Package org.openscience.cdk.isomorphism
Enum TransformOp.Type
- java.lang.Object
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- java.lang.Enum<TransformOp.Type>
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- org.openscience.cdk.isomorphism.TransformOp.Type
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- All Implemented Interfaces:
Serializable
,Comparable<TransformOp.Type>
- Enclosing class:
- TransformOp
public static enum TransformOp.Type extends Enum<TransformOp.Type>
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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-handedparams: {foci, nbr1, nbr2, nbr3}
TotalH
Set the total hydrogen count of an atom.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static TransformOp.Type
valueOf(String name)
Returns the enum constant of this type with the specified name.static TransformOp.Type[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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NewAtom
public static final TransformOp.Type NewAtom
Create a new atom.params: {idx, elem, hcnt, isarom}
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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}
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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}
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DeleteBond
public static final TransformOp.Type DeleteBond
Delete a bond.params: {idx1, idx2}
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DeleteAtom
public static final TransformOp.Type DeleteAtom
Delete an atom.params: {idx}
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BondOrder
public static final TransformOp.Type BondOrder
Set the bond order.params: {idx1, idx2, order, old-order}
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Mass
public static final TransformOp.Type Mass
Set the mass number (isotope) of an atom.params: {idx, mass}
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Element
public static final TransformOp.Type Element
Set the atomic number (element) of an atom.params: {idx, elem}
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Aromatic
public static final TransformOp.Type Aromatic
Set or clear the aromatic flag of an atom.params: {idx, isarom}
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AromaticBond
public static final TransformOp.Type AromaticBond
Set or clear the aromatic flag of an bond.params: {idx1, idx2, isarom}
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Charge
public static final TransformOp.Type Charge
Set the formal charge of an atom.params: {idx, charg}
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ImplH
public static final TransformOp.Type ImplH
Set the implicit hydrogen count of an atom.params: {idx, hcnt}
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TotalH
public static final TransformOp.Type TotalH
Set the total hydrogen count of an atom.params: {idx, hcnt}
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AdjustH
public static final TransformOp.Type AdjustH
Adjust the total hydrogen count (up or down) of an atom.params: {idx, hdelta}
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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}
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MoveH
public static final TransformOp.Type MoveH
Move a hydrogen from one atom to another.params: {idx1, idx2}
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Tetrahedral
public static final TransformOp.Type Tetrahedral
Set the tetrahedral left-handedparams: {foci, nbr1, nbr2, nbr3}
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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}
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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}
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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}
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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}
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RemoveUnmapped
public static final TransformOp.Type RemoveUnmapped
Remove unmapped fragments.
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RecomputeHydrogens
public static final TransformOp.Type RecomputeHydrogens
Recalculate hydrogens on changed atoms.
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Method Detail
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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
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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 nameNullPointerException
- if the argument is null
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