) {\n        // top cap\n        t = -baoc / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    } else if(bottomCap && y >= 0.0) {\n        // bottom cap\n        t = (baba - baoc) / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    }\n\n    if (uDoubleSided) {\n        // body inside\n        h = -h;\n        t = (-k1 - h) / k2;\n        y = baoc + t * bard;\n        if (y > 0.0 && y < baba) {\n            interior = true;\n            intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n            return true;\n        }\n\n        // TODO: handle inside caps???\n    }\n\n    return false;\n}\n\nvoid main() {\n    #include clip_pixel\n\n    vec3 rayDir = mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n\n    vec4 intersection;\n    bool interior;\n    bool hit = CylinderImpostor(vModelPosition, rayDir, vStart, vEnd, vSize, intersection, interior);\n    if (!hit) discard;\n\n    vec3 vViewPosition = vModelPosition + intersection.x * rayDir;\n    vViewPosition = (uView * vec4(vViewPosition, 1.0)).xyz;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            mat3 normalMatrix = transpose3(inverse3(mat3(uView)));\n            vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export declare const cylinders_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\nuniform mat4 uView;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform vec3 uCameraDir;\nuniform vec3 uCameraPosition;\nuniform mat4 uInvView;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\n// adapted from https://www.shadertoy.com/view/4lcSRn\n// The MIT License, Copyright 2016 Inigo Quilez\nbool CylinderImpostor(\n    in vec3 rayOrigin, in vec3 rayDir,\n    in vec3 start, in vec3 end, in float radius,\n    out vec4 intersection, out bool interior\n){\n    vec3 ba = end - start;\n    vec3 oc = rayOrigin - start;\n\n    float baba = dot(ba, ba);\n    float bard = dot(ba, rayDir);\n    float baoc = dot(ba, oc);\n\n    float k2 = baba - bard*bard;\n    float k1 = baba * dot(oc, rayDir) - baoc * bard;\n    float k0 = baba * dot(oc, oc) - baoc * baoc - radius * radius * baba;\n\n    float h = k1 * k1 - k2 * k0;\n    if (h < 0.0) return false;\n\n    bool topCap = (vCap > 0.9 && vCap < 1.1) || vCap >= 2.9;\n    bool bottomCap = (vCap > 1.9 && vCap < 2.1) || vCap >= 2.9;\n\n    // body outside\n    h = sqrt(h);\n    float t = (-k1 - h) / k2;\n    float y = baoc + t * bard;\n    if (y > 0.0 && y < baba) {\n        interior = false;\n        intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n        return true;\n    }\n\n    if (topCap && y < 0.0) {\n        // top cap\n        t = -baoc / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    } else if(bottomCap && y >= 0.0) {\n        // bottom cap\n        t = (baba - baoc) / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    }\n\n    if (uDoubleSided) {\n        // body inside\n        h = -h;\n        t = (-k1 - h) / k2;\n        y = baoc + t * bard;\n        if (y > 0.0 && y < baba) {\n            interior = true;\n            intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n            return true;\n        }\n\n        // TODO: handle inside caps???\n    }\n\n    return false;\n}\n\nvoid main() {\n    #include clip_pixel\n\n    vec3 rayDir = mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n\n    vec4 intersection;\n    bool interior;\n    bool hit = CylinderImpostor(vModelPosition, rayDir, vStart, vEnd, vSize, intersection, interior);\n    if (!hit) discard;\n\n    vec3 vViewPosition = vModelPosition + intersection.x * rayDir;\n    vViewPosition = (uView * vec4(vViewPosition, 1.0)).xyz;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        mat3 normalMatrix = transpose3(inverse3(mat3(uView)));\n        vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";

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

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var cylinders_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\nuniform mat4 uView;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform vec3 uCameraDir;\nuniform vec3 uCameraPosition;\nuniform mat4 uInvView;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\n// adapted from https://www.shadertoy.com/view/4lcSRn\n// The MIT License, Copyright 2016 Inigo Quilez\nbool CylinderImpostor(\n    in vec3 rayOrigin, in vec3 rayDir,\n    in vec3 start, in vec3 end, in float radius,\n    out vec4 intersection, out bool interior\n){\n    vec3 ba = end - start;\n    vec3 oc = rayOrigin - start;\n\n    float baba = dot(ba, ba);\n    float bard = dot(ba, rayDir);\n    float baoc = dot(ba, oc);\n\n    float k2 = baba - bard*bard;\n    float k1 = baba * dot(oc, rayDir) - baoc * bard;\n    float k0 = baba * dot(oc, oc) - baoc * baoc - radius * radius * baba;\n\n    float h = k1 * k1 - k2 * k0;\n    if (h < 0.0) return false;\n\n    bool topCap = (vCap > 0.9 && vCap < 1.1) || vCap >= 2.9;\n    bool bottomCap = (vCap > 1.9 && vCap < 2.1) || vCap >= 2.9;\n\n    // body outside\n    h = sqrt(h);\n    float t = (-k1 - h) / k2;\n    float y = baoc + t * bard;\n    if (y > 0.0 && y < baba) {\n        interior = false;\n        intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n        return true;\n    }\n\n    if (topCap && y < 0.0) {\n        // top cap\n        t = -baoc / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    } else if(bottomCap && y >= 0.0) {\n        // bottom cap\n        t = (baba - baoc) / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    }\n\n    if (uDoubleSided) {\n        // body inside\n        h = -h;\n        t = (-k1 - h) / k2;\n        y = baoc + t * bard;\n        if (y > 0.0 && y < baba) {\n            interior = true;\n            intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n            return true;\n        }\n\n        // TODO: handle inside caps???\n    }\n\n    return false;\n}\n\nvoid main() {\n    #include clip_pixel\n\n    vec3 rayDir = mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n\n    vec4 intersection;\n    bool interior;\n    bool hit = CylinderImpostor(vModelPosition, rayDir, vStart, vEnd, vSize, intersection, interior);\n    if (!hit) discard;\n\n    vec3 vViewPosition = vModelPosition + intersection.x * rayDir;\n    vViewPosition = (uView * vec4(vViewPosition, 1.0)).xyz;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            mat3 normalMatrix = transpose3(inverse3(mat3(uView)));\n            vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export var cylinders_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\nuniform mat4 uView;\n\nvarying mat4 vTransform;\nvarying vec3 vStart;\nvarying vec3 vEnd;\nvarying float vSize;\nvarying float vCap;\n\nuniform vec3 uCameraDir;\nuniform vec3 uCameraPosition;\nuniform mat4 uInvView;\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\n// adapted from https://www.shadertoy.com/view/4lcSRn\n// The MIT License, Copyright 2016 Inigo Quilez\nbool CylinderImpostor(\n    in vec3 rayOrigin, in vec3 rayDir,\n    in vec3 start, in vec3 end, in float radius,\n    out vec4 intersection, out bool interior\n){\n    vec3 ba = end - start;\n    vec3 oc = rayOrigin - start;\n\n    float baba = dot(ba, ba);\n    float bard = dot(ba, rayDir);\n    float baoc = dot(ba, oc);\n\n    float k2 = baba - bard*bard;\n    float k1 = baba * dot(oc, rayDir) - baoc * bard;\n    float k0 = baba * dot(oc, oc) - baoc * baoc - radius * radius * baba;\n\n    float h = k1 * k1 - k2 * k0;\n    if (h < 0.0) return false;\n\n    bool topCap = (vCap > 0.9 && vCap < 1.1) || vCap >= 2.9;\n    bool bottomCap = (vCap > 1.9 && vCap < 2.1) || vCap >= 2.9;\n\n    // body outside\n    h = sqrt(h);\n    float t = (-k1 - h) / k2;\n    float y = baoc + t * bard;\n    if (y > 0.0 && y < baba) {\n        interior = false;\n        intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n        return true;\n    }\n\n    if (topCap && y < 0.0) {\n        // top cap\n        t = -baoc / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    } else if(bottomCap && y >= 0.0) {\n        // bottom cap\n        t = (baba - baoc) / bard;\n        if (abs(k1 + k2 * t) < h) {\n            interior = false;\n            intersection = vec4(t, ba * sign(y) / baba);\n            return true;\n        }\n    }\n\n    if (uDoubleSided) {\n        // body inside\n        h = -h;\n        t = (-k1 - h) / k2;\n        y = baoc + t * bard;\n        if (y > 0.0 && y < baba) {\n            interior = true;\n            intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);\n            return true;\n        }\n\n        // TODO: handle inside caps???\n    }\n\n    return false;\n}\n\nvoid main() {\n    #include clip_pixel\n\n    vec3 rayDir = mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);\n\n    vec4 intersection;\n    bool interior;\n    bool hit = CylinderImpostor(vModelPosition, rayDir, vStart, vEnd, vSize, intersection, interior);\n    if (!hit) discard;\n\n    vec3 vViewPosition = vModelPosition + intersection.x * rayDir;\n    vViewPosition = (uView * vec4(vViewPosition, 1.0)).xyz;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        mat3 normalMatrix = transpose3(inverse3(mat3(uView)));\n        vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
 //# sourceMappingURL=cylinders.frag.js.map

