@datagrok-libraries/bio 5.41.10 → 5.41.12

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 (20) hide show
  1. package/.eslintrc.json +1 -0
  2. package/CHANGELOG.md +14 -0
  3. package/package.json +1 -1
  4. package/src/pdb/format/types-base.d.ts +1 -0
  5. package/src/pdb/format/types-base.d.ts.map +1 -1
  6. package/src/pdb/format/types-base.js +63 -0
  7. package/src/pdb/format/types-base.js.map +1 -1
  8. package/src/pdb/format/types-pdb.d.ts +1 -1
  9. package/src/pdb/format/types-pdb.d.ts.map +1 -1
  10. package/src/pdb/format/types-pdb.js +6 -2
  11. package/src/pdb/format/types-pdb.js.map +1 -1
  12. package/src/pdb/format/types-pdbqt.d.ts.map +1 -1
  13. package/src/pdb/format/types-pdbqt.js +0 -10
  14. package/src/pdb/format/types-pdbqt.js.map +1 -1
  15. package/src/pdb/format/types.d.ts +1 -0
  16. package/src/pdb/format/types.d.ts.map +1 -1
  17. package/src/utils/cell-renderer-async-base.d.ts +1 -1
  18. package/src/utils/cell-renderer-async-base.d.ts.map +1 -1
  19. package/src/utils/cell-renderer-async-base.js +4 -0
  20. package/src/utils/cell-renderer-async-base.js.map +1 -1
package/.eslintrc.json CHANGED
@@ -17,6 +17,7 @@
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  "rules": {
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  "indent": ["error", 2, {"SwitchCase": 0}],
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  "max-len": ["error", 120],
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+ "no-throw-literal": "error",
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  "no-unused-vars": "off",
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  "@typescript-eslint/no-unused-vars": [
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  "warn", {"varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}
package/CHANGELOG.md CHANGED
@@ -1,5 +1,19 @@
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  # bio changelog
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2
 
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+ ## 5.41.12 (2024-06-12)
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+
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+ ### Bug fixes
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+
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+ * Fix .pdbqt to .pdb sorting atoms, add tests
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+ * Fix cell renderer async base to reset errorCount
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+
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+ ## 5.41.11 (2024-06-11)
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+
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+ ### Bug fixes
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+
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+ Fix Pdbqt parser to assume ROOT as MODEL
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+ Fix Pdbqt.toPdb sorting atoms, tests
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+
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  ## 5.41.10 (2024-06-10)
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  NGL typings
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": "5.41.10",
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+ "version": "5.41.12",
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  "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.71",
package/src/pdb/format/types-base.d.ts CHANGED
@@ -26,6 +26,7 @@ export declare class AtomBase extends LineBase implements IAtomBase {
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  */
