Nonvirtual member functions

• void init_atoms(int) - initializes storage to store data for N atoms. This only allocates memory, it does not store anything in that memory. This should be called when constructing a new molecule, when the number of atoms has been determined but before the atom data itself is stored into the BaseMolecule structures.
• int add_atom(char *, char *, char *, char *, char *, char *, float *pos, float *extra) - add a new atom to the molecule, with the specified names, and given starting x, y, z position (pos) and given starting extra data (such as beta value and occupancy).
• int add_bond(int, int, Atom::BackboneType = Atom::NORMAL) - add a new bond between the atoms specified as the first two arguments, where the bond is of the specified type. See the description of Atom for a list of the different bond types.
• int find_backbone(void) - determines which bonds are backbone bonds, and stores this data in the Atom objects stored in the atomList member. Returns the number of backbone bonds found.
• int find_residues(void) - find which atoms are in which residues, and store this data. Returns the number of residues found.
• int find_waters(void) - Find the waters, based on their residue name, and return the number found.
• int find_segments(void) - Find the segments in the molecule, and store this data. Return the number round.
• int find_fragments(void) - Find the fragments in the molecule, and store this data. Return the number found.
• int find_atom_in_residue(char *nm, int r) - find the index of the first atom in the specified residue with the given name, or return -1 if none is found with that name.
• int id(void) - return the ID of the molecule.
• Atom *atom(int) - return the Nth Atom for the molecule.
• char *atom_full_name(int, char * = NULL) - return a string containing the full name specification for the Nth atom. If the second argument is not NULL, the name will be placed in the given character array. Otherwise, an internal static buffer will be used to hold the name. The name is of the form: <mol ID>:<atom index> This name is guaranteed to be unique for each atom.
• char *atom_short_name(int, char * = NULL) - the same as for the full name, except the name returned is of the form: <residue name><residue ID>:<atom name> This form is nicer to read, but is not generally unique for a given atom.
• float default_charge(char *) - returns a default partial charge to use for the specified atom name. Used when this information is not supplied by the source of molecular structure. The following routines also supply default data based on a given atom name.
• float default_mass(char *)
• float default_radius(char *)
• float default_occup(char *)
• float default_beta(char *)