molstar 2.3.9 → 2.4.0

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

@@ -3,7 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { getInstancedArrays, getStandardDerivatives, getElementIndexUint, getTextureFloat, getTextureFloatLinear, getBlendMinMax, getFragDepth, getColorBufferFloat, getDrawBuffers, getShaderTextureLod, getDepthTexture, getSRGB, getTextureHalfFloat, getTextureHalfFloatLinear, getColorBufferHalfFloat } from './compat';
+import { getInstancedArrays, getStandardDerivatives, getElementIndexUint, getTextureFloat, getTextureFloatLinear, getBlendMinMax, getFragDepth, getColorBufferFloat, getDrawBuffers, getShaderTextureLod, getDepthTexture, getSRGB, getTextureHalfFloat, getTextureHalfFloatLinear, getColorBufferHalfFloat, getVertexArrayObject } from './compat';
 import { isDebugMode } from '../../mol-util/debug';
 export function createExtensions(gl) {
     var instancedArrays = getInstancedArrays(gl);
@@ -50,11 +50,7 @@ export 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 = getVertexArrayObject(gl);
     if (isDebugMode && vertexArrayObject === null) {
         console.log('Could not find support for "vertex_array_object"');
     }

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

@@ -1 +1 @@
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+{"version":3,"file":"extensions.js","sourceRoot":"","sources":["../../../src/mol-gl/webgl/extensions.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAwG,kBAAkB,EAAE,sBAAsB,EAA6B,mBAAmB,EAAwB,eAAe,EAA+B,qBAAqB,EAAuB,cAAc,EAAE,YAAY,EAAgD,mBAAmB,EAAuB,cAAc,EAAE,mBAAmB,EAA6B,eAAe,EAAqC,OAAO,EAAE,mBAAmB,EAAE,yBAAyB,EAA+F,uBAAuB,EAAE,oBAAoB,EAAE,MAAM,UAAU,CAAC;AAC3vB,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AAsBnD,MAAM,UAAU,gBAAgB,CAAC,EAAsB;IACnD,IAAM,eAAe,GAAG,kBAAkB,CAAC,EAAE,CAAC,CAAC;IAC/C,IAAI,eAAe,KAAK,IAAI,EAAE;QAC1B,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAC;KACpE;IACD,IAAM,gBAAgB,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAC;IACjD,IAAI,gBAAgB,KAAK,IAAI,EAAE;QAC3B,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAC;KACtE;IAED,IAAM,mBAAmB,GAAG,sBAAsB,CAAC,EAAE,CAAC,CAAC;IACvD,IAAI,WAAW,IAAI,mBAAmB,KAAK,IAAI,EAAE;QAC7C,oEAAoE;QACpE,+EAA+E;QAC/E,OAAO,CAAC,GAAG,CAAC,mDAAmD,CAAC,CAAC;KACpE;IACD,IAAM,YAAY,GAAG,eAAe,CAAC,EAAE,CAAC,CAAC;IACzC,IAAI,WAAW,IAAI,YAAY,KAAK,IAAI,EAAE;QACtC,OAAO,CAAC,GAAG,CAAC,4CAA4C,CAAC,CAAC;KAC7D;IACD,IAAM,kBAAkB,GAAG,qBAAqB,CAAC,EAAE,CAAC,CAAC;IACrD,IAAI,WAAW,IAAI,kBAAkB,KAAK,IAAI,EAAE;QAC5C,0EAA0E;QAC1E,+EAA+E;QAC/E,OAAO,CAAC,GAAG,CAAC,mDAAmD,CAAC,CAAC;KACpE;IACD,IAAM,gBAAgB,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAC;IACjD,IAAI,WAAW,IAAI,gBAAgB,KAAK,IAAI,EAAE;QAC1C,OAAO,CAAC,GAAG,CAAC,iDAAiD,CAAC,CAAC;KAClE;IACD,IAAM,sBAAsB,GAAG,yBAAyB,CAAC,EAAE,CAAC,CAAC;IAC7D,IAAI,WAAW,IAAI,sBAAsB,KAAK,IAAI,EAAE;QAChD,0EAA0E;QAC1E,+EAA+E;QAC/E,OAAO,CAAC,GAAG,CAAC,wDAAwD,CAAC,CAAC;KACzE;IACD,IAAM,YAAY,GAAG,eAAe,CAAC,EAAE,CAAC,CAAC;IACzC,IAAI,WAAW,IAAI,YAAY,KAAK,IAAI,EAAE;QACtC,OAAO,CAAC,GAAG,CAAC,4CAA4C,CAAC,CAAC;KAC7D;IACD,IAAM,WAAW,GAAG,cAAc,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,WAAW,IAAI,WAAW,KAAK,IAAI,EAAE;QACrC,iEAAiE;QACjE,+EAA+E;QAC/E,OAAO,CAAC,GAAG,CAAC,2CAA2C,CAAC,CAAC;KAC5D;IACD,IAAM,iBAAiB,GAAG,oBAAoB,CAAC,EAAE,CAAC,CAAC;IACnD,IAAI,WAAW,IAAI,iBAAiB,KAAK,IAAI,EAAE;QAC3C,OAAO,CAAC,GAAG,CAAC,kDAAkD,CAAC,CAAC;KACnE;IACD,IAAM,SAAS,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC;IACnC,IAAI,WAAW,IAAI,SAAS,KAAK,IAAI,EAAE;QACnC,OAAO,CAAC,GAAG,CAAC,yCAAyC,CAAC,CAAC;KAC1D;IACD,IAAM,gBAAgB,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAC;IACjD,IAAI,WAAW,IAAI,gBAAgB,KAAK,IAAI,EAAE;QAC1C,OAAO,CAAC,GAAG,CAAC,iDAAiD,CAAC,CAAC;KAClE;IACD,IAAM,oBAAoB,GAAG,uBAAuB,CAAC,EAAE,CAAC,CAAC;IACzD,IAAI,WAAW,IAAI,oBAAoB,KAAK,IAAI,EAAE;QAC9C,OAAO,CAAC,GAAG,CAAC,sDAAsD,CAAC,CAAC;KACvE;IACD,IAAM,WAAW,GAAG,cAAc,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,WAAW,IAAI,WAAW,KAAK,IAAI,EAAE;QACrC,OAAO,CAAC,GAAG,CAAC,2CAA2C,CAAC,CAAC;KAC5D;IACD,IAAM,gBAAgB,GAAG,mBAAmB,CAAC,EAAE,CAAC,CAAC;IACjD,IAAI,WAAW,IAAI,gBAAgB,KAAK,IAAI,EAAE;QAC1C,OAAO,CAAC,GAAG,CAAC,iDAAiD,CAAC,CAAC;KAClE;IACD,IAAM,IAAI,GAAG,OAAO,CAAC,EAAE,CAAC,CAAC;IACzB,IAAI,WAAW,IAAI,IAAI,KAAK,IAAI,EAAE;QAC9B,OAAO,CAAC,GAAG,CAAC,mCAAmC,CAAC,CAAC;KACpD;IAED,OAAO;QACH,eAAe,iBAAA;QACf,mBAAmB,qBAAA;QACnB,YAAY,cAAA;QACZ,kBAAkB,oBAAA;QAClB,gBAAgB,kBAAA;QAChB,sBAAsB,wBAAA;QACtB,gBAAgB,kBAAA;QAChB,YAAY,cAAA;QAEZ,WAAW,aAAA;QACX,iBAAiB,mBAAA;QACjB,SAAS,WAAA;QACT,gBAAgB,kBAAA;QAChB,oBAAoB,sBAAA;QACpB,WAAW,aAAA;QACX,gBAAgB,kBAAA;QAChB,IAAI,MAAA;KACP,CAAC;AACN,CAAC"}

