molstar 3.6.1 → 3.7.0

package/lib/commonjs/mol-gl/renderable/spheres.d.ts

@@ -1,5 +1,5 @@
 /**
- * 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>
  */
@@ -16,6 +16,7 @@ export declare const SpheresSchema: {
     uDoubleSided: UniformSpec<"b">;
     dIgnoreLight: DefineSpec<"boolean">;
     dXrayShaded: DefineSpec<"boolean">;
+    dOpaqueBackfaces: DefineSpec<"boolean">;
     uBumpFrequency: UniformSpec<"f">;
     uBumpAmplitude: UniformSpec<"f">;
     uSize: UniformSpec<"f">;

package/lib/commonjs/mol-gl/renderable/spheres.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -12,7 +12,7 @@ var render_item_1 = require("../webgl/render-item");
 var schema_1 = require("./schema");
 var shader_code_1 = require("../shader-code");
 var mol_util_1 = require("../../mol-util");
-exports.SpheresSchema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), schema_1.SizeSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aPosition: (0, schema_1.AttributeSpec)('float32', 3, 0), aMapping: (0, schema_1.AttributeSpec)('float32', 2, 0), elements: (0, schema_1.ElementsSpec)('uint32'), padding: (0, schema_1.ValueSpec)('number'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f') });
+exports.SpheresSchema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), schema_1.SizeSchema), { aGroup: (0, schema_1.AttributeSpec)('float32', 1, 0), aPosition: (0, schema_1.AttributeSpec)('float32', 3, 0), aMapping: (0, schema_1.AttributeSpec)('float32', 2, 0), elements: (0, schema_1.ElementsSpec)('uint32'), padding: (0, schema_1.ValueSpec)('number'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), dOpaqueBackfaces: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f') });
 function SpheresRenderable(ctx, id, values, state, materialId, variants) {
     var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.SpheresSchema);
     var internalValues = {

package/lib/commonjs/mol-gl/renderable/texture-mesh.d.ts

@@ -1,5 +1,5 @@
 /**
- * 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>
  */
@@ -17,6 +17,7 @@ export declare const TextureMeshSchema: {
     dFlipSided: DefineSpec<"boolean">;
     dIgnoreLight: DefineSpec<"boolean">;
     dXrayShaded: DefineSpec<"boolean">;
+    dOpaqueBackfaces: DefineSpec<"boolean">;
     uBumpFrequency: UniformSpec<"f">;
     uBumpAmplitude: UniformSpec<"f">;
     meta: ValueSpec<"unknown">;

package/lib/commonjs/mol-gl/renderable/texture-mesh.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -12,7 +12,7 @@ var render_item_1 = require("../webgl/render-item");
 var schema_1 = require("./schema");
 var shader_code_1 = require("../shader-code");
 var mol_util_1 = require("../../mol-util");
-exports.TextureMeshSchema = tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), { uGeoTexDim: (0, schema_1.UniformSpec)('v2', 'buffered'), tPosition: (0, schema_1.TextureSpec)('texture', 'rgb', 'float', 'nearest'), tGroup: (0, schema_1.TextureSpec)('texture', 'alpha', 'float', 'nearest'), tNormal: (0, schema_1.TextureSpec)('texture', 'rgb', 'float', 'nearest'), dFlatShaded: (0, schema_1.DefineSpec)('boolean'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dFlipSided: (0, schema_1.DefineSpec)('boolean'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f'), meta: (0, schema_1.ValueSpec)('unknown') });
+exports.TextureMeshSchema = tslib_1.__assign(tslib_1.__assign({}, schema_1.BaseSchema), { uGeoTexDim: (0, schema_1.UniformSpec)('v2', 'buffered'), tPosition: (0, schema_1.TextureSpec)('texture', 'rgb', 'float', 'nearest'), tGroup: (0, schema_1.TextureSpec)('texture', 'alpha', 'float', 'nearest'), tNormal: (0, schema_1.TextureSpec)('texture', 'rgb', 'float', 'nearest'), dFlatShaded: (0, schema_1.DefineSpec)('boolean'), uDoubleSided: (0, schema_1.UniformSpec)('b'), dFlipSided: (0, schema_1.DefineSpec)('boolean'), dIgnoreLight: (0, schema_1.DefineSpec)('boolean'), dXrayShaded: (0, schema_1.DefineSpec)('boolean'), dOpaqueBackfaces: (0, schema_1.DefineSpec)('boolean'), uBumpFrequency: (0, schema_1.UniformSpec)('f'), uBumpAmplitude: (0, schema_1.UniformSpec)('f'), meta: (0, schema_1.ValueSpec)('unknown') });
 function TextureMeshRenderable(ctx, id, values, state, materialId, variants) {
     var schema = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, schema_1.GlobalUniformSchema), schema_1.GlobalTextureSchema), schema_1.InternalSchema), exports.TextureMeshSchema);
     var internalValues = {

