molstar 2.3.6 → 2.4.0

package/lib/commonjs/mol-io/reader/cif/text/parser.js

@@ -587,7 +587,7 @@ function handleLoop(tokenizer, ctx) {
                         return [2 /*return*/, {
                                 hasError: true,
                                 errorLine: tokenizer.lineNumber,
-                                errorMessage: "The number of values for loop starting at line " + loopLine + " is not a multiple of the number of columns."
+                                errorMessage: "The number of values for loop starting at line ".concat(loopLine, " is not a multiple of the number of columns.")
                             }];
                     }
                     rowCount = (state.tokenCount / fieldCount) | 0;
@@ -707,7 +707,7 @@ function parseInternal(data, runtimeCtx) {
                 case 7:
                     // Check if the latest save frame was closed.
                     if (tokenizer.inSaveFrame) {
-                        return [2 /*return*/, error(tokenizer.lineNumber, "Unfinished save frame (" + saveFrame.header + ").")];
+                        return [2 /*return*/, error(tokenizer.lineNumber, "Unfinished save frame (".concat(saveFrame.header, ")."))];
                     }
                     if (blockCtx.categoryNames.length > 0 || saveFrames.length > 0) {
                         dataBlocks.push(CifBlock(blockCtx, blockHeader, saveFrames));

package/lib/commonjs/mol-io/reader/cif/text/parser.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-io/reader/dcd/parser.js

@@ -125,7 +125,7 @@ function _parseDcd(data) {
         // xyz coordinates
         for (var j = 0; j < 3; ++j) {
             if (dv.getInt32(nextPos, ef) !== natom4) {
-                throw new Error("dcd bad format, coord block start: " + i + ", " + j);
+                throw new Error("dcd bad format, coord block start: ".concat(i, ", ").concat(j));
             }
             nextPos += 4; // block start
             var c = new Float32Array(data.buffer, nextPos, natom);
@@ -137,7 +137,7 @@ function _parseDcd(data) {
                 frame.z = c;
             nextPos += natom4;
             if (dv.getInt32(nextPos, ef) !== natom4) {
-                throw new Error("dcd bad format, coord block end: " + i + ", " + j);
+                throw new Error("dcd bad format, coord block end: ".concat(i, ", ").concat(j));
             }
             nextPos += 4; // block end
         }

package/lib/commonjs/mol-io/reader/dcd/parser.js.map

@@ -1 +1 @@
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package/lib/commonjs/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): "int" | "float" | "float32" | "int32" | "uint16" | "uint32" | "uint8" | "int8" | "int16" | "ushort" | "short" | "double" | "char" | "uchar" | "uint" | "float64";
+export declare function PlyType(str: string): "ushort" | "float" | "int" | "float32" | "int32" | "uint32" | "uint16" | "int8" | "int16" | "char" | "uchar" | "short" | "uint" | "double" | "uint8" | "float64";
 export interface PlyFile {
     readonly comments: ReadonlyArray<string>;
     readonly elementNames: ReadonlyArray<string>;

package/lib/commonjs/mol-io/reader/ply/schema.js

@@ -29,7 +29,7 @@ exports.PlyTypeByteLength = {
 exports.PlyTypes = new Set(Object.keys(exports.PlyTypeByteLength));
 function PlyType(str) {
     if (!exports.PlyTypes.has(str))
-        throw new Error("unknown ply type '" + str + "'");
+        throw new Error("unknown ply type '".concat(str, "'"));
     return str;
 }
 exports.PlyType = PlyType;

