Enum TransformOp.Type

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description
      AdjustH
      Adjust the total hydrogen count (up or down) of an atom.
      Aromatic
      Set or clear the aromatic flag of an atom.
      AromaticBond
      Set or clear the aromatic flag of an bond.
      BondOrder
      Set the bond order.
      Charge
      Set the formal charge of an atom.
      DbOpposite
      Set the double bond (ndr1-idx1=idx2-nbr2) such that the neighbours are on opposite (trans) sides of the double bond.
      DbTogether
      Set the double bond (ndr1-idx1=idx2-nbr2) such that the neighbours are on together (cis) on the same side of the double bond.
      DeleteAtom
      Delete an atom.
      DeleteBond
      Delete a bond.
      Element
      Set the atomic number (element) of an atom.
      ImplH
      Set the implicit hydrogen count of an atom.
      Mass
      Set the mass number (isotope) of an atom.
      MoveH
      Move a hydrogen from one atom to another.
      NewAtom
      Create a new atom.
      NewBond
      Create a new bond with between the two atom indexes.
      OverwriteBond
      Create a new bond with between the two atom indexes.
      PromoteH
      Move a hydrogen from one atom to another and create a new one at the given index.
      RecomputeHydrogens
      Recalculate hydrogens on changed atoms.
      RemoveUnmapped
      Remove unmapped fragments.
      ReplaceAtom
      Replace an existing atom, keep bonding to other mapped atoms intact but removing bonds to unmapped atoms.
      ReplaceHydrogen
      Replace an existing implicit or explicit atom, If it's an explicit hydrogen, and bond to unmapped atoms are removed.
      Tetrahedral
      Set the tetrahedral left-handed params: {foci, nbr1, nbr2, nbr3}
      TotalH
      Set the total hydrogen count of an atom.
    • Enum Constant Detail

      • NewAtom

        public static final TransformOp.Type NewAtom
        Create a new atom. params: {idx, elem, hcnt, isarom}
      • NewBond

        public static final TransformOp.Type NewBond
        Create a new bond with between the two atom indexes. If the bond already exists the pattern will fail to apply. params: {idx1, idx2, order}
      • OverwriteBond

        public static final TransformOp.Type OverwriteBond
        Create a new bond with between the two atom indexes. If the bond already exists the order is updated. params: {idx1, idx2, order}
      • DeleteBond

        public static final TransformOp.Type DeleteBond
        Delete a bond. params: {idx1, idx2}
      • DeleteAtom

        public static final TransformOp.Type DeleteAtom
        Delete an atom. params: {idx}
      • BondOrder

        public static final TransformOp.Type BondOrder
        Set the bond order. params: {idx1, idx2, order, old-order}
      • Mass

        public static final TransformOp.Type Mass
        Set the mass number (isotope) of an atom. params: {idx, mass}
      • Element

        public static final TransformOp.Type Element
        Set the atomic number (element) of an atom. params: {idx, elem}
      • Aromatic

        public static final TransformOp.Type Aromatic
        Set or clear the aromatic flag of an atom. params: {idx, isarom}
      • AromaticBond

        public static final TransformOp.Type AromaticBond
        Set or clear the aromatic flag of an bond. params: {idx1, idx2, isarom}
      • Charge

        public static final TransformOp.Type Charge
        Set the formal charge of an atom. params: {idx, charg}
      • ImplH

        public static final TransformOp.Type ImplH
        Set the implicit hydrogen count of an atom. params: {idx, hcnt}
      • TotalH

        public static final TransformOp.Type TotalH
        Set the total hydrogen count of an atom. params: {idx, hcnt}
      • AdjustH

        public static final TransformOp.Type AdjustH
        Adjust the total hydrogen count (up or down) of an atom. params: {idx, hdelta}
      • PromoteH

        public static final TransformOp.Type PromoteH
        Move a hydrogen from one atom to another and create a new one at the given index. params: {idx1, idx2}
      • MoveH

        public static final TransformOp.Type MoveH
        Move a hydrogen from one atom to another. params: {idx1, idx2}
      • Tetrahedral

        public static final TransformOp.Type Tetrahedral
        Set the tetrahedral left-handed params: {foci, nbr1, nbr2, nbr3}
      • DbTogether

        public static final TransformOp.Type DbTogether
        Set the double bond (ndr1-idx1=idx2-nbr2) such that the neighbours are on together (cis) on the same side of the double bond. params: {idx1, idx2, nbr1, nbr2}
      • DbOpposite

        public static final TransformOp.Type DbOpposite
        Set the double bond (ndr1-idx1=idx2-nbr2) such that the neighbours are on opposite (trans) sides of the double bond.

        params: {idx1, idx2, nbr1, nbr2}

      • ReplaceAtom

        public static final TransformOp.Type ReplaceAtom
        Replace an existing atom, keep bonding to other mapped atoms intact but removing bonds to unmapped atoms. This is a convenient way to preserve stereochemistry when we delete and then add a atom/bond pair. Note this op-code is automatically put in by an optimisation pass.

        params: {idx, elem, hcnt, isarom}

      • ReplaceHydrogen

        public static final TransformOp.Type ReplaceHydrogen
        Replace an existing implicit or explicit atom, If it's an explicit hydrogen, and bond to unmapped atoms are removed. This is a convenient way to preserve stereochemistry when we delete a hydrogen then bond a new atom. Note this op-code is automatically put in by an optimisation pass.

        params: {idx1, idx2, elem, hcnt}

      • RemoveUnmapped

        public static final TransformOp.Type RemoveUnmapped
        Remove unmapped fragments.
      • RecomputeHydrogens

        public static final TransformOp.Type RecomputeHydrogens
        Recalculate hydrogens on changed atoms.
    • Method Detail

      • values

        public static TransformOp.Type[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (TransformOp.Type c : TransformOp.Type.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static TransformOp.Type valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null