@datagrok-libraries/bio 5.39.11 → 5.39.13

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Files changed (38) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/package.json +3 -1
  3. package/src/molecule/molecule-units-handler.d.ts +2 -0
  4. package/src/molecule/molecule-units-handler.d.ts.map +1 -1
  5. package/src/molecule/molecule-units-handler.js +12 -0
  6. package/src/molecule/molecule-units-handler.js.map +1 -1
  7. package/src/molecule-3d/molecule-3d-units-handler.d.ts +2 -0
  8. package/src/molecule-3d/molecule-3d-units-handler.d.ts.map +1 -1
  9. package/src/molecule-3d/molecule-3d-units-handler.js +23 -0
  10. package/src/molecule-3d/molecule-3d-units-handler.js.map +1 -1
  11. package/src/pdb/auto-dock-service.d.ts +3 -1
  12. package/src/pdb/auto-dock-service.d.ts.map +1 -1
  13. package/src/pdb/auto-dock-service.js +1 -1
  14. package/src/pdb/auto-dock-service.js.map +1 -1
  15. package/src/pdb/format/types-base.d.ts +54 -0
  16. package/src/pdb/format/types-base.d.ts.map +1 -0
  17. package/src/pdb/format/types-base.js +125 -0
  18. package/src/pdb/format/types-base.js.map +1 -0
  19. package/src/pdb/format/types-pdb.d.ts +22 -0
  20. package/src/pdb/format/types-pdb.d.ts.map +1 -0
  21. package/src/pdb/format/types-pdb.js +41 -0
  22. package/src/pdb/format/types-pdb.js.map +1 -0
  23. package/src/pdb/format/types-pdbqt.d.ts +30 -0
  24. package/src/pdb/format/types-pdbqt.d.ts.map +1 -0
  25. package/src/pdb/format/types-pdbqt.js +64 -0
  26. package/src/pdb/format/types-pdbqt.js.map +1 -0
  27. package/src/pdb/format/types.d.ts +36 -0
  28. package/src/pdb/format/types.d.ts.map +1 -0
  29. package/src/pdb/format/types.js +2 -0
  30. package/src/pdb/format/types.js.map +1 -0
  31. package/src/types/ngl.d.ts +126 -0
  32. package/src/types/ngl.d.ts.map +1 -0
  33. package/src/types/ngl.js +2 -0
  34. package/src/types/ngl.js.map +1 -0
  35. package/src/viewers/molstar-viewer.d.ts +1 -0
  36. package/src/viewers/molstar-viewer.d.ts.map +1 -1
  37. package/src/viewers/molstar-viewer.js +6 -0
  38. package/src/viewers/molstar-viewer.js.map +1 -1
package/CHANGELOG.md CHANGED
@@ -8,6 +8,10 @@
8
8
  * Add WebLogo `valueAggrType`, `valueColumnName` properties.
9
9
  * Add routines to get/set user monomer library settings.
10
10
  * Add Molecule3DUnitsHandler
11
+ * Move NGL typings to bio lib
12
+ * Move pdb, pdbqt parser to bio lib
13
+ * Add IAutoDockService checkOpenCl, dockLigandColumn
14
+ * Add Molecule, Molecule3D units handler getAsPdb
11
15
 
12
16
  ### Bug fixes
13
17
 
package/package.json CHANGED
@@ -8,7 +8,7 @@
8
8
  "access": "public"
9
9
  },
10
10
  "friendlyName": "Datagrok bio library",
11
- "version": "5.39.11",
11
+ "version": "5.39.13",
12
12
  "description": "",
13
13
  "dependencies": {
14
14
  "@datagrok-libraries/gridext": "^1.3.68",
@@ -26,6 +26,8 @@
26
26
  "wu": "latest"
27
27
  },
28
28
  "devDependencies": {
29
+ "@types/three": "^0.159.0",
30
+ "@types/signals": "1.0.1",
29
31
  "@types/uuid": "^9.0.1",
30
32
  "@types/wu": "latest",
31
33
  "@typescript-eslint/eslint-plugin": "latest",
package/src/molecule/molecule-units-handler.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { BuildDataFunc, UnitsHandlerBase } from '../utils/units-handler-base';
3
3
  import { MoleculeBuildDataFunc, MoleculeBase } from './types';
4
+ import { IPdbHelper } from '../pdb/pdb-helper';
4
5
  export declare const Temps: {
5
6
  uh: string;
6
7
  data: string;
@@ -20,6 +21,7 @@ export declare class MoleculeUnitsHandler extends UnitsHandlerBase<string, Molec
20
21
  constructor(col: DG.Column);
21
22
  protected getFileExt(): string;
22
23
  protected getBuildDataFunc(): BuildDataFunc<string, MoleculeBase>;
24
+ getAsPdb(ph: IPdbHelper): Promise<DG.Column<string>>;
23
25
  static getOrCreate(col: DG.Column): MoleculeUnitsHandler;
24
26
  }
25
27
  //# sourceMappingURL=molecule-units-handler.d.ts.map
package/src/molecule/molecule-units-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"molecule-units-handler.d.ts","sourceRoot":"","sources":["molecule-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,aAAa,EAAE,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAE5E,OAAO,EAAC,qBAAqB,EAAE,YAAY,EAAC,MAAM,SAAS,CAAC;AAE5D,eAAO,MAAM,KAAK;;;CAGf,CAAC;AAEJ,oBAAY,aAAa;IACvB,QAAQ,aAAa;IACrB,QAAQ,aAAa;CACtB;AAED,eAAO,MAAM,gBAAgB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAGvD,CAAC;AAEF,eAAO,MAAM,sBAAsB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,qBAAqB,CAAA;CAG5E,CAAC;AAEF,eAAO,MAAM,uBAAuB,EAAE,MAAM,EAAuB,CAAC;AAEpE,qBAAa,oBAAqB,SAAQ,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC;gBAClE,GAAG,EAAE,EAAE,CAAC,MAAM;cAIP,UAAU,IAAI,MAAM;cAIpB,gBAAgB,IAAI,aAAa,CAAC,MAAM,EAAE,YAAY,CAAC;WAI5D,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,oBAAoB;CAMhE"}
1
+ {"version":3,"file":"molecule-units-handler.d.ts","sourceRoot":"","sources":["molecule-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,aAAa,EAAE,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAE5E,OAAO,EAAC,qBAAqB,EAAE,YAAY,EAAC,MAAM,SAAS,CAAC;AAC5D,OAAO,EAAC,UAAU,EAAC,MAAM,mBAAmB,CAAC;AAE7C,eAAO,MAAM,KAAK;;;CAGf,CAAC;AAEJ,oBAAY,aAAa;IACvB,QAAQ,aAAa;IACrB,QAAQ,aAAa;CACtB;AAED,eAAO,MAAM,gBAAgB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAGvD,CAAC;AAEF,eAAO,MAAM,sBAAsB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,qBAAqB,CAAA;CAG5E,CAAC;AAEF,eAAO,MAAM,uBAAuB,EAAE,MAAM,EAAuB,CAAC;AAEpE,qBAAa,oBAAqB,SAAQ,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC;gBAClE,GAAG,EAAE,EAAE,CAAC,MAAM;cAIP,UAAU,IAAI,MAAM;cAIpB,gBAAgB,IAAI,aAAa,CAAC,MAAM,EAAE,YAAY,CAAC;IAI7D,QAAQ,CAAC,EAAE,EAAE,UAAU,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;WAanD,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,oBAAoB;CAMhE"}
package/src/molecule/molecule-units-handler.js CHANGED
@@ -31,6 +31,18 @@ export class MoleculeUnitsHandler extends UnitsHandlerBase {
31
31
  getBuildDataFunc() {
32
32
  return MoleculeBuildDataFuncs[this.units];
33
33
  }
34
+ async getAsPdb(ph) {
35
+ if (this.units !== 'mol')
36
+ throw new Error(`Unsupported units '${this.units}' of the molecule column, must be 'mol'.`);
37
+ const colLength = this.column.length;
38
+ const resCol = DG.Column.fromType(DG.TYPE.STRING, this.column.name, colLength);
39
+ for (let rowI = 0; rowI < colLength; ++rowI) {
40
+ const molVal = this.column.get(rowI);
41
+ const pdbVal = molVal === null ? null : await ph.molToPdb(molVal);
42
+ resCol.set(rowI, pdbVal);
43
+ }
44
+ return resCol;
45
+ }
34
46
  static getOrCreate(col) {
35
47
  let res = col.temp[Temps.uh];
36
48
  if (!res)
