molstar 2.3.9 → 3.0.0-dev.10

package/lib/commonjs/mol-gl/shader-code.js

@@ -73,7 +73,8 @@ var ShaderChunks = {
     texture3d_from_2d_nearest: texture3d_from_2d_nearest_glsl_1.texture3d_from_2d_nearest,
     wboit_write: wboit_write_glsl_1.wboit_write
 };
-var reInclude = /^(?!\/\/)\s*#include\s+(\S+)/gmi;
+var reInclude = /^(?!\/\/)\s*#include\s+(\S+)/gm;
+var reUnrollLoop = /#pragma unroll_loop_start\s+for\s*\(\s*int\s+i\s*=\s*(\d+)\s*;\s*i\s*<\s*(\d+)\s*;\s*\+\+i\s*\s*\)\s*{([\s\S]+?)}\s+#pragma unroll_loop_end/g;
 var reSingleLineComment = /[ \t]*\/\/.*\n/g;
 var reMultiLineComment = /[ \t]*\/\*[\s\S]*?\*\//g;
 var reMultipleLinebreaks = /\n{2,}/g;
@@ -90,42 +91,92 @@ function addIncludes(text) {
         .replace(reMultiLineComment, '\n')
         .replace(reMultipleLinebreaks, '\n');
 }
-function ShaderCode(name, vert, frag, extensions, outTypes) {
+function unrollLoops(str) {
+    return str.replace(reUnrollLoop, loopReplacer);
+}
+function loopReplacer(match, start, end, snippet) {
+    var out = '';
+    for (var i = parseInt(start); i < parseInt(end); ++i) {
+        out += snippet
+            .replace(/\[\s*i\s*\]/g, "[".concat(i, "]"))
+            .replace(/UNROLLED_LOOP_INDEX/g, "".concat(i));
+    }
+    return out;
+}
+function replaceCounts(str, defines) {
+    if (defines.dLightCount)
+        str = str.replace(/dLightCount/g, "".concat(defines.dLightCount.ref.value));
+    if (defines.dClipObjectCount)
+        str = str.replace(/dClipObjectCount/g, "".concat(defines.dClipObjectCount.ref.value));
+    return str;
+}
+function preprocess(str, defines) {
+    return unrollLoops(replaceCounts(str, defines));
+}
+function ShaderCode(name, vert, frag, extensions, outTypes, ignoreDefine) {
     if (extensions === void 0) { extensions = {}; }
     if (outTypes === void 0) { outTypes = {}; }
-    return { id: shaderCodeId(), name: name, vert: addIncludes(vert), frag: addIncludes(frag), extensions: extensions, outTypes: outTypes };
+    return { id: shaderCodeId(), name: name, vert: addIncludes(vert), frag: addIncludes(frag), extensions: extensions, outTypes: outTypes, ignoreDefine: ignoreDefine };
 }
 exports.ShaderCode = ShaderCode;
 // Note: `drawBuffers` need to be 'optional' for wboit
+function ignoreDefine(name, variant, defines) {
+    var _a;
+    if (variant.startsWith('color')) {
+        if (name === 'dLightCount') {
+            return !!((_a = defines.dIgnoreLight) === null || _a === void 0 ? void 0 : _a.ref.value);
+        }
+    }
+    else {
+        return [
+            'dColorType', 'dUsePalette',
+            'dLightCount',
+            'dOverpaintType', 'dOverpaint',
+            'dSubstanceType', 'dSubstance',
+        ].includes(name);
+    }
+    return false;
+}
+;
+function ignoreDefineUnlit(name, variant, defines) {
+    if (name === 'dLightCount')
+        return true;
+    return ignoreDefine(name, variant, defines);
+}
+;
 var points_vert_1 = require("./shader/points.vert");
 var points_frag_1 = require("./shader/points.frag");
-exports.PointsShaderCode = ShaderCode('points', points_vert_1.points_vert, points_frag_1.points_frag, { drawBuffers: 'optional' });
+exports.PointsShaderCode = ShaderCode('points', points_vert_1.points_vert, points_frag_1.points_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
 var spheres_vert_1 = require("./shader/spheres.vert");
 var spheres_frag_1 = require("./shader/spheres.frag");
-exports.SpheresShaderCode = ShaderCode('spheres', spheres_vert_1.spheres_vert, spheres_frag_1.spheres_frag, { fragDepth: 'required', drawBuffers: 'optional' });
+exports.SpheresShaderCode = ShaderCode('spheres', spheres_vert_1.spheres_vert, spheres_frag_1.spheres_frag, { fragDepth: 'required', drawBuffers: 'optional' }, {}, ignoreDefine);
 var cylinders_vert_1 = require("./shader/cylinders.vert");
 var cylinders_frag_1 = require("./shader/cylinders.frag");
-exports.CylindersShaderCode = ShaderCode('cylinders', cylinders_vert_1.cylinders_vert, cylinders_frag_1.cylinders_frag, { fragDepth: 'required', drawBuffers: 'optional' });
+exports.CylindersShaderCode = ShaderCode('cylinders', cylinders_vert_1.cylinders_vert, cylinders_frag_1.cylinders_frag, { fragDepth: 'required', drawBuffers: 'optional' }, {}, ignoreDefine);
 var text_vert_1 = require("./shader/text.vert");
 var text_frag_1 = require("./shader/text.frag");
-exports.TextShaderCode = ShaderCode('text', text_vert_1.text_vert, text_frag_1.text_frag, { standardDerivatives: 'required', drawBuffers: 'optional' });