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

@@ -41,7 +41,7 @@ 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<"colorBlended" | "colorWboit" | "pickObject" | "pickInstance" | "pickGroup" | "depth" | "markingDepth" | "markingMask">;
+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 type ComputeRenderItem = RenderItem<ComputeRenderVariant>;
 export declare function createComputeRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId?: number): RenderItem<"compute">;
 /**

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

@@ -73,7 +73,7 @@ export function createResources(gl, state, stats, extensions) {
             return wrap('texture', createTexture(gl, extensions, kind, format, type, filter));
         },
         vertexArray: function (program, attributeBuffers, elementsBuffer) {
-            return wrap('vertexArray', createVertexArray(extensions, program, attributeBuffers, elementsBuffer));
+            return wrap('vertexArray', createVertexArray(gl, extensions, program, attributeBuffers, elementsBuffer));
         },
         getByteCounts: function () {
             var texture = 0;

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

@@ -1 +1 @@
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package/lib/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/mol-gl/webgl/vertex-array.js

@@ -1,5 +1,5 @@
 /**
- * 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>
  */
@@ -23,7 +23,7 @@ function getVertexArrayObject(extensions) {
     }
     return vertexArrayObject;
 }
-export function createVertexArray(extensions, program, attributeBuffers, elementsBuffer) {
+export function createVertexArray(gl, extensions, program, attributeBuffers, elementsBuffer) {
     var id = getNextVertexArrayId();
     var vertexArray = getVertexArray(extensions);
     var vertexArrayObject = getVertexArrayObject(extensions);
@@ -50,6 +50,13 @@ export function createVertexArray(extensions, program, attributeBuffers, element
         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/mol-gl/webgl/vertex-array.js.map