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  constructor(l: LineBase, number: number, atomElement: string, atomName: string, altLoc: string, resName: string, chain: string, resNumber: number, insCode: string);
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  static fromStr(line: string): AtomBase;
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+ compare(b: AtomBase): number;
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  toStr(): string;
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  }
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  /** 1-66 */
package/src/pdb/format/types-base.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types-base.d.ts","sourceRoot":"","sources":["types-base.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,WAAW,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AAEzD,qBAAa,QAAQ;aAED,SAAS,EAAE,MAAM;gBAAjB,SAAS,EAAE,MAAM;IAGnC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAMtC,KAAK,IAAI,MAAM;CAQhB;AAED,WAAW;AACX,qBAAa,QAAS,SAAQ,QAAS,YAAW,SAAS;aAYvC,MAAM,EAAE,MAAM;aACA,WAAW,EAAE,MAAM;aACK,QAAQ,EAAE,MAAM;aACtD,MAAM,EAAE,MAAM;aACY,OAAO,EAAE,MAAM;aACzC,KAAK,EAAE,MAAM;aACb,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAlBjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,MAAM,EAAE,MAAM,EACA,WAAW,EAAE,MAAM,EACK,QAAQ,EAAE,MAAM,EACtD,MAAM,EAAE,MAAM,EACY,OAAO,EAAE,MAAM,EACzC,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAetC,KAAK,IAAI,MAAM;CAgBhB;AAED,WAAW;AACX,qBAAa,cAAe,SAAQ,QAAS,YAAW,WAAW;aAY/C,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAfjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc;IAa5C,OAAO,IAAI,OAAO;IAgBlB,KAAK,IAAI,MAAM;CAahB;AAED,qBAAa,WAAY,SAAQ,QAAS,YAAW,QAAQ;CAAG"}
1
+ {"version":3,"file":"types-base.d.ts","sourceRoot":"","sources":["types-base.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAE,WAAW,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AAEzD,qBAAa,QAAQ;aAED,SAAS,EAAE,MAAM;gBAAjB,SAAS,EAAE,MAAM;IAGnC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAMtC,KAAK,IAAI,MAAM;CAQhB;AASD,WAAW;AACX,qBAAa,QAAS,SAAQ,QAAS,YAAW,SAAS;aAYvC,MAAM,EAAE,MAAM;aACA,WAAW,EAAE,MAAM;aACK,QAAQ,EAAE,MAAM;aACtD,MAAM,EAAE,MAAM;aACY,OAAO,EAAE,MAAM;aACzC,KAAK,EAAE,MAAM;aACb,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAlBjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,MAAM,EAAE,MAAM,EACA,WAAW,EAAE,MAAM,EACK,QAAQ,EAAE,MAAM,EACtD,MAAM,EAAE,MAAM,EACY,OAAO,EAAE,MAAM,EACzC,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ;IAetC,OAAO,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM;IAyD5B,KAAK,IAAI,MAAM;CAgBhB;AAED,WAAW;AACX,qBAAa,cAAe,SAAQ,QAAS,YAAW,WAAW;aAY/C,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,SAAS,EAAE,MAAM;aACjB,OAAO,EAAE,MAAM;IAfjC;;;;;;;;OAQG;gBAED,CAAC,EAAE,QAAQ,EACK,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM;IAKjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc;IAa5C,OAAO,IAAI,OAAO;IAgBlB,KAAK,IAAI,MAAM;CAahB;AAED,qBAAa,WAAY,SAAQ,QAAS,YAAW,QAAQ;CAAG"}
package/src/pdb/format/types-base.js CHANGED
@@ -14,6 +14,12 @@ export class LineBase {
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  return res;
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  }
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  }
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+ const backboneRanks = { 'N': 1, 'CA': 2, 'C': 3, 'O': 4 };
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+ const atomNameRanks = {
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+ /* backbone */ '': 0, /**/ 'N': 0,
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+ 'A': 1, 'B': 2, 'G': 3, 'D': 4, 'E': 5, 'Z': 6, 'H': 7,
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+ /* terminal */ 'X': 1000
