npm - molstar - Versions diffs - 2.3.6 → 2.4.0 - Mend

molstar 2.3.6 → 2.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1610) hide show

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

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

@@ -584,7 +584,7 @@ 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;
@@ -704,7 +704,7 @@ 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/mol-io/reader/cif/text/parser.js.map CHANGED Viewed

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

@@ -122,7 +122,7 @@ export 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);
@@ -134,7 +134,7 @@ export 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/mol-io/reader/dcd/parser.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"parser.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/dcd/parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAEH,OAAO,EAAE,YAAY,IAAI,MAAM,EAAE,MAAM,WAAW,CAAC;AACnD,OAAO,EAAE,IAAI,EAAE,MAAM,mBAAmB,CAAC;AAEzC,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AA6BpD,MAAM,UAAU,SAAS,CAAC,IAAgB;IACtC,qEAAqE;IAErE,0CAA0C;IAC1C,gEAAgE;IAChE,0EAA0E;IAC1E,6EAA6E;IAC7E,mCAAmC;IACnC,uEAAuE;IACvE,6EAA6E;IAC7E,wBAAwB;IACxB,4BAA4B;IAC5B,wBAAwB;IACxB,6EAA6E;IAC7E,QAAQ;IACR,SAAS;IACT,MAAM;IACN,6EAA6E;IAC7E,mCAAmC;IACnC,kBAAkB;IAClB,kBAAkB;IAClB,6EAA6E;IAE7E,IAAM,EAAE,GAAG,IAAI,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAErC,IAAM,MAAM,GAAuB,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IACvD,IAAM,MAAM,GAAe,EAAE,CAAC;IAE9B,IAAI,OAAO,GAAG,CAAC,CAAC;IAEhB,eAAe;IAEf,IAAM,OAAO,GAAG,IAAI,UAAU,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;IACnD,IAAM,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,iBAAiB;IAC3D,+DAA+D;IAC/D,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,EAAE;QACnB,IAAM,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC;QAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;YAC3B,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC;SAC5C;KACJ;IACD,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,EAAE;QACnB,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;KACzD;IAED,uCAAuC;IACvC,IAAM,YAAY,GAAG,MAAM,CAAC,YAAY,CACpC,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,EAC9B,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CACjC,CAAC;IACF,IAAI,YAAY,KAAK,MAAM,EAAE;QACzB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAC;KACpD;IACD,IAAI,QAAQ,GAAG,KAAK,CAAC;IACrB,IAAI,UAAU,GAAG,KAAK,CAAC;IACvB,IAAI,QAAQ,GAAG,KAAK,CAAC;IACrB,4CAA4C;IAC5C,IAAI,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE;QACnB,QAAQ,GAAG,IAAI,CAAC;QAChB,IAAI,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC;YAAE,UAAU,GAAG,IAAI,CAAC;QACzC,IAAI,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC;YAAE,QAAQ,GAAG,IAAI,CAAC;KAC1C;IACD,MAAM,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;IACzB,MAAM,CAAC,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;IAC3B,MAAM,CAAC,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;IAC1B,MAAM,CAAC,KAAK,GAAG,OAAO,CAAC,EAAE,CAAC,CAAC;IAE3B,IAAI,QAAQ,EAAE;QACV,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC,UAAU,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;KACxC;SAAM;QACH,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC,UAAU,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;KACxC;IAED,IAAI,OAAO,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE;QACpB,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACvD;IACD,OAAO,GAAG,OAAO,GAAG,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC;IAE/B,cAAc;IAEd,IAAM,QAAQ,GAAG,EAAE,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;IAC1C,IAAM,UAAU,GAAG,OAAO,GAAG,CAAC,CAAC;IAC/B,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE;QAC3B,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACxD;IACD,MAAM,CAAC,KAAK,GAAG,aAAa,CAAC,IAAI,CAAC,QAAQ,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,CAAC;IAClE,IAAI,EAAE,CAAC,QAAQ,CAAC,UAAU,GAAG,QAAQ,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,KAAK,QAAQ,EAAE;QAC7D,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACtD;IAED,OAAO,GAAG,OAAO,GAAG,QAAQ,GAAG,CAAC,CAAC;IAEjC,cAAc;IAEd,IAAI,EAAE,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,KAAK,CAAC,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACxD;IACD,MAAM,CAAC,KAAK,GAAG,EAAE,CAAC,QAAQ,CAAC,OAAO,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC;IAC5C,IAAI,EAAE,CAAC,QAAQ,CAAC,OAAO,GAAG,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,EAAE;QACpC,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACtD;IACD,OAAO,GAAG,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC;IAE1B,oBAAoB;IAEpB,IAAI,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE;QAClB,mDAAmD;QACnD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAC;KACxE;IAED,SAAS;IACT,IAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC;IAC3B,IAAM,MAAM,GAAG,KAAK,GAAG,CAAC,CAAC;IAEzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;QACzC,IAAM,KAAK,GAAsB,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QACrD,KAAK,CAAC,YAAY,GAAG,KAAK,CAAC;QAE3B,IAAI,UAAU,EAAE;YACZ,OAAO,IAAI,CAAC,CAAC,CAAC,cAAc;YAC5B,KAAK,CAAC,IAAI,GAAG;gBACT,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC;gBAC1B,EAAE,CAAC,UAAU,CAAC,OAAO,GAAG,CAAC,EAAE,EAAE,CAAC;gBAC9B,EAAE,CAAC,UAAU,CAAC,OAAO,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBAClC,EAAE,CAAC,UAAU,CAAC,OAAO,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBAClC,EAAE,CAAC,UAAU,CAAC,OAAO,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBAClC,EAAE,CAAC,UAAU,CAAC,OAAO,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;aAC5B,CAAC;YACX,OAAO,IAAI,EAAE,CAAC;YACd,OAAO,IAAI,CAAC,CAAC,CAAC,YAAY;SAC7B;QAED,kBAAkB;QAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;YACxB,IAAI,EAAE,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,KAAK,MAAM,EAAE;gBACrC,MAAM,IAAI,KAAK,CAAC,6CAAsC,CAAC,eAAK,CAAC,CAAE,CAAC,CAAC;aACpE;YACD,OAAO,IAAI,CAAC,CAAC,CAAC,cAAc;YAC5B,IAAM,CAAC,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC;YACxD,IAAI,CAAC,KAAK,CAAC;gBAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;iBACpB,IAAI,CAAC,KAAK,CAAC;gBAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;;gBACzB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;YAEjB,OAAO,IAAI,MAAM,CAAC;YAClB,IAAI,EAAE,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,KAAK,MAAM,EAAE;gBACrC,MAAM,IAAI,KAAK,CAAC,2CAAoC,CAAC,eAAK,CAAC,CAAE,CAAC,CAAC;aAClE;YACD,OAAO,IAAI,CAAC,CAAC,CAAC,YAAY;SAC7B;QAED,IAAI,QAAQ,EAAE;YACV,IAAM,KAAK,GAAG,EAAE,CAAC,QAAQ,CAAC,OAAO,EAAE,EA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package/lib/mol-io/reader/ply/schema.d.ts CHANGED Viewed