@@ -1 +1 @@
-{"version":3,"file":"vertex-array.js","sourceRoot":"","sources":["../../../src/mol-gl/webgl/vertex-array.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAC;AAEtD,IAAM,oBAAoB,GAAG,SAAS,EAAE,CAAC;AAEzC,SAAS,cAAc,CAAC,UAA2B;IACvC,IAAA,iBAAiB,GAAK,UAAU,kBAAf,CAAgB;IACzC,IAAI,CAAC,iBAAiB,EAAE;QACpB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACtD;IACD,IAAM,WAAW,GAAG,iBAAiB,CAAC,iBAAiB,EAAE,CAAC;IAC1D,IAAI,CAAC,WAAW,EAAE;QACd,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;KAC1D;IACD,OAAO,WAAW,CAAC;AACvB,CAAC;AAED,SAAS,oBAAoB,CAAC,UAA2B;IAC7C,IAAA,iBAAiB,GAAK,UAAU,kBAAf,CAAgB;IACzC,IAAI,iBAAiB,KAAK,IAAI,EAAE;QAC5B,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACtD;IACD,OAAO,iBAAiB,CAAC;AAC7B,CAAC;AAWD,MAAM,UAAU,iBAAiB,CAAC,UAA2B,EAAE,OAAgB,EAAE,gBAAkC,EAAE,cAA+B;IAChJ,IAAM,EAAE,GAAG,oBAAoB,EAAE,CAAC;IAClC,IAAI,WAAW,GAAG,cAAc,CAAC,UAAU,CAAC,CAAC;IAC7C,IAAI,iBAAiB,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAC;IAEzD,SAAS,MAAM;QACX,iBAAiB,CAAC,eAAe,CAAC,WAAW,CAAC,CAAC;QAC/C,IAAI,cAAc;YAAE,cAAc,CAAC,IAAI,EAAE,CAAC;QAC1C,OAAO,CAAC,cAAc,CAAC,gBAAgB,CAAC,CAAC;QACzC,iBAAiB,CAAC,eAAe,CAAC,IAAI,CAAC,CAAC;IAC5C,CAAC;IAED,MAAM,EAAE,CAAC;IACT,IAAI,SAAS,GAAG,KAAK,CAAC;IAEtB,OAAO;QACH,EAAE,IAAA;QACF,IAAI,EAAE;YACF,iBAAiB,CAAC,eAAe,CAAC,WAAW,CAAC,CAAC;QACnD,CAAC;QACD,MAAM,QAAA;QACN,KAAK,EAAE;YACH,WAAW,GAAG,cAAc,CAAC,UAAU,CAAC,CAAC;YACzC,iBAAiB,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAC;YACrD,MAAM,EAAE,CAAC;QACb,CAAC;QACD,OAAO,EAAE;YACL,IAAI,SAAS;gBAAE,OAAO;YACtB,iBAAiB,CAAC,iBAAiB,CAAC,WAAW,CAAC,CAAC;YACjD,SAAS,GAAG,IAAI,CAAC;QACrB,CAAC;KACJ,CAAC;AACN,CAAC"}
+{"version":3,"file":"vertex-array.js","sourceRoot":"","sources":["../../../src/mol-gl/webgl/vertex-array.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAC;AAGtD,IAAM,oBAAoB,GAAG,SAAS,EAAE,CAAC;AAEzC,SAAS,cAAc,CAAC,UAA2B;IACvC,IAAA,iBAAiB,GAAK,UAAU,kBAAf,CAAgB;IACzC,IAAI,CAAC,iBAAiB,EAAE;QACpB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACtD;IACD,IAAM,WAAW,GAAG,iBAAiB,CAAC,iBAAiB,EAAE,CAAC;IAC1D,IAAI,CAAC,WAAW,EAAE;QACd,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;KAC1D;IACD,OAAO,WAAW,CAAC;AACvB,CAAC;AAED,SAAS,oBAAoB,CAAC,UAA2B;IAC7C,IAAA,iBAAiB,GAAK,UAAU,kBAAf,CAAgB;IACzC,IAAI,iBAAiB,KAAK,IAAI,EAAE;QAC5B,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACtD;IACD,OAAO,iBAAiB,CAAC;AAC7B,CAAC;AAWD,MAAM,UAAU,iBAAiB,CAAC,EAAsB,EAAE,UAA2B,EAAE,OAAgB,EAAE,gBAAkC,EAAE,cAA+B;IACxK,IAAM,EAAE,GAAG,oBAAoB,EAAE,CAAC;IAClC,IAAI,WAAW,GAAG,cAAc,CAAC,UAAU,CAAC,CAAC;IAC7C,IAAI,iBAAiB,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAC;IAEzD,SAAS,MAAM;QACX,iBAAiB,CAAC,eAAe,CAAC,WAAW,CAAC,CAAC;QAC/C,IAAI,cAAc;YAAE,cAAc,CAAC,IAAI,EAAE,CAAC;QAC1C,OAAO,CAAC,cAAc,CAAC,gBAAgB,CAAC,CAAC;QACzC,iBAAiB,CAAC,eAAe,CAAC,IAAI,CAAC,CAAC;IAC5C,CAAC;IAED,MAAM,EAAE,CAAC;IACT,IAAI,SAAS,GAAG,KAAK,CAAC;IAEtB,OAAO;QACH,EAAE,IAAA;QACF,IAAI,EAAE;YACF,iBAAiB,CAAC,eAAe,CAAC,WAAW,CAAC,CAAC;QACnD,CAAC;QACD,MAAM,QAAA;QACN,KAAK,EAAE;YACH,WAAW,GAAG,cAAc,CAAC,UAAU,CAAC,CAAC;YACzC,iBAAiB,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAC;YACrD,MAAM,EAAE,CAAC;QACb,CAAC;QACD,OAAO,EAAE;YACL,IAAI,SAAS;gBAAE,OAAO;YACtB,IAAI,cAAc,EAAE;gBAChB,oCAAoC;gBACpC,mEAAmE;gBACnE,kEAAkE;gBAClE,iBAAiB,CAAC,eAAe,CAAC,WAAW,CAAC,CAAC;gBAC/C,EAAE,CAAC,UAAU,CAAC,EAAE,CAAC,oBAAoB,EAAE,IAAI,CAAC,CAAC;aAChD;YACD,iBAAiB,CAAC,iBAAiB,CAAC,WAAW,CAAC,CAAC;YACjD,SAAS,GAAG,IAAI,CAAC;QACrB,CAAC;KACJ,CAAC;AACN,CAAC"}