package/src/molecule/molecule-units-handler.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"molecule-units-handler.js","sourceRoot":"","sources":["molecule-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAgB,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAC5E,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,MAAM,uBAAuB,CAAC;AAG3E,MAAM,CAAC,MAAM,KAAK,GAAG,IAAI;IAAA;QACvB,OAAE,GAAG,iBAAiB,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;QAC5C,SAAI,GAAG,QAAQ,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;IACvC,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAN,IAAY,aAGX;AAHD,WAAY,aAAa;IACvB,sCAAqB,CAAA;IACrB,sCAAqB,CAAA;AACvB,CAAC,EAHW,aAAa,KAAb,aAAa,QAGxB;AAED,MAAM,CAAC,MAAM,gBAAgB,GAAgC;IAC3D,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,KAAK;IAC/B,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,KAAK;CAChC,CAAC;AAEF,MAAM,CAAC,MAAM,sBAAsB,GAA+C;IAChF,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,iBAAiB;IAC3C,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,iBAAiB;CAC5C,CAAC;AAEF,MAAM,CAAC,MAAM,uBAAuB,GAAa,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;AAEpE,MAAM,OAAO,oBAAqB,SAAQ,gBAAsC;IAC9E,YAAY,GAAc;QACxB,KAAK,CAAC,GAAG,EAAE,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,uBAAuB,CAAC,CAAC;IAC3D,CAAC;IAEkB,UAAU;QAC3B,OAAO,gBAAgB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACtC,CAAC;IAEkB,gBAAgB;QACjC,OAAO,sBAAsB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC5C,CAAC;IAEM,MAAM,CAAC,WAAW,CAAC,GAAc;QACtC,IAAI,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAC7B,IAAI,CAAC,GAAG;YACN,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,IAAI,oBAAoB,CAAC,GAAG,CAAC,CAAC;QAC3D,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
1
+ {"version":3,"file":"molecule-units-handler.js","sourceRoot":"","sources":["molecule-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAgB,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAC5E,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,MAAM,uBAAuB,CAAC;AAI3E,MAAM,CAAC,MAAM,KAAK,GAAG,IAAI;IAAA;QACvB,OAAE,GAAG,iBAAiB,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;QAC5C,SAAI,GAAG,QAAQ,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;IACvC,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAN,IAAY,aAGX;AAHD,WAAY,aAAa;IACvB,sCAAqB,CAAA;IACrB,sCAAqB,CAAA;AACvB,CAAC,EAHW,aAAa,KAAb,aAAa,QAGxB;AAED,MAAM,CAAC,MAAM,gBAAgB,GAAgC;IAC3D,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,KAAK;IAC/B,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,KAAK;CAChC,CAAC;AAEF,MAAM,CAAC,MAAM,sBAAsB,GAA+C;IAChF,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,iBAAiB;IAC3C,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE,iBAAiB;CAC5C,CAAC;AAEF,MAAM,CAAC,MAAM,uBAAuB,GAAa,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;AAEpE,MAAM,OAAO,oBAAqB,SAAQ,gBAAsC;IAC9E,YAAY,GAAc;QACxB,KAAK,CAAC,GAAG,EAAE,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,uBAAuB,CAAC,CAAC;IAC3D,CAAC;IAEkB,UAAU;QAC3B,OAAO,gBAAgB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACtC,CAAC;IAEkB,gBAAgB;QACjC,OAAO,sBAAsB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC5C,CAAC;IAEM,KAAK,CAAC,QAAQ,CAAC,EAAc;QAClC,IAAI,IAAI,CAAC,KAAK,KAAK,KAAK;YACtB,MAAM,IAAI,KAAK,CAAC,sBAAsB,IAAI,CAAC,KAAK,0CAA0C,CAAC,CAAC;QAC9F,MAAM,SAAS,GAAW,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC;QAC7C,MAAM,MAAM,GAAc,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;QAC1F,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,SAAS,EAAE,EAAE,IAAI,EAAE;YAC3C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;YACrC,MAAM,MAAM,GAAG,MAAM,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;YAClE,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;SAC1B;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEM,MAAM,CAAC,WAAW,CAAC,GAAc;QACtC,IAAI,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAC7B,IAAI,CAAC,GAAG;YACN,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,IAAI,oBAAoB,CAAC,GAAG,CAAC,CAAC;QAC3D,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
package/src/molecule-3d/molecule-3d-units-handler.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
2
  import { BuildDataFunc, UnitsHandlerBase } from '../utils/units-handler-base';
3
3
  import { Molecule3DBase, Molecule3DBuildDataFunc } from './types';
4
+ import { IPdbHelper } from '../pdb/pdb-helper';
4
5
  export declare const Temps: {
5
6
  uh: string;
6
7
  data: string;
@@ -21,6 +22,7 @@ export declare class Molecule3DUnitsHandler extends UnitsHandlerBase<any, Molecu
21
22
  constructor(col: DG.Column);
22
23
  protected getFileExt(): string;
23
24
  protected getBuildDataFunc(): BuildDataFunc<any, Molecule3DBase>;
25
+ getAsPdb(ph: IPdbHelper): Promise<DG.Column<string>>;
24
26
  static getOrCreate(col: DG.Column): Molecule3DUnitsHandler;
25
27
  }
26
28
  //# sourceMappingURL=molecule-3d-units-handler.d.ts.map
package/src/molecule-3d/molecule-3d-units-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"molecule-3d-units-handler.d.ts","sourceRoot":"","sources":["molecule-3d-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,aAAa,EAAE,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAC5E,OAAO,EAAC,cAAc,EAAE,uBAAuB,EAAC,MAAM,SAAS,CAAC;AAGhE,eAAO,MAAM,KAAK;;;CAGf,CAAC;AAEJ,oBAAY,eAAe;IACzB,GAAG,QAAQ;IACX,KAAK,UAAU;IACf,KAAK,UAAU;CAChB;AAED,eAAO,MAAM,kBAAkB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAIzD,CAAC;AAEF,eAAO,MAAM,wBAAwB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,uBAAuB,CAAA;CAIhF,CAAC;AAEF,eAAO,MAAM,yBAAyB,EAAE,MAAM,EAAuB,CAAC;AAGtE,qBAAa,sBAAuB,SAAQ,gBAAgB,CAAC,GAAG,EAAE,cAAc,CAAC;gBACnE,GAAG,EAAE,EAAE,CAAC,MAAM;IAI1B,SAAS,CAAC,UAAU,IAAI,MAAM;IAI9B,SAAS,CAAC,gBAAgB,IAAI,aAAa,CAAC,GAAG,EAAE,cAAc,CAAC;WAIlD,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,sBAAsB;CAMlE"}
1
+ {"version":3,"file":"molecule-3d-units-handler.d.ts","sourceRoot":"","sources":["molecule-3d-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,aAAa,EAAE,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAC5E,OAAO,EAAC,cAAc,EAAE,uBAAuB,EAAC,MAAM,SAAS,CAAC;AAEhE,OAAO,EAAC,UAAU,EAAC,MAAM,mBAAmB,CAAC;AAE7C,eAAO,MAAM,KAAK;;;CAGf,CAAC;AAEJ,oBAAY,eAAe;IACzB,GAAG,QAAQ;IACX,KAAK,UAAU;IACf,KAAK,UAAU;CAChB;AAED,eAAO,MAAM,kBAAkB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAIzD,CAAC;AAEF,eAAO,MAAM,wBAAwB,EAAE;IAAE,CAAC,KAAK,EAAE,MAAM,GAAG,uBAAuB,CAAA;CAIhF,CAAC;AAEF,eAAO,MAAM,yBAAyB,EAAE,MAAM,EAAuB,CAAC;AAGtE,qBAAa,sBAAuB,SAAQ,gBAAgB,CAAC,GAAG,EAAE,cAAc,CAAC;gBACnE,GAAG,EAAE,EAAE,CAAC,MAAM;IAI1B,SAAS,CAAC,UAAU,IAAI,MAAM;IAI9B,SAAS,CAAC,gBAAgB,IAAI,aAAa,CAAC,GAAG,EAAE,cAAc,CAAC;IAInD,QAAQ,CAAC,EAAE,EAAE,UAAU,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;WAwBnD,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,sBAAsB;CAMlE"}
package/src/molecule-3d/molecule-3d-units-handler.js CHANGED
@@ -34,6 +34,29 @@ export class Molecule3DUnitsHandler extends UnitsHandlerBase {
34
34
  getBuildDataFunc() {
35
35
  return Molecule3DBuildDataFuncs[this.units];
36
36
  }
37
+ async getAsPdb(ph) {
38
+ if (this.units === 'pdb')
39
+ return this.column;
40
+ let convertToPdb;
41
+ switch (this.units) {
42
+ case 'pdbqt': {
43
+ convertToPdb = (srcPdbqt) => {
44
+ return ph.pdbqtToMol(srcPdbqt);
45
+ };
46
+ break;
47
+ }
48
+ default:
49
+ throw new Error('Unsupported units \'${this.units}\' of the Molecule3D column');
50
+ }
51
+ const colLength = this.column.length;
52
+ const resCol = DG.Column.fromType(DG.TYPE.STRING, this.column.name, colLength);
53
+ for (let rowI = 0; rowI < colLength; ++rowI) {
54
+ const srcVal = this.column.get(rowI);
55
+ const pdbVal = srcVal === null ? null : await convertToPdb(srcVal);
56
+ resCol.set(rowI, pdbVal);
57
+ }
58
+ return resCol;
59
+ }
37
60
  static getOrCreate(col) {
38
61
  let res = col.temp[Temps.uh];
39
62
  if (!res)
