OEAtomBondSet

class OEAtomBondSet : public OESystem::OERoleSet

This class represents OEAtomBondSet that is a container that holds atom and bond pointers.

The following methods are publicly inherited from OERoleSet:

`AddRole`	`GetRoles`
`ClearRoles`	`HasRole`
`DeleteRole`	`NumRoles`

Constructors

OEAtomBondSet() -> OEAtomBondSet

Default constructor that generates an empty container.

OEAtomBondSet(rhs: OEAtomBondSet, amap: OEAtomBase = (OEAtomBase, bmap: OEBondBase = (OEBondBase) -> OEAtomBondSet

Copy constructor.

OEAtomBondSet(atoms: OEAtomIter) -> OEAtomBondSet
OEAtomBondSet(bonds: OEBondIter) -> OEAtomBondSet
OEAtomBondSet(atoms: OEAtomIter, bonds: OEBondIter) -> OEAtomBondSet

Constructors that generate an OEAtomBondSet container with the given atoms and bonds.

Add

Add(mol: Union[OEGraphMol,OEMol,OEQMol], atompred: OEUnaryAtomPred) -> bool
Add(mol: Union[OEGraphMol,OEMol,OEQMol], bondpred: OEUnaryBondPred) -> bool
Add(mol: Union[OEGraphMol,OEMol,OEQMol], atompred: OEUnaryAtomPred,
    bondpred: OEUnaryBondPred) -> bool
Add(abset: OEAtomBondSet) -> bool

Adds the atom and bond objects to the container. Returns false if given a null pointer or if the atoms or bonds being added do not belong to the same molecule previous objects in the set belong to.

See also

OEAtomBondSet.GetParent method

AddAtom

AddAtom(atom: OEAtomBase) -> bool

Adds an atom to the container. Returns false if given a null pointer or if the atom being added does not belong to the same molecule previous atoms and bonds in the set belong to.

See also

OEAtomBondSet.GetParent method

AddAtoms

AddAtoms(atoms: OEAtomVector) -> bool

Adds all the atoms to the container. Returns false if given a null pointer or if any atom being added does not belong to the same molecule previous atoms and bonds in the set belong to.

See also

OEAtomBondSet.GetParent method

AddBond

AddBond(bond: OEBondBase) -> bool

Adds a bond to the container. Returns false if given a null pointer or if the bond being added does not belong to the same molecule previous atoms and bonds in the set belong to.

See also

OEAtomBondSet.GetParent method

AddBonds

AddBonds(bonds: OEBondVector) -> bool

Adds all the bonds to the container. Returns false if given a null pointer or if any bond being added does not belong to the same molecule previous atoms and bonds in the set belong to.

See also

OEAtomBondSet.GetParent method

Clear

Clear() -> None

Removes all atoms and bonds from the OEAtomBondSet and clears the OERoleSet.

ClearAtoms

ClearAtoms() -> None

Removes all atoms from the OEAtomBondSet.

ClearAtomsAndBonds

ClearAtomsAndBonds() -> None

Removes all atoms and bonds from the OEAtomBondSet but retains the existing OERoleSet.

ClearBonds

ClearBonds() -> None

Removes all bonds from the OEAtomBondSet.

CreateCopy

CreateCopy() -> OEAtomBondSet

Deep copy constructor that returns a copy of the object. The memory for the returned object derived from OEAtomBondSet is dynamically allocated and owned by the caller.

HasAtom

HasAtom(atom: OEAtomBase) -> bool

Returns whether atom already belongs to the set.

HasBond

HasBond(bond: OEBondBase) -> bool

Returns whether bond already belongs to the set.

IsEmpty

IsEmpty() -> bool

Returns whether the set contains any atoms or bonds.

GetAtoms

GetAtoms() -> OEAtomIter

Returns an iterator over the atoms that are stored in the OEAtomBondSet object.

GetAtoms(atompred: OEUnaryAtomPred) -> OEAtomIter

Returns an iterator over all of the atoms in the container that match the specified atom predicate (OEUnaryPredicate).

GetBonds

GetBonds() -> OEBondIter

Returns an iterator over the bonds that are stored in the OEAtomBondSet object.

GetBonds(bondpred: OEUnaryBondPred) -> OEBondIter

Returns an iterator over all of the bonds in the container that match the specified bond predicate (OEUnaryPredicate).

GetParent

GetParent() -> OEGraphMol

Returns the parent molecule of a OEAtomBondSet object. This method can be used to determine the molecule of which atoms and bonds the container stores. The ‘parent molecule’ property of a OEAtomBondSet object cannot be altered, as it is determined at the point the container is created. The OEAtomBondSet.GetParent method returns a null pointer if the container is empty.

NumAtoms

NumAtoms() -> int

Returns the number of atoms stored in the OEAtomBondSet object.

NumAtoms(atompred: OEUnaryAtomPred) -> int

Returns the number of atoms stored in the OEAtomBondSet object matching the provided predicate.

NumBonds

NumBonds() -> int

Returns the number of bonds stored in the OEAtomBondSet object.

NumBonds(bondpred: OEUnaryBondPred) -> int

Returns the number of bonds stored in the OEAtomBondSet object matching the provided predicate.

Remove

Remove(mol: Union[OEGraphMol,OEMol,OEQMol],
       atompred: OEUnaryAtomPred) -> bool
Remove(mol: Union[OEGraphMol,OEMol,OEQMol],
       bondpred: OEUnaryBondPred) -> bool
Remove(mol: Union[OEGraphMol,OEMol,OEQMol],
       atompred: OEUnaryAtomPred, bondpred: OEUnaryBondPred) -> bool
Remove(abset: OEAtomBondSet) -> bool

Removes the objects from the container. Returns false if given a null pointer or if any of the objects being removed do not belong to the same molecule previous objects in the set belong to.

RemoveAtom

RemoveAtom(atom: OEAtomBase) -> bool

Removes an atom from the container. Returns false if given a null pointer or if the atom being removed does not belong to the same molecule previous atoms in the set belong to.

RemoveAtoms

RemoveAtoms(atoms: OEAtomVector) -> bool

Removes atoms from the container. Returns false if given a null pointer or if any atoms being removed do not belong to the same molecule previous atoms in the set belong to.

RemoveBond

RemoveBond(bond: OEBondBase) -> bool

Removes a bond from the container. Returns false if given a null pointer or if the bond being removed does not belong to the same molecule previous bonds in the set belong to.

RemoveBonds

RemoveBonds(bonds: OEBondVector) -> bool

Removes bonds from the container. Returns false if given a null pointer or if any bonds being removed do not belong to the same molecule previous bonds in the set belong to.

Sweep

Sweep() -> bool

Removes deleted atoms and bonds from the container.

Translate

Translate(amap: OEAtomBase, bmap: OEBondBase) -> bool

Translates the pointers in the container based on the provided mapping between the atoms or bonds in the array arguments. This can be used to convert an existing OEAtomBondSet container to refer to a copy of the molecule made from a subset operations.

See also

OESubsetMol