package/lib/mol-io/common/typed-array.d.ts

@@ -25,6 +25,6 @@ export interface TypedArrayBufferContext {
 }
 export declare function getElementByteSize(type: TypedArrayValueType): 1 | 2 | 4;
 export declare function makeTypedArray(type: TypedArrayValueType, buffer: ArrayBuffer, byteOffset?: number, length?: number): TypedArrayValueArray;
-export declare function createTypedArray(type: TypedArrayValueType, size: number): Int8Array | Int16Array | Uint16Array | Float32Array;
+export declare function createTypedArray(type: TypedArrayValueType, size: number): Float32Array | Uint16Array | Int8Array | Int16Array;
 export declare function createTypedArrayBufferContext(size: number, type: TypedArrayValueType): TypedArrayBufferContext;
 export declare function readTypedArray(ctx: TypedArrayBufferContext, file: FileHandle, position: number, byteCount: number, valueByteOffset: number, littleEndian?: boolean): Promise<TypedArrayValueArray>;

package/lib/mol-io/reader/_spec/sdf.spec.js

@@ -1,6 +1,7 @@
 import { __awaiter, __generator } from "tslib";
 import { parseSdf } from '../sdf/parser';
 var SdfString = "\n  Mrv1718007121815122D\n\n  5  4  0  0  0  0            999 V2000\n    0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n    0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n  4  1  1  0  0  0  0\n  4  2  2  0  0  0  0\n  4  3  1  0  0  0  0\n  4  5  1  0  0  0  0\nM  CHG  3   1  -1   3  -1   5  -1\nM  END\n> <DATABASE_ID>\n0\n\n> <DATABASE_NAME>\ndrugbank\n\n> 5225 <TEST_FIELD>\nwhatever\n\n> <INCHI_IDENTIFIER>\nInChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3\n\n> <INCHI_KEY>\nNBIIXXVUZAFLBC-UHFFFAOYSA-K\n\n> <FORMULA>\nO4P\n\n> <MOLECULAR_WEIGHT>\n94.9714\n\n> <EXACT_MASS>\n94.95342\n\n> <JCHEM_ACCEPTOR_COUNT>\n4\n\n> <JCHEM_ATOM_COUNT>\n5\n\n> <JCHEM_AVERAGE_POLARIZABILITY>\n4.932162910070488\n\n> <JCHEM_BIOAVAILABILITY>\n1\n\n> <JCHEM_DONOR_COUNT>\n0\n\n> <JCHEM_FORMAL_CHARGE>\n-3\n\n> <JCHEM_GHOSE_FILTER>\n0\n\n> <JCHEM_IUPAC>\nphosphate\n\n> <JCHEM_LOGP>\n-1.0201038226666665\n\n> <JCHEM_MDDR_LIKE_RULE>\n0\n\n> <JCHEM_NUMBER_OF_RINGS>\n0\n\n> <JCHEM_PHYSIOLOGICAL_CHARGE>\n-2\n\n> <JCHEM_PKA>\n6.951626889535468\n\n> <JCHEM_PKA_STRONGEST_ACIDIC>\n1.7961261340181292\n\n> <JCHEM_POLAR_SURFACE_AREA>\n86.25\n\n> <JCHEM_REFRACTIVITY>\n11.2868\n\n> <JCHEM_ROTATABLE_BOND_COUNT>\n0\n\n> <JCHEM_RULE_OF_FIVE>\n1\n\n> <JCHEM_TRADITIONAL_IUPAC>\nphosphate\n\n> <JCHEM_VEBER_RULE>\n0\n\n> <DRUGBANK_ID>\nDB14523\n\n> <DRUG_GROUPS>\nexperimental\n\n> <GENERIC_NAME>\nPhosphate ion\n\n> <SYNONYMS>\nOrthophosphate; Phosphate\n\n$$$$\n\nComp 2\n\n5  4  0  0  0  0            999 V2000\n  0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n  0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n4  1  1  0  0  0  0\n4  2  2  0  0  0  0\n4  3  1  0  0  0  0\n4  5  1  0  0  0  0\nM  CHG  3   1  -1   3  -1   5  -1\nM  END\n> <DATABASE_ID>\n1\n\n$$$$\n\n2244\n  -OEChem-04122119123D\n\n 21 21  0     0  0  0  0  0  0999 V2000\n    1.2333    0.5540    0.7792 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6952   -2.7148   -0.7502 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7958   -2.1843    0.8685 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7813    0.8105   -1.4821 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0857    0.6088    0.4403 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7927   -0.5515    0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7288    1.8464    0.4133 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1426   -0.4741   -0.2184 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.0787    1.9238    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7855    0.7636   -0.2453 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1409   -1.8536    0.1477 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1094    0.6715   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5305    0.5996    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1851    2.7545    0.6593 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7247   -1.3605   -0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5797    2.8872    