@@ -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" | "ushort" | "float32" | "int32" | "uint32" | "uint16" | "char" | "uchar" | "short" | "uint" | "double" | "int8" | "uint8" | "int16" | "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/ply/schema.js CHANGED Viewed

@@ -26,7 +26,7 @@ export var PlyTypeByteLength = {
 export var PlyTypes = new Set(Object.keys(PlyTypeByteLength));
 export function PlyType(str) {
     if (!PlyTypes.has(str))
-        throw new Error("unknown ply type '" + str + "'");
+        throw new Error("unknown ply type '".concat(str, "'"));
     return str;
 }
 export function PlyFile(elements, elementNames, comments) {

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

	@@ -1 +1 @@
1	- {"version":3,"file":"schema.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/ply/schema.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,yCAAyC;AACzC,kDAAkD;AAElD,MAAM,CAAC,IAAM,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;AAEF,MAAM,CAAC,IAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC;AAChE,MAAM,UAAU,OAAO,CAAC,GAAW;IAC/B,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,MAAM,IAAI,KAAK,CAAC,~~uBAAqB~~,GAAG,MAAG,CAAC,CAAC;IACrE,OAAO,GAAc,CAAC;AAC1B,CAAC;AAQD,MAAM,UAAU,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"}
1	+ {"version":3,"file":"schema.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/ply/schema.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,yCAAyC;AACzC,kDAAkD;AAElD,MAAM,CAAC,IAAM,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;AAEF,MAAM,CAAC,IAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC;AAChE,MAAM,UAAU,OAAO,CAAC,GAAW;IAC/B,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,MAAM,IAAI,KAAK,CAAC,4BAAqB,GAAG,MAAG,CAAC,CAAC;IACrE,OAAO,GAAc,CAAC;AAC1B,CAAC;AAQD,MAAM,UAAU,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"}

package/lib/mol-io/reader/result.js CHANGED Viewed

@@ -24,7 +24,7 @@ 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/mol-io/reader/result.js.map CHANGED Viewed

	@@ -1 +1 @@
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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,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;AAED,OAAO,EAAE,YAAY,EAAE,CAAC"}

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

@@ -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/mol-io/reader/sdf/parser-v3-util.js ADDED Viewed

@@ -0,0 +1,84 @@
+import { Column } from '../../../mol-data/db';
+import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
+import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+export function isV3(versionLine) {
+    return versionLine.trim().endsWith('V3000');
+}
+export function handleCountsV3(tokenizer) {
+    var atomCount = TokenBuilder.create(tokenizer.data, 1);
+    var bondCount = TokenBuilder.create(tokenizer.data, 1);
+    Tokenizer.eatLine(tokenizer); // BEGIN CTAB
+    skipSingleValue(tokenizer); // M
+    skipSingleValue(tokenizer); // V30
+    skipSingleValue(tokenizer); // COUNTS
+    addSingleValue(tokenizer, atomCount);
+    addSingleValue(tokenizer, bondCount);
+    Tokenizer.eatLine(tokenizer);
+    return {
+        atomCount: TokenColumn(atomCount)(Column.Schema.int).value(0),
+        bondCount: TokenColumn(bondCount)(Column.Schema.int).value(0)
+    };
+}
+export function handleAtomsV3(tokenizer, atomCount) {
+    var x = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var y = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var z = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    var type_symbol = TokenBuilder.create(tokenizer.data, atomCount * 2);
+    for (var i = 0; i < atomCount; ++i) {
+        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.eatLine(tokenizer); // Previous Line
+    Tokenizer.eatLine(tokenizer); // END ATOM
+    return {
+        count: atomCount,
+        x: TokenColumn(x)(Column.Schema.float),
+        y: TokenColumn(y)(Column.Schema.float),
+        z: TokenColumn(z)(Column.Schema.float),
+        type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+    };
+}
+export function handleBondsV3(tokenizer, bondCount) {
+    var atomIdxA = TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var atomIdxB = TokenBuilder.create(tokenizer.data, bondCount * 2);
+    var order = TokenBuilder.create(tokenizer.data, bondCount * 2);
+    for (var i = 0; i < bondCount; ++i) {
+        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.eatLine(tokenizer); // Previous Line
+    Tokenizer.eatLine(tokenizer); // END BOND
+    return {
+        count: bondCount,
+        atomIdxA: TokenColumn(atomIdxA)(Column.Schema.float),
+        atomIdxB: TokenColumn(atomIdxB)(Column.Schema.float),
+        order: TokenColumn(order)(Column.Schema.float),
+    };
+}
+function skipSingleValue(tokenizer) {
+    Tokenizer.skipWhitespace(tokenizer);
+    Tokenizer.eatValue(tokenizer);
+}
+function addSingleValue(tokenizer, tokens) {
+    var valueStart = tokenizer.position;
+    Tokenizer.skipWhitespace(tokenizer);
+    Tokenizer.eatValue(tokenizer);
+    Tokenizer.trim(tokenizer, valueStart, tokenizer.position);
+    TokenBuilder.addUnchecked(tokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+}
+//# sourceMappingURL=parser-v3-util.js.map