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

@@ -125,7 +125,8 @@ var Renderer;
         };
         var globalUniformList = Object.entries(globalUniforms);
         var globalUniformsNeedUpdate = true;
-        var renderObject = function (r, variant) {
+        var renderObject = function (r, variant, flag) {
+            var _a, _b, _c;
             if (r.state.disposed || !r.state.visible || (!r.state.pickable && variant === 'pick')) {
                 return;
             }
@@ -160,6 +161,28 @@ var Renderer;
                     state.depthMask(false);
                 }
             }
+            else if (flag === 1 /* BlendedFront */) {
+                state.enable(gl.CULL_FACE);
+                if ((_a = r.values.dFlipSided) === null || _a === void 0 ? void 0 : _a.ref.value) {
+                    state.frontFace(gl.CW);
+                    state.cullFace(gl.FRONT);
+                }
+                else {
+                    state.frontFace(gl.CCW);
+                    state.cullFace(gl.BACK);
+                }
+            }
+            else if (flag === 2 /* BlendedBack */) {
+                state.enable(gl.CULL_FACE);
+                if ((_b = r.values.dFlipSided) === null || _b === void 0 ? void 0 : _b.ref.value) {
+                    state.frontFace(gl.CW);
+                    state.cullFace(gl.BACK);
+                }
+                else {
+                    state.frontFace(gl.CCW);
+                    state.cullFace(gl.FRONT);
+                }
+            }
             else {
                 if (r.values.uDoubleSided) {
                     if (r.values.uDoubleSided.ref.value || r.values.hasReflection.ref.value) {
@@ -173,15 +196,9 @@ var Renderer;
                     // webgl default
                     state.disable(gl.CULL_FACE);
                 }
-                if (r.values.dFlipSided) {
-                    if (r.values.dFlipSided.ref.value) {
-                        state.frontFace(gl.CW);
-                        state.cullFace(gl.FRONT);
-                    }
-                    else {
-                        state.frontFace(gl.CCW);
-                        state.cullFace(gl.BACK);
-                    }
+                if ((_c = r.values.dFlipSided) === null || _c === void 0 ? void 0 : _c.ref.value) {
+                    state.frontFace(gl.CW);
+                    state.cullFace(gl.FRONT);
                 }
                 else {
                     // webgl default
@@ -232,7 +249,7 @@ var Renderer;
             var renderables = group.renderables;
             for (var i = 0, il = renderables.length; i < il; ++i) {
                 if (!renderables[i].state.colorOnly) {
-                    renderObject(renderables[i], variant);
+                    renderObject(renderables[i], variant, 0 /* None */);
                 }
             }
         };
@@ -243,7 +260,7 @@ var Renderer;
             updateInternal(group, camera, depthTexture, false, false);
             var renderables = group.renderables;
             for (var i = 0, il = renderables.length; i < il; ++i) {
-                renderObject(renderables[i], 'depth');
+                renderObject(renderables[i], 'depth', 0 /* None */);
             }
         };
         var renderMarkingDepth = function (group, camera, depthTexture) {
@@ -256,7 +273,7 @@ var Renderer;
             for (var i = 0, il = renderables.length; i < il; ++i) {
                 var r = renderables[i];
                 if (r.values.markerAverage.ref.value !== 1) {
-                    renderObject(renderables[i], 'marking');
+                    renderObject(renderables[i], 'marking', 0 /* None */);
                 }
             }
         };
@@ -270,7 +287,7 @@ var Renderer;
             for (var i = 0, il = renderables.length; i < il; ++i) {
                 var r = renderables[i];
                 if (r.values.markerAverage.ref.value > 0) {
-                    renderObject(renderables[i], 'marking');
+                    renderObject(renderables[i], 'marking', 0 /* None */);
                 }
             }
         };
@@ -279,6 +296,7 @@ var Renderer;
             renderBlendedTransparent(group, camera, depthTexture);
         };
         var renderBlendedOpaque = function (group, camera, depthTexture) {
+            var _a, _b;
             state.disable(gl.BLEND);
             state.enable(gl.DEPTH_TEST);
             state.depthMask(true);
@@ -287,11 +305,15 @@ var Renderer;
             for (var i = 0, il = renderables.length; i < il; ++i) {
                 var r = renderables[i];
                 if (r.state.opaque) {
-                    renderObject(r, 'colorBlended');
+                    renderObject(r, 'colorBlended', 0 /* None */);
+                }
+                else if (((_a = r.values.uDoubleSided) === null || _a === void 0 ? void 0 : _a.ref.value) && ((_b = r.values.dOpaqueBackfaces) === null || _b === void 0 ? void 0 : _b.ref.value)) {