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.8374    0.8238   -0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7290    1.4184    0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.2045    0.6969   -0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7105   -0.3659    0.6426 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.2555   -3.5916   -0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  5  1  0  0  0  0\n  1 12  1  0  0  0  0\n  2 11  1  0  0  0  0\n  2 21  1  0  0  0  0\n  3 11  2  0  0  0  0\n  4 12  2  0  0  0  0\n  5  6  1  0  0  0  0\n  5  7  2  0  0  0  0\n  6  8  2  0  0  0  0\n  6 11  1  0  0  0  0\n  7  9  1  0  0  0  0\n  7 14  1  0  0  0  0\n  8 10  1  0  0  0  0\n  8 15  1  0  0  0  0\n  9 10  2  0  0  0  0\n  9 16  1  0  0  0  0\n 10 17  1  0  0  0  0\n 12 13  1  0  0  0  0\n 13 18  1  0  0  0  0\n 13 19  1  0  0  0  0\n 13 20  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_CID>\n2244\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.6\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n11\n10\n3\n15\n17\n13\n5\n16\n7\n14\n9\n8\n4\n18\n6\n12\n2\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n18\n1 -0.23\n10 -0.15\n11 0.63\n12 0.66\n13 0.06\n14 0.15\n15 0.15\n16 0.15\n17 0.15\n2 -0.65\n21 0.5\n3 -0.57\n4 -0.57\n5 0.08\n6 0.09\n7 -0.15\n8 -0.15\n9 -0.15\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n3\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n5\n1 2 acceptor\n1 3 acceptor\n1 4 acceptor\n3 2 3 11 anion\n6 5 6 7 8 9 10 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n13\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n000008C400000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n39.5952\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n25.432\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n1 1 18265615372930943622\n100427 49 16967750034970055351\n12138202 97 18271247217817981012\n12423570 1 16692715976000295083\n12524768 44 16753525617747228747\n12716758 59 18341332292274886536\n13024252 1 17968377969333732145\n14181834 199 17830728755827362645\n14614273 12 18262232214645093005\n15207287 21 17703787037639964108\n15775835 57 18340488876329928641\n16945 1 18271533103414939405\n193761 8 17907860604865584321\n20645476 183 17677348215414174190\n20871998 184 18198632231250704846\n21040471 1 18411412921197846465\n21501502 16 18123463883164380929\n23402539 116 18271795865171824860\n23419403 2 13539898140662769886\n23552423 10 18048876295495619569\n23559900 14 18272369794190581304\n241688 4 16179044415907240795\n257057 1 17478316999871287486\n2748010 2 18339085878070479087\n305870 269 18263645056784260212\n528862 383 18117272558388284091\n53812653 8 18410289211719108569\n7364860 26 17910392788380644719\n81228 2 18050568744116491203\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n244.06\n3.86\n2.45\n0.89\n1.95\n1.58\n0.15\n-1.85\n0.38\n-0.61\n-0.02\n0.29\n0.01\n-0.33\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n513.037\n\n> <PUBCHEM_SHAPE_VOLUME>\n136\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n";
+var V3000SdfString = "FYI-001\nFYICenter.com\n123456789012345678901234567890123456789012345678901234567890\n 0  0  0     0  0            999 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 13 14 0 0 0\nM  V30 BEGIN ATOM\nM  V30 1 N 0.84 -0.16 0 0\nM  V30 2 N 1.48 0.43 0 0\nM  V30 3 N 0.09 0.27 0 0\nM  V30 4 C 1.11 1.21 0 0\nM  V30 5 C 0.27 1.12 0 0\nM  V30 6 C 0.84 -1.03 0 0\nM  V30 7 C 1.53 1.99 0 0\nM  V30 8 Cl 1.07 2.74 0.01 0\nM  V30 9 C 1.59 -1.46 0 0\nM  V30 10 C 0.08 -1.46 0 0\nM  V30 11 C 1.59 -2.33 0 0\nM  V30 12 C 0.07 -2.32 0 0\nM  V30 13 C 0.84 -2.76 0 0\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 1 1 2 1\nM  V30 2 1 3 1\nM  V30 3 1 6 1\nM  V30 4 2 4 2\nM  V30 5 2 5 3\nM  V30 6 1 7 4\nM  V30 7 1 4 5\nM  V30 8 1 9 6\nM  V30 9 2 10 6\nM  V30 10 1 8 7\nM  V30 11 2 11 9\nM  V30 12 1 12 10\nM  V30 13 1 13 11\nM  V30 14 2 13 12\nM  V30 END BOND\nM  V30 END CTAB\nM  END\n> <Comment>\nThis is an SDF example.\nWith a multi-line comment.\n\n> <source>\nThis was retrieved from biotech.fyicenter.com\n\n$$$$\nL-Alanine\nGSMACCS-II07189510252D 1 0.00366 0.00000 0\nFigure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992\n 0 0 0 0 0 999 V3000\nM V30 BEGIN CTAB\nM V30 COUNTS 6 5 0 0 1\nM V30 BEGIN ATOM\nM V30 1 C -0.6622 0.5342 0 0 CFG=2\nM V30 2 C 0.6622 -0.3 0 0\nM V30 3 C -0.7207 2.0817 0 0 MASS=13\nM V30 4 N -1.8622 -0.3695 0 0 CHG=1\nM V30 5 O 0.622 -1.8037 0 0\nM V30 6 O 1.9464 0.4244 0 0 CHG=-1\nM V30 END ATOM\nM V30 BEGIN BOND\nM V30 1 1 1 2\nM V30 2 1 1 3 CFG=1\nM V30 3 1 1 4\nM V30 4 2 2 5\nM V30 5 1 2 6\nM V30 END BOND\nM V30 END CTAB\nM END\n\n$$$$\n";
