molstar 3.8.2 → 3.9.0

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

@@ -373,7 +373,7 @@ function getTokenString(state) {
 function moveNextInternal(state) {
     var prev = skipWhitespace(state);
     if (state.position >= state.length) {
-        state.tokenType = 6 /* End */;
+        state.tokenType = 6 /* CifTokenType.End */;
         return;
     }
     state.tokenStart = state.position;
@@ -383,17 +383,17 @@ function moveNextInternal(state) {
     switch (c) {
         case 35: // #, comment
             skipCommentLine(state);
-            state.tokenType = 5 /* Comment */;
+            state.tokenType = 5 /* CifTokenType.Comment */;
             break;
         case 39: // ', escaped value
             if (isTripleQuoteAtPosition(state)) {
                 eatTripleQuote(state);
-                state.tokenType = 3 /* Value */;
+                state.tokenType = 3 /* CifTokenType.Value */;
                 break;
             }
         case 34: // ", escaped value
             eatEscaped(state, c);
-            state.tokenType = 3 /* Value */;
+            state.tokenType = 3 /* CifTokenType.Value */;
             break;
         case 59: // ;, possible multiline value
             // multiline value must start at the beginning of the line.
@@ -403,7 +403,7 @@ function moveNextInternal(state) {
             else {
                 eatValue(state);
             }
-            state.tokenType = 3 /* Value */;
+            state.tokenType = 3 /* CifTokenType.Value */;
             break;
         default:
             if (state.isImportGet) {
@@ -414,29 +414,29 @@ function moveNextInternal(state) {
             }
             // escaped is always Value
             if (state.isEscaped) {
-                state.tokenType = 3 /* Value */;
+                state.tokenType = 3 /* CifTokenType.Value */;
                 // _ means column name, including _import.get
             }
             else if (state.data.charCodeAt(state.tokenStart) === 95) { // _
                 if (state.inSaveFrame && isImportGet(state)) {
                     state.isImportGet = true;
                 }
-                state.tokenType = 4 /* ColumnName */;
+                state.tokenType = 4 /* CifTokenType.ColumnName */;
                 // 5th char needs to be _ for data_, save_ or loop_
             }
             else if (state.tokenEnd - state.tokenStart >= 5 && state.data.charCodeAt(state.tokenStart + 4) === 95) {
                 if (isData(state))
-                    state.tokenType = 0 /* Data */;
+                    state.tokenType = 0 /* CifTokenType.Data */;
                 else if (isSave(state))
-                    state.tokenType = 1 /* Save */;
+                    state.tokenType = 1 /* CifTokenType.Save */;
                 else if (isLoop(state))
-                    state.tokenType = 2 /* Loop */;
+                    state.tokenType = 2 /* CifTokenType.Loop */;
                 else
-                    state.tokenType = 3 /* Value */;
+                    state.tokenType = 3 /* CifTokenType.Value */;
                 // all other tests failed, we are at Value token.
             }
             else {
-                state.tokenType = 3 /* Value */;
+                state.tokenType = 3 /* CifTokenType.Value */;
             }
             break;
     }
@@ -446,7 +446,7 @@ function moveNextInternal(state) {
  */
 function moveNext(state) {
     moveNextInternal(state);
-    while (state.tokenType === 5 /* Comment */)
+    while (state.tokenType === 5 /* CifTokenType.Comment */)
         moveNextInternal(state);
 }
 function createTokenizer(data, runtimeCtx) {
@@ -456,7 +456,7 @@ function createTokenizer(data, runtimeCtx) {
         position: 0,
         tokenStart: 0,
         tokenEnd: 0,
-        tokenType: 6 /* End */,
+        tokenType: 6 /* CifTokenType.End */,
         lineNumber: 1,
         isEscaped: false,
         isImportGet: false,
@@ -504,13 +504,13 @@ function handleSingle(tokenizer, ctx) {
     var fieldNames = [];
     var readingNames = true;
     while (readingNames) {