package/lib/mol-gl/shader/direct-volume.frag.d.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
  */
-export declare const directVolume_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include light_frag_params\n\n#if dClipObjectCount != 0\n    uniform int uClipObjectType[dClipObjectCount];\n    uniform bool uClipObjectInvert[dClipObjectCount];\n    uniform vec3 uClipObjectPosition[dClipObjectCount];\n    uniform vec4 uClipObjectRotation[dClipObjectCount];\n    uniform vec3 uClipObjectScale[dClipObjectCount];\n#endif\n#include common_clip\n\n#include read_from_texture\n#include texture3d_from_1d_trilinear\n#include texture3d_from_2d_nearest\n#include texture3d_from_2d_linear\n\nuniform mat4 uProjection, uTransform, uModelView, uModel, uView;\nuniform vec3 uCameraDir;\n\nuniform sampler2D tDepth;\nuniform vec2 uDrawingBufferSize;\n\nvarying vec3 vOrigPos;\nvarying float vInstance;\nvarying vec4 vBoundingSphere;\nvarying mat4 vTransform;\n\nuniform mat4 uInvView;\nuniform vec3 uGridDim;\nuniform vec3 uBboxSize;\nuniform sampler2D tTransferTex;\nuniform float uTransferScale;\nuniform float uStepScale;\nuniform float uJumpLength;\n\nuniform int uObjectId;\nuniform int uVertexCount;\nuniform int uInstanceCount;\nuniform int uGroupCount;\n\nuniform vec3 uHighlightColor;\nuniform vec3 uSelectColor;\nuniform float uHighlightStrength;\nuniform float uSelectStrength;\nuniform int uMarkerPriority;\n\nuniform float uMarker;\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nuniform float uMetalness;\nuniform float uRoughness;\n\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform float uPickingAlphaThreshold;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\n\nuniform float uInteriorDarkening;\nuniform bool uInteriorColorFlag;\nuniform vec3 uInteriorColor;\n\nuniform bool uRenderWboit;\nuniform bool uDoubleSided;\n\nuniform float uNear;\nuniform float uFar;\nuniform float uIsOrtho;\n\nuniform vec3 uCellDim;\nuniform vec3 uCameraPosition;\nuniform mat4 uCartnToUnit;\n\n#if __VERSION__ != 100\n    // for webgl1 this is given as a 'define'\n    uniform int uMaxSteps;\n#endif\n\n#if defined(dGridTexType_2d)\n    precision highp sampler2D;\n    uniform sampler2D tGridTex;\n    uniform vec3 uGridTexDim;\n#elif defined(dGridTexType_3d)\n    precision highp sampler3D;\n    uniform sampler3D tGridTex;\n#endif\n\n#if defined(dColorType_uniform)\n    uniform vec3 uColor;\n#elif defined(dColorType_texture)\n    uniform vec2 uColorTexDim;\n    uniform sampler2D tColor;\n#endif\n\n#ifdef dOverpaint\n    #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n        uniform vec2 uOverpaintTexDim;\n        uniform sampler2D tOverpaint;\n    #endif\n#endif\n\n#ifdef dUsePalette\n    uniform sampler2D tPalette;\n#endif\n\n#if defined(dGridTexType_2d)\n    vec4 textureVal(vec3 pos) {\n        return texture3dFrom2dLinear(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texture3dFrom2dNearest(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n#elif defined(dGridTexType_3d)\n    vec4 textureVal(vec3 pos) {\n        return texture(tGridTex, pos + (vec3(0.5) / uGridDim));\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texelFetch(tGridTex, ivec3(pos * uGridDim), 0);\n    }\n#endif\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n\nfloat transferFunction(float value) {\n    return texture2D(tTransferTex, vec2(value, 0.0)).a;\n}\n\nfloat getDepth(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        if (!uRenderWboit) {\n            // in case of opaque volumes (and depth texture support)\n            return texture2D(tDepth, coords).r;\n        } else {\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\n    #else\n        return unpackRGBAToDepth(texture2D(tDepth, coords));\n    #endif\n}\n\nconst float gradOffset = 0.5;\n\nvec3 v3m4(vec3 p, mat4 m) {\n    return (m * vec4(p, 1.0)).xyz;\n}\n\nfloat preFogAlphaBlended = 0.0;\n\nvec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {\n    #if !defined(dIgnoreLight)\n        mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    #endif\n    mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);\n    #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n        mat4 modelTransform = uModel * vTransform * uTransform;\n    #endif\n    mat4 modelViewTransform = uModelView * vTransform * uTransform;\n\n    vec3 scaleVol = vec3(1.0) / uGridDim;\n    vec3 pos = startLoc;\n    vec4 cell;\n    float prevValue = -1.0;\n    float value = 0.0;\n    vec4 src = vec4(0.0);\n    vec4 dst = vec4(0.0);\n    float fragmentDepth;\n\n    vec3 posMin = vec3(0.0);\n    vec3 posMax = vec3(1.0) - vec3(1.0) / uGridDim;\n\n    vec3 unitPos;\n\n    vec3 nextPos;\n    float nextValue;\n\n    vec4 material;\n    vec4 overpaint;\n    float metalness = uMetalness;\n    float roughness = uRoughness;\n\n    vec3 gradient = vec3(1.0);\n    vec3 dx = vec3(gradOffset * scaleVol.x, 0.0, 0.0);\n    vec3 dy = vec3(0.0, gradOffset * scaleVol.y, 0.0);\n    vec3 dz = vec3(0.0, 0.0, gradOffset * scaleVol.z);\n\n    float maxDist = min(vBoundingSphere.w * 2.0, uFar - uNear);\n    float maxDistSq = maxDist * maxDist;\n\n    for (int i = 0; i < uMaxSteps; ++i) {\n        // break when beyond bounding-sphere or far-plane\n        vec3 distVec = startLoc - pos;\n        if (dot(distVec, distVec) > maxDistSq) break;\n\n        unitPos = v3m4(pos, cartnToUnit);\n\n        // continue when outside of grid\n        if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||\n            unitPos.x < posMin.x || unitPos.y < posMin.y || unitPos.z < posMin.z\n        ) {\n            prevValue = value;\n            pos += step;\n            continue;\n        }\n\n        cell = textureVal(unitPos);\n        value = cell.a; // current voxel value\n\n        if (uJumpLength > 0.0 && value < 0.01) {\n            nextPos = pos + rayDir * uJumpLength;\n            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;\n            if (nextValue < 0.01) {\n                prevValue = nextValue;\n                pos = nextPos;\n                continue;\n            }\n        }\n\n        vec4 mvPosition = modelViewTransform * vec4(unitPos * uGridDim, 1.0);\n        if (calcDepth(mvPosition.xyz) > getDepth(gl_FragCoord.xy / uDrawingBufferSize))\n            break;\n\n        #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);\n            if (clipTest(vec4(vModelPosition, 0.0), 0)) {\n                prevValue = value;\n                pos += step;\n                continue;\n            }\n        #endif\n\n        vec3 vViewPosition = mvPosition.xyz;\n        material.a = transferFunction(value);\n\n        #ifdef dPackedGroup\n            float group = unpackRGBToInt(textureGroup(floor(unitPos * uGridDim + 0.5) / uGridDim).rgb);\n        #else\n            vec3 g = floor(unitPos * uGridDim + 0.5);\n            // note that we swap x and z because the texture is flipped around y\n            #if defined(dAxisOrder_012)\n                float group = g.z + g.y * uGridDim.z + g.x * uGridDim.z * uGridDim.y; // 210\n            #elif defined(dAxisOrder_021)\n                float group = g.y + g.z * uGridDim.y + g.x * uGridDim.y * uGridDim.z; // 120\n            #elif defined(dAxisOrder_102)\n                float group = g.z + g.x * uGridDim.z + g.y * uGridDim.z * uGridDim.x; // 201\n            #elif defined(dAxisOrder_120)\n                float group = g.x + g.z * uGridDim.x + g.y * uGridDim.x * uGridDim.z; // 021\n            #elif defined(dAxisOrder_201)\n                float group = g.y + g.x * uGridDim.y + g.z * uGridDim.y * uGridDim.x; // 102\n            #elif defined(dAxisOrder_210)\n                float group = g.x + g.y * uGridDim.x + g.z * uGridDim.x * uGridDim.y; // 012\n            #endif\n        #endif\n\n        #if defined(dColorType_direct) && defined(dUsePalette)\n            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;\n        #elif defined(dColorType_uniform)\n            material.rgb = uColor;\n        #elif defined(dColorType_instance)\n            material.rgb = readFromTexture(tColor, vInstance, uColorTexDim).rgb;\n        #elif defined(dColorType_group)\n            material.