@datagrok/bio 2.15.2 → 2.15.5

package/files/tests/to-atomic-level-msa-separator-output.csv

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+M  V30 158 O 22.8638 1.6507 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
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@@ -319,7 +319,7 @@ M  V30 150 2 147 148
 M  V30 151 1 148 149
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 M  V30 153 1 150 151
-M  V30 154 1 152 151 CFG=1
+M  V30 154 1 152 151 CFG=3
 M  V30 155 1 152 153
 M  V30 156 1 152 154
 M  V30 157 2 154 155
@@ -484,19 +484,19 @@ M  V30 144 C 20.72 -0.4122  0.000000 0
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 M  V30 END ATOM
 M  V30 BEGIN BOND
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@@ -655,7 +655,7 @@ M  V30 153 2 149 150
 M  V30 154 1 150 151
 M  V30 155 2 151 152
 M  V30 156 1 152 153
-M  V30 157 1 154 153 CFG=1
+M  V30 157 1 154 153 CFG=3
 M  V30 158 1 154 155
 M  V30 159 1 154 156
 M  V30 160 2 156 157
@@ -827,19 +827,19 @@ M  V30 151 C 20.7201 -0.4123  0.000000 0
 M  V30 152 N 20.0056 0.0002  0.000000 0
 M  V30 153 C 21.4346 0.0003  0.000000 0
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-M  V30 166 C 23.5781 3.7127  0.000000 0
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 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2
@@ -1004,7 +1004,7 @@ M  V30 159 2 156 157
 M  V30 160 1 157 158
 M  V30 161 2 158 159
 M  V30 162 1 159 160
-M  V30 163 1 161 160 CFG=1
+M  V30 163 1 161 160 CFG=3
 M  V30 164 1 161 162
 M  V30 165 1 161 163
 M  V30 166 2 163 164
@@ -1169,19 +1169,19 @@ M  V30 144 C 20.7201 -0.4123  0.000000 0
 M  V30 145 N 20.0056 0.0002  0.000000 0
 M  V30 146 C 21.4346 0.0003  0.000000 0
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-M  V30 150 C 24.2925 2.4752  0.000000 0
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-M  V30 154 C 22.1491 1.2378  0.000000 0
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 M  V30 END ATOM
 M  V30 BEGIN BOND
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@@ -1339,7 +1339,7 @@ M  V30 152 2 149 150
 M  V30 153 1 150 151
 M  V30 154 2 151 152
 M  V30 155 1 152 153
-M  V30 156 1 154 153 CFG=1
+M  V30 156 1 154 153 CFG=3
 M  V30 157 1 154 155
 M  V30 158 1 154 156
 M  V30 159 2 156 157
@@ -1503,19 +1503,19 @@ M  V30 143 C 20.7201 -0.412  0.000000 0
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-M  V30 152 C 22.1491 2.063  0.000000 0
-M  V30 153 C 22.1491 1.2381  0.000000 0
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+M  V30 153 C 22.1491 0.4131  0.000000 0
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-M  V30 155 C 22.8636 0.8255  0.000000 0
-M  V30 156 O 23.578 1.238  0.000000 0
-M  V30 157 C 22.8636 3.3005  0.000000 0
-M  V30 158 C 23.5781 3.713  0.000000 0
-M  V30 159 O 22.8636 -0.0005 0.000000 0
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+M  V30 159 O 22.8636 1.6507 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2
@@ -1673,7 +1673,7 @@ M  V30 152 2 148 149
 M  V30 153 1 149 150
 M  V30 154 2 150 151
 M  V30 155 1 151 152
-M  V30 156 1 153 152 CFG=1
+M  V30 156 1 153 152 CFG=3
 M  V30 157 1 153 154
 M  V30 158 1 153 155
 M  V30 159 2 155 156
@@ -2767,19 +2767,19 @@ M  V30 136 C 20.9147 -0.6603  0.000000 0
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-M  V30 142 C 24.4871 2.2272  0.000000 0
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-M  V30 152 O 23.0582 0.2478 0.000000 0
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+M  V30 152 O 23.0582 1.4024 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2
@@ -2930,7 +2930,7 @@ M  V30 145 2 141 142
 M  V30 146 1 142 143
 M  V30 147 2 143 144
 M  V30 148 1 144 145
-M  V30 149 1 146 145 CFG=1
+M  V30 149 1 146 145 CFG=3
 M  V30 150 1 146 147
 M  V30 151 1 146 148
 M  V30 152 2 148 149
@@ -3085,19 +3085,19 @@ M  V30 134 C 20.7201 -0.4121  0.000000 0
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 M  V30 136 C 21.4346 0.0005  0.000000 0
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-M  V30 138 C 25.007 3.7129  0.000000 0
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-M  V30 140 C 24.2925 2.4754  0.000000 0
-M  V30 141 C 23.578 2.063  0.000000 0
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-M  V30 144 C 22.1491 1.238  0.000000 0
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-M  V30 148 C 22.8636 3.3004  0.000000 0
-M  V30 149 C 23.5781 3.7129  0.000000 0
-M  V30 150 O 22.8636 -0.0004 0.000000 0
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+M  V30 150 O 22.8636 1.6506 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2
@@ -3244,7 +3244,7 @@ M  V30 141 2 139 140
 M  V30 142 1 140 141
 M  V30 143 2 141 142
 M  V30 144 1 142 143
-M  V30 145 1 144 143 CFG=1
+M  V30 145 1 144 143 CFG=3
 M  V30 146 1 144 145
 M  V30 147 1 144 146
 M  V30 148 2 146 147
@@ -3404,19 +3404,19 @@ M  V30 139 C 20.9148 -0.6602  0.000000 0
 M  V30 140 N 20.2003 -0.2477  0.000000 0
 M  V30 141 C 21.6293 -0.2476  0.000000 0
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-M  V30 143 C 25.2017 3.4648  0.000000 0
-M  V30 144 C 24.4873 3.0523  0.000000 0
-M  V30 145 C 24.4872 2.2273  0.000000 0
-M  V30 146 C 23.7727 1.8149  0.000000 0
-M  V30 147 C 23.0583 2.2273  0.000000 0
-M  V30 148 C 22.3438 1.8148  0.000000 0
-M  V30 149 C 22.3438 0.9899  0.000000 0
+M  V30 143 C 25.2017 -2.31  0.000000 0
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 M  V30 150 N 21.6293 0.5774  0.000000 0
-M  V30 151 C 23.0583 0.5773  0.000000 0
-M  V30 152 O 23.7727 0.9898  0.000000 0
-M  V30 153 C 23.0583 3.0523  0.000000 0
-M  V30 154 C 23.7728 3.4648  0.000000 0
-M  V30 155 O 23.0583 0.2477 0.000000 0
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+M  V30 153 C 23.0583 -1.8975  0.000000 0
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+M  V30 155 O 23.0583 1.4025 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
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@@ -3570,7 +3570,7 @@ M  V30 148 2 144 145
 M  V30 149 1 145 146
 M  V30 150 2 146 147
 M  V30 151 1 147 148
-M  V30 152 1 149 148 CFG=1
+M  V30 152 1 149 148 CFG=3
 M  V30 153 1 149 150
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package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.15.2",
+  "version": "2.15.5",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,12 +37,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.43.0",
-    "@datagrok-libraries/chem-meta": "^1.2.5",
+    "@datagrok-libraries/bio": "^5.44.1",
+    "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.0",
     "@datagrok-libraries/ml": "^6.7.1",
     "@datagrok-libraries/tutorials": "^1.4.0",
-    "@datagrok-libraries/utils": "^4.3.3",
+    "@datagrok-libraries/utils": "^4.3.4",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -60,9 +60,9 @@
   "devDependencies": {
     "@datagrok-libraries/helm-web-editor": "^1.1.11",
     "@datagrok-libraries/js-draw-lite": "^0.0.8",
-    "@datagrok/chem": "^1.12.0",
+    "@datagrok/chem": "^1.12.1",
     "@datagrok/dendrogram": "^1.2.33",
-    "@datagrok/helm": "latest",
+    "@datagrok/helm": "^2.5.0",
     "@types/node": "^17.0.24",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",
@@ -83,12 +83,12 @@
     "link-bio": "npm link @datagrok-libraries/bio",
     "link-ml": "npm link @datagrok-libraries/ml",
     "link-utils": "npm link @datagrok-libraries/utils",
-    "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/math @datagrok-libraries/utils @datagrok-libraries/ml @datagrok-libraries/bio @datagrok-libraries/tutorials",
+    "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/math @datagrok-libraries/ml @datagrok-libraries/bio @datagrok-libraries/tutorials",
     "debug-sequences1": "webpack && grok publish",
     "release-sequences1": "webpack && grok publish --release",
     "build-sequences1": "webpack",
     "build": "webpack",
-    "build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/math run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm --prefix ./../../libraries/bio run build && npm --prefix ./../../libraries/tutorials run build && npm run build",
+    "build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/math run build && npm --prefix ./../../libraries/ml run build && npm --prefix ./../../libraries/bio run build && npm --prefix ./../../libraries/tutorials run build && npm run build",
     "debug-sequences1-local": "webpack && grok publish local",
     "release-sequences1-local": "webpack && grok publish local --release",
     "debug-sequences1-dev": "webpack && grok publish dev",
@@ -153,4 +153,4 @@
       }
     }
   }
-}
+}