package/src/molecule-3d/molecule-3d-units-handler.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"molecule-3d-units-handler.js","sourceRoot":"","sources":["molecule-3d-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAgB,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAE5E,OAAO,EAAC,cAAc,EAAE,YAAY,EAAE,cAAc,EAAC,MAAM,0BAA0B,CAAC;AAEtF,MAAM,CAAC,MAAM,KAAK,GAAG,IAAI;IAAA;QACvB,OAAE,GAAG,iBAAiB,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,CAAC;QAC9C,SAAI,GAAG,QAAQ,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,CAAC;IACzC,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAN,IAAY,eAIX;AAJD,WAAY,eAAe;IACzB,8BAAW,CAAA;IACX,kCAAe,CAAA;IACf,kCAAe,CAAA;AACjB,CAAC,EAJW,eAAe,KAAf,eAAe,QAI1B;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAgC;IAC7D,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,KAAK;IAC5B,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,OAAO;IAChC,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,OAAO;CACjC,CAAC;AAEF,MAAM,CAAC,MAAM,wBAAwB,GAAiD;IACpF,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,YAAY;IACnC,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,cAAc;IACvC,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,cAAc;CACxC,CAAC;AAEF,MAAM,CAAC,MAAM,yBAAyB,GAAa,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;AAGtE,MAAM,OAAO,sBAAuB,SAAQ,gBAAqC;IAC/E,YAAY,GAAc;QACxB,KAAK,CAAC,GAAG,EAAE,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,yBAAyB,CAAC,CAAC;IAC/D,CAAC;IAES,UAAU;QAClB,OAAO,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACxC,CAAC;IAES,gBAAgB;QACxB,OAAO,wBAAwB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC9C,CAAC;IAEM,MAAM,CAAC,WAAW,CAAC,GAAc;QACtC,IAAI,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAC7B,IAAI,CAAC,GAAG;YACN,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,IAAI,sBAAsB,CAAC,GAAG,CAAC,CAAC;QAC7D,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
1
+ {"version":3,"file":"molecule-3d-units-handler.js","sourceRoot":"","sources":["molecule-3d-units-handler.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAgB,gBAAgB,EAAC,MAAM,6BAA6B,CAAC;AAE5E,OAAO,EAAC,cAAc,EAAE,YAAY,EAAE,cAAc,EAAC,MAAM,0BAA0B,CAAC;AAGtF,MAAM,CAAC,MAAM,KAAK,GAAG,IAAI;IAAA;QACvB,OAAE,GAAG,iBAAiB,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,CAAC;QAC9C,SAAI,GAAG,QAAQ,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,CAAC;IACzC,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAN,IAAY,eAIX;AAJD,WAAY,eAAe;IACzB,8BAAW,CAAA;IACX,kCAAe,CAAA;IACf,kCAAe,CAAA;AACjB,CAAC,EAJW,eAAe,KAAf,eAAe,QAI1B;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAgC;IAC7D,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,KAAK;IAC5B,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,OAAO;IAChC,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,OAAO;CACjC,CAAC;AAEF,MAAM,CAAC,MAAM,wBAAwB,GAAiD;IACpF,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,YAAY;IACnC,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,cAAc;IACvC,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE,cAAc;CACxC,CAAC;AAEF,MAAM,CAAC,MAAM,yBAAyB,GAAa,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;AAGtE,MAAM,OAAO,sBAAuB,SAAQ,gBAAqC;IAC/E,YAAY,GAAc;QACxB,KAAK,CAAC,GAAG,EAAE,EAAE,CAAC,OAAO,CAAC,UAAU,EAAE,yBAAyB,CAAC,CAAC;IAC/D,CAAC;IAES,UAAU;QAClB,OAAO,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACxC,CAAC;IAES,gBAAgB;QACxB,OAAO,wBAAwB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAC9C,CAAC;IAEM,KAAK,CAAC,QAAQ,CAAC,EAAc;QAClC,IAAI,IAAI,CAAC,KAAK,KAAK,KAAK;YAAE,OAAO,IAAI,CAAC,MAAM,CAAC;QAC7C,IAAI,YAA8C,CAAC;QACnD,QAAQ,IAAI,CAAC,KAAK,EAAE;YAClB,KAAK,OAAO,CAAC,CAAC;gBACZ,YAAY,GAAG,CAAC,QAAgB,EAAmB,EAAE;oBACnD,OAAO,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;gBACjC,CAAC,CAAC;gBACF,MAAM;aACP;YACD;gBACE,MAAM,IAAI,KAAK,CAAC,8DAA8D,CAAC,CAAC;SACnF;QAED,MAAM,SAAS,GAAW,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC;QAC7C,MAAM,MAAM,GAAc,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;QAC1F,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,SAAS,EAAE,EAAE,IAAI,EAAE;YAC3C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;YACrC,MAAM,MAAM,GAAG,MAAM,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,YAAY,CAAC,MAAM,CAAC,CAAC;YACnE,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;SAC1B;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEM,MAAM,CAAC,WAAW,CAAC,GAAc;QACtC,IAAI,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAC7B,IAAI,CAAC,GAAG;YACN,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,GAAG,IAAI,sBAAsB,CAAC,GAAG,CAAC,CAAC;QAC7D,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
package/src/pdb/auto-dock-service.d.ts CHANGED
@@ -29,12 +29,14 @@ export interface IAutoDockService {
29
29
  get ready(): boolean;
30
30
  awaitStatus(targetStatus: DockerContainerStatus, timeout?: number): Promise<void>;
31
31
  startDockerContainer(timeout?: number): Promise<void>;
32
+ checkOpenCl(): Promise<number>;
32
33
  /**
33
34
  * @param receptor PDB string of target (receptor) structure
34
35
  * @param ligand PDB or mol structure of the ligand to be docked
35
36
  * @param npts Grid
36
37
  */
37
- run(receptor: string, ligand: BiostructureData, npts: GridSize, poseCount?: number, posColName?: string): Promise<AutoDockRunResult>;
38
+ dockLigand(receptor: BiostructureData, ligand: BiostructureData, autodockGpf: string, poseCount?: number, posColName?: string): Promise<DG.DataFrame>;
39
+ dockLigandColumn(receptor: BiostructureData, ligandCol: DG.Column<string>, autodockGpf: string, poseCount?: number, posColName?: string): Promise<DG.DataFrame>;
38
40
  }
39
41
  export declare function getAutoDockService(): Promise<IAutoDockService>;
40
42
  //# sourceMappingURL=auto-dock-service.d.ts.map
package/src/pdb/auto-dock-service.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"auto-dock-service.d.ts","sourceRoot":"","sources":["auto-dock-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,gBAAgB,EAAC,MAAM,SAAS,CAAC;AACzC,OAAO,EAAC,qBAAqB,EAAC,MAAM,iBAAiB,CAAC;AAEtD,oBAAY,kBAAkB;IAAG,IAAI,IAAA;IAAE,OAAO,IAAA;IAAE,KAAK,IAAA;CAAC;AAEtD,qBAAa,aAAc,SAAQ,KAAK;aAEpB,KAAK,EAAE,kBAAkB;gBAAzB,KAAK,EAAE,kBAAkB,EACzC,OAAO,EAAE,MAAM;CAIlB;AAED,qBAAa,QAAQ;IACnB,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,MAAM,GAAG,aAAa;IAI5C,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,GAAG,aAAa;IAI9C,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,aAAa;CAG5C;AAED,oEAAoE;AACpE,qBAAa,QAAQ;aAED,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;gBAFT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM;CAM5B;AAED,MAAM,MAAM,iBAAiB,GAAG;IAC9B,OAAO,EAAE,EAAE,CAAC,SAAS,CAAA;CACtB,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,IAAI,KAAK,IAAI,OAAO,CAAC;IAErB,WAAW,CAAC,YAAY,EAAE,qBAAqB,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAElF,oBAAoB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEtD;;;;OAIG;IACH,GAAG,CACD,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,gBAAgB,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,CAAC,EAAE,MAAM,EAC9E,UAAU,CAAC,EAAE,MAAM,GAClB,OAAO,CAAC,iBAAiB,CAAC,CAAC;CAC/B;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,gBAAgB,CAAC,CAQpE"}
1