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;\n        #elif defined(dColorType_groupInstance)\n            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;\n        #elif defined(dColorType_vertex)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;\n        #endif\n\n        #ifdef dOverpaint\n            #if defined(dOverpaintType_groupInstance)\n                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);\n            #elif defined(dOverpaintType_vertexInstance)\n                overpaint = texture3dFrom1dTrilinear(tOverpaint, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        #ifdef dIgnoreLight\n            gl_FragColor.rgb = material.rgb;\n        #else\n            if (material.a >= 0.01) {\n                #ifdef dPackedGroup\n                    // compute gradient by central differences\n                    gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;\n                    gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;\n                    gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;\n                #else\n                    gradient = cell.xyz * 2.0 - 1.0;\n                #endif\n                vec3 normal = -normalize(normalMatrix * normalize(gradient));\n                #include apply_light_color\n            } else {\n                gl_FragColor.rgb = material.rgb;\n            }\n        #endif\n\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n            marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n        }\n        #include apply_marker_color\n\n        preFogAlphaBlended = (1.0 - preFogAlphaBlended) * gl_FragColor.a + preFogAlphaBlended;\n        fragmentDepth = calcDepth(mvPosition.xyz);\n        #include apply_fog\n\n        src = gl_FragColor;\n\n        if (!uTransparentBackground) {\n            // done in 'apply_fog' otherwise\n            src.rgb *= src.a;\n        }\n        dst = (1.0 - dst.a) * src + dst; // standard blending\n\n        // break if the color is opaque enough\n        if (dst.a > 0.95)\n            break;\n\n        pos += step;\n    }\n\n    return dst;\n}\n\n// TODO: support float texture for higher precision values???\n// TODO: support clipping exclusion texture support\n\nvoid main() {\n    if (gl_FrontFacing)\n        discard;\n\n    vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 step = rayDir * uStepScale;\n\n    float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;\n    float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);\n    vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);\n    gl_FragColor = raymarch(start, step, rayDir);\n\n    float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);\n    float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);\n    bool interior = false;\n    #include wboit_write\n}\n";
+export declare const directVolume_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include light_frag_params\n\n#if dClipObjectCount != 0\n    uniform int uClipObjectType[dClipObjectCount];\n    uniform bool uClipObjectInvert[dClipObjectCount];\n    uniform vec3 uClipObjectPosition[dClipObjectCount];\n    uniform vec4 uClipObjectRotation[dClipObjectCount];\n    uniform vec3 uClipObjectScale[dClipObjectCount];\n#endif\n#include common_clip\n\n#include read_from_texture\n#include texture3d_from_1d_trilinear\n#include texture3d_from_2d_nearest\n#include texture3d_from_2d_linear\n\nuniform mat4 uProjection, uTransform, uModelView, uModel, uView;\nuniform vec3 uCameraDir;\n\nuniform sampler2D tDepth;\nuniform vec2 uDrawingBufferSize;\n\nvarying vec3 vOrigPos;\nvarying float vInstance;\nvarying vec4 vBoundingSphere;\nvarying mat4 vTransform;\n\nuniform mat4 uInvView;\nuniform vec3 uGridDim;\nuniform vec3 uBboxSize;\nuniform sampler2D tTransferTex;\nuniform float uTransferScale;\nuniform float uStepScale;\nuniform float uJumpLength;\n\nuniform int uObjectId;\nuniform int uVertexCount;\nuniform int uInstanceCount;\nuniform int uGroupCount;\n\nuniform vec3 uHighlightColor;\nuniform vec3 uSelectColor;\nuniform float uHighlightStrength;\nuniform float uSelectStrength;\nuniform int uMarkerPriority;\n\nuniform float uMarker;\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nuniform float uMetalness;\nuniform float uRoughness;\n\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform float uPickingAlphaThreshold;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\n\nuniform float uInteriorDarkening;\nuniform bool uInteriorColorFlag;\nuniform vec3 uInteriorColor;\n\nuniform bool uRenderWboit;\nuniform bool uDoubleSided;\n\nuniform float uNear;\nuniform float uFar;\nuniform float uIsOrtho;\n\nuniform vec3 uCellDim;\nuniform vec3 uCameraPosition;\nuniform mat4 uCartnToUnit;\n\n#if __VERSION__ != 100\n    // for webgl1 this is given as a 'define'\n    uniform int uMaxSteps;\n#endif\n\n#if defined(dGridTexType_2d)\n    precision highp sampler2D;\n    uniform sampler2D tGridTex;\n    uniform vec3 uGridTexDim;\n#elif defined(dGridTexType_3d)\n    precision highp sampler3D;\n    uniform sampler3D tGridTex;\n#endif\n\n#if defined(dColorType_uniform)\n    uniform vec3 uColor;\n#elif defined(dColorType_texture)\n    uniform vec2 uColorTexDim;\n    uniform sampler2D tColor;\n#endif\n\n#ifdef dOverpaint\n    #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n        uniform vec2 uOverpaintTexDim;\n        uniform sampler2D tOverpaint;\n    #endif\n#endif\n\n#ifdef dUsePalette\n    uniform sampler2D tPalette;\n#endif\n\n#if defined(dGridTexType_2d)\n    vec4 textureVal(vec3 pos) {\n        return texture3dFrom2dLinear(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texture3dFrom2dNearest(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n#elif defined(dGridTexType_3d)\n    vec4 textureVal(vec3 pos) {\n        return texture(tGridTex, pos + (vec3(0.5) / uGridDim));\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texelFetch(tGridTex, ivec3(pos * uGridDim), 0);\n    }\n#endif\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n\nfloat transferFunction(float value) {\n    return texture2D(tTransferTex, vec2(value, 0.0)).a;\n}\n\nfloat getDepth(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        if (!uRenderWboit) {\n            // in case of opaque