package/lib/commonjs/mol-io/reader/ply/schema.js.map

@@ -1 +1 @@
-{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../../../../src/mol-io/reader/ply/schema.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAIH,yCAAyC;AACzC,kDAAkD;AAErC,QAAA,iBAAiB,GAAG;IAC7B,MAAM,EAAE,CAAC;IACT,OAAO,EAAE,CAAC;IACV,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IACX,KAAK,EAAE,CAAC;IACR,MAAM,EAAE,CAAC;IACT,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IAEX,MAAM,EAAE,CAAC;IACT,OAAO,EAAE,CAAC;IACV,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IACX,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IACX,SAAS,EAAE,CAAC;IACZ,SAAS,EAAE,CAAC;CACf,CAAC;AAEW,QAAA,QAAQ,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,yBAAiB,CAAC,CAAC,CAAC;AAChE,SAAgB,OAAO,CAAC,GAAW;IAC/B,IAAI,CAAC,gBAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,MAAM,IAAI,KAAK,CAAC,uBAAqB,GAAG,MAAG,CAAC,CAAC;IACrE,OAAO,GAAc,CAAC;AAC1B,CAAC;AAHD,0BAGC;AAQD,SAAgB,OAAO,CAAC,QAAsB,EAAE,YAAsB,EAAE,QAAkB;IACtF,IAAM,UAAU,GAAG,IAAI,GAAG,EAAsB,CAAC;IACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,EAAE;QACnD,UAAU,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;KAChD;IACD,OAAO;QACH,QAAQ,UAAA;QACR,YAAY,cAAA;QACZ,UAAU,EAAE,UAAC,IAAY;YACrB,OAAO,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAChC,CAAC;KACJ,CAAC;AACN,CAAC;AAZD,0BAYC"}
+{"version":3,"file":"schema.js","sourceRoot":"","sources":["../../../../../src/mol-io/reader/ply/schema.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAIH,yCAAyC;AACzC,kDAAkD;AAErC,QAAA,iBAAiB,GAAG;IAC7B,MAAM,EAAE,CAAC;IACT,OAAO,EAAE,CAAC;IACV,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IACX,KAAK,EAAE,CAAC;IACR,MAAM,EAAE,CAAC;IACT,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IAEX,MAAM,EAAE,CAAC;IACT,OAAO,EAAE,CAAC;IACV,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IACX,OAAO,EAAE,CAAC;IACV,QAAQ,EAAE,CAAC;IACX,SAAS,EAAE,CAAC;IACZ,SAAS,EAAE,CAAC;CACf,CAAC;AAEW,QAAA,QAAQ,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,yBAAiB,CAAC,CAAC,CAAC;AAChE,SAAgB,OAAO,CAAC,GAAW;IAC/B,IAAI,CAAC,gBAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,MAAM,IAAI,KAAK,CAAC,4BAAqB,GAAG,MAAG,CAAC,CAAC;IACrE,OAAO,GAAc,CAAC;AAC1B,CAAC;AAHD,0BAGC;AAQD,SAAgB,OAAO,CAAC,QAAsB,EAAE,YAAsB,EAAE,QAAkB;IACtF,IAAM,UAAU,GAAG,IAAI,GAAG,EAAsB,CAAC;IACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,EAAE;QACnD,UAAU,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;KAChD;IACD,OAAO;QACH,QAAQ,UAAA;QACR,YAAY,cAAA;QACZ,UAAU,EAAE,UAAC,IAAY;YACrB,OAAO,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAChC,CAAC;KACJ,CAAC;AACN,CAAC;AAZD,0BAYC"}

package/lib/commonjs/mol-io/reader/result.js

@@ -27,7 +27,7 @@ var ReaderResult;
         }
         Error.prototype.toString = function () {
             if (this.line >= 0) {
-                return "[Line " + this.line + "] " + this.message;
+                return "[Line ".concat(this.line, "] ").concat(this.message);
             }
             return this.message;
         };