+                    renderObject(r, 'colorBlended', 2 /* BlendedBack */);
                 }
             }
         };
         var renderBlendedTransparent = function (group, camera, depthTexture) {
+            var _a, _b;
             state.enable(gl.DEPTH_TEST);
             updateInternal(group, camera, depthTexture, false, false);
             var renderables = group.renderables;
@@ -306,14 +328,23 @@ var Renderer;
             for (var i = 0, il = renderables.length; i < il; ++i) {
                 var r = renderables[i];
                 if (!r.state.opaque && r.state.writeDepth) {
-                    renderObject(r, 'colorBlended');
+                    renderObject(r, 'colorBlended', 0 /* None */);
                 }
             }
             state.depthMask(false);
             for (var i = 0, il = renderables.length; i < il; ++i) {
                 var r = renderables[i];
                 if (!r.state.opaque && !r.state.writeDepth) {
-                    renderObject(r, 'colorBlended');
+                    if ((_a = r.values.uDoubleSided) === null || _a === void 0 ? void 0 : _a.ref.value) {
+                        // render frontfaces and backfaces separately to avoid artefacts
+                        if (!((_b = r.values.dOpaqueBackfaces) === null || _b === void 0 ? void 0 : _b.ref.value)) {
+                            renderObject(r, 'colorBlended', 2 /* BlendedBack */);
+                        }
+                        renderObject(r, 'colorBlended', 1 /* BlendedFront */);
+                    }
+                    else {
+                        renderObject(r, 'colorBlended', 0 /* None */);
+                    }
                 }
             }
         };
@@ -329,7 +360,7 @@ var Renderer;
                 // uAlpha is updated in "render" so we need to recompute it here
                 var alpha = (0, interpolate_1.clamp)(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
                 if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && !((_a = r.values.dXrayShaded) === null || _a === void 0 ? void 0 : _a.ref.value)) {
-                    renderObject(r, 'colorBlended');
+                    renderObject(r, 'colorBlended', 0 /* None */);
                 }
             }
         };
@@ -345,12 +376,12 @@ var Renderer;
                 // uAlpha is updated in "render" so we need to recompute it here
                 var alpha = (0, interpolate_1.clamp)(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
                 if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || ((_a = r.values.dXrayShaded) === null || _a === void 0 ? void 0 : _a.ref.value)) {
-                    renderObject(r, 'colorBlended');
+                    renderObject(r, 'colorBlended', 0 /* None */);
                 }
             }
         };
         var renderWboitOpaque = function (group, camera, depthTexture) {
-            var _a, _b;
+            var _a, _b, _c;
             state.disable(gl.BLEND);
             state.enable(gl.DEPTH_TEST);
             state.depthMask(true);
@@ -361,8 +392,8 @@ var Renderer;
                 // TODO: simplify, handle in renderable.state???
                 // uAlpha is updated in "render" so we need to recompute it here
                 var alpha = (0, interpolate_1.clamp)(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
-                if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dGeometryType.ref.value !== 'directVolume' && ((_a = r.values.dPointStyle) === null || _a === void 0 ? void 0 : _a.ref.value) !== 'fuzzy' && !((_b = r.values.dXrayShaded) === null || _b === void 0 ? void 0 : _b.ref.value)) {
-                    renderObject(r, 'colorWboit');
+                if ((alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dGeometryType.ref.value !== 'directVolume' && ((_a = r.values.dPointStyle) === null || _a === void 0 ? void 0 : _a.ref.value) !== 'fuzzy' && !((_b = r.values.dXrayShaded) === null || _b === void 0 ? void 0 : _b.ref.value)) || ((_c = r.values.dOpaqueBackfaces) === null || _c === void 0 ? void 0 : _c.ref.value)) {
+                    renderObject(r, 'colorWboit', 0 /* None */);
                 }
             }
         };
@@ -376,7 +407,7 @@ var Renderer;
                 // uAlpha is updated in "render" so we need to recompute it here
                 var alpha = (0, interpolate_1.clamp)(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
                 if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dGeometryType.ref.value === 'directVolume' || ((_a = r.values.dPointStyle) === null || _a === void 0 ? void 0 : _a.ref.value) === 'fuzzy' || !!r.values.uBackgroundColor || ((_b = r.values.dXrayShaded) === null || _b === void 0 ? void 0 : _b.ref.value)) {
-                    renderObject(r, 'colorWboit');
+                    renderObject(r, 'colorWboit', 0 /* None */);
                 }
             }
         };

