@datagrok-libraries/bio 5.40.3 → 5.40.5

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Files changed (10) hide show
  1. package/CHANGELOG.md +13 -1
  2. package/package.json +1 -1
  3. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  4. package/src/monomer-works/monomer-utils.js +6 -0
  5. package/src/monomer-works/monomer-utils.js.map +1 -1
  6. package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
  7. package/src/monomer-works/to-atomic-level-utils.js +16 -13
  8. package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
  9. package/src/utils/const.js +2 -2
  10. package/src/utils/const.js.map +1 -1
package/CHANGELOG.md CHANGED
@@ -1,5 +1,17 @@
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  # bio changelog
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+ ## 5.40.5 (2024-04-10)
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+
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+ ### Bug fixes
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+
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+ * Fix SDF to JSON for Biovia lib
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+
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+ ## 5.40.4 (2024-04-09)
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+
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+ ### Features
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+
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+ * Modified STEABS block generation when linking monomers (adding not more than 80 symbols per row)
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+
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  ## 5.40.3 (2024-04-08)
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  ### Features
@@ -11,7 +23,7 @@
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  ### Bug fixes
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- Bio: Fix SeqHandler for column version
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+ * Fix SeqHandler for column version
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  ## 5.40.1 (2024-04-05)
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package/package.json CHANGED
@@ -8,7 +8,7 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.40.3",
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+ "version": "5.40.5",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.68",
package/src/monomer-works/monomer-utils.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAa,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAMtE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhG;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,CA8BpE;AAED,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AA6DhJ;;+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,CAmC1F"}
1
+ {"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAa,YAAY,EAAC,MAAM,8BAA8B,CAAC;AAMtE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAkBhG;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,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAG1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AA6DhJ;;+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,CAmC1F"}
package/src/monomer-works/monomer-utils.js CHANGED
@@ -86,6 +86,7 @@ export function createMomomersMolDict(lib) {
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  return dict;
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  }
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  export function createJsonMonomerLibFromSdf(table) {
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+ var _a, _b, _c, _d, _e;
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  const resultLib = [];
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  for (let i = 0; i < table.rowCount; i++) {
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  const monomer = {};
@@ -114,6 +115,11 @@ export function createJsonMonomerLibFromSdf(table) {
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  monomer[key] = table.get(jsonSdfMonomerLibDict[key], i);
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  }
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  });
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+ monomer[_a = "author" /* HELM_REQUIRED_FIELD.AUTHOR */] ?? (monomer[_a] = '');
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+ monomer[_b = "id" /* HELM_REQUIRED_FIELD.ID */] ?? (monomer[_b] = 0);
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+ monomer[_c = "smiles" /* HELM_REQUIRED_FIELD.SMILES */] ?? (monomer[_c] = '');
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+ monomer[_d = "monomerType" /* HELM_REQUIRED_FIELD.MONOMER_TYPE */] ?? (monomer[_d] = 'Backbone');
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+ monomer[_e = "createDate" /* HELM_REQUIRED_FIELD.CREATE_DATE */] ?? (monomer[_e] = null);
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  resultLib.push(monomer);
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  }
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  return resultLib;
package/src/monomer-works/monomer-utils.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AACA,OAAO,EACL,QAAQ,EAAC,MAAM,SAAS,CAAC;AAC3B,OAAO,EAC0B,iBAAiB,EACjD,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAC,QAAQ,EAAC,MAAM,+BAA+B,CAAC;AACvD,OAAO,EAAC,WAAW,EAAU,MAAM,UAAU,CAAC;AAG9C;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC1E,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAsBlB;AAED;;;;;qCAKqC;AACrC,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,EACzD,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,GACjD,MAAM,CAkFR;AAqPD;;;EAGE;AACF,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}
package/src/monomer-works/to-atomic-level-utils.js CHANGED
@@ -104,21 +104,24 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
104
104
  return result;
105
105
  }
106
106
  function getCollectionBlock(collection) {
107
- let collectionBlock = 'M V30 BEGIN COLLECTION\n';
108
- const entries = 4;
109
- const collNumber = Math.ceil(collection.length / entries);
110
- collectionBlock += 'M V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
111
- for (let i = 0; i < collNumber; i++) {
112
- collectionBlock += 'M V30 ';
113
- const entriesCurrent = i + 1 === collNumber ? collection.length - (collNumber - 1) * entries : entries;
114
- for (let j = 0; j < entriesCurrent; j++) {
115
- collectionBlock += (j + 1 === entriesCurrent) ?
116
- (i === collNumber - 1 ? collection[entries * i + j] + ')\n' : collection[entries * i + j] + ' -\n') :
117
- collection[entries * i + j] + ' ';
107
+ //one row in STEABS block can be no longer than 80 symbols
108
+ //maxSymbols = 80 symbols minus ' -\n' (4 symbols)
109
+ const maxSymbols = 76;
110
+ const rowsArray = [];
111
+ let newCollectionRow = `M V30 MDLV30/STEABS ATOMS=(${collection.length}`;
112
+ for (let i = 0; i < collection.length; i++) {
113
+ const updatedRow = `${newCollectionRow} ${collection[i]}`;
114
+ if (updatedRow.length > maxSymbols) {
115
+ rowsArray.push(`${newCollectionRow} -\n`);
116
+ newCollectionRow = `M V30 ${collection[i]}`;
118
117
  }
118
+ else
119
+ newCollectionRow = updatedRow;
120
+ //in case last atom was added - close the block
121
+ if (i === collection.length - 1)
122
+ rowsArray.push(`${newCollectionRow})\n`);
119
123
  }
120
- collectionBlock += 'M V30 END COLLECTION\n';
121
- return collectionBlock;
124
+ return `M V30 BEGIN COLLECTION\n${rowsArray.join('')}M V30 END COLLECTION\n`;
122
125
  }
123
126
  /** Cap the resulting (after sewing up all the monomers) molfile with 'O'
124
127
  * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block
package/src/monomer-works/to-atomic-level-utils.js.map CHANGED
@@ -1 +1 @@
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package/src/utils/const.js CHANGED
@@ -12,7 +12,7 @@ export const SDF_MONOMER_NAME = 'MonomerName';
12
12
  export const jsonSdfMonomerLibDict = {
13
13
  'monomerType': null,
14
14
  'smiles': null,
15
- 'name': 'MonomerName',
15
+ 'name': 'Name',
16
16
  'author': null,
17
17
  'molfile': 'molecule',
18
18
  'naturalAnalog': 'MonomerNaturalAnalogCode',
@@ -20,7 +20,7 @@ export const jsonSdfMonomerLibDict = {
20
20
  'createDate': null,
21
21
  'id': null,
22
22
  'polymerType': 'MonomerType',
23
- 'symbol': 'MonomerCode'
23
+ 'symbol': 'MonomerName'
24
24
  };
25
25
  export const DUMMY_MONOMER = {
26
26
  'monomerType': 'Backbone',
package/src/utils/const.js.map CHANGED
@@ -1 +1 @@
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