-        if (tokenizer.tokenType !== 4 /* ColumnName */ || !isNamespace(tokenizer, nsStart, nsEnd)) {
+        if (tokenizer.tokenType !== 4 /* CifTokenType.ColumnName */ || !isNamespace(tokenizer, nsStart, nsEnd)) {
             readingNames = false;
             break;
         }
         var fieldName = getTokenString(tokenizer).substring(name.length + 1);
         moveNext(tokenizer);
-        if (tokenizer.tokenType !== 3 /* Value */) {
+        if (tokenizer.tokenType !== 3 /* CifTokenType.Value */) {
             return {
                 hasError: true,
                 errorLine: tokenizer.lineNumber,
@@ -532,7 +532,7 @@ function readLoopChunk(chunkSize, state) {
     var tokenizer = state.tokenizer, tokens = state.tokens, fieldCount = state.fieldCount;
     var tokenCount = state.tokenCount;
     var counter = 0;
-    while (tokenizer.tokenType === 3 /* Value */ && counter < chunkSize) {
+    while (tokenizer.tokenType === 3 /* CifTokenType.Value */ && counter < chunkSize) {
         TokenBuilder.add(tokens[(tokenCount++) % fieldCount], tokenizer.tokenStart, tokenizer.tokenEnd);
         moveNext(tokenizer);
         counter++;
@@ -560,7 +560,7 @@ function handleLoop(tokenizer, ctx) {
                     name = getNamespace(tokenizer, getNamespaceEnd(tokenizer));
                     isFlat = isFlatNamespace(tokenizer);
                     fieldNames = [];
-                    while (tokenizer.tokenType === 4 /* ColumnName */) {
+                    while (tokenizer.tokenType === 4 /* CifTokenType.ColumnName */) {
                         fieldNames[fieldNames.length] = isFlat
                             ? getTokenString(tokenizer)
                             : getTokenString(tokenizer).substring(name.length + 1);
@@ -645,9 +645,9 @@ function parseInternal(data, runtimeCtx) {
                     moveNext(tokenizer);
                     _a.label = 1;
                 case 1:
-                    if (!(tokenizer.tokenType !== 6 /* End */)) return [3 /*break*/, 7];
+                    if (!(tokenizer.tokenType !== 6 /* CifTokenType.End */)) return [3 /*break*/, 7];
                     token = tokenizer.tokenType;
-                    if (!(token === 0 /* Data */)) return [3 /*break*/, 2];
+                    if (!(token === 0 /* CifTokenType.Data */)) return [3 /*break*/, 2];
                     if (tokenizer.inSaveFrame) {
                         return [2 /*return*/, error(tokenizer.lineNumber, 'Unexpected data block inside a save frame.')];
                     }
@@ -660,7 +660,7 @@ function parseInternal(data, runtimeCtx) {
                     moveNext(tokenizer);
                     return [3 /*break*/, 6];
                 case 2:
-                    if (!(token === 1 /* Save */)) return [3 /*break*/, 3];
+                    if (!(token === 1 /* CifTokenType.Save */)) return [3 /*break*/, 3];
                     if (tokenizer.tokenEnd - tokenizer.tokenStart === 5) { // end of save frame
                         if (saveCtx.categoryNames.length > 0) {
                             saveFrames[saveFrames.length] = CifSaveFrame(saveCtx, saveHeader);
@@ -679,7 +679,7 @@ function parseInternal(data, runtimeCtx) {
                     moveNext(tokenizer);
                     return [3 /*break*/, 6];
                 case 3:
-                    if (!(token === 2 /* Loop */)) return [3 /*break*/, 5];
+                    if (!(token === 2 /* CifTokenType.Loop */)) return [3 /*break*/, 5];
                     return [4 /*yield*/, handleLoop(tokenizer, tokenizer.inSaveFrame ? saveCtx : blockCtx)];
                 case 4:
                     cat = _a.sent();
@@ -688,7 +688,7 @@ function parseInternal(data, runtimeCtx) {
                     }
                     return [3 /*break*/, 6];
                 case 5:
-                    if (token === 4 /* ColumnName */) {
+                    if (token === 4 /* CifTokenType.ColumnName */) {
                         cat = handleSingle(tokenizer, tokenizer.inSaveFrame ? saveCtx : blockCtx);
                         if (cat.hasError) {
                             return [2 /*return*/, error(cat.errorLine, cat.errorMessage)];