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

@@ -1 +1 @@
-export declare const apply_interior_color = "\nif (interior) {\n    if (uInteriorColorFlag) {\n        gl_FragColor.rgb = uInteriorColor;\n    } else {\n        gl_FragColor.rgb *= 1.0 - uInteriorDarkening;\n    }\n}\n";
+export declare const apply_interior_color = "\nif (interior) {\n    if (uInteriorColorFlag) {\n        gl_FragColor.rgb = uInteriorColor;\n    } else {\n        gl_FragColor.rgb *= 1.0 - uInteriorDarkening;\n    }\n\n    #ifdef dOpaqueBackfaces\n        gl_FragColor.a = 1.0;\n    #endif\n}\n";

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

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.apply_interior_color = void 0;
-exports.apply_interior_color = "\nif (interior) {\n    if (uInteriorColorFlag) {\n        gl_FragColor.rgb = uInteriorColor;\n    } else {\n        gl_FragColor.rgb *= 1.0 - uInteriorDarkening;\n    }\n}\n";
+exports.apply_interior_color = "\nif (interior) {\n    if (uInteriorColorFlag) {\n        gl_FragColor.rgb = uInteriorColor;\n    } else {\n        gl_FragColor.rgb *= 1.0 - uInteriorDarkening;\n    }\n\n    #ifdef dOpaqueBackfaces\n        gl_FragColor.a = 1.0;\n    #endif\n}\n";

package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.d.ts

@@ -1 +1 @@
-export declare const check_picking_alpha = "\nfloat viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);\nfloat fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));\nfloat alpha = (1.0 - fogFactor) * uAlpha;\nif (uAlpha < uPickingAlphaThreshold || alpha < 0.1)\n    discard; // ignore so the element below can be picked\n";
+export declare const check_picking_alpha = "\nfloat viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);\nfloat fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));\nfloat alpha = (1.0 - fogFactor) * uAlpha;\n// if not opaque enough ignore so the element below can be picked\nif (uAlpha < uPickingAlphaThreshold || alpha < 0.1) {\n    #ifdef dOpaqueBackfaces\n        if (!interior) discard;\n    #else\n        discard;\n    #endif\n}\n";

package/lib/commonjs/mol-gl/shader/chunks/check-picking-alpha.glsl.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.check_picking_alpha = void 0;
-exports.check_picking_alpha = "\nfloat viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);\nfloat fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));\nfloat alpha = (1.0 - fogFactor) * uAlpha;\nif (uAlpha < uPickingAlphaThreshold || alpha < 0.1)\n    discard; // ignore so the element below can be picked\n";
+exports.check_picking_alpha = "\nfloat viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);\nfloat fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));\nfloat alpha = (1.0 - fogFactor) * uAlpha;\n// if not opaque enough ignore so the element below can be picked\nif (uAlpha < uPickingAlphaThreshold || alpha < 0.1) {\n    #ifdef dOpaqueBackfaces\n        if (!interior) discard;\n    #else\n        discard;\n    #endif\n}\n";