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+ };
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  /** 1-27 */
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  export class AtomBase extends LineBase {
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  /**
@@ -45,6 +51,63 @@ export class AtomBase extends LineBase {
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  /* number */ parseInt(line.slice(7 - 1, 11)), `${line.slice(13 - 1, 14).trim()}`, `${line.slice(15 - 1, 16).trim()}`, `${line.slice(17 - 1, 17).trim()}`, `${line.slice(18 - 1, 20).trim()}`, `${line.slice(22 - 1, 22).trim()}`,
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  /* resNumber */ parseInt(line.slice(23 - 1, 26)), `${line.slice(27 - 1, 27).trim()}`);
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  }
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+ compare(b) {
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+ // https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
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+ const a = this;
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+ if (a.chain != b.chain)
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+ return a.chain.localeCompare(b.chain);
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+ if (a.resNumber !== b.resNumber)
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+ return a.resNumber - b.resNumber;
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+ else {
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+ const aFullName = `${a.atomElement}${a.atomName}`;
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+ const bFullName = `${b.atomElement}${b.atomName}`;
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+ const aBackboneRank = backboneRanks[aFullName] ?? -1;
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+ const bBackboneRank = backboneRanks[bFullName] ?? -1;
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+ if (aBackboneRank !== -1 && bBackboneRank !== -1)
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+ return aBackboneRank - bBackboneRank;
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+ else if (aBackboneRank !== -1)
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+ return -1;
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+ else if (bBackboneRank !== -1)
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+ return +1;
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+ else {
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+ const aElement = a.atomElement.replaceAll(/\d+/g, '');
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+ const bElement = b.atomElement.replaceAll(/\d+/g, '');
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+ const aRemoteness = a.atomName.replaceAll(/\d+/g, '').slice(0, 1);
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+ const bRemoteness = b.atomName.replaceAll(/\d+/g, '').slice(0, 1);
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+ const aAtomNameRank = atomNameRanks[aRemoteness];
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+ const bAtomNameRank = atomNameRanks[bRemoteness];
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+ if (aAtomNameRank === undefined || bAtomNameRank === undefined) {
80
+ return a.atomName.localeCompare(b.atomName);
81
+ }
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+ if (aElement !== 'H' && bElement !== 'H') {
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+ // Both atoms are not hydrogen
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+ if (aAtomNameRank !== bAtomNameRank)
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+ return aAtomNameRank - bAtomNameRank;