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

@@ -0,0 +1 @@

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

@@ -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/mol-io/reader/sdf/parser.js CHANGED Viewed

@@ -11,6 +11,7 @@ import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+import { handleAtomsV3, handleBondsV3, handleCountsV3, isV3 } from './parser-v3-util';
 var delimiter = '$$$$';
 function handleDataItems(tokenizer) {
     var dataHeader = TokenBuilder.create(tokenizer.data, 32);
@@ -46,12 +47,19 @@ function handleDataItems(tokenizer) {
         data: TokenColumn(data)(Column.Schema.str)
     };
 }
+function handleCountsV2(countsAndVersion) {
+    return {
+        atomCount: +countsAndVersion.substr(0, 3),
+        bondCount: +countsAndVersion.substr(3, 3)
+    };
+}
 function handleMolFile(tokenizer) {
     var title = Tokenizer.readLine(tokenizer).trim();
     var program = Tokenizer.readLine(tokenizer).trim();
     var comment = Tokenizer.readLine(tokenizer).trim();
-    var counts = Tokenizer.readLine(tokenizer);
-    var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
+    var countsAndVersion = Tokenizer.readLine(tokenizer);
+    var molIsV3 = isV3(countsAndVersion);
+    var _a = molIsV3 ? 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) {
@@ -61,8 +69,8 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
-    var atoms = handleAtoms(tokenizer, atomCount);
-    var bonds = handleBonds(tokenizer, bondCount);
+    var atoms = molIsV3 ? handleAtomsV3(tokenizer, atomCount) : handleAtoms(tokenizer, atomCount);
+    var bonds = molIsV3 ? handleBondsV3(tokenizer, bondCount) : handleBonds(tokenizer, bondCount);
     var dataItems = handleDataItems(tokenizer);
     return {
         molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },

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

	@@ -1 +1 @@
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package/lib/mol-io/writer/cif/encoder/text.js CHANGED Viewed

@@ -29,7 +29,7 @@ var TextEncoder = /** @class */ (function () {
     };
     TextEncoder.prototype.startDataBlock = function (header) {
         this.dataBlockCreated = true;
-        StringBuilder.write(this.builder, "data_" + (header || '').replace(/[ \n\t]/g, '').toUpperCase() + "\n#\n");
+        StringBuilder.write(this.builder, "data_".concat((header || '').replace(/[ \n\t]/g, '').toUpperCase(), "\n#\n"));
     };
     TextEncoder.prototype.writeCategory = function (category, context, options) {
         if (this.encoded) {
@@ -126,7 +126,7 @@ function writeCifSingleRecord(category, instance, source, builder, filter, forma
         var f = fields[_f];
         if (!filter.includeField(category.name, f.name))
             continue;
-        StringBuilder.writePadRight(builder, "_" + category.name + "." + f.name, width);
+        StringBuilder.writePadRight(builder, "_".concat(category.name, ".").concat(f.name), width);
         var multiline = writeValue(builder, data, key, f, precisions[_f], 0);
         if (!multiline)
             StringBuilder.newline(builder);
@@ -142,7 +142,7 @@ 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/mol-io/writer/cif/encoder/text.js.map CHANGED Viewed

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

@@ -57,7 +57,7 @@ export 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;
         };
@@ -209,7 +209,7 @@ 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 });
         }
     }
@@ -217,7 +217,7 @@ 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 });
             }
         }
@@ -227,7 +227,7 @@ 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 });
                 }
             }
@@ -259,7 +259,7 @@ 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;