+ {"version":3,"file":"auto-dock-service.d.ts","sourceRoot":"","sources":["auto-dock-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,gBAAgB,EAAC,MAAM,SAAS,CAAC;AACzC,OAAO,EAAC,qBAAqB,EAAC,MAAM,iBAAiB,CAAC;AAEtD,oBAAY,kBAAkB;IAAG,IAAI,IAAA;IAAE,OAAO,IAAA;IAAE,KAAK,IAAA;CAAC;AAEtD,qBAAa,aAAc,SAAQ,KAAK;aAEpB,KAAK,EAAE,kBAAkB;gBAAzB,KAAK,EAAE,kBAAkB,EACzC,OAAO,EAAE,MAAM;CAIlB;AAED,qBAAa,QAAQ;IACnB,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,MAAM,GAAG,aAAa;IAI5C,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,MAAM,GAAG,aAAa;IAI9C,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,GAAG,aAAa;CAG5C;AAED,oEAAoE;AACpE,qBAAa,QAAQ;aAED,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;aACT,CAAC,EAAE,MAAM;gBAFT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM,EACT,CAAC,EAAE,MAAM;CAM5B;AAED,MAAM,MAAM,iBAAiB,GAAG;IAC9B,OAAO,EAAE,EAAE,CAAC,SAAS,CAAA;CACtB,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,IAAI,KAAK,IAAI,OAAO,CAAC;IAErB,WAAW,CAAC,YAAY,EAAE,qBAAqB,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAElF,oBAAoB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAEtD,WAAW,IAAI,OAAO,CAAC,MAAM,CAAC,CAAC;IAE/B;;;;OAIG;IACH,UAAU,CAAC,QAAQ,EAAE,gBAAgB,EAAE,MAAM,EAAE,gBAAgB,EAAE,WAAW,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,EACtG,UAAU,CAAC,EAAE,MAAM,GAClB,OAAO,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC;IAEzB,gBAAgB,CAAC,QAAQ,EAAE,gBAAgB,EAAE,SAAS,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM,EAChH,UAAU,CAAC,EAAE,MAAM,GAClB,OAAO,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC;CAC1B;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,gBAAgB,CAAC,CAQpE"}
package/src/pdb/auto-dock-service.js CHANGED
@@ -38,7 +38,7 @@ export class GridSize {
38
38
  }
39
39
  }
40
40
  export async function getAutoDockService() {
41
- const packageName = 'BiostructureViewer';
41
+ const packageName = 'Docking';
42
42
  const funcName = 'getAutoDockService';
43
43
  const funcList = DG.Func.find({ package: packageName, name: funcName });
44
44
  if (funcList.length === 0)
package/src/pdb/auto-dock-service.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"auto-dock-service.js","sourceRoot":"","sources":["auto-dock-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,MAAM,CAAN,IAAY,kBAA0C;AAAtD,WAAY,kBAAkB;IAAG,2DAAI,CAAA;IAAE,iEAAO,CAAA;IAAE,6DAAK,CAAA;AAAA,CAAC,EAA1C,kBAAkB,KAAlB,kBAAkB,QAAwB;AAAA,CAAC;AAEvD,MAAM,OAAO,aAAc,SAAQ,KAAK;IACtC,YACkB,KAAyB,EACzC,OAAe;QAEf,KAAK,CAAC,OAAO,CAAC,CAAC;QAHC,UAAK,GAAL,KAAK,CAAoB;IAI3C,CAAC;CACF;AAED,MAAM,OAAO,QAAQ;IACnB,MAAM,CAAC,KAAK,CAAC,OAAe;QAC1B,OAAO,IAAI,aAAa,CAAC,kBAAkB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;IAC9D,CAAC;IAED,MAAM,CAAC,OAAO,CAAC,OAAe;QAC5B,OAAO,IAAI,aAAa,CAAC,kBAAkB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IAChE,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,OAAe;QACzB,OAAO,IAAI,aAAa,CAAC,kBAAkB,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IAC7D,CAAC;CACF;AAED,oEAAoE;AACpE,MAAM,OAAO,QAAQ;IACnB,YACkB,CAAS,EACT,CAAS,EACT,CAAS;QAFT,MAAC,GAAD,CAAC,CAAQ;QACT,MAAC,GAAD,CAAC,CAAQ;QACT,MAAC,GAAD,CAAC,CAAQ;QAEzB,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,MAAM,QAAQ,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAC;QACrE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,MAAM,QAAQ,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAC;QACrE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,MAAM,QAAQ,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAC;IACvE,CAAC;CACF;AAwBD,MAAM,CAAC,KAAK,UAAU,kBAAkB;IACtC,MAAM,WAAW,GAAW,oBAAoB,CAAC;IACjD,MAAM,QAAQ,GAAW,oBAAoB,CAAC;IAC9C,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,QAAQ,EAAC,CAAC,CAAC;IACtE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,2CAA2C,CAAC,CAAC;IACtF,MAAM,GAAG,GAAqB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAE,CAAC;IACzF,OAAO,GAAG,CAAC;AACb,CAAC"}
1
+ {"version":3,"file":"auto-dock-service.js","sourceRoot":"","sources":["auto-dock-service.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,MAAM,CAAN,IAAY,kBAA0C;AAAtD,WAAY,kBAAkB;IAAG,2DAAI,CAAA;IAAE,iEAAO,CAAA;IAAE,6DAAK,CAAA;AAAA,CAAC,EAA1C,kBAAkB,KAAlB,kBAAkB,QAAwB;AAAA,CAAC;AAEvD,MAAM,OAAO,aAAc,SAAQ,KAAK;IACtC,YACkB,KAAyB,EACzC,OAAe;QAEf,KAAK,CAAC,OAAO,CAAC,CAAC;QAHC,UAAK,GAAL,KAAK,CAAoB;IAI3C,CAAC;CACF;AAED,MAAM,OAAO,QAAQ;IACnB,MAAM,CAAC,KAAK,CAAC,OAAe;QAC1B,OAAO,IAAI,aAAa,CAAC,kBAAkB,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;IAC9D,CAAC;IAED,MAAM,CAAC,OAAO,CAAC,OAAe;QAC5B,OAAO,IAAI,aAAa,CAAC,kBAAkB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IAChE,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,OAAe;QACzB,OAAO,IAAI,aAAa,CAAC,kBAAkB,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;IAC7D,CAAC;CACF;AAED,oEAAoE;AACpE,MAAM,OAAO,QAAQ;IACnB,YACkB,CAAS,EACT,CAAS,EACT,CAAS;QAFT,MAAC,GAAD,CAAC,CAAQ;QACT,MAAC,GAAD,CAAC,CAAQ;QACT,MAAC,GAAD,CAAC,CAAQ;QAEzB,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,MAAM,QAAQ,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAC;QACrE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,MAAM,QAAQ,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAC;QACrE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,MAAM,QAAQ,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAC;IACvE,CAAC;CACF;AA6BD,MAAM,CAAC,KAAK,UAAU,kBAAkB;IACtC,MAAM,WAAW,GAAW,SAAS,CAAC;IACtC,MAAM,QAAQ,GAAW,oBAAoB,CAAC;IAC9C,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,WAAW,EAAE,IAAI,EAAE,QAAQ,EAAC,CAAC,CAAC;IACtE,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,YAAY,WAAW,2CAA2C,CAAC,CAAC;IACtF,MAAM,GAAG,GAAqB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAE,CAAC;IACzF,OAAO,GAAG,CAAC;AACb,CAAC"}
package/src/pdb/format/types-base.d.ts ADDED
@@ -0,0 +1,54 @@
1
+ import { IAtomBase, IAtomCoords, IAtomTer } from './types';
2
+ export declare class LineBase {
3
+ readonly lineTitle: string;
4
+ constructor(lineTitle: string);
5
+ static fromStr(line: string): LineBase;
6
+ toStr(): string;
7
+ }
8
+ /** 1-27 */
9
+ export declare class AtomBase extends LineBase implements IAtomBase {
10
+ readonly number: number;
11
+ readonly atomElement: string;
12
+ readonly atomName: string;
13
+ readonly altLoc: string;
14
+ readonly resName: string;
15
+ readonly chain: string;
16
+ readonly resNumber: number;
17
+ readonly insCode: string;
18
+ /**
19
+ * @param number cols: 7-11 Atom serial number
20
+ * @param name cols: 13-16
21
+ * @param altLoc cols: 17 Alternate location indicator
22
+ * @param resName cols: 18-20
23
+ * @param chain cols: 22
24
+ * @param resNumber cols: 23-26
25
+ * @param insCode cols: 27 Insertion code
26
+ */
27
+ constructor(l: LineBase, number: number, atomElement: string, atomName: string, altLoc: string, resName: string, chain: string, resNumber: number, insCode: string);
28
+ static fromStr(line: string): AtomBase;
29
+ toStr(): string;
30
+ }
31
+ /** 1-66 */
32
+ export declare class AtomCoordsBase extends AtomBase implements IAtomCoords {
33
+ readonly x: number;
34
+ readonly y: number;
35
+ readonly z: number;
36
+ readonly occupancy: number;
37
+ readonly bFactor: number;
38
+ /**
39
+ *
40
+ * cols: 28-30 SPACE
41
+ * @param x cols: 31-38, f:8.3
42
+ * @param y cols: 39-46, f:8.3
43
+ * @param z cols: 47-54, f:8.3
44
+ * @param occupancy cols: 55-60, f:6.2, vdW (occupancy?)