86
+ else {
87
+ const aAtomNameNum = parseInt(a.atomName.slice(1));
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+ const bAtomNameNum = parseInt(b.atomName.slice(1));
89
+ if (aAtomNameNum !== bAtomNameNum)
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+ return aAtomNameNum - bAtomNameNum;
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+ return a.atomName.localeCompare(b.atomName);
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+ }
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+ }
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+ else if (a.atomElement !== 'H' && b.atomElement === 'H')
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+ return -1;
96
+ else if (a.atomElement === 'H' && b.atomElement !== 'H')
97
+ return +1;
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+ else {
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+ // Both atoms are hydrogen
100
+ if (aAtomNameRank !== bAtomNameRank)
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+ return aAtomNameRank - bAtomNameRank;
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+ else {
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+ const aAtomNameNum = parseInt(a.atomName.slice(1));
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+ const bAtomNameNum = parseInt(b.atomName.slice(1));
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+ return aAtomNameNum - bAtomNameNum;
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+ }
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+ }
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+ }
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+ }
110
+ }
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  toStr() {
49
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  const res = [
50
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  super.toStr() /* 1-6 */,
package/src/pdb/format/types-base.js.map CHANGED
@@ -1 +1 @@
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package/src/pdb/format/types-pdb.d.ts CHANGED
@@ -15,7 +15,7 @@ export declare class PdbAtomCoords extends AtomCoordsBase implements IPdbAtomCoo
15
15
  * @param charge cols: 79-80, examples: '1+', '1-'
16
16
  */
17
17
  constructor(a: AtomCoordsBase, segment: string, element: string, charge: string);
18
- static fromStr(src: string): PdbAtomCoords;
18
+ static fromStr(line: string): PdbAtomCoords;
19
19
  isValid(): boolean;
20
20
  toStr(): string;
21
21
  }
package/src/pdb/format/types-pdb.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types-pdb.d.ts","sourceRoot":"","sources":["types-pdb.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAC,MAAM,cAAc,CAAC;AACnE,OAAO,EAAC,cAAc,EAAE,WAAW,EAAC,MAAM,SAAS,CAAC;AAEpD,qBAAa,UAAW,SAAQ,WAAY,YAAW,WAAW;gBACpD,CAAC,EAAE,QAAQ;CAGxB;AAED,+EAA+E;AAC/E,qBAAa,aAAc,SAAQ,cAAe,YAAW,cAAc;aAQvD,OAAO,EAAE,MAAM;aACf,OAAO,EAAE,MAAM;aACf,MAAM,EAAE,MAAM;IAThC;;;;;OAKG;gBACS,CAAC,EAAE,cAAc,EACX,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM;IAKhC,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,MAAM,GAAG,aAAa;IAIjC,OAAO,IAAI,OAAO;IAOlB,KAAK,IAAI,MAAM;CAUzB"}
1
+ {"version":3,"file":"types-pdb.d.ts","sourceRoot":"","sources":["types-pdb.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAC,MAAM,cAAc,CAAC;AACnE,OAAO,EAAC,cAAc,EAAE,WAAW,EAAC,MAAM,SAAS,CAAC;AAEpD,qBAAa,UAAW,SAAQ,WAAY,YAAW,WAAW;gBACpD,CAAC,EAAE,QAAQ;CAGxB;AAED,+EAA+E;AAC/E,qBAAa,aAAc,SAAQ,cAAe,YAAW,cAAc;aAQvD,OAAO,EAAE,MAAM;aACf,OAAO,EAAE,MAAM;aACf,MAAM,EAAE,MAAM;IAThC;;;;;OAKG;gBACS,CAAC,EAAE,cAAc,EACX,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM;IAKhC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa;IAUlC,OAAO,IAAI,OAAO;IAOlB,KAAK,IAAI,MAAM;CAUzB"}
