openchemlib 8.1.0 → 8.2.0

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Files changed (6) hide show
  1. package/dist/openchemlib-core.js +142 -142
  2. package/dist/openchemlib-full.js +157 -156
  3. package/dist/openchemlib-full.pretty.js +421 -314
  4. package/dist/openchemlib-minimal.js +110 -110
  5. package/package.json +1 -1
  6. package/types.d.ts +82 -19
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
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  "name": "openchemlib",
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- "version": "8.1.0",
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+ "version": "8.2.0",
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  "description": "Manipulate molecules",
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  "keywords": [
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  "chemistry",
package/types.d.ts CHANGED
@@ -89,6 +89,8 @@ export declare class Molecule {
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  */
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  constructor(maxAtoms: number, maxBonds: number);
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+ // based on JSMolecule.java you can do a regexp ".*static.* (int|long|double)(.*) = .*;" and replace with "$2: number;"
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+
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  static CANONIZER_CREATE_SYMMETRY_RANK: number;
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  static CANONIZER_CONSIDER_DIASTEREOTOPICITY: number;
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  static CANONIZER_CONSIDER_ENANTIOTOPICITY: number;
@@ -99,22 +101,22 @@ export declare class Molecule {
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  static CANONIZER_COORDS_ARE_3D: number;
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  static CANONIZER_CREATE_PSEUDO_STEREO_GROUPS: number;
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  static CANONIZER_DISTINGUISH_RACEMIC_OR_GROUPS: number;
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+ static CANONIZER_TIE_BREAK_FREE_VALENCE_ATOMS: number;
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+ static CANONIZER_ENCODE_ATOM_CUSTOM_LABELS_WITHOUT_RANKING: number;
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+ static CANONIZER_NEGLECT_ANY_STEREO_INFORMATION: number;
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107
 