package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.d.ts

@@ -1 +1 @@
-export declare const color_vert_params = "\nuniform float uMetalness;\nuniform float uRoughness;\nuniform float uBumpiness;\n\n#if defined(dRenderVariant_color)\n    #if defined(dColorType_uniform)\n        uniform vec3 uColor;\n    #elif defined(dColorType_attribute)\n        varying vec4 vColor;\n        attribute vec3 aColor;\n    #elif defined(dColorType_texture)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform sampler2D tColor;\n    #elif defined(dColorType_grid)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform vec3 uColorGridDim;\n        uniform vec4 uColorGridTransform;\n        uniform sampler2D tColorGrid;\n    #endif\n\n    #ifdef dUsePalette\n        varying float vPaletteV;\n    #endif\n\n    #ifdef dOverpaint\n        #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform sampler2D tOverpaint;\n        #elif defined(dOverpaintType_volumeInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform vec3 uOverpaintGridDim;\n            uniform vec4 uOverpaintGridTransform;\n            uniform sampler2D tOverpaintGrid;\n        #endif\n    #endif\n\n    #ifdef dSubstance\n        #if defined(dSubstanceType_groupInstance) || defined(dSubstanceType_vertexInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform sampler2D tSubstance;\n        #elif defined(dSubstanceType_volumeInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform vec3 uSubstanceGridDim;\n            uniform vec4 uSubstanceGridTransform;\n            uniform sampler2D tSubstanceGrid;\n        #endif\n    #endif\n#elif defined(dRenderVariant_pick)\n    #if __VERSION__ == 100\n        varying vec4 vColor;\n    #else\n        flat out vec4 vColor;\n    #endif\n#endif\n\n#ifdef dTransparency\n    varying float vGroup;\n    #if defined(dTransparencyType_groupInstance) || defined(dTransparencyType_vertexInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform sampler2D tTransparency;\n    #elif defined(dTransparencyType_volumeInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform vec3 uTransparencyGridDim;\n        uniform vec4 uTransparencyGridTransform;\n        uniform sampler2D tTransparencyGrid;\n    #endif\n#endif\n";
+export declare const color_vert_params = "\nuniform float uMetalness;\nuniform float uRoughness;\nuniform float uBumpiness;\n\n#if defined(dRenderVariant_color)\n    #if defined(dColorType_uniform)\n        uniform vec3 uColor;\n    #elif defined(dColorType_attribute)\n        varying vec4 vColor;\n        attribute vec3 aColor;\n    #elif defined(dColorType_texture)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform sampler2D tColor;\n    #elif defined(dColorType_grid)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform vec3 uColorGridDim;\n        uniform vec4 uColorGridTransform;\n        uniform sampler2D tColorGrid;\n    #elif defined(dColorType_direct)\n        varying vec4 vColor;\n    #endif\n\n    #ifdef dUsePalette\n        varying float vPaletteV;\n    #endif\n\n    #ifdef dOverpaint\n        #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform sampler2D tOverpaint;\n        #elif defined(dOverpaintType_volumeInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform vec3 uOverpaintGridDim;\n            uniform vec4 uOverpaintGridTransform;\n            uniform sampler2D tOverpaintGrid;\n        #endif\n    #endif\n\n    #ifdef dSubstance\n        #if defined(dSubstanceType_groupInstance) || defined(dSubstanceType_vertexInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform sampler2D tSubstance;\n        #elif defined(dSubstanceType_volumeInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform vec3 uSubstanceGridDim;\n            uniform vec4 uSubstanceGridTransform;\n            uniform sampler2D tSubstanceGrid;\n        #endif\n    #endif\n#elif defined(dRenderVariant_pick)\n    #if __VERSION__ == 100\n        varying vec4 vColor;\n    #else\n        flat out vec4 vColor;\n    #endif\n#endif\n\n#ifdef dTransparency\n    varying float vGroup;\n    #if defined(dTransparencyType_groupInstance) || defined(dTransparencyType_vertexInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform sampler2D tTransparency;\n    #elif defined(dTransparencyType_volumeInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform vec3 uTransparencyGridDim;\n        uniform vec4 uTransparencyGridTransform;\n        uniform sampler2D tTransparencyGrid;\n    #endif\n#endif\n";