45
+ * @param bFactor cols: 61-66, f:6.2, Elec (temperature-/B-factor?)
46
+ */
47
+ constructor(a: AtomBase, x: number, y: number, z: number, occupancy: number, bFactor: number);
48
+ static fromStr(line: string): AtomCoordsBase;
49
+ isValid(): boolean;
50
+ toStr(): string;
51
+ }
52
+ export declare class AtomTerBase extends AtomBase implements IAtomTer {
53
+ }
54
+ //# sourceMappingURL=types-base.d.ts.map
package/src/pdb/format/types-base.d.ts.map ADDED
@@ -0,0 +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"}
package/src/pdb/format/types-base.js ADDED
@@ -0,0 +1,125 @@
1
+ export class LineBase {
2
+ constructor(lineTitle) {
3
+ this.lineTitle = lineTitle;
4
+ }
5
+ static fromStr(line) {
6
+ return new LineBase(`${line.slice(1 - 1, 6).trim()}`);
7
+ }
8
+ toStr() {
9
+ const res = [
10
+ this.lineTitle.padEnd(6) /* 1-6*/,
11
+ ].join('');
12
+ if (res.length !== 6)
13
+ throw new Error(`Invalid length ${res.length}, expected ${6}`);
14
+ return res;
15
+ }
16
+ }
17
+ /** 1-27 */
18
+ export class AtomBase extends LineBase {
19
+ /**
20
+ * @param number cols: 7-11 Atom serial number
21
+ * @param name cols: 13-16
22
+ * @param altLoc cols: 17 Alternate location indicator
23
+ * @param resName cols: 18-20
24
+ * @param chain cols: 22
25
+ * @param resNumber cols: 23-26
26
+ * @param insCode cols: 27 Insertion code
27
+ */
28
+ constructor(l, number,
29
+ /* Element */ atomElement,
30
+ /* Name of the atom in the residue */ atomName, altLoc,
31
+ /* Name of the residue */ resName, chain, resNumber, insCode) {
32
+ super(l.lineTitle);
33
+ this.number = number;
34
+ this.atomElement = atomElement;
35
+ this.atomName = atomName;
36
+ this.altLoc = altLoc;
37
+ this.resName = resName;
38
+ this.chain = chain;
39
+ this.resNumber = resNumber;
40
+ this.insCode = insCode;
41
+ }
42
+ static fromStr(line) {
43
+ // TODO: Check line start (?)
44
+ return new AtomBase(LineBase.fromStr(line.slice(1 - 1, 6)),
45
+ /* number */ parseInt(line.slice(7 - 1, 11)), `${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()}`,
46
+ /* resNumber */ parseInt(line.slice(23 - 1, 26)), `${line.slice(27 - 1, 27).trim()}`);
47
+ }
48
+ toStr() {
49
+ const res = [
50
+ super.toStr() /* 1-6 */,
51
+ (this.number > 0 ? this.number.toFixed(0) : '').padStart(5) /* 7-11 */, ' ' /* 12 */,
52
+ this.atomElement.padStart(2) /* 13-14 */,
53
+ this.atomName.padEnd(2) /* 15-16*/,
54
+ this.altLoc.padEnd(1) /* 17 */,
55
+ this.resName.padStart(3) /* 18-20 */, ' ' /* 21 */,
56
+ this.chain.padEnd(1).slice(0, 1) /* 22 */,
57
+ (this.resNumber >= 0 ? this.resNumber.toFixed(0) : '').padStart(4) /* 23-26 */,
58
+ this.insCode.padEnd(1).slice(0, 1) /* 27 */,
59
+ ].join('');
60
+ if (res.length !== 27)
61
+ throw new Error(`Invalid length ${res.length}, expected 27`);
62
+ return res;
63
+ }
64
+ }
65
+ /** 1-66 */
66
+ export class AtomCoordsBase extends AtomBase {
67
+ /**
68
+ *
69
+ * cols: 28-30 SPACE
70
+ * @param x cols: 31-38, f:8.3
71
+ * @param y cols: 39-46, f:8.3
72
+ * @param z cols: 47-54, f:8.3
73
+ * @param occupancy cols: 55-60, f:6.2, vdW (occupancy?)
74
+ * @param bFactor cols: 61-66, f:6.2, Elec (temperature-/B-factor?)
75
+ */
76
+ constructor(a, x, y, z, occupancy, bFactor) {
77
+ super(a, a.number, a.atomElement, a.atomName, a.altLoc, a.resName, a.chain, a.resNumber, a.insCode);
78
+ this.x = x;
79
+ this.y = y;
80
+ this.z = z;
81
+ this.occupancy = occupancy;
82
+ this.bFactor = bFactor;
83
+ }
84
+ static fromStr(line) {
85
+ if (!(line.startsWith('ATOM ') || line.startsWith('HETATM')))
86
+ throw new Error('');
87
+ return new AtomCoordsBase(AtomBase.fromStr(line.slice(1 - 1, 27)),
88
+ /* x */ parseFloat(line.slice(31 - 1, 38)),
89
+ /* y */ parseFloat(line.slice(39 - 1, 46)),
90
+ /* z */ parseFloat(line.slice(47 - 1, 54)),
91
+ /* occupancy */ parseFloat(line.slice(55 - 1, 60)),
92
+ /* bFactor*/ parseFloat(line.slice(61 - 1, 66)));
93
+ }
94
+ isValid() {
95
+ return this.number.toFixed(0).length <= 5 &&
96
+ this.atomElement.length <= 2 &&
97
+ this.atomName.length <= 2 &&
98
+ this.altLoc.length == 1 &&
99
+ this.resName.length <= 3 &&
100
+ this.chain.length == 1 &&
101
+ this.resNumber.toFixed(0).length <= 4 &&
102
+ this.insCode.length == 1 &&
103
+ this.x.toFixed(3).length <= 8 &&
104
+ this.y.toFixed(3).length <= 8 &&
105
+ this.z.toFixed(3).length <= 8 &&
106
+ this.occupancy.toFixed(2).length <= 6 &&
107
+ this.bFactor.toFixed(2).length <= 6;
108
+ }
109
+ toStr() {
110
+ const res = [
111
+ super.toStr() /* 1 - 27 */, ' ' /* 28-30 */,
112
+ this.x.toFixed(3).padStart(8) /* 31-38 */,
113
+ this.y.toFixed(3).padStart(8) /* 39-46 */,
114
+ this.z.toFixed(3).padStart(8) /* 47-54 */,
115
+ this.occupancy.toFixed(2).padStart(6) /* 55-60 */,
116
+ this.bFactor.toFixed(2).padStart(6) /* 61-66 */,
117
+ ].join('');
118
+ if (res.length !== 66)
119
+ throw new Error(`ATOM base line of invalid length ${res.length} != 66.`);
120
+ return res;
121
+ }
122
+ }
123
+ export class AtomTerBase extends AtomBase {
124
+ }
125
+ //# sourceMappingURL=types-base.js.map
package/src/pdb/format/types-base.js.map ADDED
@@ -0,0 +1 @@
1
+ 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package/src/pdb/format/types-pdb.d.ts ADDED
@@ -0,0 +1,22 @@
1
+ import { AtomBase, AtomCoordsBase, AtomTerBase } from './types-base';
2
+ import { IPdbAtomCoords, IPdbAtomTer } from './types';
3
+ export declare class PdbAtomTer extends AtomTerBase implements IPdbAtomTer {
4
+ constructor(a: AtomBase);
5
+ }
6
+ /** https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html */
7
+ export declare class PdbAtomCoords extends AtomCoordsBase implements IPdbAtomCoords {
8
+ readonly segment: string;
9
+ readonly element: string;
10
+ readonly charge: string;
11
+ /**
12
+ * cols: 67-72, SPACE
13
+ * @param segment cols: 73-76
14
+ * @param element cols: 77-78
15
+ * @param charge cols: 79-80, examples: '1+', '1-'
16
+ */
17
+ constructor(a: AtomCoordsBase, segment: string, element: string, charge: string);
18
+ static fromStr(src: string): PdbAtomCoords;
19
+ isValid(): boolean;
20
+ toStr(): string;
21
+ }
22
+ //# sourceMappingURL=types-pdb.d.ts.map
package/src/pdb/format/types-pdb.d.ts.map ADDED