package/lib/commonjs/mol-io/reader/result.js.map

@@ -1 +1 @@
-{"version":3,"file":"result.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/result.ts"],"names":[],"mappings":";AAAA;;;;;GAKG;;;AAIH,IAAU,YAAY,CA8BrB;AA9BD,WAAU,YAAY;IAClB,SAAgB,KAAK,CAAI,OAAe,EAAE,IAAS;QAAT,qBAAA,EAAA,QAAQ,CAAC;QAC/C,OAAO,IAAI,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IACpC,CAAC;IAFe,kBAAK,QAEpB,CAAA;IAED,SAAgB,OAAO,CAAI,MAAS,EAAE,QAAuB;QAAvB,yBAAA,EAAA,aAAuB;QACzD,OAAO,IAAI,OAAO,CAAI,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC5C,CAAC;IAFe,oBAAO,UAEtB,CAAA;IAED;QAUI,eACW,OAAe,EACf,IAAY;YADZ,YAAO,GAAP,OAAO,CAAQ;YACf,SAAI,GAAJ,IAAI,CAAQ;YAXvB,YAAO,GAAS,IAAI,CAAC;QAYrB,CAAC;QAVD,wBAAQ,GAAR;YACI,IAAI,IAAI,CAAC,IAAI,IAAI,CAAC,EAAE;gBAChB,OAAO,WAAS,IAAI,CAAC,IAAI,UAAK,IAAI,CAAC,OAAS,CAAC;aAChD;YACD,OAAO,IAAI,CAAC,OAAO,CAAC;QACxB,CAAC;QAML,YAAC;IAAD,CAAC,AAdD,IAcC;IAdY,kBAAK,QAcjB,CAAA;IAED;QAGI,iBAAmB,MAAS,EAAS,QAAkB;YAApC,WAAM,GAAN,MAAM,CAAG;YAAS,aAAQ,GAAR,QAAQ,CAAU;YAFvD,YAAO,GAAU,KAAK,CAAC;QAEoC,CAAC;QAChE,cAAC;IAAD,CAAC,AAJD,IAIC;IAJY,oBAAO,UAInB,CAAA;AACL,CAAC,EA9BS,YAAY,KAAZ,YAAY,QA8BrB;AAEQ,oCAAY"}
+{"version":3,"file":"result.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/result.ts"],"names":[],"mappings":";AAAA;;;;;GAKG;;;AAIH,IAAU,YAAY,CA8BrB;AA9BD,WAAU,YAAY;IAClB,SAAgB,KAAK,CAAI,OAAe,EAAE,IAAS;QAAT,qBAAA,EAAA,QAAQ,CAAC;QAC/C,OAAO,IAAI,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;IACpC,CAAC;IAFe,kBAAK,QAEpB,CAAA;IAED,SAAgB,OAAO,CAAI,MAAS,EAAE,QAAuB;QAAvB,yBAAA,EAAA,aAAuB;QACzD,OAAO,IAAI,OAAO,CAAI,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC5C,CAAC;IAFe,oBAAO,UAEtB,CAAA;IAED;QAUI,eACW,OAAe,EACf,IAAY;YADZ,YAAO,GAAP,OAAO,CAAQ;YACf,SAAI,GAAJ,IAAI,CAAQ;YAXvB,YAAO,GAAS,IAAI,CAAC;QAYrB,CAAC;QAVD,wBAAQ,GAAR;YACI,IAAI,IAAI,CAAC,IAAI,IAAI,CAAC,EAAE;gBAChB,OAAO,gBAAS,IAAI,CAAC,IAAI,eAAK,IAAI,CAAC,OAAO,CAAE,CAAC;aAChD;YACD,OAAO,IAAI,CAAC,OAAO,CAAC;QACxB,CAAC;QAML,YAAC;IAAD,CAAC,AAdD,IAcC;IAdY,kBAAK,QAcjB,CAAA;IAED;QAGI,iBAAmB,MAAS,EAAS,QAAkB;YAApC,WAAM,GAAN,MAAM,CAAG;YAAS,aAAQ,GAAR,QAAQ,CAAU;YAFvD,YAAO,GAAU,KAAK,CAAC;QAEoC,CAAC;QAChE,cAAC;IAAD,CAAC,AAJD,IAIC;IAJY,oBAAO,UAInB,CAAA;AACL,CAAC,EA9BS,YAAY,KAAZ,YAAY,QA8BrB;AAEQ,oCAAY"}

package/lib/commonjs/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'];