package/src/pdb/format/types-pdb.js CHANGED
@@ -18,8 +18,12 @@ export class PdbAtomCoords extends AtomCoordsBase {
18
18
  this.element = element;
19
19
  this.charge = charge;
20
20
  }
21
- static fromStr(src) {
22
- throw new Error('Not implemented');
21
+ static fromStr(line) {
22
+ const res = new PdbAtomCoords(AtomCoordsBase.fromStr(line),
23
+ /* segment */ line.slice(73 - 1, 76),
24
+ /* element */ line.slice(77 - 1, 78),
25
+ /* charge */ line.slice(79 - 1, 80));
26
+ return res;
23
27
  }
24
28
  isValid() {
25
29
  return super.isValid() &&
package/src/pdb/format/types-pdb.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"types-pdb.js","sourceRoot":"","sources":["types-pdb.ts"],"names":[],"mappings":"AAIA,OAAO,EAAW,cAAc,EAAE,WAAW,EAAC,MAAM,cAAc,CAAC;AAGnE,MAAM,OAAO,UAAW,SAAQ,WAAW;IACzC,YAAY,CAAW;QACrB,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC;IACtG,CAAC;CACF;AAED,+EAA+E;AAC/E,MAAM,OAAO,aAAc,SAAQ,cAAc;IAC/C;;;;;OAKG;IACH,YAAY,CAAiB,EACX,OAAe,EACf,OAAe,EACf,MAAc;QAE9B,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC;QAJhC,YAAO,GAAP,OAAO,CAAQ;QACf,YAAO,GAAP,OAAO,CAAQ;QACf,WAAM,GAAN,MAAM,CAAQ;IAGhC,CAAC;IAED,MAAM,CAAC,OAAO,CAAC,IAAY;QACzB,MAAM,GAAG,GAAG,IAAI,aAAa,CAC3B,cAAc,CAAC,OAAO,CAAC,IAAI,CAAC;QAC5B,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;QACpC,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;QACpC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CACpC,CAAC;QACF,OAAO,GAAG,CAAC;IACb,CAAC;IAEQ,OAAO;QACd,OAAO,KAAK,CAAC,OAAO,EAAE;YACpB,IAAI,CAAC,OAAO,CAAC,MAAM,IAAI,CAAC;YACxB,IAAI,CAAC,OAAO,CAAC,MAAM,IAAI,CAAC;YACxB,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACtC,CAAC;IAEQ,KAAK;QACZ,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,UAAU,EAAE,QAAQ,CAAA,UAAU;YACvD,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW;YAClC,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,WAAW;YACpC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW;SAClC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACX,IAAI,GAAG,CAAC,MAAM,KAAK,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,mCAAmC,GAAG,CAAC,MAAM,SAAS,CAAC,CAAC;QAC1E,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
package/src/pdb/format/types-pdbqt.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types-pdbqt.d.ts","sourceRoot":"","sources":["types-pdbqt.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAC,MAAM,cAAc,CAAC;AACnE,OAAO,EAAC,WAAW,EAAE,gBAAgB,EAAE,aAAa,EAAC,MAAM,SAAS,CAAC;AACrE,OAAO,EAAC,aAAa,EAAa,MAAM,aAAa,CAAC;AAEtD,MAAM,MAAM,cAAc,GAAG;IAC3B,QAAQ,EAAE,MAAM,CAAC;IACjB,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,CAAA;CACvB,CAAC;AAEF,qBAAa,YAAa,SAAQ,WAAY,YAAW,aAAa;gBACxD,CAAC,EAAE,QAAQ;IAIhB,KAAK,IAAI,WAAW;IAI3B,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,YAAY;CAG3C;AAED,mGAAmG;AACnG,qBAAa,eAAgB,SAAQ,cAAe,YAAW,gBAAgB;aAO3D,UAAU,EAAE,MAAM;aAClB,QAAQ,EAAE,MAAM;IAPlC;;;;OAIG;gBACS,CAAC,EAAE,cAAc,EACX,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM;IAKlC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,eAAe;IAoB7C,yBAAyB,CAAC,IAAI,aAAa,IAAI,MAAM,CAEpD;IAGD,OAAO,IAAI,OAAO;IAMlB,KAAK,IAAI,aAAa;IAKtB,KAAK,IAAI,MAAM;CAShB"}
1
+ {"version":3,"file":"types-pdbqt.d.ts","sourceRoot":"","sources":["types-pdbqt.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAC,MAAM,cAAc,CAAC;AACnE,OAAO,EAAC,WAAW,EAAE,gBAAgB,EAAE,aAAa,EAAC,MAAM,SAAS,CAAC;AACrE,OAAO,EAAC,aAAa,EAAa,MAAM,aAAa,CAAC;AAEtD,MAAM,MAAM,cAAc,GAAG;IAC3B,QAAQ,EAAE,MAAM,CAAC;IACjB,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,CAAA;CACvB,CAAC;AAEF,qBAAa,YAAa,SAAQ,WAAY,YAAW,aAAa;gBACxD,CAAC,EAAE,QAAQ;IAIhB,KAAK,IAAI,WAAW;IAI3B,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,YAAY;CAG3C;AAED,mGAAmG;AACnG,qBAAa,eAAgB,SAAQ,cAAe,YAAW,gBAAgB;aAO3D,UAAU,EAAE,MAAM;aAClB,QAAQ,EAAE,MAAM;IAPlC;;;;OAIG;gBACS,CAAC,EAAE,cAAc,EACX,UAAU,EAAE,MAAM,EAClB,QAAQ,EAAE,MAAM;IAKlC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,eAAe;IAS7C,yBAAyB,CAAC,IAAI,aAAa,IAAI,MAAM,CAEpD;IAGD,OAAO,IAAI,OAAO;IAMlB,KAAK,IAAI,aAAa;IAKtB,KAAK,IAAI,MAAM;CAShB"}