package/lib/mol-io/reader/common/text/column/fixed.js

@@ -39,7 +39,7 @@ export function FixedColumn(lines, offset, width, schema) {
         isDefined: true,
         rowCount: rowCount,
         value: value,
-        valueKind: function (row) { return 0 /* Present */; },
+        valueKind: function (row) { return 0 /* Column.ValueKind.Present */; },
         toArray: function (params) { return ColumnHelpers.createAndFillArray(rowCount, value, params); },
         areValuesEqual: function (rowA, rowB) { return value(rowA) === value(rowB); }
     };

package/lib/mol-io/reader/common/text/column/token.js

@@ -25,7 +25,7 @@ export function TokenColumn(tokens, schema) {
         isDefined: true,
         rowCount: rowCount,
         value: value,
-        valueKind: function (row) { return 0 /* Present */; },
+        valueKind: function (row) { return 0 /* Column.ValueKind.Present */; },
         toArray: function (params) { return ColumnHelpers.createAndFillArray(rowCount, value, params); },
         areValuesEqual: areValuesEqualProvider(tokens)
     };

package/lib/mol-io/reader/common/text/number-parser.js

@@ -104,7 +104,7 @@ function getNumberTypeScientific(str, start, end) {
     // handle + in '1e+1' separately.
     if (str.charCodeAt(start) === 43 /* + */)
         start++;
-    return isInt(str, start, end) ? 2 /* Scientific */ : 3 /* NaN */;
+    return isInt(str, start, end) ? 2 /* NumberType.Scientific */ : 3 /* NumberType.NaN */;
 }
 /** The whole range must match, otherwise returns NaN */
 export function getNumberType(str) {
@@ -115,7 +115,7 @@ export function getNumberType(str) {
     }
     // string is . or -.
     if (str.charCodeAt(start) === 46 && end - start === 1) {
-        return 3 /* NaN */;
+        return 3 /* NumberType.NaN */;
     }
     while (start < end) {
         var c = str.charCodeAt(start) - 48;
@@ -135,14 +135,14 @@ export function getNumberType(str) {
                     return getNumberTypeScientific(str, start + 1, end);
                 }
                 else {
-                    return 3 /* NaN */;
+                    return 3 /* NumberType.NaN */;
                 }
             }
-            return hasDigit ? 1 /* Float */ : 0 /* Int */;
+            return hasDigit ? 1 /* NumberType.Float */ : 0 /* NumberType.Int */;
         }
         else if (c === 53 || c === 21) { // 'e'/'E'
             if (start === 0 || start === 1 && str.charCodeAt(0) === 45) {
-                return 3 /* NaN */; // string starts with e/E or -e/-E
+                return 3 /* NumberType.NaN */; // string starts with e/E or -e/-E
             }
             return getNumberTypeScientific(str, start + 1, end);
         }
@@ -150,5 +150,5 @@ export function getNumberType(str) {
             break;
         }
     }
-    return start === end ? 0 /* Int */ : 3 /* NaN */;
+    return start === end ? 0 /* NumberType.Int */ : 3 /* NumberType.NaN */;
 }

package/lib/mol-io/reader/csv/parser.js

@@ -15,7 +15,7 @@ function State(data, runtimeCtx, opts) {
     return {
         data: data,
         tokenizer: tokenizer,
-        tokenType: 2 /* End */,
+        tokenType: 2 /* CsvTokenType.End */,
         runtimeCtx: runtimeCtx,
         tokens: [],
         fieldCount: 0,
@@ -134,7 +134,7 @@ function moveNextInternal(state) {
     var tokenizer = state.tokenizer;
     skipWhitespace(tokenizer);
     if (tokenizer.position >= tokenizer.length) {
-        state.tokenType = 2 /* End */;
+        state.tokenType = 2 /* CsvTokenType.End */;
         return false;
     }
     tokenizer.tokenStart = tokenizer.position;
@@ -142,14 +142,14 @@ function moveNextInternal(state) {
     var c = state.data.charCodeAt(tokenizer.position);
     switch (c) {
         case state.commentCharCode:
-            state.tokenType = 1 /* Comment */;
+            state.tokenType = 1 /* CsvTokenType.Comment */;
             skipLine(tokenizer);
             break;
         case state.quoteCharCode:
-            state.tokenType = 0 /* Value */;
+            state.tokenType = 0 /* CsvTokenType.Value */;
             return eatQuoted(tokenizer, state.quoteCharCode, state.delimiterCharCode);
         default:
-            state.tokenType = 0 /* Value */;
+            state.tokenType = 0 /* CsvTokenType.Value */;
             return eatValue(tokenizer, state.delimiterCharCode);
     }
 }
@@ -159,18 +159,18 @@ function moveNextInternal(state) {
  */
 function moveNext(state) {
     var newRecord = moveNextInternal(state);
-    while (state.tokenType === 1 /* Comment */) {
+    while (state.tokenType === 1 /* CsvTokenType.Comment */) {
         newRecord = moveNextInternal(state);
     }
     return newRecord;
 }
 function readRecordsChunk(chunkSize, state) {
-    if (state.tokenType === 2 /* End */)
+    if (state.tokenType === 2 /* CsvTokenType.End */)
         return 0;
     var counter = 0;
     var newRecord;
     var tokens = state.tokens, tokenizer = state.tokenizer;
-    while (state.tokenType === 0 /* Value */ && counter < chunkSize) {
+    while (state.tokenType === 0 /* CsvTokenType.Value */ && counter < chunkSize) {
         TokenBuilder.add(tokens[state.fieldCount % state.columnCount], tokenizer.tokenStart, tokenizer.tokenEnd);
         ++state.fieldCount;
         newRecord = moveNext(state);

