Internal data structures

• int index - the index of this atom, as provided in the constructor.
• int bonds - the total number of bonds which this atoms participates in. Note that a bond will be stored twice, once for each of the atoms it connects.
• int uniq_resid - a unique integer indicating which residue this atom is in. This is not the same as te residue ID, since that is not necessarily unique in a given structure (particularly if the structure contains more than one segment or chain).
• int fragment - which fragment this atom belongs in.
• int bondTo[MAXATOMBONDS] - the indices of the other atoms to which this atom is bonded. An atom can bond to a maximum number of other atoms before an error occurs, this maximum is currently 8.
• BackboneType bondType[MAXATOMBONDS] - lists what type of bond each to the bonds to this atom are.
• BackboneType atomType - indicates if this atom is part of the backbone, and if so what kind of backbone.
• ResidueType residueType - what type of residue this atom is a part of.
• float pos[], extra[] - position and `extra' data values for this atom. These are initial, or `default', values for the atom when no other coordinates or extra values are known.
• char namestr[], int nameindex - the atom name, and the index of that name in the unique atom name array in the BaseMolecule which created the Atom object.
• char typestr[], int typeindex - the atom type name, and the index of that name in the unique atomtype name array in the BaseMolecule which created the Atom object.
• char resnamestr[], int resnameindex - the residue name, and the index of that name in the unique residue name array in the BaseMolecule which created the Atom object.
• char residstr[], int residindex - the residue ID, and the index of that name in the unique residue ID array in the BaseMolecule which created the Atom object.
• char segnamestr[], int segnameindex - the segment name, and the index of that name in the unique segment name array in the BaseMolecule which created the Atom object.
• char chainstr[], int chainindex - the chain ID, and the index of that ID in the unique chain ID array in the BaseMolecule which created the Atom object.