molstar 3.6.0 → 3.8.0

package/lib/commonjs/mol-gl/shader/ssao.frag.js

@@ -1,10 +1,10 @@
 "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>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ssao_frag = void 0;
-exports.ssao_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n\nuniform sampler2D tDepth;\nuniform vec2 uTexSize;\nuniform vec4 uBounds;\n\nuniform vec3 uSamples[dNSamples];\n\nuniform mat4 uProjection;\nuniform mat4 uInvProjection;\n\nuniform float uRadius;\nuniform float uBias;\n\nfloat smootherstep(float edge0, float edge1, float x) {\n    x = clamp((x - edge0) / (edge1 - edge0), 0.0, 1.0);\n    return x * x * x * (x * (x * 6.0 - 15.0) + 10.0);\n}\n\nfloat noise(const in vec2 coords) {\n    float a = 12.9898;\n    float b = 78.233;\n    float c = 43758.5453;\n    float dt = dot(coords, vec2(a,b));\n    float sn = mod(dt, PI);\n    return abs(fract(sin(sn) * c)); // is abs necessary?\n}\n\nvec2 getNoiseVec2(const in vec2 coords) {\n    return vec2(noise(coords), noise(coords + vec2(PI, 2.71828)));\n}\n\nbool isBackground(const in float depth) {\n    return depth == 1.0;\n}\n\nbool outsideBounds(const in vec2 p) {\n    return p.x < uBounds.x || p.y < uBounds.y || p.x > uBounds.z || p.y > uBounds.w;\n}\n\nfloat getDepth(const in vec2 coords) {\n    return outsideBounds(coords) ? 1.0 : unpackRGBAToDepth(texture2D(tDepth, coords));\n}\n\nvec3 normalFromDepth(const in float depth, const in float depth1, const in float depth2, vec2 offset1, vec2 offset2) {\n    vec3 p1 = vec3(offset1, depth1 - depth);\n    vec3 p2 = vec3(offset2, depth2 - depth);\n\n    vec3 normal = cross(p1, p2);\n    normal.z = -normal.z;\n\n    return normalize(normal);\n}\n\n// StarCraft II Ambient Occlusion by [Filion and McNaughton 2008]\nvoid main(void) {\n    vec2 invTexSize = 1.0 / uTexSize;\n    vec2 selfCoords = gl_FragCoord.xy * invTexSize;\n\n    float selfDepth = getDepth(selfCoords);\n    vec2 selfPackedDepth = packUnitIntervalToRG(selfDepth);\n\n    if (isBackground(selfDepth)) {\n        gl_FragColor = vec4(packUnitIntervalToRG(0.0), selfPackedDepth);\n        return;\n    }\n\n    vec2 offset1 = vec2(0.0, invTexSize.y);\n    vec2 offset2 = vec2(invTexSize.x, 0.0);\n\n    float selfDepth1 = getDepth(selfCoords + offset1);\n    float selfDepth2 = getDepth(selfCoords + offset2);\n\n    vec3 selfViewNormal = normalFromDepth(selfDepth, selfDepth1, selfDepth2, offset1, offset2);\n    vec3 selfViewPos = screenSpaceToViewSpace(vec3(selfCoords, selfDepth), uInvProjection);\n\n    vec3 randomVec = normalize(vec3(getNoiseVec2(selfCoords) * 2.0 - 1.0, 0.0));\n\n    vec3 tangent = normalize(randomVec - selfViewNormal * dot(randomVec, selfViewNormal));\n    vec3 bitangent = cross(selfViewNormal, tangent);\n    mat3 TBN = mat3(tangent, bitangent, selfViewNormal);\n\n    float occlusion = 0.0;\n    for(int i = 0; i < dNSamples; i++){\n        vec3 sampleViewPos = TBN * uSamples[i];\n        sampleViewPos = selfViewPos + sampleViewPos * uRadius;\n\n        vec4 offset = vec4(sampleViewPos, 1.0);\n        offset = uProjection * offset;\n        offset.xyz = (offset.xyz / offset.w) * 0.5 + 0.5;\n\n        float sampleViewZ = screenSpaceToViewSpace(vec3(offset.xy, getDepth(offset.xy)), uInvProjection).z;\n\n        occlusion += step(sampleViewPos.z + 0.025, sampleViewZ) * smootherstep(0.0, 1.0, uRadius / abs(selfViewPos.z - sampleViewZ));\n    }\n    occlusion = 1.0 - (uBias * occlusion / float(dNSamples));\n\n    vec2 packedOcclusion = packUnitIntervalToRG(occlusion);\n\n    gl_FragColor = vec4(packedOcclusion, selfPackedDepth);\n}\n";