 describe('sdf reader', function () {
     it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
         var parsed, compound1, compound2, compound3, molFile, dataItems, atoms, bonds;
@@ -48,5 +49,55 @@ describe('sdf reader', function () {
             }
         });
     }); });
+    it('v3000', function () { return __awaiter(void 0, void 0, void 0, function () {
+        var parsed, compound1, compound2;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, parseSdf(V3000SdfString).run()];
+                case 1:
+                    parsed = _a.sent();
+                    if (parsed.isError) {
+                        throw new Error(parsed.message);
+                    }
+                    expect(parsed.result.compounds.length).toBe(2);
+                    compound1 = parsed.result.compounds[0];
+                    expect(compound1.molFile.atoms.count).toBe(13);
+                    expect(compound1.molFile.atoms.x.rowCount).toBe(13);
+                    expect(compound1.molFile.atoms.y.rowCount).toBe(13);
+                    expect(compound1.molFile.atoms.z.rowCount).toBe(13);
+                    expect(compound1.molFile.atoms.type_symbol.rowCount).toBe(13);
+                    expect(compound1.molFile.bonds.count).toBe(14);
+                    expect(compound1.molFile.bonds.atomIdxA.rowCount).toBe(14);
+                    expect(compound1.molFile.bonds.atomIdxB.rowCount).toBe(14);
+                    expect(compound1.molFile.bonds.order.rowCount).toBe(14);
+                    expect(compound1.molFile.atoms.x.value(7)).toBe(1.07);
+                    expect(compound1.molFile.atoms.y.value(7)).toBe(2.74);
+                    expect(compound1.molFile.atoms.z.value(7)).toBe(0.01);
+                    expect(compound1.molFile.atoms.type_symbol.value(7)).toBe('Cl');
+                    expect(compound1.molFile.bonds.atomIdxA.value(10)).toBe(11);
+                    expect(compound1.molFile.bonds.atomIdxB.value(10)).toBe(9);
+                    expect(compound1.molFile.bonds.order.value(10)).toBe(2);
+                    expect(compound1.dataItems.dataHeader.rowCount).toBe(2);
+                    expect(compound1.dataItems.data.rowCount).toBe(2);
+                    expect(compound1.dataItems.dataHeader.value(0)).toBe('<Comment>');
+                    expect(compound1.dataItems.data.value(0)).toBe("This is an SDF example.\nWith a multi-line comment.");
+                    expect(compound1.dataItems.dataHeader.value(1)).toBe('<source>');
+                    expect(compound1.dataItems.data.value(1)).toBe('This was retrieved from biotech.fyicenter.com');
+                    compound2 = parsed.result.compounds[1];
+                    expect(compound2.molFile.atoms.count).toBe(6);
+                    expect(compound2.molFile.bonds.count).toBe(5);
+                    expect(compound2.molFile.atoms.x.value(4)).toBe(0.622);
+                    expect(compound2.molFile.atoms.y.value(4)).toBe(-1.8037);
+                    expect(compound2.molFile.atoms.z.value(4)).toBe(0);
+                    expect(compound2.molFile.atoms.type_symbol.value(4)).toBe('O');
+                    expect(compound2.molFile.bonds.atomIdxA.value(1)).toBe(1);
+                    expect(compound2.molFile.bonds.atomIdxB.value(1)).toBe(3);
+                    expect(compound2.molFile.bonds.order.value(1)).toBe(1);
+                    expect(compound2.dataItems.dataHeader.rowCount).toBe(0);
+                    expect(compound2.dataItems.data.rowCount).toBe(0);
+                    return [2 /*return*/];
+            }
+        });
+    }); });
 });
 //# sourceMappingURL=sdf.spec.js.map