@@ -0,0 +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"}
package/src/pdb/format/types-pdb.js ADDED
@@ -0,0 +1,41 @@
1
+ import { AtomCoordsBase, AtomTerBase } from './types-base';
2
+ export class PdbAtomTer extends AtomTerBase {
3
+ constructor(a) {
4
+ super(a, a.number, a.atomElement, a.atomName, a.altLoc, a.resName, a.chain, a.resNumber, a.insCode);
5
+ }
6
+ }
7
+ /** https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html */
8
+ export class PdbAtomCoords extends AtomCoordsBase {
9
+ /**
10
+ * cols: 67-72, SPACE
11
+ * @param segment cols: 73-76
12
+ * @param element cols: 77-78
13
+ * @param charge cols: 79-80, examples: '1+', '1-'
14
+ */
15
+ constructor(a, segment, element, charge) {
16
+ super(a, a.x, a.y, a.z, a.occupancy, a.bFactor);
17
+ this.segment = segment;
18
+ this.element = element;
19
+ this.charge = charge;
20
+ }
21
+ static fromStr(src) {
22
+ throw new Error('Not implemented');
23
+ }
24
+ isValid() {
25
+ return super.isValid() &&
26
+ this.segment.length <= 4 &&
27
+ this.element.length <= 2 &&
28
+ /^()|(\d[+-])$/.test(this.charge);
29
+ }
30
+ toStr() {
31
+ const res = [super.toStr() /* 1-66 */, ' ' /* 67-72*/,
32
+ this.segment.padEnd(4) /* 73-76 */,
33
+ this.element.padStart(2) /* 77-78 */,
34
+ this.charge.padEnd(2) /* 79-80 */,
35
+ ].join('');
36
+ if (res.length !== 80)
37
+ throw new Error(`ATOM PDB line of invalid length ${res.length} != 80.`);
38
+ return res;
39
+ }
40
+ }
41
+ //# sourceMappingURL=types-pdb.js.map
package/src/pdb/format/types-pdb.js.map ADDED
@@ -0,0 +1 @@
1
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package/src/pdb/format/types-pdbqt.d.ts ADDED
@@ -0,0 +1,30 @@
1
+ import { AtomBase, AtomCoordsBase, AtomTerBase } from './types-base';
2
+ import { IPdbAtomTer, IPdbqtAtomCoords, IPdbqtAtomTer } from './types';
3
+ import { PdbAtomCoords } from './types-pdb';
4
+ export type VinaResultType = {
5
+ affinity: number;
6
+ lbDistFromBest: number;
7
+ ubDistFromBest: number;
8
+ };
9
+ export declare class PdbqtAtomTer extends AtomTerBase implements IPdbqtAtomTer {
10
+ constructor(a: AtomBase);
11
+ toPdb(): IPdbAtomTer;
12
+ static fromStr(line: string): PdbqtAtomTer;
13
+ }
14
+ /** https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf */
15
+ export declare class PdbqtAtomCoords extends AtomCoordsBase implements IPdbqtAtomCoords {
16
+ readonly partCharge: number;
17
+ readonly atomType: string;
18
+ /**
19
+ * cols: 67-70, SPACE
20
+ * @param partCharge cols: 71-76 f:+1.3
21
+ * @param atomType cols: 78-79, right
22
+ */
23
+ constructor(a: AtomCoordsBase, partCharge: number, atomType: string);
24
+ static fromStr(line: string): PdbqtAtomCoords;
25
+ /** cols: 71-76 f:+5.3 */ get partChargeStr(): string;
26
+ isValid(): boolean;
27
+ toPdb(): PdbAtomCoords;
28
+ toStr(): string;
29
+ }
30
+ //# sourceMappingURL=types-pdbqt.d.ts.map
package/src/pdb/format/types-pdbqt.d.ts.map ADDED
@@ -0,0 +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"}
package/src/pdb/format/types-pdbqt.js ADDED
@@ -0,0 +1,64 @@
1
+ import { AtomBase, AtomCoordsBase, AtomTerBase } from './types-base';
2
+ import { PdbAtomCoords, PdbAtomTer } from './types-pdb';
3
+ export class PdbqtAtomTer extends AtomTerBase {
4
+ constructor(a) {
5
+ super(a, a.number, a.atomElement, a.atomName, a.altLoc, a.resName, a.chain, a.resNumber, a.insCode);
6
+ }
7
+ toPdb() {
8
+ return new PdbAtomTer(this);
9
+ }
10
+ static fromStr(line) {
11
+ return new PdbqtAtomTer(AtomBase.fromStr(line));
12
+ }
13
+ }
14
+ /** https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf */
15
+ export class PdbqtAtomCoords extends AtomCoordsBase {
16
+ /**
17
+ * cols: 67-70, SPACE
18
+ * @param partCharge cols: 71-76 f:+1.3
19
+ * @param atomType cols: 78-79, right
20
+ */
21
+ constructor(a, partCharge, atomType) {
22
+ super(a, a.x, a.y, a.z, a.occupancy, a.bFactor);
23
+ this.partCharge = partCharge;
24
+ this.atomType = atomType;
25
+ }
26
+ static fromStr(line) {
27
+ const res = new PdbqtAtomCoords(AtomCoordsBase.fromStr(line),
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(`^${res.atomElement}`), '');
31
+ // res = new PdbqtAtomCoords(
32
+ // new AtomCoordsBase(
33
+ // new AtomBase(res, res.number, res.atomElement,
34
+ // atomName /* replacing res.atomName*/,
35
+ // res.altLoc, res.resName, res.chain, res.resNumber, res.insCode),
36
+ // res.x, res.y, res.z, res.occupancy, res.bFactor),
37
+ // res.partCharge, res.atomType);
38
+ // }
39
+ return res;
40
+ }
41
+ /** cols: 71-76 f:+5.3 */ get partChargeStr() {
42
+ return `${this.partCharge >= 0 ? '+' : ''}${this.partCharge.toFixed(3)}`;
43
+ }
44
+ // /** cols: 73-76, left */ segment: string;
45
+ isValid() {
46
+ return super.isValid() &&
47
+ this.partChargeStr.length <= 6 &&
48
+ this.atomType.length <= 2;
49
+ }
50
+ toPdb() {
51
+ const res = new PdbAtomCoords(this, '', this.atomElement /* from base */, '');
52
+ return res;
53
+ }
54
+ toStr() {
55
+ const res = [super.toStr() /* 1-66 */, ' ' /* 67-70 */,
56
+ this.partChargeStr.padStart(6) /* 71-76*/, ' ' /* 77 */,
57
+ this.atomType.padEnd(2) /* 78-79 */,
58
+ ].join('');
59
+ if (res.length !== 79)
60
+ throw new Error(`ATOM Pdbqt line of invalid length ${res.length} != 79.`);
61
+ return res;
62
+ }
63
+ }
64
+ //# sourceMappingURL=types-pdbqt.js.map
package/src/pdb/format/types-pdbqt.js.map ADDED
@@ -0,0 +1 @@
1
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package/src/pdb/format/types.d.ts ADDED
@@ -0,0 +1,36 @@
1
+ export interface IAtomBase {
2
+ get number(): number;
3
+ get atomElement(): string;
4
+ get atomName(): string;
5
+ get altLoc(): string;
6
+ get resName(): string;
7
+ get chain(): string;
8
+ get resNumber(): number;
9
+ get insCode(): string;
10
+ toStr(): string;
11
+ }
12
+ export interface IAtomTer extends IAtomBase {
13
+ }
14
+ export interface IAtomCoords extends IAtomBase {
15
+ get x(): number;
16
+ get y(): number;
17
+ get z(): number;
18
+ get occupancy(): number;
19
+ get bFactor(): number;
20
+ }
21
+ export interface IPdbAtomBase extends IAtomBase {
22
+ }
23
+ export interface IPdbAtomCoords extends IPdbAtomBase, IAtomCoords {
24
+ }
