paramagpy.protein.CustomAtom

class paramagpy.protein.CustomAtom(*arg, **kwargs)

__init__(*arg, **kwargs)

Initialize Atom object.

Parameters

• name (string) – atom name (eg. “CA”). Note that spaces are normally stripped.

• coord (Numeric array (Float0, size 3)) – atomic coordinates (x,y,z)

• bfactor (number) – isotropic B factor

• occupancy (number) – occupancy (0.0-1.0)

• altloc (string) – alternative location specifier for disordered atoms

• fullname (string) – full atom name, including spaces, e.g. ” CA “. Normally these spaces are stripped from the atom name.

• element (uppercase string (or None if unknown)) – atom element, e.g. “C” for Carbon, “HG” for mercury,

• pqr_charge (number) – atom charge

• radius (number) – atom radius

Methods

copy()	Create a copy of the Atom.
detach_parent()	Remove reference to parent.
dipole_shift_tensor(position)	Calculate the magnetic field shielding tensor at the given postition due to the nuclear dipole
flag_disorder()	Set the disordered flag to 1.
get_altloc()	Return alternative location specifier.
get_anisou()	Return anisotropic B factor.
get_bfactor()	Return B factor.
get_charge()	Return charge.
get_coord()	Return atomic coordinates.
get_full_id()	Return the full id of the atom.
get_fullname()	Return the atom name, including leading and trailing spaces.
get_id()	Return the id of the atom (which is its atom name).
get_level()	Return level.
get_name()	Return atom name.
get_occupancy()	Return occupancy.
get_parent()	Return parent residue.
get_radius()	Return radius.
get_serial_number()	Return the serial number.
get_sigatm()	Return standard deviation of atomic parameters.
get_siguij()	Return standard deviations of anisotropic temperature factors.
get_vector()	Return coordinates as Vector.
is_disordered()	Return the disordered flag (1 if disordered, 0 otherwise).
set_altloc(altloc)	Set alternative location specifier.
set_anisou(anisou_array)	Set anisotropic B factor.
set_bfactor(bfactor)	Set isotroptic B factor.
set_charge(pqr_charge)	Set charge.
set_coord(coord)	Set coordinates.
set_occupancy(occupancy)	Set occupancy.
set_parent(parent)	Set the parent residue.
set_radius(radius)	Set radius.
set_serial_number(n)	Set serial number.
set_sigatm(sigatm_array)	Set standard deviation of atomic parameters.
set_siguij(siguij_array)	Set standard deviations of anisotropic temperature factors.
top()
transform(rot, tran)	Apply rotation and translation to the atomic coordinates.

Attributes

HBAR
MU0
csa	Get the CSA tensor at the nuclear position This uses the geometry of neighbouring atoms and a standard library from Bax J.
csa_lib	docstring for CustomAtom
gyro_lib
position