Internal data structures

• MoleculeType type - type of this molecule (from above list).
• int nAtoms - number of atoms in this molecule. Can be zero.
• int nBonds - number of bonds in this molecule.
• int nBackProtein - number of protein backbone bonds.
• int nBackDNA - number of nucleic-acid backbone bonds.
• int nResidues - number of residues.
• int nSegments - number of segments.
• int ID - molecule integer ID number.
• int maxAtoms - maximum storage currently allotted to store the atoms (i.e. size of atomList array, which may be larger than the actual number of atoms stored there).
• Atom **atomList - array of Atom objects.
• NameList<int> atomNames - list of unique atom names in this molecule.
• NameList<int> atomTypes - list of unique atom types in this molecule.
• NameList<int> resNames - list of unique residue names in this molecule.
• NameList<int> resIds - list of unique residue ID's in this molecule.
• NameList<int> chainNames - list of unique chain ID's in this molecule.
• NameList<int> segNames - list of unique segment names in this molecule.
• ResizeArray<Residue *> residueList - list of which residues are connected to which.
• ResizeArray<Fragment *> fragList - list of connected residues, which form fragments.
• ResizeArray<Fragment *> pfragList - list of connected protein residues which form protein fragments. A protein fragment is a single chain from N to C.
• ResizeArray<Fragment *> nfragList - list of connected nucleic acid residues, which form nucleic acid fragments. A nucleic acid fragment is a single chain from 5' to 3'.