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js

@@ -0,0 +1,91 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handleBondsV3 = exports.handleAtomsV3 = exports.handleCountsV3 = exports.isV3 = void 0;
+var db_1 = require("../../../mol-data/db");
+var tokenizer_1 = require("../common/text/tokenizer");
+var token_1 = require("../common/text/column/token");
+function isV3(versionLine) {
+    return versionLine.trim().endsWith('V3000');
+}
+exports.isV3 = isV3;
+function handleCountsV3(tokenizer) {
+    var atomCount = tokenizer_1.TokenBuilder.create(tokenizer.data, 1);
+    var bondCount = tokenizer_1.TokenBuilder.create(tokenizer.data, 1);
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // BEGIN CTAB
+    skipSingleValue(tokenizer); // M
+    skipSingleValue(tokenizer); // V30
+    skipSingleValue(tokenizer); // COUNTS
+    addSingleValue(tokenizer, atomCount);
+    addSingleValue(tokenizer, bondCount);
+    tokenizer_1.Tokenizer.eatLine(tokenizer);
+    return {
+        atomCount: (0, token_1.TokenColumnProvider)(atomCount)(db_1.Column.Schema.int).value(0),
+        bondCount: (0, token_1.TokenColumnProvider)(bondCount)(db_1.Column.Schema.int).value(0)
+    };
+}
+exports.handleCountsV3 = handleCountsV3;
+function handleAtomsV3(tokenizer, atomCount) {
+    var x = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var y = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var z = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var type_symbol = tokenizer_1.TokenBuilder.create(tokenizer.data, atomCount * 2);
+    for (var i = 0; i < atomCount; ++i) {
+        tokenizer_1.Tokenizer.markLine(tokenizer);
+        skipSingleValue(tokenizer); // M
+        skipSingleValue(tokenizer); // V30
+        skipSingleValue(tokenizer); // Index
+        var position = tokenizer.position;
+        addSingleValue(tokenizer, type_symbol);
+        addSingleValue(tokenizer, x);
+        addSingleValue(tokenizer, y);
+        addSingleValue(tokenizer, z);
+        tokenizer.position = position;
+    }
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // Previous Line
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // END ATOM
+    return {
+        count: atomCount,
+        x: (0, token_1.TokenColumnProvider)(x)(db_1.Column.Schema.float),
+        y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
+        z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
+        type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str),
+    };
+}
+exports.handleAtomsV3 = handleAtomsV3;
+function handleBondsV3(tokenizer, bondCount) {
+    var atomIdxA = tokenizer_1.TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var atomIdxB = tokenizer_1.TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var order = tokenizer_1.TokenBuilder.create(tokenizer.data, bondCount * 2);
+    for (var i = 0; i < bondCount; ++i) {
+        tokenizer_1.Tokenizer.markLine(tokenizer);
+        skipSingleValue(tokenizer); // M
+        skipSingleValue(tokenizer); // V30
+        skipSingleValue(tokenizer); // Index
+        var position = tokenizer.position;
+        addSingleValue(tokenizer, order);
+        addSingleValue(tokenizer, atomIdxA);
+        addSingleValue(tokenizer, atomIdxB);
+        tokenizer.position = position;
+    }
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // Previous Line
+    tokenizer_1.Tokenizer.eatLine(tokenizer); // END BOND
+    return {
+        count: bondCount,
+        atomIdxA: (0, token_1.TokenColumnProvider)(atomIdxA)(db_1.Column.Schema.float),
+        atomIdxB: (0, token_1.TokenColumnProvider)(atomIdxB)(db_1.Column.Schema.float),
+        order: (0, token_1.TokenColumnProvider)(order)(db_1.Column.Schema.float),
+    };
+}
+exports.handleBondsV3 = handleBondsV3;
+function skipSingleValue(tokenizer) {
+    tokenizer_1.Tokenizer.skipWhitespace(tokenizer);
+    tokenizer_1.Tokenizer.eatValue(tokenizer);
+}
+function addSingleValue(tokenizer, tokens) {
+    var valueStart = tokenizer.position;
+    tokenizer_1.Tokenizer.skipWhitespace(tokenizer);
+    tokenizer_1.Tokenizer.eatValue(tokenizer);
+    tokenizer_1.Tokenizer.trim(tokenizer, valueStart, tokenizer.position);
+    tokenizer_1.TokenBuilder.addUnchecked(tokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+}
+//# sourceMappingURL=parser-v3-util.js.map