package/lib/mol-io/writer/cif/encoder/binary.js

@@ -91,14 +91,14 @@ function getArrayCtor(field, format) {
         return format.typedArray;
     if (field.defaultFormat && field.defaultFormat.typedArray)
         return field.defaultFormat.typedArray;
-    if (field.type === 0 /* Str */)
+    if (field.type === 0 /* Field.Type.Str */)
         return Array;
-    if (field.type === 1 /* Int */)
+    if (field.type === 1 /* Field.Type.Int */)
         return Int32Array;
     return Float64Array;
 }
 function getDefaultEncoder(type) {
-    if (type === 0 /* Str */)
+    if (type === 0 /* Field.Type.Str */)
         return ArrayEncoder.by(E.stringArray);
     return ArrayEncoder.by(E.byteArray);
 }
@@ -117,9 +117,9 @@ function tryGetEncoder(categoryName, field, format, provider) {
     }
 }
 function classify(type, data) {
-    if (type === 0 /* Str */)
+    if (type === 0 /* Field.Type.Str */)
         return ArrayEncoder.by(E.stringArray);
-    if (type === 1 /* Int */)
+    if (type === 1 /* Field.Type.Int */)
         return classifyIntArray(data);
     return classifyFloatArray(data);
 }
@@ -150,7 +150,7 @@ function encodeField(categoryName, field, data, totalCount, format, encoderProvi
     };
 }
 function getFieldData(field, arrayCtor, totalCount, data) {
-    var isStr = field.type === 0 /* Str */;
+    var isStr = field.type === 0 /* Field.Type.Str */;
     var array = new arrayCtor(totalCount);
     var mask = new Uint8Array(totalCount);
     var valueKind = field.valueKind;
@@ -162,8 +162,8 @@ function getFieldData(field, arrayCtor, totalCount, data) {
         var keys = data[_d].keys();
         while (keys.hasNext) {
             var key = keys.move();
-            var p = valueKind ? valueKind(key, d) : 0 /* Present */;
-            if (p !== 0 /* Present */) {
+            var p = valueKind ? valueKind(key, d) : 0 /* Column.ValueKind.Present */;
+            if (p !== 0 /* Column.ValueKind.Present */) {
                 mask[offset] = p;
                 if (isStr)
                     array[offset] = '';
@@ -172,11 +172,11 @@ function getFieldData(field, arrayCtor, totalCount, data) {
             else {
                 var value = getter(key, d, offset);
                 if (typeof value === 'string' && !value) {
-                    mask[offset] = 1 /* NotPresent */;
+                    mask[offset] = 1 /* Column.ValueKind.NotPresent */;
                     allPresent = false;
                 }
                 else {
-                    mask[offset] = 0 /* Present */;
+                    mask[offset] = 0 /* Column.ValueKind.Present */;
                 }
                 array[offset] = value;
             }

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

@@ -70,9 +70,9 @@ var TextEncoder = /** @class */ (function () {
 export { TextEncoder };
 function writeValue(builder, data, key, f, floatPrecision, index) {
     var kind = f.valueKind;
-    var p = kind ? kind(key, data) : 0 /* Present */;
-    if (p !== 0 /* Present */) {
-        if (p === 1 /* NotPresent */)
+    var p = kind ? kind(key, data) : 0 /* Column.ValueKind.Present */;
+    if (p !== 0 /* Column.ValueKind.Present */) {
+        if (p === 1 /* Column.ValueKind.NotPresent */)
             writeNotPresent(builder);
         else
             writeUnknown(builder);
@@ -80,7 +80,7 @@ function writeValue(builder, data, key, f, floatPrecision, index) {
     else {
         var val = f.value(key, data, index);
         var t = f.type;
-        if (t === 0 /* Str */) {
+        if (t === 0 /* Field.Type.Str */) {
             if (isMultiline(val)) {
                 writeMultiline(builder, val);
                 return true;
@@ -89,7 +89,7 @@ function writeValue(builder, data, key, f, floatPrecision, index) {
                 return writeChecked(builder, val);
             }
         }
-        else if (t === 1 /* Int */) {
+        else if (t === 1 /* Field.Type.Int */) {
             writeInteger(builder, val);
         }
         else {
@@ -104,9 +104,9 @@ function getFloatPrecisions(categoryName, fields, formatter) {
         var f = fields_1[_a];
         var format = formatter.getFormat(categoryName, f.name);
         if (format && typeof format.digitCount !== 'undefined')
-            ret[ret.length] = f.type === 2 /* Float */ ? Math.pow(10, Math.max(0, Math.min(format.digitCount, 15))) : 0;
+            ret[ret.length] = f.type === 2 /* Field.Type.Float */ ? Math.pow(10, Math.max(0, Math.min(format.digitCount, 15))) : 0;
         else
-            ret[ret.length] = f.type === 2 /* Float */ ? Math.pow(10, getFieldDigitCount(f)) : 0;
+            ret[ret.length] = f.type === 2 /* Field.Type.Float */ ? Math.pow(10, getFieldDigitCount(f)) : 0;
     }
     return ret;
 }