+exports.ssao_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n\nuniform sampler2D tDepth;\nuniform vec2 uTexSize;\nuniform vec4 uBounds;\n\nuniform vec3 uSamples[dNSamples];\n\nuniform mat4 uProjection;\nuniform mat4 uInvProjection;\n\nuniform float uRadius;\nuniform float uBias;\n\nfloat smootherstep(float edge0, float edge1, float x) {\n    x = clamp((x - edge0) / (edge1 - edge0), 0.0, 1.0);\n    return x * x * x * (x * (x * 6.0 - 15.0) + 10.0);\n}\n\nfloat noise(const in vec2 coords) {\n    float a = 12.9898;\n    float b = 78.233;\n    float c = 43758.5453;\n    float dt = dot(coords, vec2(a,b));\n    float sn = mod(dt, PI);\n    return abs(fract(sin(sn) * c)); // is abs necessary?\n}\n\nvec2 getNoiseVec2(const in vec2 coords) {\n    return vec2(noise(coords), noise(coords + vec2(PI, 2.71828)));\n}\n\nbool isBackground(const in float depth) {\n    return depth == 1.0;\n}\n\nbool outsideBounds(const in vec2 p) {\n    return p.x < uBounds.x || p.y < uBounds.y || p.x > uBounds.z || p.y > uBounds.w;\n}\n\nfloat getDepth(const in vec2 coords) {\n    if (outsideBounds(coords)) {\n        return 1.0;\n    } else {\n        #ifdef depthTextureSupport\n            return texture2D(tDepth, coords).r;\n        #else\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        #endif\n    }\n}\n\nvec3 normalFromDepth(const in float depth, const in float depth1, const in float depth2, vec2 offset1, vec2 offset2) {\n    vec3 p1 = vec3(offset1, depth1 - depth);\n    vec3 p2 = vec3(offset2, depth2 - depth);\n\n    vec3 normal = cross(p1, p2);\n    normal.z = -normal.z;\n\n    return normalize(normal);\n}\n\n// StarCraft II Ambient Occlusion by [Filion and McNaughton 2008]\nvoid main(void) {\n    vec2 invTexSize = 1.0 / uTexSize;\n    vec2 selfCoords = gl_FragCoord.xy * invTexSize;\n\n    float selfDepth = getDepth(selfCoords);\n    vec2 selfPackedDepth = packUnitIntervalToRG(selfDepth);\n\n    if (isBackground(selfDepth)) {\n        gl_FragColor = vec4(packUnitIntervalToRG(0.0), selfPackedDepth);\n        return;\n    }\n\n    vec2 offset1 = vec2(0.0, invTexSize.y);\n    vec2 offset2 = vec2(invTexSize.x, 0.0);\n\n    float selfDepth1 = getDepth(selfCoords + offset1);\n    float selfDepth2 = getDepth(selfCoords + offset2);\n\n    vec3 selfViewNormal = normalFromDepth(selfDepth, selfDepth1, selfDepth2, offset1, offset2);\n    vec3 selfViewPos = screenSpaceToViewSpace(vec3(selfCoords, selfDepth), uInvProjection);\n\n    vec3 randomVec = normalize(vec3(getNoiseVec2(selfCoords) * 2.0 - 1.0, 0.0));\n\n    vec3 tangent = normalize(randomVec - selfViewNormal * dot(randomVec, selfViewNormal));\n    vec3 bitangent = cross(selfViewNormal, tangent);\n    mat3 TBN = mat3(tangent, bitangent, selfViewNormal);\n\n    float occlusion = 0.0;\n    for(int i = 0; i < dNSamples; i++){\n        vec3 sampleViewPos = TBN * uSamples[i];\n        sampleViewPos = selfViewPos + sampleViewPos * uRadius;\n\n        vec4 offset = vec4(sampleViewPos, 1.0);\n        offset = uProjection * offset;\n        offset.xyz = (offset.xyz / offset.w) * 0.5 + 0.5;\n\n        float sampleViewZ = screenSpaceToViewSpace(vec3(offset.xy, getDepth(offset.xy)), uInvProjection).z;\n\n        occlusion += step(sampleViewPos.z + 0.025, sampleViewZ) * smootherstep(0.0, 1.0, uRadius / abs(selfViewPos.z - sampleViewZ));\n    }\n    occlusion = 1.0 - (uBias * occlusion / float(dNSamples));\n\n    vec2 packedOcclusion = packUnitIntervalToRG(occlusion);\n\n    gl_FragColor = vec4(packedOcclusion, selfPackedDepth);\n}\n";

