Package chemaxon.marvin.alignment

Class RotatableBondDetector

java.lang.Object
chemaxon.marvin.alignment.RotatableBondDetector
@PublicApi public final class RotatableBondDetector extends Object

  • Constructor Summary

    Constructors
    Constructor
    Description
    RotatableBondDetector(Molecule m, boolean forcedFlexible)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    isRotatableBond(int bond)
    Not flexible if:
    double, aromatic, triple bond single bond neighboring a triple like at cyanide chain end bonds amide thioamide: -C(=S)-NR2 sulphonamide R-S(=O)2-NR2 aniline N : C(aromatic)-N(sp3) aromatic amidine : C(aromatic)-C(=NH)-NH2 aromatic nitroso : C(aromatic)-N=O aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable) C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature: Ring bonds may be rotatable also.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • RotatableBondDetector

      public RotatableBondDetector(Molecule m, boolean forcedFlexible)

  • Method Details

    • isRotatableBond

      public boolean isRotatableBond(int bond)
      Not flexible if:
      • double, aromatic, triple bond
      • single bond neighboring a triple like at cyanide
      • chain end bonds
      • amide
      • thioamide: -C(=S)-NR2
      • sulphonamide R-S(=O)2-NR2
      • aniline N : C(aromatic)-N(sp3)
      • aromatic amidine : C(aromatic)-C(=NH)-NH2
      • aromatic nitroso : C(aromatic)-N=O
      • aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable)
      C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature:
      • Ring bonds may be rotatable also.
      • The single bond in biphenyl is also rotatable.
      • Single bond in acetylene, which should be rotatable, kept rigid.
      Parameters:
      bond - bondSeq in molecule
      Returns:
      if rotatable or not