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

@@ -11,13 +11,13 @@ import { assertUnreachable } from '../../../mol-util/type-helpers';
 export var Field;
 (function (Field) {
     function str(name, value, params) {
-        return { name: name, type: 0 /* Str */, value: value, valueKind: params && params.valueKind, defaultFormat: params && params.encoder ? { encoder: params.encoder } : void 0, shouldInclude: params && params.shouldInclude };
+        return { name: name, type: 0 /* Type.Str */, value: value, valueKind: params && params.valueKind, defaultFormat: params && params.encoder ? { encoder: params.encoder } : void 0, shouldInclude: params && params.shouldInclude };
     }
     Field.str = str;
     function int(name, value, params) {
         return {
             name: name,
-            type: 1 /* Int */,
+            type: 1 /* Type.Int */,
             value: value,
             valueKind: params && params.valueKind,
             defaultFormat: params ? { encoder: params.encoder, typedArray: params.typedArray } : void 0,
@@ -28,7 +28,7 @@ export var Field;
     function float(name, value, params) {
         return {
             name: name,
-            type: 2 /* Float */,
+            type: 2 /* Type.Float */,
             value: value,
             valueKind: params && params.valueKind,
             defaultFormat: params ? { encoder: params.encoder, typedArray: params.typedArray, digitCount: typeof params.digitCount !== 'undefined' ? params.digitCount : void 0 } : void 0,
@@ -205,7 +205,7 @@ function columnValueKind(k) {
 }
 function getTensorDefinitions(field, space) {
     var fieldDefinitions = [];
-    var type = 2 /* Float */;
+    var type = 2 /* Field.Type.Float */;
     var valueKind = columnValueKind(field);
     if (space.rank === 1) {
         var rows = space.dimensions[0];
@@ -245,16 +245,16 @@ function cifFieldsFromTableSchema(schema) {
         var k = _a[_i];
         var t = schema[k];
         if (t.valueType === 'int') {
-            fields.push({ name: k, type: 1 /* Int */, value: columnValue(k), valueKind: columnValueKind(k) });
+            fields.push({ name: k, type: 1 /* Field.Type.Int */, value: columnValue(k), valueKind: columnValueKind(k) });
         }
         else if (t.valueType === 'float') {
-            fields.push({ name: k, type: 2 /* Float */, value: columnValue(k), valueKind: columnValueKind(k) });
+            fields.push({ name: k, type: 2 /* Field.Type.Float */, value: columnValue(k), valueKind: columnValueKind(k) });
         }
         else if (t.valueType === 'str') {
-            fields.push({ name: k, type: 0 /* Str */, value: columnValue(k), valueKind: columnValueKind(k) });
+            fields.push({ name: k, type: 0 /* Field.Type.Str */, value: columnValue(k), valueKind: columnValueKind(k) });
         }
         else if (t.valueType === 'list') {
-            fields.push({ name: k, type: 0 /* Str */, value: columnListValue(k), valueKind: columnValueKind(k) });
+            fields.push({ name: k, type: 0 /* Field.Type.Str */, value: columnListValue(k), valueKind: columnValueKind(k) });
         }
         else if (t.valueType === 'tensor') {
             fields.push.apply(fields, getTensorDefinitions(k, t.space));