package/src/pdb/format/types-pdbqt.js CHANGED
@@ -26,16 +26,6 @@ export class PdbqtAtomCoords extends AtomCoordsBase {
26
26
  static fromStr(line) {
27
27
  const res = new PdbqtAtomCoords(AtomCoordsBase.fromStr(line),
28
28
  /* partCharge */ parseFloat(line.slice(71 - 1, 76)), `${line.slice(78 - 1, 79).trim()}`);
29
- // if (!res.atomName && res.atomType.startsWith(res.atomElement) && res.atomType.length > res.atomElement.length) {
30
- // const atomName = res.atomType.replace(new RegExp(`^${res.atomElement}`), '');
31
- // res = new PdbqtAtomCoords(
32
- // new AtomCoordsBase(
33
- // new AtomBase(res, res.number, res.atomElement,
34
- // atomName /* replacing res.atomName*/,
35
- // res.altLoc, res.resName, res.chain, res.resNumber, res.insCode),
36
- // res.x, res.y, res.z, res.occupancy, res.bFactor),
37
- // res.partCharge, res.atomType);
38
- // }
39
29
  return res;
40
30
  }
41
31
  /** cols: 71-76 f:+5.3 */ get partChargeStr() {
package/src/pdb/format/types-pdbqt.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"types-pdbqt.js","sourceRoot":"","sources":["types-pdbqt.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAC,MAAM,cAAc,CAAC;AAEnE,OAAO,EAAC,aAAa,EAAE,UAAU,EAAC,MAAM,aAAa,CAAC;AAQtD,MAAM,OAAO,YAAa,SAAQ,WAAW;IAC3C,YAAY,CAAW;QACrB,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC;IACtG,CAAC;IAEM,KAAK;QACV,OAAO,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC;IAC9B,CAAC;IAED,MAAM,CAAC,OAAO,CAAC,IAAY;QACzB,OAAO,IAAI,YAAY,CAAC,QAAQ,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC;IAClD,CAAC;CACF;AAED,mGAAmG;AACnG,MAAM,OAAO,eAAgB,SAAQ,cAAc;IACjD;;;;OAIG;IACH,YAAY,CAAiB,EACX,UAAkB,EAClB,QAAgB;QAEhC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC;QAHhC,eAAU,GAAV,UAAU,CAAQ;QAClB,aAAQ,GAAR,QAAQ,CAAQ;IAGlC,CAAC;IAED,MAAM,CAAC,OAAO,CAAC,IAAY;QACzB,MAAM,GAAG,GAAG,IAAI,eAAe,CAC7B,cAAc,CAAC,OAAO,CAAC,IAAI,CAAC;QAC5B,gBAAgB,CAAC,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,EACnD,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,EAAE,CACnC,CAAC;QACF,OAAO,GAAG,CAAC;IACb,CAAC;IAED,yBAAyB,CAAC,IAAI,aAAa;QACzC,OAAO,GAAG,IAAI,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;IAC3E,CAAC;IAED,4CAA4C;IAC5C,OAAO;QACL,OAAO,KAAK,CAAC,OAAO,EAAE;YACpB,IAAI,CAAC,aAAa,CAAC,MAAM,IAAI,CAAC;YAC9B,IAAI,CAAC,QAAQ,CAAC,MAAM,IAAI,CAAC,CAAC;IAC9B,CAAC;IAED,KAAK;QACH,MAAM,GAAG,GAAG,IAAI,aAAa,CAAC,IAAI,EAAE,EAAE,EAAE,IAAI,CAAC,WAAW,CAAC,eAAe,EAAE,EAAE,CAAC,CAAC;QAC9E,OAAO,GAAG,CAAC;IACb,CAAC;IAED,KAAK;QACH,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,UAAU,EAAE,MAAM,CAAC,WAAW;YACvD,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,GAAG,CAAC,QAAQ;YACvD,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW;SACpC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACX,IAAI,GAAG,CAAC,MAAM,KAAK,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,qCAAqC,GAAG,CAAC,MAAM,SAAS,CAAC,CAAC;QAC5E,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
package/src/pdb/format/types.d.ts CHANGED
@@ -7,6 +7,7 @@ export interface IAtomBase {
7
7
  get chain(): string;
8
8
  get resNumber(): number;
9
9
  get insCode(): string;
10
+ compare(b: IAtomBase): any;
10
11
  toStr(): string;
11
12
  }
12
13
  export interface IAtomTer extends IAtomBase {
