paramagpy.metal.Metal

class paramagpy.metal.Metal(position=(0, 0, 0), eulers=(0, 0, 0), axrh=(0, 0), mueff=0.0, g_axrh=(0, 0), t1e=0.0, shift=0.0, temperature=298.15, B0=18.79, taur=0.0)

An object for paramagnetic chi tensors and delta-chi tensors. This class has basic attributes that specify position, axiality/rhombicity, isotropy and euler angles. It also has methods for calculating PCS, RDC, PRE and CCR values.

__init__(position=(0, 0, 0), eulers=(0, 0, 0), axrh=(0, 0), mueff=0.0, g_axrh=(0, 0), t1e=0.0, shift=0.0, temperature=298.15, B0=18.79, taur=0.0)

Instantiate ChiTensor object

Parameters

• position (array of floats, optional) – the (x,y,z) position in meters. Default is (0,0,0) stored as a np.matrix object.

• eulers (array of floats, optional) – the euler angles [alpha,beta,gamma] in radians by ZYZ convention. Defualt is (0,0,0)

• axrh (array of floats, optional) – the axial and rhombic values defining the magnetic susceptibility anisotropy

• g_axrh (array of floats, optional) – the axial and rhombic values defining the power spectral density tensor

• mueff (float) – the effective magnetic moment in units of A.m^2

• shift (float) – a bulk shift value applied to all PCS calculations. This is a correction parameter that may arise due to an offset between diamagnetic and paramagnetic PCS datasets.