package/lib/commonjs/mol-gl/webgl/render-target.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>
  */
@@ -7,10 +7,12 @@ import { Texture, TextureFilter } from './texture';
 import { Framebuffer } from './framebuffer';
 import { WebGLResources } from './resources';
 import { GLRenderingContext } from './compat';
+import { Renderbuffer } from './renderbuffer';
 export interface RenderTarget {
     readonly id: number;
     readonly texture: Texture;
     readonly framebuffer: Framebuffer;
+    readonly depthRenderbuffer: Renderbuffer | null;
     getWidth: () => number;
     getHeight: () => number;
     /** binds framebuffer */

package/lib/commonjs/mol-gl/webgl/render-target.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -39,6 +39,7 @@ function createRenderTarget(gl, resources, _width, _height, depth, type, filter)
         id: getNextRenderTargetId(),
         texture: targetTexture,
         framebuffer: framebuffer,
+        depthRenderbuffer: depthRenderbuffer,
         getWidth: function () { return _width; },
         getHeight: function () { return _height; },
         bind: function () {
@@ -75,6 +76,7 @@ function createNullRenderTarget(gl) {
         id: getNextRenderTargetId(),
         texture: (0, texture_1.createNullTexture)(gl),
         framebuffer: (0, framebuffer_1.createNullFramebuffer)(),
+        depthRenderbuffer: null,
         getWidth: function () { return 0; },
         getHeight: function () { return 0; },
         bind: function () {

package/lib/commonjs/mol-gl/webgl/renderbuffer.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>
  */
@@ -13,6 +13,7 @@ export interface Renderbuffer {
     readonly id: number;
     bind: () => void;
     attachFramebuffer: (framebuffer: Framebuffer) => void;
+    detachFramebuffer: (framebuffer: Framebuffer) => void;
     setSize: (width: number, height: number) => void;
     reset: () => void;
     destroy: () => void;

package/lib/commonjs/mol-gl/webgl/renderbuffer.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -62,6 +62,13 @@ function createRenderbuffer(gl, format, attachment, _width, _height) {
             if (debug_1.isDebugMode)
                 (0, framebuffer_1.checkFramebufferStatus)(gl);
         },
+        detachFramebuffer: function (framebuffer) {
+            framebuffer.bind();
+            bind();
+            gl.framebufferRenderbuffer(gl.FRAMEBUFFER, _attachment, gl.RENDERBUFFER, null);
+            if (debug_1.isDebugMode)
+                (0, framebuffer_1.checkFramebufferStatus)(gl);
+        },
         setSize: function (width, height) {
             _width = width;
             _height = height;

package/lib/commonjs/mol-gl/webgl/state.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>
  */
@@ -40,6 +40,10 @@ export declare type WebGLState = {
     cullFace: (mode: number) => void;
     /** sets whether writing into the depth buffer is enabled or disabled */
     depthMask: (flag: boolean) => void;
+    /** specifies the depth value used when clearing depth buffer, used when calling `gl.clear` */
+    clearDepth: (depth: number) => void;
+    /** sets the depth comparison function */
+    depthFunc: (func: number) => void;
     /** sets which color components to enable or to disable */
     colorMask: (red: boolean, green: boolean, blue: boolean, alpha: boolean) => void;
     /** specifies the color values used when clearing color buffers, used when calling `gl.clear`, clamped to [0, 1] */
@@ -52,6 +56,8 @@ export declare type WebGLState = {
     blendEquation: (mode: number) => void;
     /** set the RGB blend equation and alpha blend equation separately, determines how a new pixel is combined with an existing */
     blendEquationSeparate: (modeRGB: number, modeAlpha: number) => void;
+    /** specifies the source and destination blending factors, clamped to [0, 1] */
+    blendColor: (red: number, green: number, blue: number, alpha: number) => void;
     enableVertexAttrib: (index: number) => void;
     clearVertexAttribsState: () => void;
     disableUnusedVertexAttribs: () => void;

