Class Residue

Initialize the class

Parameters
    atoms:      A list of Atom objects to be stored in this class
                (list)

Add the atom object to the residue.

Parameters
    atom: The object to be added (ATOM)

Add the value to the list of missing atoms

Parameters
    value: The name of the missing atom (string)

Add a new atom object to the residue. Uses an atom
currently in the residue to seed the new atom
object, then replaces the coordinates and name accordingly.

Parameters
    name:      The name of the new atom (string)
    newcoords: The x,y,z coordinates of the new atom (list)
    type:      The type of atom, ATOM or HETATM

Get a member of the Residue class

Parameters
    name:          The name of the member (string)
Possible Values
    atoms:         The atoms in the residue
    name:          The name of the residue
    chainID:       The chainID associated with the residue
    resSeq:        The sequence number of the residue
    icode:         The iCode of the residue
    SSbonded:      1 if the residue has a SS bond, 0 otherwise
    SSbondpartner: The residue of the bond partner
    type:          The type associated with this residue
    isNterm:       # of hydrogens if the residue is the N-Terminus, 0 otherwise
    isCterm:       1 if the residue is the C-Terminus, 0 otherwise
    missing:     List of missing atoms of the residue
Returns
    item:          The value of the member

Retrieve an atom from the mapping

Parameters
    resname: The name of the residue to retrieve (string)

Get the total charge of the residue.  In order to get rid
of floating point rounding error, do the string
transformation.

Returns:
    charge: The charge of the residue (float)

Get the number of atoms for the residue

Returns
    count:  Number of atoms in the residue (int)

Remove an atom from the residue object.

Parameters
    atomname: The name of the atom to be removed (string)

Rename an atom to a new name

Parameters
    oldname: The old atom name (string)
    newname: The new atom name (string)

Rename a given residue

Parameters
    name:       The new name of the residue

Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.

Parameters:
    atom1:  The first atom of the bond to rotate about (atom)
    atom2:  The second atom of the bond to rotate about (atom)
    angle:  The number of degrees to rotate (float)

Set a member of the Residue class to a specific value 

Parameters
    name:          The name of the object to set (string)
    value:         The object to append
Possible Values
    atoms:         The atoms in the residue
    name:          The name of the residue
    chain:         The chainID associated with the residue
    resSeq:        The sequence number of the residue
    icode:         The iCode of the residue
    SSbonded:      1 if the residue has a SS bond, 0 otherwise
    SSbondpartner: The residue of the bond partner
    type:          The type associated with this residue
    isNterm:       # of hydrogens if the residue is the N-Terminus, 0 otherwise
    isCterm:       1 if the residue is the C-Terminus, 0 otherwise
    isDirty:       1 if the residue is not missing atoms,
                   0 otherwise
Notes
    resSeq points to the residue.setResSeq function
Returns
    item:          The value of the member   

Set the atom field resSeq to a certain value and
change the residue's information.  The icode field is no longer
useful.

Parameters
    value:  The new value of resSeq (int)