openchemlib 8.1.0 → 8.3.0

package/minimal.d.ts

@@ -8,6 +8,9 @@ export {
   IDepictorOptions,
   Reaction,
   SDFileParser,
+  ISmilesParserOptions,
+  ISmilesParserParseMoleculeOptions,
+  SmilesParser,
   SSSearcher,
   SSSearcherWithIndex,
   Util,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "openchemlib",
-  "version": "8.1.0",
+  "version": "8.3.0",
   "description": "Manipulate molecules",
   "keywords": [
     "chemistry",
@@ -27,9 +27,6 @@
     "test": "npm run build && npm run test-only && npm run eslint",
     "test-only": "jest"
   },
-  "jest": {
-    "testEnvironment": "node"
-  },
   "main": "./core.js",
   "files": [
     "dist",
@@ -56,14 +53,12 @@
   "homepage": "https://github.com/cheminfo/openchemlib-js",
   "devDependencies": {
     "benchmark": "^2.1.4",
-    "eslint": "^8.25.0",
-    "eslint-config-cheminfo": "^8.0.2",
-    "fs-extra": "^10.1.0",
+    "eslint": "^8.37.0",
+    "eslint-config-cheminfo": "^8.2.0",
     "gwt-api-exporter": "^2.0.0",
-    "jest": "^29.2.0",
-    "openchemlib-utils": "^2.1.3",
-    "prettier": "^2.7.1",
-    "rimraf": "^3.0.2",
-    "yargs": "^17.6.0"
+    "jest": "^29.5.0",
+    "openchemlib-utils": "^2.4.0",
+    "prettier": "^2.8.7",
+    "yargs": "^17.7.1"
   }
 }

package/types.d.ts

@@ -2,12 +2,14 @@
 
 export interface IMoleculeFromSmilesOptions {
   /**
-   * Disable extra coordinate computation. Default: false.
+   * Disable coordinate invention.
+   * @default `false`
    */
   noCoordinates?: boolean;
 
   /**
-   * Disable stereo features parsing. Default: false.
+   * Disable stereo features parsing.
+   * @default `false`
    */
   noStereo?: boolean;
 }
@@ -89,6 +91,8 @@ export declare class Molecule {
    */
   constructor(maxAtoms: number, maxBonds: number);
 
+  // based on JSMolecule.java you can do a regexp ".*static.* (int|long|double)(.*) = .*;" and replace with "$2: number;"
+
   static CANONIZER_CREATE_SYMMETRY_RANK: number;
   static CANONIZER_CONSIDER_DIASTEREOTOPICITY: number;
   static CANONIZER_CONSIDER_ENANTIOTOPICITY: number;
@@ -99,22 +103,22 @@ export declare class Molecule {
   static CANONIZER_COORDS_ARE_3D: number;
   static CANONIZER_CREATE_PSEUDO_STEREO_GROUPS: number;
   static CANONIZER_DISTINGUISH_RACEMIC_OR_GROUPS: number;
+  static CANONIZER_TIE_BREAK_FREE_VALENCE_ATOMS: number;
+  static CANONIZER_ENCODE_ATOM_CUSTOM_LABELS_WITHOUT_RANKING: number;
+  static CANONIZER_NEGLECT_ANY_STEREO_INFORMATION: number;
 