package/lib/commonjs/mol-gl/shader/chunks/color-vert-params.glsl.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.color_vert_params = void 0;
-exports.color_vert_params = "\nuniform float uMetalness;\nuniform float uRoughness;\nuniform float uBumpiness;\n\n#if defined(dRenderVariant_color)\n    #if defined(dColorType_uniform)\n        uniform vec3 uColor;\n    #elif defined(dColorType_attribute)\n        varying vec4 vColor;\n        attribute vec3 aColor;\n    #elif defined(dColorType_texture)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform sampler2D tColor;\n    #elif defined(dColorType_grid)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform vec3 uColorGridDim;\n        uniform vec4 uColorGridTransform;\n        uniform sampler2D tColorGrid;\n    #endif\n\n    #ifdef dUsePalette\n        varying float vPaletteV;\n    #endif\n\n    #ifdef dOverpaint\n        #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform sampler2D tOverpaint;\n        #elif defined(dOverpaintType_volumeInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform vec3 uOverpaintGridDim;\n            uniform vec4 uOverpaintGridTransform;\n            uniform sampler2D tOverpaintGrid;\n        #endif\n    #endif\n\n    #ifdef dSubstance\n        #if defined(dSubstanceType_groupInstance) || defined(dSubstanceType_vertexInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform sampler2D tSubstance;\n        #elif defined(dSubstanceType_volumeInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform vec3 uSubstanceGridDim;\n            uniform vec4 uSubstanceGridTransform;\n            uniform sampler2D tSubstanceGrid;\n        #endif\n    #endif\n#elif defined(dRenderVariant_pick)\n    #if __VERSION__ == 100\n        varying vec4 vColor;\n    #else\n        flat out vec4 vColor;\n    #endif\n#endif\n\n#ifdef dTransparency\n    varying float vGroup;\n    #if defined(dTransparencyType_groupInstance) || defined(dTransparencyType_vertexInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform sampler2D tTransparency;\n    #elif defined(dTransparencyType_volumeInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform vec3 uTransparencyGridDim;\n        uniform vec4 uTransparencyGridTransform;\n        uniform sampler2D tTransparencyGrid;\n    #endif\n#endif\n";
+exports.color_vert_params = "\nuniform float uMetalness;\nuniform float uRoughness;\nuniform float uBumpiness;\n\n#if defined(dRenderVariant_color)\n    #if defined(dColorType_uniform)\n        uniform vec3 uColor;\n    #elif defined(dColorType_attribute)\n        varying vec4 vColor;\n        attribute vec3 aColor;\n    #elif defined(dColorType_texture)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform sampler2D tColor;\n    #elif defined(dColorType_grid)\n        varying vec4 vColor;\n        uniform vec2 uColorTexDim;\n        uniform vec3 uColorGridDim;\n        uniform vec4 uColorGridTransform;\n        uniform sampler2D tColorGrid;\n    #elif defined(dColorType_direct)\n        varying vec4 vColor;\n    #endif\n\n    #ifdef dUsePalette\n        varying float vPaletteV;\n    #endif\n\n    #ifdef dOverpaint\n        #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform sampler2D tOverpaint;\n        #elif defined(dOverpaintType_volumeInstance)\n            varying vec4 vOverpaint;\n            uniform vec2 uOverpaintTexDim;\n            uniform vec3 uOverpaintGridDim;\n            uniform vec4 uOverpaintGridTransform;\n            uniform sampler2D tOverpaintGrid;\n        #endif\n    #endif\n\n    #ifdef dSubstance\n        #if defined(dSubstanceType_groupInstance) || defined(dSubstanceType_vertexInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform sampler2D tSubstance;\n        #elif defined(dSubstanceType_volumeInstance)\n            varying vec4 vSubstance;\n            uniform vec2 uSubstanceTexDim;\n            uniform vec3 uSubstanceGridDim;\n            uniform vec4 uSubstanceGridTransform;\n            uniform sampler2D tSubstanceGrid;\n        #endif\n    #endif\n#elif defined(dRenderVariant_pick)\n    #if __VERSION__ == 100\n        varying vec4 vColor;\n    #else\n        flat out vec4 vColor;\n    #endif\n#endif\n\n#ifdef dTransparency\n    varying float vGroup;\n    #if defined(dTransparencyType_groupInstance) || defined(dTransparencyType_vertexInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform sampler2D tTransparency;\n    #elif defined(dTransparencyType_volumeInstance)\n        varying float vTransparency;\n        uniform vec2 uTransparencyTexDim;\n        uniform vec3 uTransparencyGridDim;\n        uniform vec4 uTransparencyGridTransform;\n        uniform sampler2D tTransparencyGrid;\n    #endif\n#endif\n";

package/lib/commonjs/mol-io/writer/ligand-encoder.d.ts

@@ -8,11 +8,12 @@ import { Writer } from './writer';
 import { Encoder, Category } from './cif/encoder';
 import { ComponentAtom } from '../../mol-model-formats/structure/property/atoms/chem_comp';
 import { ComponentBond } from '../../mol-model-formats/structure/property/bonds/chem_comp';
+import { ElementSymbol } from '../../mol-model/structure/model/types';
 interface Atom {
     Cartn_x: number;
     Cartn_y: number;
     Cartn_z: number;
-    type_symbol: string;
+    type_symbol: ElementSymbol;
     index: number;
 }
 declare function Atom(partial: any): Atom;
@@ -39,7 +40,8 @@ export declare abstract class LigandEncoder implements Encoder<string> {
     getData(): string;
     protected getAtoms<Ctx>(instance: Category.Instance<Ctx>, source: any): Map<string, Atom>;
     private _getAtoms;
-    protected skipHydrogen(type_symbol: string): boolean;
+    protected skipHydrogen(type_symbol: ElementSymbol): boolean;
+    protected isHydrogen(type_symbol: ElementSymbol): boolean;
     private getSortedFields;
     private getField;
     protected getName<Ctx>(instance: Category.Instance<Ctx>, source: any): string;