volumes (and depth texture support)\n            return texture2D(tDepth, coords).r;\n        } else {\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\n    #else\n        return unpackRGBAToDepth(texture2D(tDepth, coords));\n    #endif\n}\n\nconst float gradOffset = 0.5;\n\nvec3 v3m4(vec3 p, mat4 m) {\n    return (m * vec4(p, 1.0)).xyz;\n}\n\nfloat preFogAlphaBlended = 0.0;\n\nvec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {\n    mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);\n    #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n        mat4 modelTransform = uModel * vTransform * uTransform;\n    #endif\n    mat4 modelViewTransform = uModelView * vTransform * uTransform;\n\n    vec3 scaleVol = vec3(1.0) / uGridDim;\n    vec3 pos = startLoc;\n    vec4 cell;\n    float prevValue = -1.0;\n    float value = 0.0;\n    vec4 src = vec4(0.0);\n    vec4 dst = vec4(0.0);\n    float fragmentDepth;\n\n    vec3 posMin = vec3(0.0);\n    vec3 posMax = vec3(1.0) - vec3(1.0) / uGridDim;\n\n    vec3 unitPos;\n\n    vec3 nextPos;\n    float nextValue;\n\n    vec4 material;\n    vec4 overpaint;\n    float metalness = uMetalness;\n    float roughness = uRoughness;\n\n    vec3 gradient = vec3(1.0);\n    vec3 dx = vec3(gradOffset * scaleVol.x, 0.0, 0.0);\n    vec3 dy = vec3(0.0, gradOffset * scaleVol.y, 0.0);\n    vec3 dz = vec3(0.0, 0.0, gradOffset * scaleVol.z);\n\n    float maxDist = min(vBoundingSphere.w * 2.0, uFar - uNear);\n    float maxDistSq = maxDist * maxDist;\n\n    for (int i = 0; i < uMaxSteps; ++i) {\n        // break when beyond bounding-sphere or far-plane\n        vec3 distVec = startLoc - pos;\n        if (dot(distVec, distVec) > maxDistSq) break;\n\n        unitPos = v3m4(pos, cartnToUnit);\n\n        // continue when outside of grid\n        if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||\n            unitPos.x < posMin.x || unitPos.y < posMin.y || unitPos.z < posMin.z\n        ) {\n            prevValue = value;\n            pos += step;\n            continue;\n        }\n\n        cell = textureVal(unitPos);\n        value = cell.a; // current voxel value\n\n        if (uJumpLength > 0.0 && value < 0.01) {\n            nextPos = pos + rayDir * uJumpLength;\n            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;\n            if (nextValue < 0.01) {\n                prevValue = nextValue;\n                pos = nextPos;\n                continue;\n            }\n        }\n\n        vec4 mvPosition = modelViewTransform * vec4(unitPos * uGridDim, 1.0);\n        if (calcDepth(mvPosition.xyz) > getDepth(gl_FragCoord.xy / uDrawingBufferSize))\n            break;\n\n        #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);\n            if (clipTest(vec4(vModelPosition, 0.0), 0)) {\n                prevValue = value;\n                pos += step;\n                continue;\n            }\n        #endif\n\n        vec3 vViewPosition = mvPosition.xyz;\n        material.a = transferFunction(value);\n\n        #ifdef dPackedGroup\n            float group = unpackRGBToInt(textureGroup(floor(unitPos * uGridDim + 0.5) / uGridDim).rgb);\n        #else\n            vec3 g = floor(unitPos * uGridDim + 0.5);\n            // note that we swap x and z because the texture is flipped around y\n            #if defined(dAxisOrder_012)\n                float group = g.z + g.y * uGridDim.z + g.x * uGridDim.z * uGridDim.y; // 210\n            #elif defined(dAxisOrder_021)\n                float group = g.y + g.z * uGridDim.y + g.x * uGridDim.y * uGridDim.z; // 120\n            #elif defined(dAxisOrder_102)\n                float group = g.z + g.x * uGridDim.z + g.y * uGridDim.z * uGridDim.x; // 201\n            #elif defined(dAxisOrder_120)\n                float group = g.x + g.z * uGridDim.x + g.y * uGridDim.x * uGridDim.z; // 021\n            #elif defined(dAxisOrder_201)\n                float group = g.y + g.x * uGridDim.y + g.z * uGridDim.y * uGridDim.x; // 102\n            #elif defined(dAxisOrder_210)\n                float group = g.x + g.y * uGridDim.x + g.z * uGridDim.x * uGridDim.y; // 012\n            #endif\n        #endif\n\n        #if defined(dColorType_direct) && defined(dUsePalette)\n            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;\n        #elif defined(dColorType_uniform)\n            material.rgb = uColor;\n        #elif defined(dColorType_instance)\n            material.rgb = readFromTexture(tColor, vInstance, uColorTexDim).rgb;\n        #elif defined(dColorType_group)\n            material.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;\n        #elif defined(dColorType_groupInstance)\n            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;\n        #elif defined(dColorType_vertex)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;\n        #endif\n\n        #ifdef dOverpaint\n            #if defined(dOverpaintType_groupInstance)\n                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);\n            #elif defined(dOverpaintType_vertexInstance)\n                overpaint = texture3dFrom1dTrilinear(tOverpaint, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        if (material.a >= 0.01) {\n            #ifdef dPackedGroup\n                // compute gradient by central differences\n                gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;\n                gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;\n                gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;\n            #else\n                gradient = cell.xyz * 2.0 - 1.0;\n            #endif\n            vec3 normal = -normalize(normalMatrix * normalize(gradient));\n            #include apply_light_color\n        } else {\n            gl_FragColor.rgb = material.rgb;\n        }\n\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n            marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n        }\n        #include apply_marker_color\n\n        preFogAlphaBlended = (1.0 - preFogAlphaBlended) * gl_FragColor.a + preFogAlphaBlended;\n        fragmentDepth = calcDepth(mvPosition.xyz);\n        #include apply_fog\n\n        src = gl_FragColor;\n\n        if (!uTransparentBackground) {\n            // done in 'apply_fog' otherwise\n            src.rgb *= src.a;\n        }\n        dst = (1.0 - dst.a) * src + dst; // standard blending\n\n        // break if the color is opaque enough\n        if (dst.a > 0.95)\n            break;\n\n        pos += step;\n    }\n\n    return dst;\n}\n\n// TODO: support float texture for higher precision values???\n// TODO: support clipping exclusion texture support\n\nvoid main() {\n    if (gl_FrontFacing)\n        discard;\n\n    vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 step = rayDir * uStepScale;\n\n    float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;\n    float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);\n    vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);\n    gl_FragColor = raymarch(start, step, rayDir);\n\n    float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);\n    float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);\n    bool interior = false;\n    #include wboit_write\n}\n";

