OEHierView

class OEHierView

The OEHierView class provides a convenient method for examining biological molecules as if they were hierarchical data. Hierarchical views can be fraught with inefficiencies. Despite this, they are such a common means of thinking about macromolecules that OEChem provides access to molecules in this manner. The OEHierView class takes a snapshot of an OEMolBase and provides convenient access to a hierarchical view of the data.

Note

Unlike typical OEChem iterators that closely track changes to a molecule, the hierarchy view is based on a snapshot of the molecule. One should use the assignment operator to update the hierarchical view after any change to the molecule.

Constructors

OEHierView()
OEHierView(OEHierViewImpl* i)
OEHierView(const OEHierView &)

Default and copy constructors.

OEHierView(OEChem::OEMolBase &,
           unsigned assume = OEAssumption::Default)

This constructor takes an OEMolBase as an argument and takes a snapshot of the molecule and sets up a hierarchical data view of the molecule. This allows hierarchical access to the molecule via the OEIter class.

Note

Unlike typical OEChem iterators that track changes to a molecule, the hierarchy view is based on a snapshot of the molecule. One should use the assignment operator to update the hierarchical view after any change to the molecule.

GetAtom

const OEChem::OEAtomBase * GetAtom(char chainID,
                                   const char* resName, int resIdx,
                                   unsigned pdbAtomIdx)
const OEChem::OEAtomBase* GetAtom(char chainID,
                                  const char* resName, int resIdx,
                                  unsigned pdbAtomIdx) const

Returns an atom specified by the chainID, residue name, residue number, and the PDB atom index.

GetAtoms

OESystem::OEIterBase<OEChem::OEAtomBase>* GetAtoms()
OESystem::OEIterBase<const OEChem::OEAtomBase>* GetAtoms() const

Returns an iterator over all of the atoms in the hierarchical view.

GetChains

OESystem::OEIterBase<OEHierChain>* GetChains()
OESystem::OEIterBase<const OEHierChain>* GetChains() const

GetFragments

OESystem::OEIterBase<OEHierFragment>* GetFragments()
OESystem::OEIterBase<const OEHierFragment>* GetFragments() const

Returns an iterator over all of the fragments in the hierarchical view.

GetResidue

OEHierResidue& GetResidue(char chainID, const char* resName,
                          int resIdx)
const OEHierResidue& GetResidue(char chainID, const char* resName,
                                int resIdx) const

Gives direct access to a residue using the typical information that a user might know about a residue of interest (e.g. - THR242 of chain 'A').

GetResidues

OESystem::OEIterBase<OEHierResidue>* GetResidues()
OESystem::OEIterBase<const OEHierResidue>* GetResidues() const

Returns an iterator over all of the residues in the hierarchical view.