+exports.TextShaderCode = ShaderCode('text', text_vert_1.text_vert, text_frag_1.text_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
 var lines_vert_1 = require("./shader/lines.vert");
 var lines_frag_1 = require("./shader/lines.frag");
-exports.LinesShaderCode = ShaderCode('lines', lines_vert_1.lines_vert, lines_frag_1.lines_frag, { drawBuffers: 'optional' });
+exports.LinesShaderCode = ShaderCode('lines', lines_vert_1.lines_vert, lines_frag_1.lines_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
 var mesh_vert_1 = require("./shader/mesh.vert");
 var mesh_frag_1 = require("./shader/mesh.frag");
-exports.MeshShaderCode = ShaderCode('mesh', mesh_vert_1.mesh_vert, mesh_frag_1.mesh_frag, { standardDerivatives: 'optional', drawBuffers: 'optional' });
+exports.MeshShaderCode = ShaderCode('mesh', mesh_vert_1.mesh_vert, mesh_frag_1.mesh_frag, { drawBuffers: 'optional' }, {}, ignoreDefine);
 var direct_volume_vert_1 = require("./shader/direct-volume.vert");
 var direct_volume_frag_1 = require("./shader/direct-volume.frag");
-exports.DirectVolumeShaderCode = ShaderCode('direct-volume', direct_volume_vert_1.directVolume_vert, direct_volume_frag_1.directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' });
+exports.DirectVolumeShaderCode = ShaderCode('direct-volume', direct_volume_vert_1.directVolume_vert, direct_volume_frag_1.directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' }, {}, ignoreDefine);
 var image_vert_1 = require("./shader/image.vert");
 var image_frag_1 = require("./shader/image.frag");
-exports.ImageShaderCode = ShaderCode('image', image_vert_1.image_vert, image_frag_1.image_frag, { drawBuffers: 'optional' });
-function getDefinesCode(defines) {
+exports.ImageShaderCode = ShaderCode('image', image_vert_1.image_vert, image_frag_1.image_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
+function getDefinesCode(defines, ignore) {
+    var _a;
     if (defines === undefined)
         return '';
+    var variant = (((_a = defines.dRenderVariant) === null || _a === void 0 ? void 0 : _a.ref.value) || '');
     var lines = [];
     for (var name_1 in defines) {
+        if (ignore === null || ignore === void 0 ? void 0 : ignore(name_1, variant, defines))
+            continue;
         var define = defines[name_1];
         var v = define.ref.value;
         if (v !== undefined) {
@@ -147,11 +198,9 @@ function getDefinesCode(defines) {
     return lines.join('\n') + '\n';
 }
 function getGlsl100FragPrefix(extensions, shaderExtensions) {
-    var prefix = [];
-    if (shaderExtensions.standardDerivatives) {
-        prefix.push('#extension GL_OES_standard_derivatives : enable');
-        prefix.push('#define enabledStandardDerivatives');
-    }
+    var prefix = [
+        '#extension GL_OES_standard_derivatives : enable'
+    ];
     if (shaderExtensions.fragDepth) {
         if (extensions.fragDepth) {
             prefix.push('#extension GL_EXT_frag_depth : enable');
@@ -192,9 +241,6 @@ function getGlsl300FragPrefix(gl, extensions, shaderExtensions, outTypes) {
         '#version 300 es',
         "layout(location = 0) out highp ".concat(outTypes[0] || 'vec4', " out_FragData0;")
     ];
-    if (shaderExtensions.standardDerivatives) {
-        prefix.push('#define enabledStandardDerivatives');
-    }
     if (shaderExtensions.fragDepth) {
         prefix.push('#define enabledFragDepth');
     }
@@ -215,7 +261,8 @@ function transformGlsl300Frag(frag) {
     return frag.replace(/gl_FragData\[([0-9]+)\]/g, 'out_FragData$1');
 }
 function addShaderDefines(gl, extensions, defines, shaders) {
-    var header = getDefinesCode(defines);
+    var vertHeader = getDefinesCode(defines, shaders.ignoreDefine);
+    var fragHeader = getDefinesCode(defines, shaders.ignoreDefine);
     var vertPrefix = (0, compat_1.isWebGL2)(gl) ? glsl300VertPrefix : '';
     var fragPrefix = (0, compat_1.isWebGL2)(gl)
         ? getGlsl300FragPrefix(gl, extensions, shaders.extensions, shaders.outTypes)
@@ -224,8 +271,8 @@ function addShaderDefines(gl, extensions, defines, shaders) {
     return {
         id: shaderCodeId(),
         name: shaders.name,
-        vert: "".concat(vertPrefix).concat(header).concat(shaders.vert),
-        frag: "".concat(fragPrefix).concat(header).concat(frag),
+        vert: "".concat(vertPrefix).concat(vertHeader).concat(preprocess(shaders.vert, defines)),
+        frag: "".concat(fragPrefix).concat(fragHeader).concat(preprocess(frag, defines)),
         extensions: shaders.extensions,
         outTypes: shaders.outTypes
     };