package/lib/mol-io/writer/mol2/encoder.js

@@ -55,7 +55,7 @@ var Mol2Encoder = /** @class */ (function (_super) {
                     var i2 = atom2.index;
                     if (i1 < i2) {
                         var order = bond.order, flags = bond.flags;
-                        var ar = BondType.is(16 /* Aromatic */, flags);
+                        var ar = BondType.is(16 /* BondType.Flag.Aromatic */, flags);
                         StringBuilder.writeSafe(b, "".concat(++bondCount, " ").concat(i1 + 1, " ").concat(i2 + 1, " ").concat(ar ? 'ar' : order));
                         StringBuilder.newline(b);
                     }
@@ -134,7 +134,7 @@ var Mol2Encoder = /** @class */ (function (_super) {
                 return 'C.3'; // 1.6.1, 3rga/ligand?encoding=mol2&auth_seq_id=307 (MOH)
             if (numBonds === 3 && this.isCat(bonds, bondMap))
                 return 'C.cat'; // 1.6.2, 1acj/ligand?encoding=mol2&auth_seq_id=44 (ARG), 5vjb/ligand?encoding=mol2&auth_seq_id=101 (GAI)
-            if (numBonds >= 2 && this.count(bonds, this, function (_k, v) { return BondType.is(16 /* Aromatic */, v.flags); }) >= 2)
+            if (numBonds >= 2 && this.count(bonds, this, function (_k, v) { return BondType.is(16 /* BondType.Flag.Aromatic */, v.flags); }) >= 2)
                 return 'C.ar'; // 1.6.3, 1acj/ligand?encoding=mol2&auth_seq_id=30 (PHE), 1acj/ligand?encoding=mol2&auth_seq_id=63 (TYR), 1acj/ligand?encoding=mol2&auth_seq_id=84 (TRP), 1acj/ligand?encoding=mol2&auth_seq_id=999 (THA)
             if ((numBonds === 1 || numBonds === 2) && this.count(bonds, this, function (_k, v) { return v.order === 3; }))
                 return 'C.1'; // 1.6.4, 3i04/ligand?encoding=mol2&auth_asym_id=C&auth_seq_id=900 (CYN)
@@ -157,7 +157,7 @@ var Mol2Encoder = /** @class */ (function (_super) {
         if (type_symbol1 === 'N') { // 1.8
             if (numNonmets === 4 && this.count(nonmets, this, function (_k, v) { return v.order === 1; }) === 4)
                 return 'N.4'; // 1.8.1, 4ikf/ligand?encoding=mol2&auth_seq_id=403 (NH4)
-            if (numBonds >= 2 && this.count(bonds, this, function (_k, v) { return BondType.is(16 /* Aromatic */, v.flags); }) >= 2)
+            if (numBonds >= 2 && this.count(bonds, this, function (_k, v) { return BondType.is(16 /* BondType.Flag.Aromatic */, v.flags); }) >= 2)
                 return 'N.ar'; // 1.8.2, 1acj/ligand?encoding=mol2&auth_seq_id=84 (TRP), 1acj/ligand?encoding=mol2&auth_seq_id=999 (THA)
             if (numNonmets === 1 && this.count(nonmets, this, function (_k, v) { return v.order === 3; }))
                 return 'N.1'; // 1.8.3, 3i04/ligand?encoding=mol2&auth_asym_id=C&auth_seq_id=900 (CYN)
@@ -198,7 +198,7 @@ var Mol2Encoder = /** @class */ (function (_super) {
         while (!result.done) {
             var label_atom_id = result.value;
             var adjacentBonds = bondMap.map.get(label_atom_id);
-            if (this.count(adjacentBonds, this, function (_k, v) { return v.order > 1 || BondType.is(16 /* Aromatic */, v.flags); })) {
+            if (this.count(adjacentBonds, this, function (_k, v) { return v.order > 1 || BondType.is(16 /* BondType.Flag.Aromatic */, v.flags); })) {
                 // TODO check accurately for 2nd criterion with coordinates
                 return true;
             }