package/lib/mol-gl/shader/direct-volume.frag.js

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
  */
-export var directVolume_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include light_frag_params\n\n#if dClipObjectCount != 0\n    uniform int uClipObjectType[dClipObjectCount];\n    uniform bool uClipObjectInvert[dClipObjectCount];\n    uniform vec3 uClipObjectPosition[dClipObjectCount];\n    uniform vec4 uClipObjectRotation[dClipObjectCount];\n    uniform vec3 uClipObjectScale[dClipObjectCount];\n#endif\n#include common_clip\n\n#include read_from_texture\n#include texture3d_from_1d_trilinear\n#include texture3d_from_2d_nearest\n#include texture3d_from_2d_linear\n\nuniform mat4 uProjection, uTransform, uModelView, uModel, uView;\nuniform vec3 uCameraDir;\n\nuniform sampler2D tDepth;\nuniform vec2 uDrawingBufferSize;\n\nvarying vec3 vOrigPos;\nvarying float vInstance;\nvarying vec4 vBoundingSphere;\nvarying mat4 vTransform;\n\nuniform mat4 uInvView;\nuniform vec3 uGridDim;\nuniform vec3 uBboxSize;\nuniform sampler2D tTransferTex;\nuniform float uTransferScale;\nuniform float uStepScale;\nuniform float uJumpLength;\n\nuniform int uObjectId;\nuniform int uVertexCount;\nuniform int uInstanceCount;\nuniform int uGroupCount;\n\nuniform vec3 uHighlightColor;\nuniform vec3 uSelectColor;\nuniform float uHighlightStrength;\nuniform float uSelectStrength;\nuniform int uMarkerPriority;\n\nuniform float uMarker;\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nuniform float uMetalness;\nuniform float uRoughness;\n\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform float uPickingAlphaThreshold;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\n\nuniform float uInteriorDarkening;\nuniform bool uInteriorColorFlag;\nuniform vec3 uInteriorColor;\n\nuniform bool uRenderWboit;\nuniform bool uDoubleSided;\n\nuniform float uNear;\nuniform float uFar;\nuniform float uIsOrtho;\n\nuniform vec3 uCellDim;\nuniform vec3 uCameraPosition;\nuniform mat4 uCartnToUnit;\n\n#if __VERSION__ != 100\n    // for webgl1 this is given as a 'define'\n    uniform int uMaxSteps;\n#endif\n\n#if defined(dGridTexType_2d)\n    precision highp sampler2D;\n    uniform sampler2D tGridTex;\n    uniform vec3 uGridTexDim;\n#elif defined(dGridTexType_3d)\n    precision highp sampler3D;\n    uniform sampler3D tGridTex;\n#endif\n\n#if defined(dColorType_uniform)\n    uniform vec3 uColor;\n#elif defined(dColorType_texture)\n    uniform vec2 uColorTexDim;\n    uniform sampler2D tColor;\n#endif\n\n#ifdef dOverpaint\n    #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n        uniform vec2 uOverpaintTexDim;\n        uniform sampler2D tOverpaint;\n    #endif\n#endif\n\n#ifdef dUsePalette\n    uniform sampler2D tPalette;\n#endif\n\n#if defined(dGridTexType_2d)\n    vec4 textureVal(vec3 pos) {\n        return texture3dFrom2dLinear(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texture3dFrom2dNearest(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n#elif defined(dGridTexType_3d)\n    vec4 textureVal(vec3 pos) {\n        return texture(tGridTex, pos + (vec3(0.5) / uGridDim));\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texelFetch(tGridTex, ivec3(pos * uGridDim), 0);\n    }\n#endif\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n\nfloat transferFunction(float value) {\n    return texture2D(tTransferTex, vec2(value, 0.0)).a;\n}\n\nfloat getDepth(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        if (!uRenderWboit) {\n            // in case of opaque volumes (and depth texture support)\n            return texture2D(tDepth, coords).r;\n        } else {\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\n    #else\n        return unpackRGBAToDepth(texture2D(tDepth, coords));\n    #endif\n}\n\nconst float gradOffset = 0.5;\n\nvec3 v3m4(vec3 p, mat4 m) {\n    return (m * vec4(p, 1.0)).xyz;\n}\n\nfloat preFogAlphaBlended = 0.0;\n\nvec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {\n    #if !defined(dIgnoreLight)\n        mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    #endif\n    mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);\n    #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n        mat4 modelTransform = uModel * vTransform * uTransform;\n    #endif\n    mat4 modelViewTransform = uModelView * vTransform * uTransform;\n\n    vec3 scaleVol = vec3(1.0) / uGridDim;\n    vec3 pos = startLoc;\n    vec4 cell;\n    float prevValue = -1.0;\n    float value = 0.0;\n    vec4 src = vec4(0.0);\n    vec4 dst = vec4(0.0);\n    float fragmentDepth;\n\n    vec3 posMin = vec3(0.0);\n    vec3 posMax = vec3(1.0) - vec3(1.0) / uGridDim;\n\n    vec3 unitPos;\n\n    vec3 nextPos;\n    float nextValue;\n\n    vec4 material;\n    vec4 overpaint;\n    float metalness = uMetalness;\n    float roughness = uRoughness;\n\n    vec3 gradient = vec3(1.0);\n    vec3 dx = vec3(gradOffset * scaleVol.x, 0.0, 0.0);\n    vec3 dy = vec3(0.0, gradOffset * scaleVol.y, 0.0);\n    vec3 dz = vec3(0.0, 0.0, gradOffset * scaleVol.z);\n\n    float maxDist = min(vBoundingSphere.w * 2.0, uFar - uNear);\n    float maxDistSq = maxDist * maxDist;\n\n    for (int i = 0; i < uMaxSteps; ++i) {\n        // break when beyond bounding-sphere or far-plane\n        vec3 distVec = startLoc - pos;\n        if (dot(distVec, distVec) > maxDistSq) break;\n\n        unitPos = v3m4(pos, cartnToUnit);\n\n        // continue when outside of grid\n        if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||\n            unitPos.x < posMin.x || unitPos.y < posMin.y || unitPos.z < posMin.z\n        ) {\n            prevValue = value;\n            pos += step;\n            continue;\n        }\n\n        cell = textureVal(unitPos);\n        value = cell.a; // current voxel value\n\n        if (uJumpLength > 0.0 && value < 0.01) {\n            nextPos = pos + rayDir * uJumpLength;\n            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;\n            if (nextValue < 0.01) {\n                prevValue = nextValue;\n                pos = nextPos;\n                continue;\n            }\n        }\n\n        vec4 mvPosition = modelViewTransform * vec4(unitPos * uGridDim, 1.0);\n        if (calcDepth(mvPosition.xyz) > getDepth(gl_FragCoord.xy / uDrawingBufferSize))\n            break;\n\n        #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);\n            if (clipTest(vec4(vModelPosition, 0.0), 0)) {\n                prevValue = value;\n                pos += step;\n                continue;\n            }\n        #endif\n\n        vec3 vViewPosition = mvPosition.xyz;\n        material.a = transferFunction(value);\n\n        #ifdef dPackedGroup\n            float group = unpackRGBToInt(textureGroup(floor(unitPos * uGridDim + 0.5) / uGridDim).rgb);\n        #else\n            vec3 g = floor(unitPos * uGridDim + 0.5);\n            // note that we swap x and z because the texture is flipped around y\n            #if defined(dAxisOrder_012)\n                float group = g.z + g.y * uGridDim.z + g.x * uGridDim.z * uGridDim.y; // 210\n            #elif defined(dAxisOrder_021)\n                float group = g.y + g.z * uGridDim.y + g.x * uGridDim.y * uGridDim.z; // 120\n            #elif defined(dAxisOrder_102)\n                float group = g.z + g.x * uGridDim.z + g.y * uGridDim.z * uGridDim.x; // 201\n            #elif defined(dAxisOrder_120)\n                float group = g.x + g.z * uGridDim.x + g.y * uGridDim.x * uGridDim.z; // 021\n            #elif defined(dAxisOrder_201)\n                float group = g.y + g.x * uGridDim.y + g.z * uGridDim.y * uGridDim.x; // 102\n            #elif defined(dAxisOrder_210)\n                float group = g.x + g.y * uGridDim.x + g.z * uGridDim.x * uGridDim.y; // 012\n            #endif\n        #endif\n\n        #if defined(dColorType_direct) && defined(dUsePalette)\n            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;\n        #elif defined(dColorType_uniform)\n            material.rgb = uColor;\n        #elif defined(dColorType_instance)\n            material.rgb = readFromTexture(tColor, vInstance, uColorTexDim).rgb;\n        #elif defined(dColorType_group)\n            material.