25
+ export interface IPdbAtomTer extends IPdbAtomBase, IAtomTer {
26
+ }
27
+ export interface IPdbqtAtomBase extends IAtomBase {
28
+ toPdb(): IPdbAtomBase;
29
+ }
30
+ export interface IPdbqtAtomCoords extends IPdbqtAtomBase, IAtomCoords {
31
+ toPdb(): IPdbAtomCoords;
32
+ }
33
+ export interface IPdbqtAtomTer extends IPdbqtAtomBase, IAtomTer {
34
+ toPdb(): IPdbAtomTer;
35
+ }
36
+ //# sourceMappingURL=types.d.ts.map
package/src/pdb/format/types.d.ts.map ADDED
@@ -0,0 +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"}
package/src/pdb/format/types.js ADDED
@@ -0,0 +1,2 @@
1
+ export {};
2
+ //# sourceMappingURL=types.js.map
package/src/pdb/format/types.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}
package/src/types/ngl.d.ts ADDED
@@ -0,0 +1,126 @@
1
+ /// <reference types="signals" />
2
+ declare module 'NGL' {
3
+ import { Signal } from 'signals';
4
+ import { Box3, Scene, WebGLRenderer } from 'three';
5
+ interface Structure {
6
+ get atomCount(): number;
7
+ get bondCount(): number;
8
+ get modelStore(): any;
9
+ getView(selection: Selection): Structure;
10
+ }
11
+ type Volume = any;
12
+ type Surface = any;
13
+ interface ColorData {
14
+ atomData?: number[];
15
+ bondData?: number[];
16
+ }
17
+ type LoaderParameters = {
18
+ ext: string;
19
+ compressed: boolean;
20
+ binary: boolean;
21
+ name: string;
22
+ defaultRepresentation: boolean;
23
+ };
24
+ type ColorMode = 'rgb' | 'hsv' | 'hsl' | 'hsi' | 'lab' | 'hcl';
25
+ type ColorSpace = 'sRGB' | 'linear';
26
+ type ScaleParameters = any;
27
+ interface ColormakerParameters extends ScaleParameters {
28
+ structure?: Structure;
29
+ volume?: Volume;
30
+ surface?: Surface;
31
+ data?: ColorData;
32
+ }
33
+ type SelectionSchemeData = [string, string, ColormakerParameters | undefined];
34
+ type Colormaker = {};
35
+ class ColormakerRegistryClass {
36
+ add(id: String, scheme: Colormaker): undefined;
37
+ addScheme(scheme: Function | Colormaker, label: String): String;
38
+ addSelectionScheme(dataList: SelectionSchemeData[], label?: String): String;
39
+ }
40
+ const ColormakerRegistry: ColormakerRegistryClass;
41
+ type RepresentationParameters = {
42
+ [k: string]: any;
43
+ };
44
+ type StructureRepresentationType = ('angle' | 'axes' | 'backbone' | 'ball+stick' | 'base' | 'cartoon' | 'contact' | 'dihedral' | 'distance' | 'helixorient' | 'hyperball' | 'label' | 'licorice' | 'line' | 'surface' | 'ribbon' | 'rocket' | 'rope' | 'spacefill' | 'trace' | 'tube' | 'unitcell');
45
+ class Component {
46
+ addRepresentation(type: StructureRepresentationType, params?: RepresentationParameters): RepresentationElement;
47
+ autoView(duration?: number): undefined;
48
+ removeAllRepresentations(): undefined;
49
+ }
50
+ class RepresentationElement extends Component {
51
+ }
52
+ class Stage {
53
+ viewer: Viewer;
54
+ get compList(): Component[];
55
+ constructor(host: HTMLElement);
56
+ handleResize(): undefined;
57
+ removeComponent(component: Component): undefined;
58
+ removeAllComponents(type?: string): undefined;
59
+ loadFile(path: String | File | Blob, params: Partial<LoaderParameters>): Promise<void>;
60
+ dispose(): undefined;
61
+ }
62
+ class Viewer {
63
+ signals: ViewerSignals;
64
+ container: HTMLElement;
65
+ wrapper: HTMLElement;
66
+ sampleLevel: number;
67
+ stats: Stats;
68
+ width: number;
69
+ height: number;
70
+ scene: Scene;
71
+ renderer: WebGLRenderer;
72
+ boundingBox: Box3;
73
+ rendering: boolean;
74
+ renderPending: boolean;
75
+ render(picking: boolean): void;
76
+ requestRender(): void;
77
+ setSize(width: number, height: number): void;
78
+ }
79
+ class Stats {
80
+ signals: {
81
+ updated: Signal;
82
+ };
83
+ maxDuration: number;
84
+ minDuration: number;
85
+ avgDuration: number;
86
+ lastDuration: number;
87
+ prevFpsTime: number;
88
+ lastFps: number;
89
+ lastFrames: number;
90
+ frames: number;
91
+ count: number;
92
+ startTime: number;
93
+ currentTime: number;
94
+ }
95
+ interface ViewerSignals {
96
+ ticked: Signal;
97
+ rendered: Signal;
98
+ }
99
+ type LoaderInput = File | Blob | string;
100
+ type InferBondsOptions = 'all' | 'none' | 'auto';
101
+ interface ParserParams {
102
+ voxelSize?: number;
103
+ firstModelOnly?: boolean;
104
+ asTrajectory?: boolean;
105
+ cAlphaOnly?: boolean;
106
+ name?: string;
107
+ path?: string;
108
+ delimiter?: string;
109
+ comment?: string;
110
+ columnNames?: string;
111
+ inferBonds?: InferBondsOptions;
112
+ }
113
+ function autoLoad(file: LoaderInput, params?: Partial<LoaderParameters & ParserParams>): Promise<Structure>;
114
+ class Selection {
115
+ constructor(query: string);
116
+ }
117
+ class PdbWriter {
118
+ constructor(src: Structure, params?: any);
119
+ getString(): string;
120
+ }
121
+ class SdfWriter {
122
+ constructor(src: Structure, params?: any);
123
+ getData(): string;
124
+ }
125
+ }
126
+ //# sourceMappingURL=ngl.d.ts.map
package/src/types/ngl.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"ngl.d.ts","sourceRoot":"","sources":["ngl.ts"],"names":[],"mappings":";AAAA,OAAO,QAAQ,KAAK,CAAC;IACnB,OAAO,EAAC,MAAM,EAAC,MAAM,SAAS,CAAC;IAC/B,OAAO,EAAC,IAAI,EAAE,KAAK,EAAE,aAAa,EAAC,MAAM,OAAO,CAAC;IAEjD,UAAiB,SAAS;QACxB,IAAI,SAAS,IAAI,MAAM,CAAC;QACxB,IAAI,SAAS,IAAI,MAAM,CAAC;QACxB,IAAI,UAAU,IAAI,GAAG,CAAC;QACtB,OAAO,CAAC,SAAS,EAAE,SAAS,GAAG,SAAS,CAAC;KAC1C;IAED,KAAY,MAAM,GAAG,GAAG,CAAC;IACzB,KAAY,OAAO,GAAG,GAAG,CAAC;IAE1B,UAAiB,SAAS;QACxB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;QACpB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAA;KACpB;IAED,KAAY,gBAAgB,GAAG;QAC7B,GAAG,EAAE,MAAM,CAAC;QACZ,UAAU,EAAE,OAAO,CAAC;QACpB,MAAM,EAAE,OAAO,CAAC;QAChB,IAAI,EAAE,MAAM,CAAC;QACb,qBAAqB,EAAE,OAAO,CAAA;KAC/B,CAAC;IAEF,KAAY,SAAS,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,CAAA;IACrE,KAAY,UAAU,GAAG,MAAM,GAAG,QAAQ,CAAA;IAE1C,KAAY,eAAe,GAAG,GAAG,CAAC;IAElC,UAAiB,oBAAqB,SAAQ,eAAe;QAC3D,SAAS,CAAC,EAAE,SAAS,CAAC;QACtB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,OAAO,CAAC,EAAE,OAAO,CAAC;QAClB,IAAI,CAAC,EAAE,SAAS,CAAC;KAClB;IAED,KAAY,mBAAmB,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,oBAAoB,GAAG,SAAS,CAAC,CAAA;IAEpF,KAAY,UAAU,GAAG,EAAE,CAAC;IAE5B,MAAa,uBAAuB;QAClC,