package/lib/commonjs/mol-io/writer/ligand-encoder.js

@@ -8,6 +8,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.LigandEncoder = void 0;
 var tslib_1 = require("tslib");
 var mol_util_1 = require("../../mol-util");
+var common_1 = require("../../mol-model/structure/structure/unit/bonds/common");
 function Atom(partial) {
     return tslib_1.__assign({}, partial);
 }
@@ -80,11 +81,12 @@ var LigandEncoder = /** @class */ (function () {
             while (it_1.hasNext) {
                 var key = it_1.move();
                 var lai = label_atom_id.value(key, data, index);
+                // ignore all alternate locations after the first
+                if (atoms.has(lai))
+                    continue;
                 var ts = type_symbol.value(key, data, index);
-                if (this.skipHydrogen(ts)) {
-                    index++;
+                if (this.skipHydrogen(ts))
                     continue;
-                }
                 var a = {};
                 for (var _f = 0, _fl = fields.length; _f < _fl; _f++) {
                     var f = fields[_f];
@@ -102,7 +104,10 @@ var LigandEncoder = /** @class */ (function () {
         if (this.hydrogens) {
             return false;
         }
-        return type_symbol === 'H';
+        return this.isHydrogen(type_symbol);
+    };
+    LigandEncoder.prototype.isHydrogen = function (type_symbol) {
+        return (0, common_1.isHydrogen)((0, common_1.getElementIdx)(type_symbol));
     };
     LigandEncoder.prototype.getSortedFields = function (instance, names) {
         var _this = this;

package/lib/commonjs/mol-io/writer/mol/encoder.js

@@ -36,13 +36,25 @@ var MolEncoder = /** @class */ (function (_super) {
         mol_util_1.StringBuilder.writeSafe(this.builder, "".concat(name, "\n  ").concat(this.encoder, "\n\n"));
         var atomMap = this.componentAtomData.entries.get(name);
         var bondMap = this.componentBondData.entries.get(name);
+        // happens for the unknown ligands (UNL)
+        if (!atomMap)
+            throw Error("The Chemical Component Dictionary doesn't hold any atom data for ".concat(name));
         var bondCount = 0;
         var chiral = false;
         // traverse once to determine all actually present atoms
         var atoms = this.getAtoms(instance, source);
         atoms.forEach(function (atom1, label_atom_id1) {
-            var i1 = atom1.index;
-            var _a = atomMap.map.get(label_atom_id1), charge = _a.charge, stereo_config = _a.stereo_config;
+            var i1 = atom1.index, type_symbol1 = atom1.type_symbol;
+            var atomMapData1 = atomMap.map.get(label_atom_id1);
+            if (!atomMapData1) {
+                if (_this.isHydrogen(type_symbol1)) {
+                    return;
+                }
+                else {
+                    throw Error("Unknown atom ".concat(label_atom_id1, " for component ").concat(name));
+                }
+            }
+            var charge = atomMapData1.charge, stereo_config = atomMapData1.stereo_config;
             mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_x.toFixed(4), 10);
             mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_y.toFixed(4), 10);
             mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_z.toFixed(4), 10);
@@ -60,8 +72,8 @@ var MolEncoder = /** @class */ (function (_super) {
                 var atom2 = atoms.get(label_atom_id2);
                 if (!atom2)
                     return;
-                var i2 = atom2.index, type_symbol2 = atom2.type_symbol;
-                if (i1 < i2 && !_this.skipHydrogen(type_symbol2)) {
+                var i2 = atom2.index;
+                if (i1 < i2) {
                     var order = bond.order;
                     mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, i1 + 1, 3);
                     mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, i2 + 1, 3);