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;\n        #elif defined(dColorType_groupInstance)\n            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;\n        #elif defined(dColorType_vertex)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;\n        #endif\n\n        #ifdef dOverpaint\n            #if defined(dOverpaintType_groupInstance)\n                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);\n            #elif defined(dOverpaintType_vertexInstance)\n                overpaint = texture3dFrom1dTrilinear(tOverpaint, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        #ifdef dIgnoreLight\n            gl_FragColor.rgb = material.rgb;\n        #else\n            if (material.a >= 0.01) {\n                #ifdef dPackedGroup\n                    // compute gradient by central differences\n                    gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;\n                    gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;\n                    gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;\n                #else\n                    gradient = cell.xyz * 2.0 - 1.0;\n                #endif\n                vec3 normal = -normalize(normalMatrix * normalize(gradient));\n                #include apply_light_color\n            } else {\n                gl_FragColor.rgb = material.rgb;\n            }\n        #endif\n\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n            marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n        }\n        #include apply_marker_color\n\n        preFogAlphaBlended = (1.0 - preFogAlphaBlended) * gl_FragColor.a + preFogAlphaBlended;\n        fragmentDepth = calcDepth(mvPosition.xyz);\n        #include apply_fog\n\n        src = gl_FragColor;\n\n        if (!uTransparentBackground) {\n            // done in 'apply_fog' otherwise\n            src.rgb *= src.a;\n        }\n        dst = (1.0 - dst.a) * src + dst; // standard blending\n\n        // break if the color is opaque enough\n        if (dst.a > 0.95)\n            break;\n\n        pos += step;\n    }\n\n    return dst;\n}\n\n// TODO: support float texture for higher precision values???\n// TODO: support clipping exclusion texture support\n\nvoid main() {\n    if (gl_FrontFacing)\n        discard;\n\n    vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 step = rayDir * uStepScale;\n\n    float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;\n    float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);\n    vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);\n    gl_FragColor = raymarch(start, step, rayDir);\n\n    float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);\n    float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);\n    bool interior = false;\n    #include wboit_write\n}\n";
+export var directVolume_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include light_frag_params\n\n#if dClipObjectCount != 0\n    uniform int uClipObjectType[dClipObjectCount];\n    uniform bool uClipObjectInvert[dClipObjectCount];\n    uniform vec3 uClipObjectPosition[dClipObjectCount];\n    uniform vec4 uClipObjectRotation[dClipObjectCount];\n    uniform vec3 uClipObjectScale[dClipObjectCount];\n#endif\n#include common_clip\n\n#include read_from_texture\n#include texture3d_from_1d_trilinear\n#include texture3d_from_2d_nearest\n#include texture3d_from_2d_linear\n\nuniform mat4 uProjection, uTransform, uModelView, uModel, uView;\nuniform vec3 uCameraDir;\n\nuniform sampler2D tDepth;\nuniform vec2 uDrawingBufferSize;\n\nvarying vec3 vOrigPos;\nvarying float vInstance;\nvarying vec4 vBoundingSphere;\nvarying mat4 vTransform;\n\nuniform mat4 uInvView;\nuniform vec3 uGridDim;\nuniform vec3 uBboxSize;\nuniform sampler2D tTransferTex;\nuniform float uTransferScale;\nuniform float uStepScale;\nuniform float uJumpLength;\n\nuniform int uObjectId;\nuniform int uVertexCount;\nuniform int uInstanceCount;\nuniform int uGroupCount;\n\nuniform vec3 uHighlightColor;\nuniform vec3 uSelectColor;\nuniform float uHighlightStrength;\nuniform float uSelectStrength;\nuniform int uMarkerPriority;\n\nuniform float uMarker;\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nuniform float uMetalness;\nuniform float uRoughness;\n\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform float uPickingAlphaThreshold;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\n\nuniform float uInteriorDarkening;\nuniform bool uInteriorColorFlag;\nuniform vec3 uInteriorColor;\n\nuniform bool uRenderWboit;\nuniform bool uDoubleSided;\n\nuniform float uNear;\nuniform float uFar;\nuniform float uIsOrtho;\n\nuniform vec3 uCellDim;\nuniform vec3 uCameraPosition;\nuniform mat4 uCartnToUnit;\n\n#if __VERSION__ != 100\n    // for webgl1 this is given as a 'define'\n    uniform int uMaxSteps;\n#endif\n\n#if defined(dGridTexType_2d)\n    precision highp sampler2D;\n    uniform sampler2D tGridTex;\n    uniform vec3 uGridTexDim;\n#elif defined(dGridTexType_3d)\n    precision highp sampler3D;\n    uniform sampler3D tGridTex;\n#endif\n\n#if defined(dColorType_uniform)\n    uniform vec3 uColor;\n#elif defined(dColorType_texture)\n    uniform vec2 uColorTexDim;\n    uniform sampler2D tColor;\n#endif\n\n#ifdef dOverpaint\n    #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n        uniform vec2 uOverpaintTexDim;\n        uniform sampler2D tOverpaint;\n    #endif\n#endif\n\n#ifdef dUsePalette\n    uniform sampler2D tPalette;\n#endif\n\n#if defined(dGridTexType_2d)\n    vec4 textureVal(vec3 pos) {\n        return texture3dFrom2dLinear(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texture3dFrom2dNearest(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n#elif defined(dGridTexType_3d)\n    vec4 textureVal(vec3 pos) {\n        return texture(tGridTex, pos + (vec3(0.5) / uGridDim));\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texelFetch(tGridTex, ivec3(pos * uGridDim), 0);\n    }\n#endif\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n\nfloat transferFunction(float value) {\n    return texture2D(tTransferTex, vec2(value, 0.0)).a;\n}\n\nfloat getDepth(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        if (!uRenderWboit) {\n            // in case of opaque volumes (and depth texture support)\n            