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

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

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

@@ -18,10 +18,8 @@ function createExtensions(gl) {
         throw new Error('Could not find support for "element_index_uint"');
     }
     var standardDerivatives = (0, compat_1.getStandardDerivatives)(gl);
-    if (debug_1.isDebugMode && standardDerivatives === null) {
-        // - non-support handled downstream (flat shading option is ignored)
-        // - can't be a required extension because it is not supported by `headless-gl`
-        console.log('Could not find support for "standard_derivatives"');
+    if (standardDerivatives === null) {
+        throw new Error('Could not find support for "standard_derivatives"');
     }
     var textureFloat = (0, compat_1.getTextureFloat)(gl);
     if (debug_1.isDebugMode && textureFloat === null) {
@@ -53,11 +51,7 @@ function createExtensions(gl) {
         // - can't be a required extension because it is not supported by `headless-gl`
         console.log('Could not find support for "blend_minmax"');
     }
-    // TODO: revisit
-    // switch off VAO support for now
-    // - https://bugs.chromium.org/p/angleproject/issues/detail?id=6599
-    // - https://bugs.chromium.org/p/chromium/issues/detail?id=1272238
-    var vertexArrayObject = null; // getVertexArrayObject(gl);
+    var vertexArrayObject = (0, compat_1.getVertexArrayObject)(gl);
     if (debug_1.isDebugMode && vertexArrayObject === null) {
         console.log('Could not find support for "vertex_array_object"');
     }

package/lib/commonjs/mol-gl/webgl/render-item.d.ts

@@ -21,18 +21,19 @@ export interface RenderItem<T extends string> {
 declare const GraphicsRenderVariant: {
     colorBlended: string;
     colorWboit: string;
-    pickObject: string;
-    pickInstance: string;
-    pickGroup: string;
+    pick: string;
     depth: string;
-    markingDepth: string;
-    markingMask: string;
+    marking: string;
 };
 export declare type GraphicsRenderVariant = keyof typeof GraphicsRenderVariant;
+export declare const GraphicsRenderVariants: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[];
+export declare const GraphicsRenderVariantsBlended: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[];
+export declare const GraphicsRenderVariantsWboit: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[];
 declare const ComputeRenderVariant: {
     compute: string;
 };
 export declare type ComputeRenderVariant = keyof typeof ComputeRenderVariant;
+export declare const ComputeRenderVariants: "compute"[];
 declare function createValueChanges(): {
     attributes: boolean;
     defines: boolean;
@@ -41,7 +42,7 @@ declare function createValueChanges(): {
 };
 declare type ValueChanges = ReturnType<typeof createValueChanges>;
 export declare type GraphicsRenderItem = RenderItem<GraphicsRenderVariant>;
-export declare function createGraphicsRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number): RenderItem<"depth" | "colorBlended" | "colorWboit" | "pickObject" | "pickInstance" | "pickGroup" | "markingDepth" | "markingMask">;
+export declare function createGraphicsRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number, variants: GraphicsRenderVariant[]): RenderItem<"depth" | "colorBlended" | "colorWboit" | "pick" | "marking">;
 export declare type ComputeRenderItem = RenderItem<ComputeRenderVariant>;
 export declare function createComputeRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId?: number): RenderItem<"compute">;
 /**