• temperature (float) – the temperature in Kelvin

• t1e (float) – the longitudinal electronic relaxation time

• B0 (float) – the magnetic field in Telsa

• taur (float) – the rotational correlation time in seconds

Methods

atom_ccr(atom, atomPartner)	Calculate R2 cross-corelated relaxation due to DDxDSA
atom_pcs(atom[, racs, rads])	Calculate the psuedo-contact shift at the given atom
atom_pre(atom[, rtype, dsa, sbm, csa])	Calculate the PRE for an atom
atom_rdc(atom1, atom2)	Calculate the residual dipolar coupling between two atoms
atom_set_position(atom)	Set the position of the Metal object to that of an atom
average(metals)	Set the attributes of the current instance to the average of a list of provided tensor objects
ccr(position, gamma, dipole_shift_tensor)	Calculate R2 cross-corelated relaxation due to DDxDSA
copy()	Copy the current Metal object to a new instance
dipole_shift_tensor(position)	Calculate the chemical shift tensor at the given postition
dsa_r1(position, gamma[, csa])	Calculate R1 relaxation due to Curie Spin
dsa_r2(position, gamma[, csa])	Calculate R2 relaxation due to Curie Spin
fast_ccr(posarray, gammaarray, dstarray)	Vectorised version of paramagpy.metal.Metal.ccr()
fast_dipole_shift_tensor(posarray)	A vectorised version of paramagpy.metal.Metal.dipole_shift_tensor()
fast_dsa_r1(posarray, gammaarray[, csaarray])	Vectorised version of paramagpy.metal.Metal.dsa_r1()
fast_dsa_r2(posarray, gammaarray[, csaarray])	Vectorised version of paramagpy.metal.Metal.dsa_r2()
fast_first_invariant_squared(t)	Vectorised version of paramagpy.metal.Metal.first_invariant_squared()
fast_g_sbm_r1(posarray, gammaarray)	Vectorised version of paramagpy.metal.Metal.g_sbm_r1()
fast_pcs(posarray)	A vectorised version of paramagpy.metal.Metal.pcs()
fast_pre(posarray, gammaarray, rtype[, dsa, …])	Calculate the PRE for a set of spins using Curie and or SBM theory
fast_racs(csaarray)	A vectorised version of paramagpy.metal.Metal.racs()
fast_rads(posarray)	A vectorised version of paramagpy.metal.Metal.rads()
fast_rdc(vecarray, gammaProdArray)	A vectorised version of paramagpy.metal.Metal.rdc() method.
fast_sbm_r1(posarray, gammaarray)	Vectorised version of paramagpy.metal.Metal.sbm_r1()
fast_sbm_r2(posarray, gammaarray)	Vectorised version of paramagpy.metal.Metal.sbm_r2()
fast_second_invariant_squared(t)	Vectorised version of paramagpy.metal.Metal.second_invariant_squared()
first_invariant_squared(t)	Calculate the antisymmetric contribution to relaxation via the first invariant of a tensor.
g_sbm_r1(position, gamma)	Calculate R1 relaxation due to Solomon-Bloembergen-Morgan theory from anisotropic power spectral density tensor
get_params(params)	Get tensor parameters that have been scaled appropriately
info([comment])	Get basic information about the Metal object
isomap([protein, isoval])
make_mesh([density, size, origin])	Construct a 3D grid of points to map an isosurface
pcs(position)	Calculate the psuedo-contact shift at the given postition
pcs_gradient(position)	Calculate the gradient of the psuedo-contact shift at the given postition.
pcs_mesh(mesh)	Calculate a PCS value at each location of cubic grid of points
pre(position, gamma, rtype[, dsa, sbm, …])	Calculate the PRE for a set of spins using Curie and or SBM theory
pre_mesh(mesh[, gamma, rtype, dsa, sbm])	Calculate a PRE value at each location of cubic grid of points
racs(csa)	Calculate the residual anisotropic chemical shift at the given postition.
rads(position)	Calculate the residual anisotropic dipolar shift at the given postition.
rdc(vector, gammaProd)	Calculate Residual Dipolar Coupling (RDC)
save([fileName])
sbm_r1(position, gamma)	Calculate R1 relaxation due to Solomon-Bloembergen-Morgan theory
sbm_r2(position, gamma)	Calculate R2 relaxation due to Solomon-Bloembergen-Morgan theory
second_invariant_squared(t)	Calculate the second invariant squared of a tensor.
set_Jg(J, g)	Set the magnetic susceptibility absolute magnitude from J/g.
set_lanthanide(lanthanide[, set_dchi])	Set the anisotropy, isotropy and T1e parameters from literature values
set_params(paramValues)	Set tensor parameters that have been scaled appropriately
set_utr()	Modify current tensor parameters to unique tensor representation (UTR)
spec_dens(tau, omega)	A spectral density function with Lorentzian shape:
write_isomap(mesh, bounds[, fileName])	Write a PyMol script to file which allows loading of the isosurface file
write_pymol_script([isoval, surfaceName, …])	Write a PyMol script to file which allows loading of the isosurface file

Attributes

B0_MHz	1H NMR frequency for the given field in MHz
GAMMA
HBAR
K
MU0
MUB
a	alpha euler anglue
alignment_factor	Factor for conversion between magnetic susceptibility and alignment tensors
ax	axiality
b	beta euler anglue
eigenvalues	The eigenvalues defining the magnitude of the principle axes
fit_scaling
fundamental_attributes
g	gamma euler anglue
g_eigenvalues	The eigenvalues defining the magnitude of the principle axes
g_isotropy	Estimate of the spectral power density tensor isotropy
g_tensor	The magnetic susceptibility tensor matrix representation
gax	axial componenet of spectral power density tensor
grh	axial componenet of spectral power density tensor
iso	isotropy
isotropy	The magnidue of the isotropic component of the tensor
lanth_axrh
lanth_lib
lower_coords
rh	rhombicity
rotationMatrix	The rotation matrix as defined by the euler angles
saupe_factor	Factor for conversion between magnetic susceptibility and saupe tensors
tauc	The effective rotational correlation time.
tensor	The magnetic susceptibility tensor matrix representation
tensor_alignment	The alignment tensor matrix representation
tensor_saupe	The saupe tensor matrix representation
tensor_traceless	The traceless magnetic susceptibility tensor matrix representation
upper_coords
upper_triang	Fetch 5 unique matrix element defining the magnetic susceptibility tensor
upper_triang_alignment	Fetch 5 unique matrix element defining the alignment tensor
upper_triang_saupe	Fetch 5 unique matrix element defining the magnetic susceptibility tensor
x	x coordinate
y	y coordinate
z	z coordinate