package/lib/commonjs/mol-gl/webgl/state.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -11,12 +11,15 @@ function createState(gl) {
     var currentFrontFace = gl.getParameter(gl.FRONT_FACE);
     var currentCullFace = gl.getParameter(gl.CULL_FACE_MODE);
     var currentDepthMask = gl.getParameter(gl.DEPTH_WRITEMASK);
+    var currentClearDepth = gl.getParameter(gl.DEPTH_CLEAR_VALUE);
+    var currentDepthFunc = gl.getParameter(gl.DEPTH_FUNC);
     var currentColorMask = gl.getParameter(gl.COLOR_WRITEMASK);
     var currentClearColor = gl.getParameter(gl.COLOR_CLEAR_VALUE);
     var currentBlendSrcRGB = gl.getParameter(gl.BLEND_SRC_RGB);
     var currentBlendDstRGB = gl.getParameter(gl.BLEND_DST_RGB);
     var currentBlendSrcAlpha = gl.getParameter(gl.BLEND_SRC_ALPHA);
     var currentBlendDstAlpha = gl.getParameter(gl.BLEND_DST_ALPHA);
+    var currentBlendColor = gl.getParameter(gl.BLEND_COLOR);
     var currentBlendEqRGB = gl.getParameter(gl.BLEND_EQUATION_RGB);
     var currentBlendEqAlpha = gl.getParameter(gl.BLEND_EQUATION_ALPHA);
     var maxVertexAttribs = gl.getParameter(gl.MAX_VERTEX_ATTRIBS);
@@ -61,6 +64,18 @@ function createState(gl) {
                 currentDepthMask = flag;
             }
         },
+        clearDepth: function (depth) {
+            if (depth !== currentClearDepth) {
+                gl.clearDepth(depth);
+                currentClearDepth = depth;
+            }
+        },
+        depthFunc: function (func) {
+            if (func !== currentDepthFunc) {
+                gl.depthFunc(func);
+                currentDepthFunc = func;
+            }
+        },
         colorMask: function (red, green, blue, alpha) {
             if (red !== currentColorMask[0] || green !== currentColorMask[1] || blue !== currentColorMask[2] || alpha !== currentColorMask[3]) {
                 gl.colorMask(red, green, blue, alpha);
@@ -111,6 +126,15 @@ function createState(gl) {
                 currentBlendEqAlpha = modeAlpha;
             }
         },
+        blendColor: function (red, green, blue, alpha) {
+            if (red !== currentBlendColor[0] || green !== currentBlendColor[1] || blue !== currentBlendColor[2] || alpha !== currentBlendColor[3]) {
+                gl.blendColor(red, green, blue, alpha);
+                currentBlendColor[0] = red;
+                currentBlendColor[1] = green;
+                currentBlendColor[2] = blue;
+                currentBlendColor[3] = alpha;
+            }
+        },
         enableVertexAttrib: function (index) {
             gl.enableVertexAttribArray(index);
             vertexAttribsState[index] = 1;
@@ -127,12 +151,15 @@ function createState(gl) {
             currentFrontFace = gl.getParameter(gl.FRONT_FACE);
             currentCullFace = gl.getParameter(gl.CULL_FACE_MODE);
             currentDepthMask = gl.getParameter(gl.DEPTH_WRITEMASK);
+            currentClearDepth = gl.getParameter(gl.DEPTH_CLEAR_VALUE);
+            currentDepthFunc = gl.getParameter(gl.DEPTH_FUNC);
             currentColorMask = gl.getParameter(gl.COLOR_WRITEMASK);
             currentClearColor = gl.getParameter(gl.COLOR_CLEAR_VALUE);
             currentBlendSrcRGB = gl.getParameter(gl.BLEND_SRC_RGB);
             currentBlendDstRGB = gl.getParameter(gl.BLEND_DST_RGB);
             currentBlendSrcAlpha = gl.getParameter(gl.BLEND_SRC_ALPHA);
             currentBlendDstAlpha = gl.getParameter(gl.BLEND_DST_ALPHA);
+            currentBlendColor = gl.getParameter(gl.BLEND_COLOR);
             currentBlendEqRGB = gl.getParameter(gl.BLEND_EQUATION_RGB);
             currentBlendEqAlpha = gl.getParameter(gl.BLEND_EQUATION_ALPHA);
             maxVertexAttribs = gl.getParameter(gl.MAX_VERTEX_ATTRIBS);

package/lib/commonjs/mol-gl/webgl/texture.js

@@ -184,6 +184,9 @@ function createTexture(gl, extensions, kind, _format, _type, _filter) {
         (kind.endsWith('depth') && _type !== 'ushort' && _type !== 'float')) {
         throw new Error("texture kind '".concat(kind, "' and type '").concat(_type, "' are incompatible"));
     }
+    if (!extensions.depthTexture && _format === 'depth') {
+        throw new Error("extension 'WEBGL_depth_texture' needed for 'depth' texture format");
+    }
     var target = getTarget(gl, kind);
     var filter = getFilter(gl, _filter);
     var format = getFormat(gl, _format, _type);