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"parser-v3-util.js","sourceRoot":"","sources":["../../../../../src/mol-io/reader/sdf/parser-v3-util.ts"],"names":[],"mappings":";;;AAAA,2CAA8C;AAE9C,sDAA2E;AAC3E,qDAAiF;AAEjF,SAAgB,IAAI,CAChB,WAAmB;IAEnB,OAAO,WAAW,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC;AAChD,CAAC;AAJD,oBAIC;AAED,SAAgB,cAAc,CAC1B,SAAoB;IAEpB,IAAM,SAAS,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IACzD,IAAM,SAAS,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAEzD,qBAAS,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,aAAa;IAC3C,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;IAChC,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM;IAClC,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS;IAErC,cAAc,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IACrC,cAAc,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IACrC,qBAAS,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IAE7B,OAAO;QACH,SAAS,EAAE,IAAA,2BAAW,EAAC,SAAS,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC;QAC7D,SAAS,EAAE,IAAA,2BAAW,EAAC,SAAS,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC;KAChE,CAAC;AACN,CAAC;AAnBD,wCAmBC;AAED,SAAgB,aAAa,CACzB,SAAoB,EACpB,SAAiB;IAEjB,IAAM,CAAC,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IAC7D,IAAM,CAAC,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IAC7D,IAAM,CAAC,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IAC7D,IAAM,WAAW,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IAEvE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,EAAE,CAAC,EAAE;QAChC,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;QAC9B,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;QAChC,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM;QAClC,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ;QAE5B,IAAA,QAAQ,GAAK,SAAS,SAAd,CAAe;QAC/B,cAAc,CAAC,SAAS,EAAE,WAAW,CAAC,CAAC;QACvC,cAAc,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QAC7B,cAAc,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QAC7B,cAAc,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QAC7B,SAAS,CAAC,QAAQ,GAAG,QAAQ,CAAC;KACjC;IACD,qBAAS,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,gBAAgB;IAC9C,qBAAS,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,WAAW;IAEzC,OAAO;QACH,KAAK,EAAE,SAAS;QAChB,CAAC,EAAE,IAAA,2BAAW,EAAC,CAAC,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,KAAK,CAAC;QACtC,CAAC,EAAE,IAAA,2BAAW,EAAC,CAAC,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,KAAK,CAAC;QACtC,CAAC,EAAE,IAAA,2BAAW,EAAC,CAAC,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,KAAK,CAAC;QACtC,WAAW,EAAE,IAAA,2BAAW,EAAC,WAAW,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,GAAG,CAAC;KAC3D,CAAC;AACN,CAAC;AAhCD,sCAgCC;AAED,SAAgB,aAAa,CACzB,SAAoB,EACpB,SAAiB;IAEjB,IAAM,QAAQ,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IACpE,IAAM,QAAQ,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IACpE,IAAM,KAAK,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,GAAG,CAAC,CAAC,CAAC;IAEjE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,EAAE,CAAC,EAAE;QAChC,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;QAC9B,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;QAChC,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM;QAClC,eAAe,CAAC,SAAS,CAAC,CAAC,CAAC,QAAQ;QAE5B,IAAA,QAAQ,GAAK,SAAS,SAAd,CAAe;QAC/B,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC;QACjC,cAAc,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QACpC,cAAc,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QACpC,SAAS,CAAC,QAAQ,GAAG,QAAQ,CAAC;KACjC;IACD,qBAAS,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,gBAAgB;IAC9C,qBAAS,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,WAAW;IAEzC,OAAO;QACH,KAAK,EAAE,SAAS;QAChB,QAAQ,EAAE,IAAA,2BAAW,EAAC,QAAQ,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,KAAK,CAAC;QACpD,QAAQ,EAAE,IAAA,2BAAW,EAAC,QAAQ,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,KAAK,CAAC;QACpD,KAAK,EAAE,IAAA,2BAAW,EAAC,KAAK,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,KAAK,CAAC;KACjD,CAAC;AACN,CAAC;AA7BD,sCA6BC;AAED,SAAS,eAAe,CAAC,SAAoB;IACzC,qBAAS,CAAC,cAAc,CAAC,SAAS,CAAC,CAAC;IACpC,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;AAClC,CAAC;AAED,SAAS,cAAc,CAAC,SAAoB,EAAE,MAAc;IAChD,IAAU,UAAU,GAAK,SAAS,SAAd,CAAe;IAC3C,qBAAS,CAAC,cAAc,CAAC,SAAS,CAAC,CAAC;IACpC,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;IAC9B,qBAAS,CAAC,IAAI,CAAC,SAAS,EAAE,UAAU,EAAE,SAAS,CAAC,QAAQ,CAAC,CAAC;IAC1D,wBAAY,CAAC,YAAY,CAAC,MAAM,EAAE,SAAS,CAAC,UAAU,EAAE,SAAS,CAAC,QAAQ,CAAC,CAAC;AAChF,CAAC"}

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

@@ -8,7 +8,7 @@ import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
-/** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 */
+/** http://c4.cabrillo.edu/404/ctfile.pdf - page 41 & 79 */
 export interface SdfFileCompound {
     readonly molFile: MolFile;
     readonly dataItems: {

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

@@ -14,6 +14,7 @@ var mol_task_1 = require("../../../mol-task");
 var result_1 = require("../result");
 var tokenizer_1 = require("../common/text/tokenizer");
 var token_1 = require("../common/text/column/token");
+var parser_v3_util_1 = require("./parser-v3-util");
 var delimiter = '$$$$';
 function handleDataItems(tokenizer) {
     var dataHeader = tokenizer_1.TokenBuilder.create(tokenizer.data, 32);
@@ -49,12 +50,19 @@ function handleDataItems(tokenizer) {
         data: (0, token_1.TokenColumnProvider)(data)(db_1.Column.Schema.str)
     };
 }
+function handleCountsV2(countsAndVersion) {
+    return {
+        atomCount: +countsAndVersion.substr(0, 3),
+        bondCount: +countsAndVersion.substr(3, 3)
+    };
+}
 function handleMolFile(tokenizer) {
     var title = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
     var program = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
     var comment = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
-    var counts = tokenizer_1.Tokenizer.readLine(tokenizer);
-    var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
+    var countsAndVersion = tokenizer_1.Tokenizer.readLine(tokenizer);
+    var molIsV3 = (0, parser_v3_util_1.isV3)(countsAndVersion);
+    var _a = molIsV3 ? (0, parser_v3_util_1.handleCountsV3)(tokenizer) : handleCountsV2(countsAndVersion), atomCount = _a.atomCount, bondCount = _a.bondCount;
     if (Number.isNaN(atomCount) || Number.isNaN(bondCount)) {
         // try to skip to next molecule
         while (tokenizer.position < tokenizer.length) {
@@ -64,8 +72,8 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
-    var atoms = (0, parser_1.handleAtoms)(tokenizer, atomCount);
-    var bonds = (0, parser_1.handleBonds)(tokenizer, bondCount);
+    var atoms = molIsV3 ? (0, parser_v3_util_1.handleAtomsV3)(tokenizer, atomCount) : (0, parser_1.handleAtoms)(tokenizer, atomCount);
+    var bonds = molIsV3 ? (0, parser_v3_util_1.handleBondsV3)(tokenizer, bondCount) : (0, parser_1.handleBonds)(tokenizer, bondCount);
     var dataItems = handleDataItems(tokenizer);
     return {
         molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },

package/lib/commonjs/mol-io/reader/sdf/parser.js.map

@@ -1 +1 @@
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+{"version":3,"file":"parser.js","sourceRoot":"","sources":["../../../../../src/mol-io/reader/sdf/parser.ts"],"names":[],"mappings":";AAAA;;;;;GAKG;;;;AAEH,2CAA8C;AAC9C,wCAAkE;AAClE,8CAAyC;AACzC,oCAAmD;AACnD,sDAAmE;AACnE,qDAAiF;AACjF,mDAAsF;AAiBtF,IAAM,SAAS,GAAG,MAAM,CAAC;AACzB,SAAS,eAAe,CAAC,SAAoB;IACzC,IAAM,UAAU,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAC3D,IAAM,IAAI,GAAG,wBAAY,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAErD,OAAO,SAAS,CAAC,QAAQ,GAAG,SAAS,CAAC,MAAM,EAAE;QAC1C,IAAM,IAAI,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;QAC3C,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC;YAAE,MAAM;QACtC,IAAI,CAAC,IAAI;YAAE,SAAS;QAEpB,IAAI,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE;YACvB,wBAAY,CAAC,GAAG,CAAC,UAAU,EAAE,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,SAAS,CAAC,QAAQ,CAAC,CAAC;YAE3E,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;YAC9B,IAAM,KAAK,GAAG,SAAS,CAAC,UAAU,CAAC;YACnC,IAAI,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC;YAC7B,IAAI,KAAK,GAAG,KAAK,CAAC;YAClB,OAAO,SAAS,CAAC,QAAQ,GAAG,SAAS,CAAC,MAAM,EAAE;gBAC1C,IAAM,KAAK,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;gBAC5C,IAAI,CAAC,KAAK,IAAI,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC,IAAI,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE;oBACjE,wBAAY,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,EAAE,GAAG,CAAC,CAAC;oBACnC,KAAK,GAAG,IAAI,CAAC;oBACb,MAAM;iBACT;gBACD,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC;aAC5B;YAED,IAAI,CAAC,KAAK,EAAE;gBACR,wBAAY,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,EAAE,GAAG,CAAC,CAAC;aACtC;SACJ;KACJ;IAED,OAAO;QACH,UAAU,EAAE,IAAA,2BAAW,EAAC,UAAU,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,GAAG,CAAC;QACtD,IAAI,EAAE,IAAA,2BAAW,EAAC,IAAI,CAAC,CAAC,WAAM,CAAC,MAAM,CAAC,GAAG,CAAC;KAC7C,CAAC;AACN,CAAC;AAED,SAAS,cAAc,CAAC,gBAAwB;IAC5C,OAAO;QACH,SAAS,EAAE,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC;QACzC,SAAS,EAAE,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC;KAC5C,CAAC;AACN,CAAC;AAED,SAAS,aAAa,CAAC,SAAoB;IACvC,IAAM,KAAK,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,EAAE,CAAC;IACnD,IAAM,OAAO,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,EAAE,CAAC;IACrD,IAAM,OAAO,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,EAAE,CAAC;IAErD,IAAM,gBAAgB,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;IACvD,IAAM,OAAO,GAAG,IAAA,qBAAI,EAAC,gBAAgB,CAAC,CAAC;IAEjC,IAAA,KAA2B,OAAO,CAAC,CAAC,CAAC,IAAA,+BAAc,EAAC,SAAS,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,gBAAgB,CAAC,EAA/F,SAAS,eAAA,EAAE,SAAS,eAA2E,CAAC;IAExG,IAAI,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,IAAI,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE;QACpD,+BAA+B;QAC/B,OAAO,SAAS,CAAC,QAAQ,GAAG,SAAS,CAAC,MAAM,EAAE;YAC1C,IAAM,IAAI,GAAG,qBAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC;gBAAE,MAAM;SACzC;QACD,OAAO;KACV;IAED,IAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,IAAA,8BAAa,EAAC,SAAS,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAA,oBAAW,EAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IAChG,IAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,IAAA,8BAAa,EAAC,SAAS,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAA,oBAAW,EAAC,SAAS,EAAE,SAAS,CAAC,CAAC;IAChG,IAAM,SAAS,GAAG,eAAe,CAAC,SAAS,CAAC,CAAC;IAE7C,OAAO;QACH,OAAO,EAAE,EAAE,KAAK,OAAA,EAAE,OAAO,SAAA,EAAE,OAAO,SAAA,EAAE,KAAK,OAAA,EAAE,KAAK,OAAA,EAAE;QAClD,SAAS,WAAA;KACZ,CAAC;AACN,CAAC;AAED,SAAS,aAAa,CAAC,IAAY;IAC/B,IAAM,SAAS,GAAG,IAAA,qBAAS,EAAC,IAAI,CAAC,CAAC;IAElC,IAAM,SAAS,GAAyB,EAAE,CAAC;IAC3C,OAAO,SAAS,CAAC,QAAQ,GAAG,SAAS,CAAC,MAAM,EAAE;QAC1C,IAAM,CAAC,GAAG,aAAa,CAAC,SAAS,CAAC,CAAC;QACnC,IAAI,CAAC;YAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;KAC5B;IAED,OAAO,qBAAM,CAAC,OAAO,CAAC,EAAE,SAAS,WAAA,EAAE,CAAC,CAAC;AACzC,CAAC;AAED,SAAgB,QAAQ,CAAC,IAAY;IAArC,iBAIC;IAHG,OAAO,eAAI,CAAC,MAAM,CAAkB,WAAW,EAAE;;YAC7C,sBAAO,aAAa,CAAC,IAAI,CAAC,EAAC;;SAC9B,CAAC,CAAC;AACP,CAAC;AAJD,4BAIC"}