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createRenderItem = exports.createComputeRenderItem = exports.createGraphicsRenderItem = exports.getDrawMode = void 0;
+exports.createRenderItem = exports.createComputeRenderItem = exports.createGraphicsRenderItem = exports.ComputeRenderVariants = exports.GraphicsRenderVariantsWboit = exports.GraphicsRenderVariantsBlended = exports.GraphicsRenderVariants = exports.getDrawMode = void 0;
 var tslib_1 = require("tslib");
 var buffer_1 = require("./buffer");
 var texture_1 = require("./texture");
@@ -33,10 +33,12 @@ function getDrawMode(ctx, drawMode) {
 }
 exports.getDrawMode = getDrawMode;
 //
-var GraphicsRenderVariant = { 'colorBlended': '', 'colorWboit': '', 'pickObject': '', 'pickInstance': '', 'pickGroup': '', 'depth': '', 'markingDepth': '', 'markingMask': '' };
-var GraphicsRenderVariants = Object.keys(GraphicsRenderVariant);
-var ComputeRenderVariant = { 'compute': '' };
-var ComputeRenderVariants = Object.keys(ComputeRenderVariant);
+var GraphicsRenderVariant = { colorBlended: '', colorWboit: '', pick: '', depth: '', marking: '' };
+exports.GraphicsRenderVariants = Object.keys(GraphicsRenderVariant);
+exports.GraphicsRenderVariantsBlended = exports.GraphicsRenderVariants.filter(function (v) { return v !== 'colorWboit'; });
+exports.GraphicsRenderVariantsWboit = exports.GraphicsRenderVariants.filter(function (v) { return v !== 'colorBlended'; });
+var ComputeRenderVariant = { compute: '' };
+exports.ComputeRenderVariants = Object.keys(ComputeRenderVariant);
 function createProgramVariant(ctx, variant, defineValues, shaderCode, schema) {
     defineValues = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defineValues), { dRenderVariant: mol_util_1.ValueCell.create(variant) });
     if (schema.dRenderVariant === undefined) {
@@ -58,13 +60,13 @@ function resetValueChanges(valueChanges) {
     valueChanges.elements = false;
     valueChanges.textures = false;
 }
-function createGraphicsRenderItem(ctx, drawMode, shaderCode, schema, values, materialId) {
-    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, GraphicsRenderVariants);
+function createGraphicsRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, variants) {
+    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, variants);
 }
 exports.createGraphicsRenderItem = createGraphicsRenderItem;
 function createComputeRenderItem(ctx, drawMode, shaderCode, schema, values, materialId) {
     if (materialId === void 0) { materialId = -1; }
-    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, ComputeRenderVariants);
+    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, exports.ComputeRenderVariants);
 }
 exports.createComputeRenderItem = createComputeRenderItem;
 /**

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

@@ -51,8 +51,15 @@ function createResources(gl, state, stats, extensions) {
         return wrapCached(shaderCache.get({ type: type, source: source }));
     }
     var programCache = (0, reference_cache_1.createReferenceCache)(function (props) {
+        var _a;
         var array = [props.shaderCode.id];
-        Object.keys(props.defineValues).forEach(function (k) { return array.push((0, util_1.hashString)(k), defineValueHash(props.defineValues[k].ref.value)); });
+        var variant = (((_a = props.defineValues.dRenderVariant) === null || _a === void 0 ? void 0 : _a.ref.value) || '');
+        Object.keys(props.defineValues).forEach(function (k) {
+            var _a, _b;
+            if (!((_b = (_a = props.shaderCode).ignoreDefine) === null || _b === void 0 ? void 0 : _b.call(_a, k, variant, props.defineValues))) {
+                array.push((0, util_1.hashString)(k), defineValueHash(props.defineValues[k].ref.value));
+            }
+        });
         return (0, util_1.hashFnv32a)(array).toString();
     }, function (props) { return wrap('program', (0, program_1.createProgram)(gl, state, extensions, getShader, props)); }, function (program) { program.destroy(); });
     return {
@@ -76,7 +83,7 @@ function createResources(gl, state, stats, extensions) {
             return wrap('texture', (0, texture_1.createTexture)(gl, extensions, kind, format, type, filter));
         },
         vertexArray: function (program, attributeBuffers, elementsBuffer) {
-            return wrap('vertexArray', (0, vertex_array_1.createVertexArray)(extensions, program, attributeBuffers, elementsBuffer));
+            return wrap('vertexArray', (0, vertex_array_1.createVertexArray)(gl, extensions, program, attributeBuffers, elementsBuffer));
         },
         getByteCounts: function () {
             var texture = 0;