package/src/pdb/format/types.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,SAAS;IACxB,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,WAAW,IAAI,MAAM,CAAC;IAC1B,IAAI,QAAQ,IAAI,MAAM,CAAC;IACvB,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,OAAO,IAAI,MAAM,CAAC;IACtB,IAAI,KAAK,IAAI,MAAM,CAAC;IACpB,IAAI,SAAS,IAAI,MAAM,CAAC;IACxB,IAAI,OAAO,IAAI,MAAM,CAAC;IAEtB,KAAK,IAAI,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,QAAS,SAAQ,SAAS;CAAG;AAE9C,MAAM,WAAW,WAAY,SAAQ,SAAS;IAC5C,IAAI,CAAC,IAAI,MAAM,CAAC;IAChB,IAAI,CAAC,IAAI,MAAM,CAAC;IAChB,IAAI,CAAC,IAAI,MAAM,CAAC;IAChB,IAAI,SAAS,IAAI,MAAM,CAAC;IACxB,IAAI,OAAO,IAAI,MAAM,CAAC;CACvB;AAID,MAAM,WAAW,YAAa,SAAQ,SAAS;CAC9C;AAED,MAAM,WAAW,cAAe,SAAQ,YAAY,EAAE,WAAW;CAAG;AAEpE,MAAM,WAAW,WAAY,SAAQ,YAAY,EAAE,QAAQ;CAAG;AAI9D,MAAM,WAAW,cAAe,SAAQ,SAAS;IAC/C,KAAK,IAAI,YAAY,CAAC;CACvB;AAED,MAAM,WAAW,gBAAiB,SAAQ,cAAc,EAAE,WAAW;IACnE,KAAK,IAAI,cAAc,CAAC;CACzB;AAED,MAAM,WAAW,aAAc,SAAQ,cAAc,EAAE,QAAQ;IAC7D,KAAK,IAAI,WAAW,CAAC;CACtB"}
1
+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,SAAS;IACxB,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,WAAW,IAAI,MAAM,CAAC;IAC1B,IAAI,QAAQ,IAAI,MAAM,CAAC;IACvB,IAAI,MAAM,IAAI,MAAM,CAAC;IACrB,IAAI,OAAO,IAAI,MAAM,CAAC;IACtB,IAAI,KAAK,IAAI,MAAM,CAAC;IACpB,IAAI,SAAS,IAAI,MAAM,CAAC;IACxB,IAAI,OAAO,IAAI,MAAM,CAAC;IAEtB,OAAO,CAAC,CAAC,EAAE,SAAS,GAAG,GAAG,CAAC;IAC3B,KAAK,IAAI,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,QAAS,SAAQ,SAAS;CAAG;AAE9C,MAAM,WAAW,WAAY,SAAQ,SAAS;IAC5C,IAAI,CAAC,IAAI,MAAM,CAAC;IAChB,IAAI,CAAC,IAAI,MAAM,CAAC;IAChB,IAAI,CAAC,IAAI,MAAM,CAAC;IAChB,IAAI,SAAS,IAAI,MAAM,CAAC;IACxB,IAAI,OAAO,IAAI,MAAM,CAAC;CACvB;AAID,MAAM,WAAW,YAAa,SAAQ,SAAS;CAC9C;AAED,MAAM,WAAW,cAAe,SAAQ,YAAY,EAAE,WAAW;CAAG;AAEpE,MAAM,WAAW,WAAY,SAAQ,YAAY,EAAE,QAAQ;CAAG;AAI9D,MAAM,WAAW,cAAe,SAAQ,SAAS;IAC/C,KAAK,IAAI,YAAY,CAAC;CACvB;AAED,MAAM,WAAW,gBAAiB,SAAQ,cAAc,EAAE,WAAW;IACnE,KAAK,IAAI,cAAc,CAAC;CACzB;AAED,MAAM,WAAW,aAAc,SAAQ,cAAc,EAAE,QAAQ;IAC7D,KAAK,IAAI,WAAW,CAAC;CACtB"}
package/src/utils/cell-renderer-async-base.d.ts CHANGED
@@ -42,7 +42,7 @@ export declare abstract class RenderServiceBase<TProps extends PropsBase, TAux>
42
42
  protected toLog(): string;
43
43
  get errorCount(): number;
44
44
  /** Disposes MolstarViewer to free WebGL context */
45
- abstract reset(): Promise<void>;
45
+ reset(): Promise<void>;
46
46
  /** Queues render tasks
47
47
  * @param consumerId Identifier of the consumer of this render service
48
48
  * @param task Task to render
package/src/utils/cell-renderer-async-base.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"cell-renderer-async-base.d.ts","sourceRoot":"","sources":["cell-renderer-async-base.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAsB,cAAc,EAAC,MAAM,MAAM,CAAC;AAIzD,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAEjC,OAAO,EAAC,oBAAoB,EAAC,MAAM,2BAA2B,CAAC;AAE/D,qBAAa,SAAS;aAEF,SAAS,EAAE,MAAM;aACjB,KAAK,EAAE,MAAM;aACb,MAAM,EAAE,MAAM;gBAFd,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,MAAM,EACb,MAAM,EAAE,MAAM;CAEjC;AAED,qBAAa,UAAU,CAAC,MAAM,SAAS,SAAS,EAAE,IAAI;aAElC,IAAI,EAAE,MAAM;aACZ,KAAK,EAAE,MAAM;aACb,aAAa,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,IAAI,KAAK,IAAI;aAC7D,UAAU,CAAC,SAAQ,OAAO;gBAH1B,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,aAAa,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,IAAI,KAAK,IAAI,EAC7D,UAAU,CAAC,SAAQ,OAAO,aAAA;CAE7C;AAED,KAAK,eAAe,CAAC,MAAM,SAAS,SAAS,EAAE,IAAI,IAAI;IACrD,UAAU,EAAE,MAAM,CAAC;IACnB,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC;IAChB,IAAI,EAAE,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IAC/B,QAAQ,EAAE,MAAM,CAAC;IACjB,EAAE,EAAE,MAAM,CAAA;CACX,CAAA;AAED,8BAAsB,iBAAiB,CAAC,MAAM,SAAS,SAAS,EAAE,IAAI;IAWlE,SAAS,CAAC,QAAQ,CAAC,MAAM,EAAE,OAAO;IAClC,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,MAAM;IACrC,SAAS,CAAC,WAAW,EAAE,MAAM;IAC7B,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,MAAM;IACrC,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,MAAM;IAdvC,OAAO,CAAC,eAAe,CAAa;IACpC,SAAS,CAAC,QAAQ,CAAC,MAAM,EAAE,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE,CAAC;IAC3D,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE;QAC7B,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;KAC3C,CAAC;IACF,6FAA6F;IAC7F,OAAO,CAAC,KAAK,CAAkB;IAC/B,OAAO,CAAC,cAAc,CAAuB;gBAGxB,MAAM,EAAE,OAAO,EACf,UAAU,GAAE,MAAU,EAC/B,WAAW,GAAE,MAAU,EACd,UAAU,GAAE,MAAU,EACtB,UAAU,GAAE,MAAa;IAQ9C,OAAO,CAAC,MAAM,CAAC,aAAa,CAAc;IAC1C,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAA6C;IAEtE,SAAS,CAAC,KAAK,IAAI,MAAM;IAIzB,IAAW,UAAU,IAAI,MAAM,CAA6B;IAE5D,mDAAmD;IAC7C,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAI5B;;;;;OAKG;IACH,MAAM,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI,EAAE,IAAI,EAAE,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE,GAAG,CAAC,EAAE,MAAM,GAAG,EAAE,QAAQ,GAAE,MAAU,GAAG,MAAM;IA8BhH,MAAM,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO;IAInC,SAAS,CAAC,OAAO,IAAI,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,GAAG,SAAS;IA0B9D,OAAO,CAAC,aAAa;IAoFrB,oCAAoC;IACpC,OAAO,CAAC,WAAW;IAqBnB,OAAO,CAAC,YAAY;IAgBpB,SAAS,CAAC,QAAQ,CAAC,aAAa,CAC9B,GAAG,EAAE,MAAM,GAAG,GAAG,SAAS,EAAE,IAAI,EAAE,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE,aAAa,EAAE,CAAC,GAAG,EAAE,IAAI,KAAK,IAAI,GAC7F,OAAO,CAAC,CAAC,cAAc,EAAE,MAAM,EAAE,MAAM,IAAI,CAAC,CAAC;IAEhD,SAAS,CAAC,QAAQ,CAAC,UAAU,CAC3B,GAAG,EAAE,MAAM,GAAG,GAAG,SAAS,EAAE,IAAI,EAAE,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE,eAAe,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,GAC7F,OAAO;CACX;AAED,8BAAsB,yBAAyB,CAAC,MAAM,SAAS,SAAS,EAAE,IAAI,CAC5E,SAAQ,oBAAoB,CAAC,MAAM,CAAC;aAWlB,YAAY,EAAE,OAAO;IAVvC,SAAS,CAAC,QAAQ,CAAC,YAAY,wCAA6C;IAC5E,SAAS,CAAC,UAAU,yBAAgC;IAEpD,gDAAgD;IAChD,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI,CAAQ;IAE3C,SAAS,aACP,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAC7B,QAAQ,EAAE,EAAE,CAAC,MAAM,EACnB,MAAM,EAAE,OAAO,EACC,YAAY,GAAE,OAAc;cAK3B,KAAK,IAAI,IAAI;IAQhC,SAAS,CAAC,QAAQ,CAAC,gBAAgB,IAAI,iBAAiB,CAAC,MAAM,EAAE,IAAI,CAAC;IAEtE,SAAS,CAAC,QAAQ,CAAC,kBAAkB,CACnC,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GACtE,MAAM;IAEF,MAAM,CAAC,CAAC,EAAE,wBAAwB,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EACnF,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,SAAS,EAAE,EAAE,CAAC,aAAa,GACjD,IAAI;IA4FP;;;;;;OAMG;IACH,SAAS,CAAC,mBAAmB,CAC3B,IAAI,EAAE,wBAAwB,EAAE,EAAE,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,QAAQ,EAAE,aAAa,EAAE,SAAS,GACxF,OAAO;IA4BV,SAAS,CAAC,QAAQ,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE,IAAI,GAAG,IAAI;IAEnE;;;;;OAKG;IACH,SAAS,CAAC,YAAY,CACpB,IAAI,EAAE,wBAAwB,EAAE,EAAE,EAAE,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC,QAAQ,EAAE,aAAa,EAAE,SAAS,GACxF,IAAI;CAyCR"}
package/src/utils/cell-renderer-async-base.js CHANGED
@@ -37,6 +37,10 @@ export class RenderServiceBase {
37
37
  return `${this.constructor.name}<${this.viewerId}>`;
38
38
  }
39
39
  get errorCount() { return this._errorCount; }
40
+ /** Disposes MolstarViewer to free WebGL context */
41
+ async reset() {
42
+ this._errorCount = 0;
43
+ }
40
44
  /** Queues render tasks
41
45
  * @param consumerId Identifier of the consumer of this render service
42
46
  * @param task Task to render
package/src/utils/cell-renderer-async-base.js.map CHANGED
@@ -1 +1 @@
1
- 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