   static cMaxAtomicNo: number;
-
   static cAtomParityNone: number;
   static cAtomParity1: number;
   static cAtomParity2: number;
   static cAtomParityUnknown: number;
   static cAtomParityIsPseudo: number;
-
   static cAtomRadicalState: number;
   static cAtomRadicalStateShift: number;
   static cAtomRadicalStateNone: number;
   static cAtomRadicalStateS: number;
   static cAtomRadicalStateD: number;
   static cAtomRadicalStateT: number;
-
   static cAtomColorNone: number;
   static cAtomColorBlue: number;
   static cAtomColorRed: number;
@@ -123,18 +127,15 @@ export declare class Molecule {
   static cAtomColorOrange: number;
   static cAtomColorDarkGreen: number;
   static cAtomColorDarkRed: number;
-
   static cAtomCIPParityNone: number;
   static cAtomCIPParityRorM: number;
   static cAtomCIPParitySorP: number;
   static cAtomCIPParityProblem: number;
-
   static cESRTypeAbs: number;
   static cESRTypeAnd: number;
   static cESRTypeOr: number;
   static cESRMaxGroups: number;
   static cESRGroupBits: number;
-
   static cAtomQFNoOfBits: number;
   static cAtomQFAromStateBits: number;
   static cAtomQFAromStateShift: number;
@@ -146,12 +147,18 @@ export declare class Molecule {
   static cAtomQFPiElectronShift: number;
   static cAtomQFNeighbourBits: number;
   static cAtomQFNeighbourShift: number;
-  static cAtomQFRingSizeBits: number;
-  static cAtomQFRingSizeShift: number;
+  static cAtomQFSmallRingSizeBits: number;
+  static cAtomQFSmallRingSizeShift: number;
   static cAtomQFChargeBits: number;
   static cAtomQFChargeShift: number;
   static cAtomQFRxnParityBits: number;
   static cAtomQFRxnParityShift: number;
+  static cAtomQFNewRingSizeBits: number;
+  static cAtomQFNewRingSizeShift: number;
+  static cAtomQFENeighbourBits: number;
+  static cAtomQFENeighbourShift: number;
+  static cAtomQFStereoStateBits: number;
+  static cAtomQFStereoStateShift: number;
   static cAtomQFSimpleFeatures: number;
   static cAtomQFNarrowing: number;
   static cAtomQFAny: number;
@@ -181,42 +188,72 @@ export declare class Molecule {
   static cAtomQFNot2Neighbours: number;
   static cAtomQFNot3Neighbours: number;
   static cAtomQFNot4Neighbours: number;
-  static cAtomQFRingSize: number;
+  static cAtomQFSmallRingSize: number;
+
   static cAtomQFCharge: number;
   static cAtomQFNotChargeNeg: number;
   static cAtomQFNotCharge0: number;
   static cAtomQFNotChargePos: number;
   static cAtomQFFlatNitrogen: number;
+
   static cAtomQFExcludeGroup: number;
+
   static cAtomQFRxnParityHint: number;
+
   static cAtomQFRxnParityRetain: number;
   static cAtomQFRxnParityInvert: number;
   static cAtomQFRxnParityRacemize: number;
+  static cAtomQFNewRingSize: number;
+  static cAtomQFRingSize0: number;
+  static cAtomQFRingSize3: number;
+  static cAtomQFRingSize4: number;
+  static cAtomQFRingSize5: number;
+  static cAtomQFRingSize6: number;
+  static cAtomQFRingSize7: number;
+  static cAtomQFRingSizeLarge: number;
+  static cAtomQFENeighbours: number;
+  static cAtomQFNot0ENeighbours: number;
+  static cAtomQFNot1ENeighbour: number;
+  static cAtomQFNot2ENeighbours: number;
+  static cAtomQFNot3ENeighbours: number;
+  static cAtomQFNot4ENeighbours: number;
+  static cAtomQFStereoState: number;
+  static cAtomQFIsStereo: number;
+  static cAtomQFIsNotStereo: number;
+  static cAtomQFHeteroAromatic: number;
 
   static cBondTypeSingle: number;
   static cBondTypeDouble: number;
   static cBondTypeTriple: number;
+  static cBondTypeQuadruple: number;
+  static cBondTypeQuintuple: number;
+  static cBondTypeMetalLigand: number;
+  static cBondTypeDelocalized: number;
   static cBondTypeDown: number;
   static cBondTypeUp: number;
   static cBondTypeCross: number;
-  static cBondTypeMetalLigand: number;
-  static cBondTypeDelocalized: number;
   static cBondTypeDeleted: number;
   static cBondTypeIncreaseOrder: number;
 
+  static cBondTypeMaskSimple: number;
+  static cBondTypeMaskStereo: number;
+
+  static cBondFlagsHelper2: number;
+  static cBondFlagsHelper3: number;
+
   static cBondParityNone: number;
   static cBondParityEor1: number;
   static cBondParityZor2: number;
   static cBondParityUnknown: number;
-
   static cBondCIPParityNone: number;
   static cBondCIPParityEorP: number;
   static cBondCIPParityZorM: number;
   static cBondCIPParityProblem: number;
-
   static cBondQFNoOfBits: number;
   static cBondQFBondTypesBits: number;
   static cBondQFBondTypesShift: number;
+  static cBondQFRareBondTypesBits: number;
+  static cBondQFRareBondTypesShift: number;
   static cBondQFRingStateBits: number;
   static cBondQFRingStateShift: number;
   static cBondQFBridgeBits: number;
@@ -233,11 +270,14 @@ export declare class Molecule {
   static cBondQFSimpleFeatures: number;
   static cBondQFNarrowing: number;
   static cBondQFBondTypes: number;
+  static cBondQFRareBondTypes: number;
   static cBondQFSingle: number;
   static cBondQFDouble: number;
   static cBondQFTriple: number;
   static cBondQFDelocalized: number;
   static cBondQFMetalLigand: number;
+  static cBondQFQuadruple: number;
+  static cBondQFQuintuple: number;
   static cBondQFRingState: number;
   static cBondQFNotRing: number;
   static cBondQFRing: number;
@@ -249,24 +289,30 @@ export declare class Molecule {
   static cBondQFAromState: number;
   static cBondQFAromatic: number;
   static cBondQFNotAromatic: number;
+  static cBondQFMatchFormalOrder: number;
 