package/lib/commonjs/mol-gl/webgl/vertex-array.d.ts

@@ -1,11 +1,12 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Program } from './program';
 import { ElementsBuffer, AttributeBuffers } from './buffer';
 import { WebGLExtensions } from './extensions';
+import { GLRenderingContext } from './compat';
 export interface VertexArray {
     readonly id: number;
     bind: () => void;
@@ -13,4 +14,4 @@ export interface VertexArray {
     reset: () => void;
     destroy: () => void;
 }
-export declare function createVertexArray(extensions: WebGLExtensions, program: Program, attributeBuffers: AttributeBuffers, elementsBuffer?: ElementsBuffer): VertexArray;
+export declare function createVertexArray(gl: GLRenderingContext, extensions: WebGLExtensions, program: Program, attributeBuffers: AttributeBuffers, elementsBuffer?: ElementsBuffer): VertexArray;

package/lib/commonjs/mol-gl/webgl/vertex-array.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -26,7 +26,7 @@ function getVertexArrayObject(extensions) {
     }
     return vertexArrayObject;
 }
-function createVertexArray(extensions, program, attributeBuffers, elementsBuffer) {
+function createVertexArray(gl, extensions, program, attributeBuffers, elementsBuffer) {
     var id = getNextVertexArrayId();
     var vertexArray = getVertexArray(extensions);
     var vertexArrayObject = getVertexArrayObject(extensions);
@@ -53,6 +53,13 @@ function createVertexArray(extensions, program, attributeBuffers, elementsBuffer
         destroy: function () {
             if (destroyed)
                 return;
+            if (elementsBuffer) {
+                // workaround for ANGLE/Chromium bug
+                // - https://bugs.chromium.org/p/angleproject/issues/detail?id=6599
+                // - https://bugs.chromium.org/p/chromium/issues/detail?id=1272238
+                vertexArrayObject.bindVertexArray(vertexArray);
+                gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, null);
+            }
             vertexArrayObject.deleteVertexArray(vertexArray);
             destroyed = true;
         }

package/lib/commonjs/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 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */
@@ -479,7 +479,7 @@ export declare const BIRD_Schema: {
         /**
          * An identifier for the wwPDB site creating or modifying the molecule.
          */
-        processing_site: Schema.Aliased<"PDBe" | "RCSB" | "BMRB" | "PDBJ" | "PDBC">;
+        processing_site: Schema.Aliased<"RCSB" | "PDBE" | "BMRB" | "PDBJ" | "PDBC">;
         /**
          * The action associated with this audit record.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/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 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */
@@ -93,7 +93,7 @@ export declare const CCD_Schema: {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other">;
+        type: Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
         /**
          * Synonym list for the component.
          */
@@ -318,7 +318,7 @@ export declare const CCD_Schema: {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Schema.Aliased<"E" | "Z" | "N">;
+        pdbx_stereo_config: Schema.Aliased<"N" | "E" | "Z">;
         /**
          * A flag indicating an aromatic bond.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