package/lib/commonjs/mol-io/writer/mol2/encoder.js

@@ -30,20 +30,33 @@ var Mol2Encoder = /** @class */ (function (_super) {
         // write header
         var name = this.getName(instance, source);
         mol_util_1.StringBuilder.writeSafe(this.builder, "# Name: ".concat(name, "\n# Created by ").concat(this.encoder, "\n\n"));
+        var atomMap = this.componentAtomData.entries.get(name);
         var bondMap = this.componentBondData.entries.get(name);
+        // happens for the unknown ligands (UNL)
+        if (!atomMap)
+            throw Error("The Chemical Component Dictionary doesn't hold any atom data for ".concat(name));
         var bondCount = 0;
         var atoms = this.getAtoms(instance, source);
         mol_util_1.StringBuilder.writeSafe(a, '@<TRIPOS>ATOM\n');
         mol_util_1.StringBuilder.writeSafe(b, '@<TRIPOS>BOND\n');
         atoms.forEach(function (atom1, label_atom_id1) {
-            var i1 = atom1.index;
+            var i1 = atom1.index, type_symbol1 = atom1.type_symbol;
+            var atomMapData1 = atomMap.map.get(label_atom_id1);
+            if (!atomMapData1) {
+                if (_this.isHydrogen(type_symbol1)) {
+                    return;
+                }
+                else {
+                    throw Error("Unknown atom ".concat(label_atom_id1, " for component ").concat(name));
+                }
+            }
             if (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) {
                 bondMap.map.get(label_atom_id1).forEach(function (bond, label_atom_id2) {
                     var atom2 = atoms.get(label_atom_id2);
                     if (!atom2)
                         return;
-                    var i2 = atom2.index, type_symbol2 = atom2.type_symbol;
-                    if (i1 < i2 && !_this.skipHydrogen(type_symbol2)) {
+                    var i2 = atom2.index;
+                    if (i1 < i2) {
                         var order = bond.order, flags = bond.flags;
                         var ar = types_1.BondType.is(16 /* Aromatic */, flags);
                         mol_util_1.StringBuilder.writeSafe(b, "".concat(++bondCount, " ").concat(i1 + 1, " ").concat(i2 + 1, " ").concat(ar ? 'ar' : order));
@@ -51,7 +64,7 @@ var Mol2Encoder = /** @class */ (function (_super) {
                     }
                 });
             }
-            var sybyl = (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) ? _this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap) : atom1.type_symbol;
+            var sybyl = (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) ? _this.mapToSybyl(label_atom_id1, type_symbol1, bondMap) : type_symbol1;
             mol_util_1.StringBuilder.writeSafe(a, "".concat(i1 + 1, " ").concat(label_atom_id1, " ").concat(atom1.Cartn_x.toFixed(3), " ").concat(atom1.Cartn_y.toFixed(3), " ").concat(atom1.Cartn_z.toFixed(3), " ").concat(sybyl, " 1 ").concat(name, " 0.000\n"));
         });
         // could write something like 'SMALL\nNO_CHARGES', for now let's write **** indicating non-optional, yet missing, string values

package/lib/commonjs/mol-model-formats/shape/ply.d.ts

@@ -30,7 +30,7 @@ export declare const PlyShapeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -72,7 +72,7 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts

@@ -25,7 +25,7 @@ export declare const InteractionsInterUnitParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts

@@ -25,7 +25,7 @@ export declare const InteractionsIntraUnitParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-model-props/computed/representations/interactions.d.ts

@@ -29,7 +29,7 @@ export declare const InteractionsParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -72,7 +72,7 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -116,7 +116,7 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -30,7 +30,7 @@ export declare const CrossLinkRestraintCylinderParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -73,7 +73,7 @@ export declare const CrossLinkRestraintParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -115,7 +115,7 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -158,7 +158,7 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    allowTransparentBackfaces: PD.BooleanParam;
+    transparentBackfaces: PD.Select<string>;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/util.js

@@ -94,7 +94,6 @@ function getContourLevelEmdb(plugin, taskCtx, emdbId) {
                         }
                     }
                     contourLevel = parseFloat(primaryContour.getElementsByTagName('level')[0].textContent);
-                    console.log({ contourLevel: contourLevel });
                     return [2 /*return*/, contourLevel];
             }
         });

package/lib/commonjs/mol-plugin/commands.d.ts

@@ -331,7 +331,7 @@ export declare const PluginCommands: {
                         flipSided: any;
                         flatShaded: any;
                         xrayShaded: any;
-                        allowTransparentBackfaces: any;
+                        transparentBackfaces: any;
                         bumpFrequency: any;
                         bumpAmplitude: any;
                         quality: any;

package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts

@@ -37,7 +37,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
-            allowTransparentBackfaces: boolean;
+            transparentBackfaces: string;
             bumpFrequency: number;
             bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
@@ -70,7 +70,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 flipSided: boolean;
                 flatShaded: boolean;
                 xrayShaded: boolean;
-                allowTransparentBackfaces: boolean;
+                transparentBackfaces: string;
                 bumpFrequency: number;
                 bumpAmplitude: number;
                 quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
@@ -111,7 +111,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
-            allowTransparentBackfaces: boolean;
+            transparentBackfaces: string;
             bumpFrequency: number;
             bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";