- <init>
copy constructor. NOTE: this will NOT index the atoms. This is dealt with in the
Molecule copy costr
- addAtom
adds a atom.
- clearLigandInfo
- deleteLigandBonds
delete all bonds to this atom.
- detach
reroute to molecule.removeAtomArray(). also implicitly removes bondArray
- equals
- generateConcise
generates concise representation. correponds to concise attribute in schema.
only works if atomArray
- getAtomById
get atom by id.
- getAtomElements
- getAtomMap
get map of atom hash to atoms.
- getAtoms
- getBondArray
get sibling bondArray.