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

@@ -32,7 +32,7 @@ var TextEncoder = /** @class */ (function () {
     };
     TextEncoder.prototype.startDataBlock = function (header) {
         this.dataBlockCreated = true;
-        string_builder_1.StringBuilder.write(this.builder, "data_" + (header || '').replace(/[ \n\t]/g, '').toUpperCase() + "\n#\n");
+        string_builder_1.StringBuilder.write(this.builder, "data_".concat((header || '').replace(/[ \n\t]/g, '').toUpperCase(), "\n#\n"));
     };
     TextEncoder.prototype.writeCategory = function (category, context, options) {
         if (this.encoded) {
@@ -129,7 +129,7 @@ function writeCifSingleRecord(category, instance, source, builder, filter, forma
         var f = fields[_f];
         if (!filter.includeField(category.name, f.name))
             continue;
-        string_builder_1.StringBuilder.writePadRight(builder, "_" + category.name + "." + f.name, width);
+        string_builder_1.StringBuilder.writePadRight(builder, "_".concat(category.name, ".").concat(f.name), width);
         var multiline = writeValue(builder, data, key, f, precisions[_f], 0);
         if (!multiline)
             string_builder_1.StringBuilder.newline(builder);
@@ -145,7 +145,7 @@ function writeCifLoop(category, instance, source, builder, filter, formatter) {
     var precisions = getFloatPrecisions(category.name, fields, formatter);
     writeLine(builder, 'loop_');
     for (var i = 0; i < fieldCount; i++) {
-        writeLine(builder, "_" + category.name + "." + fields[i].name);
+        writeLine(builder, "_".concat(category.name, ".").concat(fields[i].name));
     }
     var index = 0;
     for (var _c = 0; _c < source.length; _c++) {

package/lib/commonjs/mol-io/writer/cif/encoder/text.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-io/writer/cif/encoder.js