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  static cMaxAtomicNo: number;
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-
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  static cAtomParityNone: number;
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  static cAtomParity1: number;
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  static cAtomParity2: number;
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  static cAtomParityUnknown: number;
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  static cAtomParityIsPseudo: number;
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-
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  static cAtomRadicalState: number;
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115
  static cAtomRadicalStateShift: number;
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  static cAtomRadicalStateNone: number;
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  static cAtomRadicalStateS: number;
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  static cAtomRadicalStateD: number;
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  static cAtomRadicalStateT: number;
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-
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  static cAtomColorNone: number;
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  static cAtomColorBlue: number;
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  static cAtomColorRed: number;
@@ -123,18 +125,15 @@ export declare class Molecule {
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  static cAtomColorOrange: number;
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  static cAtomColorDarkGreen: number;
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  static cAtomColorDarkRed: number;
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-
127
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  static cAtomCIPParityNone: number;
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  static cAtomCIPParityRorM: number;
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  static cAtomCIPParitySorP: number;
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  static cAtomCIPParityProblem: number;
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-
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  static cESRTypeAbs: number;
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  static cESRTypeAnd: number;
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  static cESRTypeOr: number;
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  static cESRMaxGroups: number;
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  static cESRGroupBits: number;
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-
138
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  static cAtomQFNoOfBits: number;
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  static cAtomQFAromStateBits: number;
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  static cAtomQFAromStateShift: number;
@@ -146,12 +145,18 @@ export declare class Molecule {
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  static cAtomQFPiElectronShift: number;
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  static cAtomQFNeighbourBits: number;
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  static cAtomQFNeighbourShift: number;
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- static cAtomQFRingSizeBits: number;
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- static cAtomQFRingSizeShift: number;
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+ static cAtomQFSmallRingSizeBits: number;
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+ static cAtomQFSmallRingSizeShift: number;
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  static cAtomQFChargeBits: number;
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  static cAtomQFChargeShift: number;
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  static cAtomQFRxnParityBits: number;
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  static cAtomQFRxnParityShift: number;
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+ static cAtomQFNewRingSizeBits: number;
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+ static cAtomQFNewRingSizeShift: number;
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+ static cAtomQFENeighbourBits: number;
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+ static cAtomQFENeighbourShift: number;
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+ static cAtomQFStereoStateBits: number;
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+ static cAtomQFStereoStateShift: number;
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  static cAtomQFSimpleFeatures: number;
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  static cAtomQFNarrowing: number;
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  static cAtomQFAny: number;
@@ -181,42 +186,72 @@ export declare class Molecule {
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  static cAtomQFNot2Neighbours: number;
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  static cAtomQFNot3Neighbours: number;
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  static cAtomQFNot4Neighbours: number;
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- static cAtomQFRingSize: number;
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+ static cAtomQFSmallRingSize: number;
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+
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  static cAtomQFCharge: number;
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  static cAtomQFNotChargeNeg: number;
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  static cAtomQFNotCharge0: number;
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  static cAtomQFNotChargePos: number;
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  static cAtomQFFlatNitrogen: number;
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+
190
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  static cAtomQFExcludeGroup: number;
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+
191
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  static cAtomQFRxnParityHint: number;
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+
192
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  static cAtomQFRxnParityRetain: number;
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  static cAtomQFRxnParityInvert: number;
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  static cAtomQFRxnParityRacemize: number;
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+ static cAtomQFNewRingSize: number;
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+ static cAtomQFRingSize0: number;
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+ static cAtomQFRingSize3: number;
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+ static cAtomQFRingSize4: number;
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+ static cAtomQFRingSize5: number;
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+ static cAtomQFRingSize6: number;
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+ static cAtomQFRingSize7: number;
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+ static cAtomQFRingSizeLarge: number;
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+ static cAtomQFENeighbours: number;
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+ static cAtomQFNot0ENeighbours: number;
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+ static cAtomQFNot1ENeighbour: number;
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+ static cAtomQFNot2ENeighbours: number;
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+ static cAtomQFNot3ENeighbours: number;
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+ static cAtomQFNot4ENeighbours: number;
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+ static cAtomQFStereoState: number;
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+ static cAtomQFIsStereo: number;
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+ static cAtomQFIsNotStereo: number;
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+ static cAtomQFHeteroAromatic: number;
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196
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  static cBondTypeSingle: number;
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  static cBondTypeDouble: number;
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  static cBondTypeTriple: number;
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+ static cBondTypeQuadruple: number;
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+ static cBondTypeQuintuple: number;
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+ static cBondTypeMetalLigand: number;
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+ static cBondTypeDelocalized: number;
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  static cBondTypeDown: number;
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  static cBondTypeUp: number;
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  static cBondTypeCross: number;
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- static cBondTypeMetalLigand: number;
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- static cBondTypeDelocalized: number;
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  static cBondTypeDeleted: number;
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  static cBondTypeIncreaseOrder: number;
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235
 
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+ static cBondTypeMaskSimple: number;
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+ static cBondTypeMaskStereo: number;
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+
239
+ static cBondFlagsHelper2: number;
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+ static cBondFlagsHelper3: number;
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+
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  static cBondParityNone: number;
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  static cBondParityEor1: number;
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  static cBondParityZor2: number;
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  static cBondParityUnknown: number;
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-
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  static cBondCIPParityNone: number;
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  static cBondCIPParityEorP: number;
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  static cBondCIPParityZorM: number;
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  static cBondCIPParityProblem: number;
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-
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  static cBondQFNoOfBits: number;
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  static cBondQFBondTypesBits: number;
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  static cBondQFBondTypesShift: number;
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+ static cBondQFRareBondTypesBits: number;
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+ static cBondQFRareBondTypesShift: number;
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  static cBondQFRingStateBits: number;
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  static cBondQFRingStateShift: number;
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  static cBondQFBridgeBits: number;
@@ -233,11 +268,14 @@ export declare class Molecule {
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  static cBondQFSimpleFeatures: number;
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  static cBondQFNarrowing: number;
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  static cBondQFBondTypes: number;
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+ static cBondQFRareBondTypes: number;
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  static cBondQFSingle: number;
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  static cBondQFDouble: number;
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  static cBondQFTriple: number;
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  static cBondQFDelocalized: number;
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  static cBondQFMetalLigand: number;
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+ static cBondQFQuadruple: number;
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+ static cBondQFQuintuple: number;
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  static cBondQFRingState: number;
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  static cBondQFNotRing: number;
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  static cBondQFRing: number;
@@ -249,24 +287,30 @@ export declare class Molecule {
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  static cBondQFAromState: number;
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  static cBondQFAromatic: number;
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  static cBondQFNotAromatic: number;
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+ static cBondQFMatchFormalOrder: number;
252
291
 