package/lib/mol-math/geometry/gaussian-density/gpu.js

@@ -16,6 +16,7 @@ import { createComputeRenderItem } from '../../../mol-gl/webgl/render-item';
 import { ValueSpec, AttributeSpec, UniformSpec, TextureSpec, DefineSpec } from '../../../mol-gl/renderable/schema';
 import { gaussianDensity_vert } from '../../../mol-gl/shader/gaussian-density.vert';
 import { gaussianDensity_frag } from '../../../mol-gl/shader/gaussian-density.frag';
+import { isTimingMode } from '../../../mol-util/debug';
 var GaussianDensitySchema = {
     drawCount: ValueSpec('number'),
     instanceCount: ValueSpec('number'),
@@ -68,10 +69,20 @@ export function GaussianDensityTexture(webgl, position, box, radius, props, oldT
         GaussianDensityTexture2d(webgl, position, box, radius, false, props, oldTexture);
 }
 export function GaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo, props, oldTexture) {
-    return finalizeGaussianDensityTexture(calcGaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo, props, oldTexture));
+    if (isTimingMode)
+        webgl.timer.mark('GaussianDensityTexture2d');
+    var data = calcGaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo, props, oldTexture);
+    if (isTimingMode)
+        webgl.timer.markEnd('GaussianDensityTexture2d');
+    return finalizeGaussianDensityTexture(data);
 }
 export function GaussianDensityTexture3d(webgl, position, box, radius, props, oldTexture) {
-    return finalizeGaussianDensityTexture(calcGaussianDensityTexture3d(webgl, position, box, radius, props, oldTexture));
+    if (isTimingMode)
+        webgl.timer.mark('GaussianDensityTexture3d');
+    var data = calcGaussianDensityTexture3d(webgl, position, box, radius, props, oldTexture);
+    if (isTimingMode)
+        webgl.timer.markEnd('GaussianDensityTexture3d');
+    return finalizeGaussianDensityTexture(data);
 }
 function finalizeGaussianDensityTexture(_a) {
     var texture = _a.texture, scale = _a.scale, bbox = _a.bbox, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, gridTexScale = _a.gridTexScale, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;

package/lib/mol-model/sequence/alignment/sequence.js

@@ -80,11 +80,11 @@ var AlignSequences;
 })(AlignSequences || (AlignSequences = {}));
 function entityKey(unit) {
     switch (unit.kind) {
-        case 0 /* Atomic */:
+        case 0 /* Unit.Kind.Atomic */:
             return unit.model.atomicHierarchy.index.getEntityFromChain(unit.chainIndex[unit.elements[0]]);
-        case 1 /* Spheres */:
+        case 1 /* Unit.Kind.Spheres */:
             return unit.model.coarseHierarchy.spheres.entityKey[unit.elements[0]];
-        case 2 /* Gaussians */:
+        case 2 /* Unit.Kind.Gaussians */:
             return unit.model.coarseHierarchy.gaussians.entityKey[unit.elements[0]];
     }
 }

package/lib/mol-model/sequence/sequence.js

@@ -18,27 +18,27 @@ var Sequence;
         for (var i = 0, _i = Math.min(names.rowCount, 10); i < _i; i++) {
             var name_1 = names.value(i) || '';
             if (getProteinOneLetterCode(name_1) !== 'X')
-                return "protein" /* Protein */;
+                return "protein" /* Kind.Protein */;
             if (getRnaOneLetterCode(name_1) !== 'X')
-                return "RNA" /* RNA */;
+                return "RNA" /* Kind.RNA */;
             if (getDnaOneLetterCode(name_1) !== 'X')
-                return "DNA" /* DNA */;
+                return "DNA" /* Kind.DNA */;
         }
-        return "generic" /* Generic */;
+        return "generic" /* Kind.Generic */;
     }
     function codeProvider(kind, map) {
         var code;
         switch (kind) {
-            case "protein" /* Protein */:
+            case "protein" /* Kind.Protein */:
                 code = getProteinOneLetterCode;
                 break;
-            case "DNA" /* DNA */:
+            case "DNA" /* Kind.DNA */:
                 code = getDnaOneLetterCode;
                 break;
-            case "RNA" /* RNA */:
+            case "RNA" /* Kind.RNA */:
                 code = getRnaOneLetterCode;
                 break;
-            case "generic" /* Generic */:
+            case "generic" /* Kind.Generic */:
                 code = function () { return 'X'; };
                 break;
             default: assertUnreachable(kind);
@@ -119,7 +119,7 @@ var Sequence;
         return ResidueNamesImpl;
     }());
     function ofSequenceRanges(seqIdBegin, seqIdEnd) {
-        var kind = "generic" /* Generic */;
+        var kind = "generic" /* Kind.Generic */;
         return new SequenceRangesImpl(kind, seqIdBegin, seqIdEnd);
     }
     Sequence.ofSequenceRanges = ofSequenceRanges;