@@ -60,7 +60,7 @@ var Field;
         };
         Builder.prototype.vec = function (name, values, params) {
             for (var i = 0; i < values.length; i++) {
-                this.fields.push(Field.int(name + "[" + (i + 1) + "]", values[i], params));
+                this.fields.push(Field.int("".concat(name, "[").concat(i + 1, "]"), values[i], params));
             }
             return this;
         };
@@ -212,7 +212,7 @@ function getTensorDefinitions(field, space) {
     if (space.rank === 1) {
         var rows = space.dimensions[0];
         for (var i = 0; i < rows; i++) {
-            var name_2 = field + "[" + (i + 1) + "]";
+            var name_2 = "".concat(field, "[").concat(i + 1, "]");
             fieldDefinitions.push({ name: name_2, type: type, value: columnTensorValue(field, i), valueKind: valueKind });
         }
     }
@@ -220,7 +220,7 @@ function getTensorDefinitions(field, space) {
         var rows = space.dimensions[0], cols = space.dimensions[1];
         for (var i = 0; i < rows; i++) {
             for (var j = 0; j < cols; j++) {
-                var name_3 = field + "[" + (i + 1) + "][" + (j + 1) + "]";
+                var name_3 = "".concat(field, "[").concat(i + 1, "][").concat(j + 1, "]");
                 fieldDefinitions.push({ name: name_3, type: type, value: columnTensorValue(field, i, j), valueKind: valueKind });
             }
         }
@@ -230,7 +230,7 @@ function getTensorDefinitions(field, space) {
         for (var i = 0; i < d0; i++) {
             for (var j = 0; j < d1; j++) {
                 for (var k = 0; k < d2; k++) {
-                    var name_4 = field + "[" + (i + 1) + "][" + (j + 1) + "][" + (k + 1) + "]";
+                    var name_4 = "".concat(field, "[").concat(i + 1, "][").concat(j + 1, "][").concat(k + 1, "]");
                     fieldDefinitions.push({ name: name_4, type: type, value: columnTensorValue(field, i, j, k), valueKind: valueKind });
                 }
             }
@@ -262,7 +262,7 @@ function cifFieldsFromTableSchema(schema) {
             fields.push.apply(fields, getTensorDefinitions(k, t.space));
         }
         else {
-            throw new Error("Unknown valueType " + t.valueType);
+            throw new Error("Unknown valueType ".concat(t.valueType));
         }
     }
     return fields;

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

@@ -1 +1 @@
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package/lib/commonjs/mol-io/writer/mol/encoder.js

@@ -33,7 +33,7 @@ var MolEncoder = /** @class */ (function (_super) {
         // write header
         var name = this.getName(instance, source);
         // 3rd lines must be present and can contain comments
-        mol_util_1.StringBuilder.writeSafe(this.builder, name + "\n  " + this.encoder + "\n\n");
+        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);
         var bondCount = 0;
@@ -74,7 +74,7 @@ var MolEncoder = /** @class */ (function (_super) {
         // write counts line
         mol_util_1.StringBuilder.writeIntegerPadLeft(this.builder, atoms.size, 3);
         mol_util_1.StringBuilder.writeIntegerPadLeft(this.builder, bondCount, 3);
-        mol_util_1.StringBuilder.writeSafe(this.builder, "  0  0  " + (chiral ? 1 : 0) + "  0  0  0  0  0  0\n");
+        mol_util_1.StringBuilder.writeSafe(this.builder, "  0  0  ".concat(chiral ? 1 : 0, "  0  0  0  0  0  0\n"));
         mol_util_1.StringBuilder.writeSafe(this.builder, mol_util_1.StringBuilder.getString(ctab));
         mol_util_1.StringBuilder.writeSafe(this.builder, mol_util_1.StringBuilder.getString(bonds));
         mol_util_1.StringBuilder.writeSafe(this.builder, 'M  END\n');
@@ -102,7 +102,7 @@ var MolEncoder = /** @class */ (function (_super) {
         var key = it.move();
         for (var _f = 0; _f < fields.length; _f++) {
             var f = fields[_f];
-            mol_util_1.StringBuilder.writeSafe(sb, "> <" + category.name + "." + f.name + ">\n");
+            mol_util_1.StringBuilder.writeSafe(sb, "> <".concat(category.name, ".").concat(f.name, ">\n"));
             var val = f.value(key, data, 0);
             mol_util_1.StringBuilder.writeSafe(sb, val);
             mol_util_1.StringBuilder.writeSafe(sb, '\n\n');
@@ -115,7 +115,7 @@ var MolEncoder = /** @class */ (function (_super) {
         }
         // terminate file (needed for SDF only)
         if (!!this.terminator) {
-            mol_util_1.StringBuilder.writeSafe(this.builder, this.terminator + "\n");
+            mol_util_1.StringBuilder.writeSafe(this.builder, "".concat(this.terminator, "\n"));
         }
         this.encoded = true;
     };