   static cHelperNone: number;
   static cHelperBitNeighbours: number;
+  static cHelperBitRingsSimple: number;
+
   static cHelperBitRings: number;
   static cHelperBitParities: number;
   static cHelperBitCIP: number;
+
   static cHelperBitSymmetrySimple: number;
-  static cHelperBitSymmetryDiastereotopic: number;
-  static cHelperBitSymmetryEnantiotopic: number;
+  static cHelperBitSymmetryStereoHeterotopicity: number;
   static cHelperBitIncludeNitrogenParities: number;
+
   static cHelperBitsStereo: number;
+
   static cHelperNeighbours: number;
+  static cHelperRingsSimple: number;
   static cHelperRings: number;
   static cHelperParities: number;
   static cHelperCIP: number;
+
   static cHelperSymmetrySimple: number;
-  static cHelperSymmetryDiastereotopic: number;
-  static cHelperSymmetryEnantiotopic: number;
+  static cHelperSymmetryStereoHeterotopicity: number;
 
   static cChiralityIsomerCountMask: number;
   static cChiralityUnknown: number;
@@ -278,17 +324,33 @@ export declare class Molecule {
   static cChiralityEpimers: number;
   static cChiralityDiastereomers: number;
 
+  static cDefaultAVBL: number;
+
   static cMoleculeColorDefault: number;
   static cMoleculeColorNeutral: number;
 
+  static cPseudoAtomsHydrogenIsotops: number;
+  static cPseudoAtomsRGroups: number;
+  static cPseudoAtomsAGroups: number;
+  static cPseudoAtomR: number;
+  static cPseudoAtomA: number;
+  static cPseudoAtomX: number;
+  static cPseudoAtomsAminoAcids: number;
+  static cPseudoAtomPolymer: number;
+  static cPseudoAtomAttachmentPoint: number;
+  static cPseudoAtomsAll: number;
+  static cDefaultAllowedPseudoAtoms: number;
+
   static cAtomLabel: string[];
 
   static cRoundedMass: number[];
 
   static cDefaultAtomValence: number;
+  static cAtomValence: number[][];
+  static cCommonOxidationState: number[][];
 
   static FISCHER_PROJECTION_LIMIT: number;
-
+  static FISCHER_PROJECTION_RING_LIMIT: number;
   static STEREO_ANGLE_LIMIT: number;
 
   static cMaxConnAtoms: number;
@@ -343,7 +405,10 @@ export declare class Molecule {
    */
   static fromIDCode(idcode: string, ensure2DCoordinates?: boolean): Molecule;
 
-  static getAtomicNoFromLabel(atomLabel: string): number;
+  static getAtomicNoFromLabel(
+    atomLabel: string,
+    allowedPseudoAtomGroups?: number,
+  ): number;
 
   static getAngle(x1: number, y1: number, x2: number, y2: number): number;
 
@@ -2510,6 +2575,77 @@ export declare class Molecule {
   setAssignParitiesToNitrogen(b: boolean): void;
 }
 
+export interface ISmilesParserOptions {
+  /**
+   * Enable SMARTS parsing with `'smarts'` or `'guess'`.
+   * @default `'smiles'`
+   */
+  smartsMode?: 'smiles' | 'smarts' | 'guess';
+
+  createSmartsWarnings?: boolean;
+
+  skipCoordinateTemplates?: boolean;
+
+  makeHydrogenExplicit?: boolean;
+
+  /**
+   * Disable parsing of CACTVS syntax.
+   */
+  noCactvs?: boolean;
+}
+
+export interface ISmilesParserParseMoleculeOptions {
+  /**
+   * Molecule to parse into.
+   */
+  molecule?: Molecule;
+
+  /**
+   * Disable coordinate invention.
+   * @default `false`
+   */
+  noCoordinates?: boolean;
+
+  /**
+   * Disable stereo features parsing.
+   * @default `false`
+   */
+  noStereo?: boolean;
+}
+
+export declare class SmilesParser {
+  /**
+   * Create a SMILES parser.
+   */
+  constructor(options?: ISmilesParserOptions);
+
+  /**
+   * Set the random seed used to invent coordinates.
+   * @param seed
+   */
+  setRandomSeed(seed: number): void;
+
+  /**
+   * Parse a SMILES string and return a molecule.
+   */
+  parseMolecule(
+    smiles: string,
+    options?: ISmilesParserParseMoleculeOptions,
+  ): Molecule;
+
+  /**
+   * Parse a SMILES string and return a reaction.
+   */
+  parseReaction(smiles: string): Reaction;
+
+  /**
+   * If createSmartsWarnings in the constructor was passed as true, then this method
+   * returns a list of all SMARTS features, which could not be interpreted in the most recently
+   * parsed SMILES/SMARTS pattern.
+   */
+  getSmartsWarning(): string;
+}
+
 export interface MolecularFormula {
   absoluteWeight: number;
 
@@ -3226,15 +3362,6 @@ export declare class ConformerGenerator {
    */
   getPotentialConformerCount(): number;
 
-  /**
-   * With best current knowledge about colliding torsion combinations
-   * and based on the individual frequencies of currently active torsions
-   * this method returns the conformers's overall contribution to the
-   * total set of non colliding conformers.
-   * @returns - This conformer's contribution to all conformers.
-   */
-  getPreviousConformerContribution(): number;
-
   /**
    * Returns an iterator of molecule conformers.
    */