package/lib/mol-model/structure/export/categories/atom_site_operator_mapping.js

@@ -30,8 +30,8 @@ export var AtomSiteOperatorMappingSchema = {
         ncs_id: Column.Schema.Int(),
     }
 };
-var asmValueKind = function (i, xs) { return typeof xs[i].operator.assembly === 'undefined' ? 1 /* NotPresent */ : 0 /* Present */; };
-var symmetryValueKind = function (i, xs) { return xs[i].operator.spgrOp === -1 ? 1 /* NotPresent */ : 0 /* Present */; };
+var asmValueKind = function (i, xs) { return typeof xs[i].operator.assembly === 'undefined' ? 1 /* Column.ValueKind.NotPresent */ : 0 /* Column.ValueKind.Present */; };
+var symmetryValueKind = function (i, xs) { return xs[i].operator.spgrOp === -1 ? 1 /* Column.ValueKind.NotPresent */ : 0 /* Column.ValueKind.Present */; };
 var Fields = CifWriter.fields()
     .str('label_asym_id', function (i, xs) { return xs[i].label_asym_id; })
     .str('auth_asym_id', function (i, xs) { return xs[i].auth_asym_id; })
@@ -62,7 +62,7 @@ function getEntries(ctx) {
         for (var _b = 0, _c = s.units; _b < _c.length; _b++) {
             var unit = _c[_b];
             var operator = unit.conformation.operator;
-            if (!operator.suffix || unit.kind !== 0 /* Atomic */)
+            if (!operator.suffix || unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;

package/lib/mol-model/structure/export/categories/secondary-structure.js

@@ -41,7 +41,7 @@ var struct_conf_fields = function () { return __spreadArray(__spreadArray(__spre
 ], residueIdFields(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), residueIdFields(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
     CifField.str('pdbx_PDB_helix_class', function (i, data) { return data[i].element.helix_class; }),
     CifField.str('details', function (i, data) { return data[i].element.details || ''; }, {
-        valueKind: function (i, d) { return !!d[i].element.details ? 0 /* Present */ : 2 /* Unknown */; }
+        valueKind: function (i, d) { return !!d[i].element.details ? 0 /* Column.ValueKind.Present */ : 2 /* Column.ValueKind.Unknown */; }
     }),
     CifField.int('pdbx_PDB_helix_length', function (i, data) { return data[i].length; })
 ], false); };
@@ -49,7 +49,7 @@ var struct_sheet_range_fields = function () { return __spreadArray(__spreadArray
     CifField.str('sheet_id', function (i, data) { return data[i].element.sheet_id; }),
     CifField.index('id')
 ], residueIdFields(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), residueIdFields(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
-    CifField.str('symmetry', function (i, data) { return ''; }, { valueKind: function (i, d) { return 2 /* Unknown */; } })
+    CifField.str('symmetry', function (i, data) { return ''; }, { valueKind: function (i, d) { return 2 /* Column.ValueKind.Unknown */; } })
 ], false); };
 function findElements(ctx, kind) {
     // TODO: encode secondary structure for different models?

package/lib/mol-model/structure/export/categories/utils.js

@@ -89,7 +89,7 @@ export function copy_source_mmCifCategory(encoder, ctx, category) {
 function classifyField(name, field) {
     var type = getCifFieldType(field);
     if (type['@type'] === 'str') {
-        return { name: name, type: 0 /* Str */, value: field.str, valueKind: field.valueKind };
+        return { name: name, type: 0 /* CifWriter.Field.Type.Str */, value: field.str, valueKind: field.valueKind };
     }
     else if (type['@type'] === 'float') {
         return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, typedArray: Float64Array });

package/lib/mol-model/structure/model/model.js

@@ -168,7 +168,7 @@ export var Model;
             var polymerResidueCount = 0;
             var polymerType = model.atomicHierarchy.derived.residue.polymerType;
             for (var i = 0; i < polymerType.length; ++i) {
-                if (polymerType[i] !== 0 /* NA */)
+                if (polymerType[i] !== 0 /* PolymerType.NA */)
                     polymerResidueCount += 1;
             }
             // check for coarse grained atom names
@@ -337,7 +337,7 @@ export var Model;
         // check if from pdb archive but missing relevant meta data
         hasPdbId(model) && (!db.exptl.method.isDefined ||
             (isFromXray(model) && (!db.pdbx_database_status.status_code_sf.isDefined ||
-                db.pdbx_database_status.status_code_sf.valueKind(0) === 2 /* Unknown */)) ||
+                db.pdbx_database_status.status_code_sf.valueKind(0) === 2 /* Column.ValueKind.Unknown */)) ||
             (isFromEm(model) && (!db.pdbx_database_related.db_name.isDefined))));
     }
     Model.probablyHasDensityMap = probablyHasDensityMap;