@datagrok-libraries/bio 6.0.4 → 6.0.7

package/.turbo/turbo-build.log

@@ -0,0 +1,5 @@
+
+> @datagrok-libraries/bio@6.0.7 build /home/runner/work/public/public/libraries/bio
+> grok tsc -p tsconfig.json
+
+copied 1 asset file(s) into dist/

package/CLAUDE.md

@@ -148,7 +148,7 @@ The core engine for converting macromolecule sequences into V3000 molfiles.
 | `composition-table.ts` | `getCompositionTable()` — builds HTML monomer composition bar chart |
 | `fasta-handler.ts` | `FastaFileHandler` — parses FASTA files into DataFrames |
 | `generator.ts` | Test data generators for synthetic macromolecule columns |
-| `sequence-position-scroller.ts` | MSA header / scroll bar engine: `MSAScrollingHeader`, abstract `MSAHeaderTrack`, plus `WebLogoTrack` and `ConservationTrack` track implementations. Renders sequence-logo + conservation tracks above an MSA grid with a scrollable position slider and composition tooltips |
+| `sequence-position-scroller.ts` | MSA header / scroll bar engine: `MSAScrollingHeader`, abstract `MSAHeaderTrack`, plus `WebLogoTrack` and `ConservationTrack` track implementations. Renders sequence-logo + conservation tracks above an MSA grid with a scrollable position slider and composition tooltips. The ruler and the tooltips name positions by the column's `.positionLabels` / `.positionNames` (`getPositionName`, passed to tracks by `addTrack`); the header shows its event element only while the grid paints it and adds `header tracks/positions of <col>` readings and `position <name> of <col> header` areas to the grid's status |
 | `annotation-track.ts` | `AnnotationTrack` — `MSAHeaderTrack` subclass that overlays region/liability annotations on the MSA scroller |
 | `cell-renderer-annotations.ts` | `AnnotationRenderer` — paints region rectangles and liability underlines on the macromolecule cell renderer |
 | `macromolecule-highlight.ts` | Cross-package monomer highlight bus: `fireMacromoleculeHighlight()`, `setMacromoleculeMonomerHighlight()` / `setMacromoleculeMonomerHighlights()`, `clear*` siblings, `MACROMOLECULE_HIGHLIGHT_EVENT_ID` / `…_TEMP` / `…_ALPHA` constants, `MacromoleculeHighlightEntry` / `EventArgs` / `Colors` / `Target` / `RowSpec` types, `macromoleculeHighlightColorToCss()` |

package/LICENSE.md

@@ -0,0 +1,16 @@
+Copyright 2020 Datagrok, INC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction,
+including without limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES
+OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

package/dist/src/aminoacids.d.ts.map

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package/dist/src/molecule/molecule-units-handler.js.map

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package/dist/src/molecule/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/molecule/types.js.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/index.js.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/molecule-3d-build-data.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/molecule-3d-build-data.js.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/molecule-3d-units-handler.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/molecule-3d-units-handler.js.map

@@ -0,0 +1 @@
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package/dist/src/molecule-3d/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/molecule-3d/types.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,aAAa,EAAE,QAAQ,EAAC,MAAM,6BAA6B,CAAC;AAEpE,qBAAa,cAAe,SAAQ,QAAQ;IAC1C,YAAY,IAAI,CAAC,EAAE,MAAM,EAExB;CACF;AAED,MAAM,MAAM,uBAAuB,GAAG,aAAa,CAAC,GAAG,EAAE,cAAc,CAAC,CAAC"}

package/dist/src/molecule-3d/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/molecule-3d/types.ts"],"names":[],"mappings":"AAIA,OAAO,EAAgB,QAAQ,EAAC,MAAM,6BAA6B,CAAC;AAEpE,MAAM,OAAO,cAAe,SAAQ,QAAQ;IAC1C,YAAY,IAAa;QACvB,KAAK,CAAC,IAAI,CAAC,CAAC;IACd,CAAC;CACF"}

package/dist/src/monomer-works/consts.d.ts

@@ -0,0 +1,36 @@
+export declare const monomerWorksConsts: {
+    readonly V2K_RGP_SHIFT: 8;
+    readonly V2K_RGP_LINE: 'M  RGP';
+    readonly V2K_A_LINE: 'A  ';
+    readonly V3K_COUNTS_SHIFT: 14;
+    readonly V3K_IDX_SHIFT: 7;
+    readonly V3K_HEADER_FIRST_LINE: '\nDatagrok macromolecule handler\n\n';
+    readonly V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\n';
+    readonly V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\n';
+    readonly V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\n';
+    readonly V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ';
+    readonly V3K_COUNTS_LINE_ENDING: ' 0 0 0\n';
+    readonly V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\n';
+    readonly V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\n';
+    readonly V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\n';
+    readonly V3K_END_BOND_BLOCK: 'M  V30 END BOND\n';
+    readonly V3K_BOND_CONFIG: ' CFG=';
+    readonly V3K_BEGIN_DATA_LINE: 'M  V30 ';
+    readonly V3K_END: 'M  END';
+    readonly PRECISION_FACTOR: 10000;
+    readonly DEOXYRIBOSE: {
+        readonly polymerType: "RNA";
+        readonly symbol: 'd';
+    };
+    readonly RIBOSE: {
+        readonly polymerType: "RNA";
+        readonly symbol: 'r';
+    };
+    readonly PHOSPHATE: {
+        readonly polymerType: "RNA";
+        readonly symbol: 'p';
+    };
+    readonly OXYGEN: 'O';
+    readonly HYDROGEN: 'H';
+};
+//# sourceMappingURL=consts.d.ts.map