return texture2D(tDepth, coords).r;\n        } else {\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\n    #else\n        return unpackRGBAToDepth(texture2D(tDepth, coords));\n    #endif\n}\n\nconst float gradOffset = 0.5;\n\nvec3 v3m4(vec3 p, mat4 m) {\n    return (m * vec4(p, 1.0)).xyz;\n}\n\nfloat preFogAlphaBlended = 0.0;\n\nvec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {\n    mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);\n    #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n        mat4 modelTransform = uModel * vTransform * uTransform;\n    #endif\n    mat4 modelViewTransform = uModelView * vTransform * uTransform;\n\n    vec3 scaleVol = vec3(1.0) / uGridDim;\n    vec3 pos = startLoc;\n    vec4 cell;\n    float prevValue = -1.0;\n    float value = 0.0;\n    vec4 src = vec4(0.0);\n    vec4 dst = vec4(0.0);\n    float fragmentDepth;\n\n    vec3 posMin = vec3(0.0);\n    vec3 posMax = vec3(1.0) - vec3(1.0) / uGridDim;\n\n    vec3 unitPos;\n\n    vec3 nextPos;\n    float nextValue;\n\n    vec4 material;\n    vec4 overpaint;\n    float metalness = uMetalness;\n    float roughness = uRoughness;\n\n    vec3 gradient = vec3(1.0);\n    vec3 dx = vec3(gradOffset * scaleVol.x, 0.0, 0.0);\n    vec3 dy = vec3(0.0, gradOffset * scaleVol.y, 0.0);\n    vec3 dz = vec3(0.0, 0.0, gradOffset * scaleVol.z);\n\n    float maxDist = min(vBoundingSphere.w * 2.0, uFar - uNear);\n    float maxDistSq = maxDist * maxDist;\n\n    for (int i = 0; i < uMaxSteps; ++i) {\n        // break when beyond bounding-sphere or far-plane\n        vec3 distVec = startLoc - pos;\n        if (dot(distVec, distVec) > maxDistSq) break;\n\n        unitPos = v3m4(pos, cartnToUnit);\n\n        // continue when outside of grid\n        if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||\n            unitPos.x < posMin.x || unitPos.y < posMin.y || unitPos.z < posMin.z\n        ) {\n            prevValue = value;\n            pos += step;\n            continue;\n        }\n\n        cell = textureVal(unitPos);\n        value = cell.a; // current voxel value\n\n        if (uJumpLength > 0.0 && value < 0.01) {\n            nextPos = pos + rayDir * uJumpLength;\n            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;\n            if (nextValue < 0.01) {\n                prevValue = nextValue;\n                pos = nextPos;\n                continue;\n            }\n        }\n\n        vec4 mvPosition = modelViewTransform * vec4(unitPos * uGridDim, 1.0);\n        if (calcDepth(mvPosition.xyz) > getDepth(gl_FragCoord.xy / uDrawingBufferSize))\n            break;\n\n        #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);\n            if (clipTest(vec4(vModelPosition, 0.0), 0)) {\n                prevValue = value;\n                pos += step;\n                continue;\n            }\n        #endif\n\n        vec3 vViewPosition = mvPosition.xyz;\n        material.a = transferFunction(value);\n\n        #ifdef dPackedGroup\n            float group = unpackRGBToInt(textureGroup(floor(unitPos * uGridDim + 0.5) / uGridDim).rgb);\n        #else\n            vec3 g = floor(unitPos * uGridDim + 0.5);\n            // note that we swap x and z because the texture is flipped around y\n            #if defined(dAxisOrder_012)\n                float group = g.z + g.y * uGridDim.z + g.x * uGridDim.z * uGridDim.y; // 210\n            #elif defined(dAxisOrder_021)\n                float group = g.y + g.z * uGridDim.y + g.x * uGridDim.y * uGridDim.z; // 120\n            #elif defined(dAxisOrder_102)\n                float group = g.z + g.x * uGridDim.z + g.y * uGridDim.z * uGridDim.x; // 201\n            #elif defined(dAxisOrder_120)\n                float group = g.x + g.z * uGridDim.x + g.y * uGridDim.x * uGridDim.z; // 021\n            #elif defined(dAxisOrder_201)\n                float group = g.y + g.x * uGridDim.y + g.z * uGridDim.y * uGridDim.x; // 102\n            #elif defined(dAxisOrder_210)\n                float group = g.x + g.y * uGridDim.x + g.z * uGridDim.x * uGridDim.y; // 012\n            #endif\n        #endif\n\n        #if defined(dColorType_direct) && defined(dUsePalette)\n            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;\n        #elif defined(dColorType_uniform)\n            material.rgb = uColor;\n        #elif defined(dColorType_instance)\n            material.rgb = readFromTexture(tColor, vInstance, uColorTexDim).rgb;\n        #elif defined(dColorType_group)\n            material.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;\n        #elif defined(dColorType_groupInstance)\n            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;\n        #elif defined(dColorType_vertex)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;\n        #endif\n\n        #ifdef dOverpaint\n            #if defined(dOverpaintType_groupInstance)\n                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);\n            #elif defined(dOverpaintType_vertexInstance)\n                overpaint = texture3dFrom1dTrilinear(tOverpaint, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        if (material.a >= 0.01) {\n            #ifdef dPackedGroup\n                // compute gradient by central differences\n                gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;\n                gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;\n                gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;\n            #else\n                gradient = cell.xyz * 2.0 - 1.0;\n            #endif\n            vec3 normal = -normalize(normalMatrix * normalize(gradient));\n            #include apply_light_color\n        } else {\n            gl_FragColor.rgb = material.rgb;\n        }\n\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n            marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n        }\n        #include apply_marker_color\n\n        preFogAlphaBlended = (1.0 - preFogAlphaBlended) * gl_FragColor.a + preFogAlphaBlended;\n        fragmentDepth = calcDepth(mvPosition.xyz);\n        #include apply_fog\n\n        src = gl_FragColor;\n\n        if (!uTransparentBackground) {\n            // done in 'apply_fog' otherwise\n            src.rgb *= src.a;\n        }\n        dst = (1.0 - dst.a) * src + dst; // standard blending\n\n        // break if the color is opaque enough\n        if (dst.a > 0.95)\n            break;\n\n        pos += step;\n    }\n\n    return dst;\n}\n\n// TODO: support float texture for higher precision values???\n// TODO: support clipping exclusion texture support\n\nvoid main() {\n    if (gl_FrontFacing)\n        discard;\n\n    vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);\n    vec3 step = rayDir * uStepScale;\n\n    float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;\n    float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);\n    vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);\n    gl_FragColor = raymarch(start, step, rayDir);\n\n    float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);\n    float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);\n    bool interior = false;\n    #include wboit_write\n}\n";
 //# sourceMappingURL=direct-volume.frag.js.map