253
292
  static cHelperNone: number;
254
293
  static cHelperBitNeighbours: number;
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+ static cHelperBitRingsSimple: number;
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+
255
296
  static cHelperBitRings: number;
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297
  static cHelperBitParities: number;
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  static cHelperBitCIP: number;
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+
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  static cHelperBitSymmetrySimple: number;
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- static cHelperBitSymmetryDiastereotopic: number;
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- static cHelperBitSymmetryEnantiotopic: number;
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+ static cHelperBitSymmetryStereoHeterotopicity: number;
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  static cHelperBitIncludeNitrogenParities: number;
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+
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  static cHelperBitsStereo: number;
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+
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  static cHelperNeighbours: number;
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+ static cHelperRingsSimple: number;
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  static cHelperRings: number;
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  static cHelperParities: number;
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  static cHelperCIP: number;
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+
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  static cHelperSymmetrySimple: number;
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- static cHelperSymmetryDiastereotopic: number;
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- static cHelperSymmetryEnantiotopic: number;
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+ static cHelperSymmetryStereoHeterotopicity: number;
270
314
 
271
315
  static cChiralityIsomerCountMask: number;
272
316
  static cChiralityUnknown: number;
@@ -278,17 +322,33 @@ export declare class Molecule {
278
322
  static cChiralityEpimers: number;
279
323
  static cChiralityDiastereomers: number;
280
324
 
325
+ static cDefaultAVBL: number;
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+
281
327
  static cMoleculeColorDefault: number;
282
328
  static cMoleculeColorNeutral: number;
283
329
 
330
+ static cPseudoAtomsHydrogenIsotops: number;
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+ static cPseudoAtomsRGroups: number;
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+ static cPseudoAtomsAGroups: number;
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+ static cPseudoAtomR: number;
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+ static cPseudoAtomA: number;
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+ static cPseudoAtomX: number;
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+ static cPseudoAtomsAminoAcids: number;
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+ static cPseudoAtomPolymer: number;
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+ static cPseudoAtomAttachmentPoint: number;
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+ static cPseudoAtomsAll: number;
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+ static cDefaultAllowedPseudoAtoms: number;
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+
284
342
  static cAtomLabel: string[];
285
343
 
286
344
  static cRoundedMass: number[];
287
345
 
288
346
  static cDefaultAtomValence: number;
347
+ static cAtomValence: number[][];
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+ static cCommonOxidationState: number[][];
289
349
 
290
350
  static FISCHER_PROJECTION_LIMIT: number;
291
-
351
+ static FISCHER_PROJECTION_RING_LIMIT: number;
292
352
  static STEREO_ANGLE_LIMIT: number;
293
353
 
294
354
  static cMaxConnAtoms: number;
@@ -343,7 +403,10 @@ export declare class Molecule {
343
403
  */
344
404
  static fromIDCode(idcode: string, ensure2DCoordinates?: boolean): Molecule;
345
405
 
346
- static getAtomicNoFromLabel(atomLabel: string): number;
406
+ static getAtomicNoFromLabel(
407
+ atomLabel: string,
408
+ allowedPseudoAtomGroups?: number,
409
+ ): number;
347
410
 
348
411
  static getAngle(x1: number, y1: number, x2: number, y2: number): number;
349
412