package/src/analysis/sequence-activity-cliffs.ts

@@ -135,7 +135,9 @@ export function createDifferenceCanvas(
   const context = canvas.getContext('2d');
   canvas.height = 30;
   drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30,
-    wu(subParts1.canonicals).toArray(), wu(subParts2.canonicals).toArray(), units, true, molDifferences);
+    wu.count(0).take(subParts1.length).map((posIdx) => subParts1.getCanonical(posIdx)).toArray(),
+    wu.count(0).take(subParts2.length).map((posIdx) => subParts2.getCanonical(posIdx)).toArray(),
+    units, true, molDifferences);
   return canvas;
 }
 

package/src/calculations/monomerLevelMols.ts

@@ -6,7 +6,8 @@ import wu from 'wu';
 
 import {getHelmMonomers} from '../package';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {GAP_SYMBOL, ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
 const V2000_ATOM_NAME_POS = 31;
 

package/src/demo/bio03-atomic-level.ts

@@ -32,7 +32,7 @@ export async function demoBio03UI(): Promise<void> {
       })
       .step('To atomic level', async () => {
         const seqCol = df.getCol(seqColName);
-        await toAtomicLevel(df, seqCol, false);
+        await toAtomicLevel(df, seqCol, false, false);
       }, {
         description: 'Get atomic level structures of Macromolecules.',
         delay: 2000,

package/src/package-test.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {runTests, TestContext, tests} from '@datagrok-libraries/utils/src/test';
+import {runTests, TestContext, tests, initAutoTests as initTests } from '@datagrok-libraries/utils/src/test';
 
 import './tests/_first-tests';
 import './tests/Palettes-test';
@@ -52,3 +52,8 @@ export async function test(category: string, test: string, testContext: TestCont
   const data = await runTests({category, test, testContext, stressTest});
   return DG.DataFrame.fromObjects(data)!;
 }
+
+//name: initAutoTests
+export async function initAutoTests() {
+  await initTests(_package, _package.getModule('package-test.js'));
+}