package/lib/mol-gl/shader/mesh.frag.d.ts

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            #if defined(dFlatShaded)\n                vec3 normal = -faceNormal;\n            #else\n                vec3 normal = -normalize(vNormal);\n                if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n            #endif\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export declare const mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #if defined(dFlatShaded)\n            vec3 normal = -faceNormal;\n        #else\n            vec3 normal = -normalize(vNormal);\n            if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n        #endif\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";

package/lib/mol-gl/shader/mesh.frag.js

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            #if defined(dFlatShaded)\n                vec3 normal = -faceNormal;\n            #else\n                vec3 normal = -normalize(vNormal);\n                if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n            #endif\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export var mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #if defined(dFlatShaded)\n            vec3 normal = -faceNormal;\n        #else\n            vec3 normal = -normalize(vNormal);\n            if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n        #endif\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
 //# sourceMappingURL=mesh.frag.js.map

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

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            vec3 normal = -cameraNormal;\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export declare const spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        vec3 normal = -cameraNormal;\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";

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

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            vec3 normal = -cameraNormal;\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export var spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        vec3 normal = -cameraNormal;\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
 //# sourceMappingURL=spheres.frag.js.map

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/bird.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/ccd.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */
@@ -203,6 +203,28 @@ export declare const mmCIF_Schema: {
          * formal charge assignment normally found in chemical diagrams.
          */
         pdbx_formal_charge: Schema.Int;
+        /**
+         * This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
+         * polymeric and non-polymeric.
+         */
+        pdbx_label_index: Schema.Int;
+        /**
+         * The name of additional external databases with residue level mapping.
+         */
+        pdbx_sifts_xref_db_name: Schema.Str;
+        /**
+         * The accession code related to the additional external database entry.
+         */
+        pdbx_sifts_xref_db_acc: Schema.Str;
+        /**
+         * The sequence position of the external database entry that corresponds
+         * to the residue mapping defined by the SIFTS process.
+         */
+        pdbx_sifts_xref_db_num: Schema.Str;
+        /**
+         * Describes the residue type of the given UniProt match
+         */
+        pdbx_sifts_xref_db_res: Schema.Str;
         /**
          * The model id corresponding to the atom site.
          * This data item is a pointer to _ihm_model_list.model_id
@@ -670,7 +692,7 @@ export declare const mmCIF_Schema: {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Schema.Aliased<"AFDB" | "CAS" | "CSD" | "EMDB" | "ICSD" | "MA" | "MDF" | "MODBASE" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "SMR" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
+        database_id: Schema.Aliased<"AlphaFoldDB" | "CAS" | "CSD" | "EMDB" | "ICSD" | "ModelArchive" | "MDF" | "MODBASE" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "SWISS-MODEL_REPOSITORY" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.

package/lib/mol-io/reader/cif/schema/mmcif.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */
@@ -211,6 +211,28 @@ export var mmCIF_Schema = {
          * formal charge assignment normally found in chemical diagrams.
          */
         pdbx_formal_charge: int,
+        /**
+         * This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
+         * polymeric and non-polymeric.
+         */
+        pdbx_label_index: int,
+        /**
+         * The name of additional external databases with residue level mapping.
+         */
+        pdbx_sifts_xref_db_name: str,
+        /**
+         * The accession code related to the additional external database entry.
+         */
+        pdbx_sifts_xref_db_acc: str,
+        /**
+         * The sequence position of the external database entry that corresponds
+         * to the residue mapping defined by the SIFTS process.
+         */
+        pdbx_sifts_xref_db_num: str,
+        /**
+         * Describes the residue type of the given UniProt match
+         */
+        pdbx_sifts_xref_db_res: str,
         /**
          * The model id corresponding to the atom site.
          * This data item is a pointer to _ihm_model_list.model_id

package/lib/mol-math/geometry/primitives/sphere3d.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>

package/lib/mol-math/geometry/primitives/sphere3d.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -7,6 +7,8 @@
 import { __spreadArray } from "tslib";
 import { Vec3, Mat4, EPSILON } from '../../linear-algebra';
 import { OrderedSet } from '../../../mol-data/int';
+import { Axes3D } from './axes3d';
+import { PrincipalAxes } from '../../linear-algebra/matrix/principal-axes';
 function Sphere3D() {
     return Sphere3D.zero();
 }
@@ -193,11 +195,22 @@ function Sphere3D() {
             return out;
         }
         if (hasExtrema(sphere)) {
+            var positions = new Float32Array(sphere.extrema.length * 3);
+            for (var i = 0; i < sphere.extrema.length; i++) {
+                Vec3.toArray(sphere.extrema[i], positions, i * 3);
+            }
+            var axes_1 = PrincipalAxes.calculateMomentsAxes(positions);
+            Axes3D.scale(axes_1, Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
                 Vec3.sub(tmpDir, e, sphere.center);
-                var dist = Vec3.distance(sphere.center, e);
-                Vec3.normalize(tmpDir, tmpDir);
-                return Vec3.scaleAndAdd(Vec3(), sphere.center, tmpDir, dist + delta);
+                var out = Vec3.clone(e);
+                var sA = Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                var sB = Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                var sC = Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
+                return out;
             }));
         }
         return out;