package/dist/src/monomer-works/consts.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/monomer-works/consts.js.map

@@ -0,0 +1 @@
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package/dist/src/monomer-works/lib-events.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/monomer-works/lib-events.js.map

@@ -0,0 +1 @@
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package/dist/src/monomer-works/lib-settings.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"lib-settings.d.ts","sourceRoot":"","sources":["../../../src/monomer-works/lib-settings.ts"],"names":[],"mappings":"AAEA,OAAO,EAAC,eAAe,EAAC,MAAM,SAAS,CAAC;AA0DxC,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,eAAe,CAAC,CAwBnE;AAED,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAmB9E"}

package/dist/src/monomer-works/lib-settings.js.map

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package/dist/src/monomer-works/monomer-utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["../../../src/monomer-works/monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAYtC,OAAO,EAAC,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAG1D,OAAO,EAAC,UAAU,EAAC,MAAM,qBAAqB,CAAC;AAG/C,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,UAAU,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAwBtF;AAED,wBAAgB,kBAAkB,CAChC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,EAAE,SAAS,EAAE,UAAU,GAC9D,GAAG,EAAE,EAAE,GAAG,IAAI,CAsBhB;AAED,wBAAgB,wBAAwB,CACtC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,EAAE,SAAS,EAAE,UAAU,GAC7D,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhB;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CAoCpE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAC1C,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AACtH,wBAAsB,sBAAsB,CAC1C,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,EAAE,SAAS,EAAE,UAAU,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAmD5H;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAqB1F;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAE,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAE,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,CAAA;CAAE,CAAC,CAuC1F"}

package/{src → dist/src}/monomer-works/monomer-utils.js

@@ -132,19 +132,16 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence,
     const libHelper = await getMonomerLibHelper();
     const monomerLib = libHelper.getMonomerLib();
     // const smilesCols: DG.Column<string>[] = new Array(monomerCols.length);
-    const rawCols = new Array(positionColumns.length);
     const rowCount = positionColumns[0].length;
     const totalSimilarity = new Float32Array(rowCount);
     // Calculate base similarity
-    for (let position = 0; position < positionColumns.length; ++position) {
-        const referenceMonomerCanonical = position < referenceSequence.length ?
-            referenceSequence.getCanonical(position) : GAP_SYMBOL;
+    for (let position = 0; position < Math.min(positionColumns.length, referenceSequence.length); ++position) {
+        const referenceMonomerCanonical = referenceSequence.getCanonical(position);
         const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomerCanonical)?.smiles ?? '';
         const monomerCol = positionColumns[position];
         const monomerColData = monomerCol.getRawData();
         const monomerColCategories = monomerCol.categories;
         const emptyCategoryIdx = monomerColCategories.indexOf('');
-        rawCols[position] = { categories: monomerColCategories, data: monomerColData, emptyIndex: emptyCategoryIdx };
         if (typeof referenceMonomerCanonical === 'undefined')
             continue;
         // Calculating similarity for
@@ -161,18 +158,8 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence,
             // Do not increase similarity on mismatch score/penalty equals 0;
         }
     }
-    for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {
-        let updatedSimilarity = totalSimilarity[similarityIndex] / referenceSequence.length;
-        for (let position = 0; position < positionColumns.length; ++position) {
-            const currentRawCol = rawCols[position];
-            if ((position >= referenceSequence.length && currentRawCol.data[similarityIndex] !== currentRawCol.emptyIndex) ||
-                (currentRawCol.data[similarityIndex] === currentRawCol.emptyIndex && position < referenceSequence.length)) {
-                updatedSimilarity = DG.FLOAT_NULL;
-                break;
-            }
-        }
-        totalSimilarity[similarityIndex] = updatedSimilarity;
-    }
+    for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex)
+        totalSimilarity[similarityIndex] /= referenceSequence.length;
     const similarityCol = DG.Column.fromFloat32Array('Similarity', totalSimilarity);
     return similarityCol;
 }

package/dist/src/monomer-works/monomer-utils.js.map

@@ -0,0 +1 @@
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package/dist/src/monomer-works/monomer-works.d.ts.map

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package/dist/src/monomer-works/to-atomic-level-utils.js.map

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package/dist/src/monomer-works/to-atomic-level.d.ts.map

@@ -0,0 +1 @@
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