package/lib/mol-io/reader/_spec/sdf.spec.js.map

@@ -1 +1 @@
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+{"version":3,"file":"sdf.spec.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/_spec/sdf.spec.ts"],"names":[],"mappings":";AACA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,IAAM,SAAS,GAAG,+1MAyUjB,CAAC;AAEF,IAAM,cAAc,GAAG,shDAwEtB,CAAC;AAEF,QAAQ,CAAC,YAAY,EAAE;IACnB,EAAE,CAAC,OAAO,EAAE;;;;wBACO,qBAAM,QAAQ,CAAC,SAAS,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAAxC,MAAM,GAAG,SAA+B;oBAC9C,IAAI,MAAM,CAAC,OAAO,EAAE;wBAChB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;qBACnC;oBACK,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBACvC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBACvC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBACrC,OAAO,GAAgB,SAAS,QAAzB,EAAE,SAAS,GAAK,SAAS,UAAd,CAAe;oBACjC,KAAK,GAAY,OAAO,MAAnB,EAAE,KAAK,GAAK,OAAO,MAAZ,CAAa;oBAEjC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAE/C,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC5B,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAE5B,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC9C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAE9C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;oBAC/C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;oBACrD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC;oBAChD,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAE7C,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAErC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC;oBAC5D,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAE1C,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;oBAC9D,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;oBAEjD,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC;oBAChE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;oBAEjD,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;oBAC1D,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;oBAEnE,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAEpD,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,kCAAkC,CAAC,CAAC;oBACzF,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,+DAA+D,CAAC,CAAC;oBAEhH,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;oBACnF,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;;;;SAC/D,CAAC,CAAC;IAEH,EAAE,CAAC,OAAO,EAAE;;;;wBACO,qBAAM,QAAQ,CAAC,cAAc,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAA7C,MAAM,GAAG,SAAoC;oBACnD,IAAI,MAAM,CAAC,OAAO,EAAE;wBAChB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;qBACnC;oBAED,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAEzC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC/C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC9D,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC/C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC3D,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC3D,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAExD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACtD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACtD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACtD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBAEhE,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC5D,MAAM,C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package/lib/mol-io/reader/cif/schema/bird.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @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<"RCSB" | "BMRB" | "PDBJ" | "PDBC" | "PDBe">;
+        processing_site: Schema.Aliased<"RCSB" | "PDBE" | "BMRB" | "PDBJ" | "PDBC">;
         /**
          * The action associated with this audit record.
          */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -110,7 +110,7 @@ export var 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'
@@ -142,7 +142,7 @@ export var 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,
@@ -474,7 +474,7 @@ export var 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.
          */
@@ -501,9 +501,9 @@ export var 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.
          */
@@ -678,12 +678,21 @@ export var 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',
     ],
@@ -694,6 +703,7 @@ export var CifCore_Aliases = {
         'database_code_NBS',
     ],
     'atom_site.adp_type': [
+        'atom_site_ADP_type',
         'atom_site_thermal_displace_type',
     ],
     'atom_site.label': [