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

@@ -106,7 +106,7 @@ export declare const CifCore_Schema: {
      * Abstracts. This ordering is used in _chemical_formula.moiety
      * and _chemical_formula.sum.
      *
-     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.IUPAC      '[Mo (C O)4 (C18 H33 P)2]'
      * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
      * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
      * _chemical_formula.sum         'C40 H66 Mo O4 P2'
@@ -138,7 +138,7 @@ export declare const CifCore_Schema: {
         sum: Schema.Str;
         /**
          * Mass corresponding to the formulae _chemical_formula.structural,
-         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
          * parameters yield the density given as _exptl_crystal.density_diffrn.
          */
         weight: Schema.Float;
@@ -470,7 +470,7 @@ export declare const CifCore_Schema: {
          * A concatenated series of single-letter codes which indicate the
          * refinement restraints or constraints applied to this site. This
          * item should not be used. It has been replaced by
-         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
          * retained in this dictionary only to provide compatibility with
          * legacy CIFs.
          */
@@ -497,9 +497,9 @@ export declare const CifCore_Schema: {
          * atomic  displacement parameter, U(equiv), in angstroms squared,
          * calculated from anisotropic atomic displacement  parameters.
          *
-         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
          *
-         * a  = the real-space cell lengths
+         * a  = the real-space cell vectors
          * a* = the reciprocal-space cell lengths
          * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
          */
@@ -659,8 +659,11 @@ export declare const CifCore_Aliases: {
     'geom_bond.atom_site_label_1': string[];
     'geom_bond.atom_site_label_2': string[];
     'geom_bond.distance': string[];
+    'audit.block_doi': string[];
     'database_code.cod': string[];
     'database_code.csd': string[];
+    'database_code.depnum_ccdc_archive': string[];
+    'database_code.depnum_ccdc_fiz': string[];
     'database_code.icsd': string[];
     'database_code.mdf': string[];
     'database_code.nbs': string[];

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

@@ -113,7 +113,7 @@ exports.CifCore_Schema = {
      * Abstracts. This ordering is used in _chemical_formula.moiety
      * and _chemical_formula.sum.
      *
-     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.IUPAC      '[Mo (C O)4 (C18 H33 P)2]'
      * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
      * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
      * _chemical_formula.sum         'C40 H66 Mo O4 P2'
@@ -145,7 +145,7 @@ exports.CifCore_Schema = {
         sum: str,
         /**
          * Mass corresponding to the formulae _chemical_formula.structural,
-         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
          * parameters yield the density given as _exptl_crystal.density_diffrn.
          */
         weight: float,
@@ -477,7 +477,7 @@ exports.CifCore_Schema = {
          * A concatenated series of single-letter codes which indicate the
          * refinement restraints or constraints applied to this site. This
          * item should not be used. It has been replaced by
-         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
          * retained in this dictionary only to provide compatibility with
          * legacy CIFs.
          */
@@ -504,9 +504,9 @@ exports.CifCore_Schema = {
          * atomic  displacement parameter, U(equiv), in angstroms squared,
          * calculated from anisotropic atomic displacement  parameters.
          *
-         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
          *
-         * a  = the real-space cell lengths
+         * a  = the real-space cell vectors
          * a* = the reciprocal-space cell lengths
          * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
          */
@@ -681,12 +681,21 @@ exports.CifCore_Aliases = {
     'geom_bond.distance': [
         'geom_bond_dist',
     ],
+    'audit.block_doi': [
+        'audit_block_DOI',
+    ],
     'database_code.cod': [
         'database_code_COD',
     ],
     'database_code.csd': [
         'database_code_CSD',
     ],
+    'database_code.depnum_ccdc_archive': [
+        'database_code_depnum_CCDC_archive',
+    ],
+    'database_code.depnum_ccdc_fiz': [
+        'database_code_depnum_CCDC_fiz',
+    ],
     'database_code.icsd': [
         'database_code_ICSD',
     ],
@@ -697,6 +706,7 @@ exports.CifCore_Aliases = {
         'database_code_NBS',
     ],
     'atom_site.adp_type': [
+        'atom_site_ADP_type',
         'atom_site_thermal_displace_type',
     ],
     'atom_site.label': [

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

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

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

@@ -23,16 +23,16 @@ export declare const mmCIF_chemCompBond_schema: {
     comp_id: Column.Schema.Str;
     value_order: Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
     pdbx_ordinal: Column.Schema.Int;
-    pdbx_stereo_config: Column.Schema.Aliased<"E" | "Z" | "N">;
+    pdbx_stereo_config: Column.Schema.Aliased<"N" | "E" | "Z">;
     pdbx_aromatic_flag: Column.Schema.Aliased<"N" | "Y">;
 };
 /** Has `type` extended with 'Ion' and 'Lipid' */
 export declare const mmCIF_chemComp_schema: {
-    type: Column.Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
+    type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
     formula: Column.Schema.Str;
     formula_weight: Column.Schema.Float;
     id: Column.Schema.Str;
-    mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+    mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
     name: Column.Schema.Str;
     pdbx_synonyms: Column.Schema.List<string>;
 };