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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.
  *
  * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
  *

package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 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.
  *
  * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
  *

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */
@@ -903,8 +903,7 @@ export declare const mmCIF_Schema: {
      */
     entity_poly_seq: {
         /**
-         * This data item is a pointer to _entity_poly.entity_id in the
-         * ENTITY_POLY category.
+         * This data item is a pointer to _entity.id in the ENTITY category.
          */
         entity_id: Schema.Str;
         /**
@@ -4926,7 +4925,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of data held in the dataset.
          */
-        content_type: Schema.Aliased<"target" | "other" | "template structure" | "polymeric template library" | "spatial restraints" | "target-template alignment" | "coevolution MSA" | "model coordinates">;
+        content_type: Schema.Aliased<"target" | "other" | "reference database" | "template structure" | "polymeric template library" | "spatial restraints" | "target-template alignment" | "coevolution MSA" | "model coordinates" | "input structure">;
         /**
          * Details for other content types.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */
@@ -915,8 +915,7 @@ exports.mmCIF_Schema = {
      */
     entity_poly_seq: {
         /**
-         * This data item is a pointer to _entity_poly.entity_id in the
-         * ENTITY_POLY category.
+         * This data item is a pointer to _entity.id in the ENTITY category.
          */
         entity_id: str,
         /**

package/lib/commonjs/mol-io/reader/dx/parser.js

@@ -119,7 +119,7 @@ function parseBinary(taskCtx, data, name) {
     });
 }
 function parseDx(data, name) {
-    return mol_task_1.Task.create('Parse Cube', function (taskCtx) {
+    return mol_task_1.Task.create('Parse DX', function (taskCtx) {
         if (typeof data === 'string')
             return parseText(taskCtx, data, name);
         return parseBinary(taskCtx, data, name);

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-math/geometry/lookup3d/grid.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/commonjs/mol-math/geometry/lookup3d/grid.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -111,12 +111,12 @@ function build(data, boundary, cellSizeOrCount) {
     // need to expand the grid bounds to avoid rounding errors
     var expandedBox = box3d_1.Box3D.expand((0, box3d_1.Box3D)(), boundary.box, linear_algebra_1.Vec3.create(0.5, 0.5, 0.5));
     var indices = data.indices;
-    var S = box3d_1.Box3D.size(linear_algebra_1.Vec3.zero(), expandedBox);
+    var S = box3d_1.Box3D.size((0, linear_algebra_1.Vec3)(), expandedBox);
     var delta, size;
     var elementCount = int_1.OrderedSet.size(indices);
     var cellCount = typeof cellSizeOrCount === 'number' ? cellSizeOrCount : 32;
     var cellSize = Array.isArray(cellSizeOrCount) && cellSizeOrCount;
-    if (cellSize) {
+    if (cellSize && !linear_algebra_1.Vec3.isZero(cellSize)) {
         size = [Math.ceil(S[0] / cellSize[0]), Math.ceil(S[1] / cellSize[1]), Math.ceil(S[2] / cellSize[2])];
         delta = cellSize;
     }

package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.d.ts

@@ -1,10 +1,12 @@
 /**
- * Copyright (c) 2017-2019 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 David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { SecondaryStructureType } from '../types';
 import { ResidueIndex } from '../indexing';
+import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
 /** Secondary structure "indexed" by residues. */
 interface SecondaryStructure {
     readonly type: ArrayLike<SecondaryStructureType>;
@@ -33,7 +35,7 @@ declare namespace SecondaryStructure {
     interface Helix {
         kind: 'helix';
         flags: SecondaryStructureType;
-        type_id: string;
+        type_id: mmCIF_Schema['struct_conf']['conf_type_id']['T'];
         helix_class: string;
         details?: string;
     }

package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.js

@@ -1,8 +1,9 @@
 "use strict";
 /**
- * Copyright (c) 2017-2019 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 David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SecondaryStructure = void 0;

package/lib/commonjs/mol-model/structure/model/types/ions.d.ts

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2020 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.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
- * @author molstar/chem-comp-dict/create-table cli
+ * @author molstar/chem-comp-dict/create-ions cli
  */
 export declare const IonNames: Set<string>;

package/lib/commonjs/mol-model/structure/model/types/ions.js

@@ -1,10 +1,10 @@
 "use strict";
 /**
- * Copyright (c) 2020 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.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
- * @author molstar/chem-comp-dict/create-table cli
+ * @author molstar/chem-comp-dict/create-ions cli
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.IonNames = void 0;