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

@@ -1 +1 @@
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package/lib/mol-io/reader/cif/schema/mmcif-extras.d.ts

@@ -32,7 +32,7 @@ export declare const mmCIF_chemComp_schema: {
     formula: Column.Schema.Str;
     formula_weight: Column.Schema.Float;
     id: Column.Schema.Str;
-    mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+    mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
     name: Column.Schema.Str;
     pdbx_synonyms: Column.Schema.List<string>;
 };

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -478,7 +478,7 @@ export declare const mmCIF_Schema: {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * The full name of the component.
          */
@@ -786,12 +786,12 @@ export declare const mmCIF_Schema: {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_linkage: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        nstd_monomer: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * The type of the polymer.
          */
@@ -885,7 +885,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -1886,7 +1886,7 @@ export declare const mmCIF_Schema: {
         /**
          * The identifying content type of the related entry.
          */
-        content_type: Schema.Aliased<"split" | "other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "re-refinement" | "complete structure" | "unspecified">;
+        content_type: Schema.Aliased<"other" | "minimized average structure" | "representative structure" | "ensemble" | "derivative structure" | "native structure" | "associated EM volume" | "other EM volume" | "associated NMR restraints" | "associated structure factors" | "associated SAS data" | "protein target sequence and/or protocol data" | "split" | "re-refinement" | "complete structure" | "unspecified">;
     };
     /**
      * The PDBX_ENTITY_NONPOLY category provides a mapping between
@@ -1974,7 +1974,7 @@ export declare const mmCIF_Schema: {
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
          */
-        occupancy_flag: Schema.Aliased<"0" | "1">;
+        occupancy_flag: Schema.Aliased<"1" | "0">;
         /**
          * Part of the identifier for the unobserved or zero occupancy residue.
          *
@@ -2660,7 +2660,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2779,7 +2779,7 @@ export declare const mmCIF_Schema: {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        hetero: Schema.Aliased<"no" | "n" | "yes" | "y">;
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3083,7 +3083,7 @@ export declare const mmCIF_Schema: {
         /**
          * The primitive object used to model this segment.
          */
-        model_object_primitive: Schema.Aliased<"sphere" | "other" | "atomistic" | "gaussian">;
+        model_object_primitive: Schema.Aliased<"other" | "atomistic" | "sphere" | "gaussian">;
         /**
          * The identifier for the starting structural model.
          * This data item is a pointer to _ihm_starting_model_details.starting_model_id
@@ -3343,11 +3343,11 @@ export declare const mmCIF_Schema: {
         /**
          * The type of post modeling analysis being carried out.
          */
-        type: Schema.Aliased<"none" | "filter" | "other" | "cluster" | "rescore" | "validation">;
+        type: Schema.Aliased<"other" | "filter" | "cluster" | "rescore" | "validation" | "none">;
         /**
          * The parameter/feature used in the post modeling analysis.
          */
-        feature: Schema.Aliased<"none" | "other" | "energy/score" | "RMSD" | "dRMSD">;
+        feature: Schema.Aliased<"other" | "none" | "energy/score" | "RMSD" | "dRMSD">;
         /**
          * The number of models at the beginning of the post processing step.
          */
@@ -3566,7 +3566,7 @@ export declare const mmCIF_Schema: {
         /**
          * The application / utilization of the dataset group in modeling.
          */
-        application: Schema.Aliased<"filter" | "other" | "validation" | "restraint" | "representation" | "sampling">;
+        application: Schema.Aliased<"other" | "filter" | "validation" | "restraint" | "representation" | "sampling">;
         /**
          * Additional details regarding the dataset group.
          */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

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

package/lib/mol-io/reader/sdf/parser-v3-util.d.ts

@@ -0,0 +1,9 @@
+import { MolFile } from '../mol/parser';
+import { Tokenizer } from '../common/text/tokenizer';
+export declare function isV3(versionLine: string): boolean;
+export declare function handleCountsV3(tokenizer: Tokenizer): {
+    atomCount: number;
+    bondCount: number;
+};
+export declare function handleAtomsV3(tokenizer: Tokenizer, atomCount: number): MolFile['atoms'];
+export declare function handleBondsV3(tokenizer: Tokenizer, bondCount: number): MolFile['bonds'];