GAAG,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,GAAG,SAAS;QAE9C,SAAS,CAAC,MAAM,EAAE,QAAQ,GAAG,UAAU,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM;QAE/D,kBAAkB,CAAC,QAAQ,EAAE,mBAAmB,EAAE,EAAE,KAAK,CAAC,EAAE,MAAM,GAAG,MAAM;KAC5E;IAEM,MAAM,kBAAkB,EAAE,uBAAuB,CAAC;IAEzD,KAAY,wBAAwB,GAAG;QAAE,CAAC,CAAC,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAA;IAE3D,KAAY,2BAA2B,GAAG,CACxC,OAAO,GAAG,MAAM,GAAG,UAAU,GAAG,YAAY,GAAG,MAAM,GAAG,SAAS,GAAG,SAAS,GAAG,UAAU,GAC1F,UAAU,GAAG,aAAa,GAAG,WAAW,GAAG,OAAO,GAAG,UAAU,GAAG,MAAM,GAAG,SAAS,GACpF,QAAQ,GAAG,QAAQ,GAAG,MAAM,GAAG,WAAW,GAAG,OAAO,GAAG,MAAM,GAAG,UAAU,CACzE,CAAA;IAEH,MAAa,SAAS;QACpB,iBAAiB,CAAC,IAAI,EAAE,2BAA2B,EAAE,MAAM,CAAC,EAAE,wBAAwB,GAAG,qBAAqB;QAE9G,QAAQ,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS;QAEtC,wBAAwB,IAAI,SAAS;KACtC;IAED,MAAa,qBAAsB,SAAQ,SAAS;KAEnD;IAED,MAAa,KAAK;QAChB,MAAM,EAAE,MAAM,CAAC;QAEf,IAAI,QAAQ,IAAI,SAAS,EAAE,CAAC;oBAGhB,IAAI,EAAE,WAAW;QAE7B,YAAY,IAAI,SAAS;QAEzB,eAAe,CAAC,SAAS,EAAE,SAAS,GAAG,SAAS;QAEhD,mBAAmB,CAAC,IAAI,CAAC,EAAE,MAAM,GAAG,SAAS;QAE7C,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,GAAG,IAAI,EAAE,MAAM,EAAE,OAAO,CAAC,gBAAgB,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC;QAEtF,OAAO,IAAI,SAAS;KACrB;IAED,MAAa,MAAM;QACjB,OAAO,EAAE,aAAa,CAAC;QAEvB,SAAS,EAAE,WAAW,CAAC;QACvB,OAAO,EAAE,WAAW,CAAC;QAErB,WAAW,EAAE,MAAM,CAAC;QAEpB,KAAK,EAAE,KAAK,CAAC;QAEb,KAAK,EAAE,MAAM,CAAC;QACd,MAAM,EAAE,MAAM,CAAC;QAEf,KAAK,EAAE,KAAK,CAAC;QAEb,QAAQ,EAAE,aAAa,CAAC;QACxB,WAAW,EAAE,IAAI,CAAC;QAElB,SAAS,EAAE,OAAO,CAAC;QACnB,aAAa,EAAE,OAAO,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI;QAE9B,aAAa,IAAI,IAAI;QAErB,OAAO,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,IAAI;KAC7C;IAED,MAAa,KAAK;QAChB,OAAO,EAAE;YACP,OAAO,EAAE,MAAM,CAAA;SAChB,CAAC;QAEF,WAAW,EAAE,MAAM,CAAC;QACpB,WAAW,EAAE,MAAM,CAAC;QACpB,WAAW,EAAE,MAAM,CAAC;QACpB,YAAY,EAAE,MAAM,CAAC;QAErB,WAAW,EAAE,MAAM,CAAC;QACpB,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;QACf,KAAK,EAAE,MAAM,CAAC;QAEd,SAAS,EAAE,MAAM,CAAC;QAClB,WAAW,EAAE,MAAM,CAAC;KACrB;IAED,UAAiB,aAAa;QAC5B,MAAM,EAAE,MAAM,CAAC;QACf,QAAQ,EAAE,MAAM,CAAA;KACjB;IAED,KAAY,WAAW,GAAG,IAAI,GAAG,IAAI,GAAG,MAAM,CAAA;IAE9C,KAAY,iBAAiB,GAAG,KAAK,GAAG,MAAM,GAAG,MAAM,CAAA;IAEvD,UAAiB,YAAY;QAC3B,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,cAAc,CAAC,EAAE,OAAO,CAAC;QACzB,YAAY,CAAC,EAAE,OAAO,CAAC;QACvB,UAAU,CAAC,EAAE,OAAO,CAAC;QACrB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,UAAU,CAAC,EAAE,iBAAiB,CAAC;KAChC;IAED,SAAgB,QAAQ,CAAC,IAAI,EAAE,WAAW,EAAE,MAAM,CAAC,EAAE,OAAO,CAAC,gBAAgB,GAAG,YAAY,CAAC,GAAG,OAAO,CAAC,SAAS,CAAC,CAAC;IAEnH,MAAa,SAAS;oBACR,KAAK,EAAE,MAAM;KAC1B;IAED,MAAa,SAAS;oBACR,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,EAAE,GAAG;QAExC,SAAS,IAAI,MAAM;KACpB;IAED,MAAa,SAAS;oBACR,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,EAAE,GAAG;QAExC,OAAO,IAAI,MAAM;KAClB;CACF"}
package/src/types/ngl.js ADDED
@@ -0,0 +1,2 @@
1
+ "use strict";
2
+ //# sourceMappingURL=ngl.js.map
package/src/types/ngl.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"ngl.js","sourceRoot":"","sources":["ngl.ts"],"names":[],"mappings":""}
package/src/viewers/molstar-viewer.d.ts CHANGED
@@ -78,4 +78,5 @@ declare module 'datagrok-api/dg' {
78
78
  fromType(viewerType: 'Biostructure', options: Partial<BiostructureProps>): Promise<DG.Viewer<BiostructureProps> & IBiostructureViewer>;
79
79
  }
80
80
  }
81
+ export declare function viewBiostructure(content: string, format?: string, name?: string): Promise<void>;
81
82
  //# sourceMappingURL=molstar-viewer.d.ts.map
package/src/viewers/molstar-viewer.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"molstar-viewer.d.ts","sourceRoot":"","sources":["molstar-viewer.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,oBAAoB,EAAC,MAAM,cAAc,CAAC;AAClD,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AACjC,OAAO,EAAC,mBAAmB,EAAC,MAAM,mBAAmB,CAAC;AAGtD,oBAAY,kBAAkB;IAC5B,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,eAAe;IAC3B,QAAQ,aAAa;IACrB,SAAS,cAAc;IACvB,OAAO,YAAY;CACpB;AAED,oBAAY,sBAAsB;IAChC,IAAI,SAAS;IACb,SAAS,cAAc;IACvB,MAAM,WAAW;CAClB;AAED,oBAAY,4BAA4B;IACtC,IAAI,SAAS;IACb,MAAM,WAAW;CAClB;AAED,oBAAY,+BAA+B;IACzC,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,SAAS,cAAc;IACvB,QAAQ,aAAa;CACtB;AAED,eAAO,MAAM,wBAAwB;cAEzB,oBAAoB;SACzB,MAAM,GAAG,IAAI;YACV,MAAM,GAAG,IAAI;sBACH,MAAM,GAAG,IAAI;iBAClB,MAAM;kBACL,MAAM;oBAGJ,kBAAkB;sBAGhB,OAAO;wBACL,OAAO;2BACJ,sBAAsB;0BACvB,4BAA4B;4BAC1B,4BAA4B;6BAC3B,4BAA4B;2BAC9B,+BAA+B;wBAElC,OAAO;yBACN,OAAO;iCACC,OAAO;+BAGT,OAAO;kCAMJ,OAAO;mCAEN,OAAO;IAGtC;;;OAGG;wBACiB,OAAO;2BAEJ,OAAO;wBACV,OAAO;mBACZ,OAAO;yBACD,OAAO;uBAET,OAAO;wBACN,OAAO;wBACP,OAAO;0BACL,OAAO;+BAEF,OAAO;2BACX,MAAM;qBACZ,MAAM;sBACL,OAAO;uBAEN,MAAM;wBACL,OAAO;CAC1B,CAAC;AAEJ,MAAM,MAAM,iBAAiB,GAAG,OAAO,wBAAwB,CAAC;AAEhE,MAAM,WAAW,mBAAoB,SAAQ,OAAO;IAClD,UAAU,CAAC,OAAO,EAAE,OAAO,CAAC,iBAAiB,CAAC,GAAG,IAAI,CAAC;CACvD;AAGD,MAAM,WAAW,cAAe,SAAQ,OAAO;IAC7C,OAAO,CAAC,EAAE,EAAE,mBAAmB,GAAG,EAAE,CAAC,SAAS,GAAG,IAAI,CAAC;CACvD;AAED,OAAO,QAAQ,iBAAiB,CAAC;IAC/B,UAAU,mBAAmB;QAE3B,QAAQ,CAAC,UAAU,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,CAAC,iBAAiB,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,GAAG,mBAAmB,CAAC,CAAC;KACxI;CACF;AAED,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,MAAM,GAAE,MAAc,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAI5G"}
package/src/viewers/molstar-viewer.js CHANGED
@@ -1,3 +1,4 @@
1
+ import * as grok from 'datagrok-api/grok';
1
2
  import { BiostructureDataJson } from '../pdb/types';
2
3
  import { TAGS as pdbTAGS } from '../pdb/index';
3
4
  export var RepresentationType;
@@ -80,4 +81,9 @@ export const BiostructurePropsDefault = new class {
80
81
  this.showExportControls = false;
81
82
  }
82
83
  }();
84
+ export async function viewBiostructure(content, format = 'pdb', name) {
85
+ const packageName = 'BiostructureViewer';
86
+ const funcName = 'viewBiostructure';
87
+ await grok.functions.call(`${packageName}:${funcName}`, { content, format, name });
88
+ }
83
89
  //# sourceMappingURL=molstar-viewer.js.map
package/src/viewers/molstar-viewer.js.map CHANGED
@@ -1 +1 @@
1
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