Module physical_constants

Module containing all physical constants used in relax, as well as all associated functions.

Functions

dipolar_constant(gx, gh, r)
Calculate the dipolar constant.

pcs_constant(T, Bo, r)
Calculate the pseudocontact shift constant.

float return_gyromagnetic_ratio(nucleus=None)
Return the gyromagnetic ratio for the given nucleus type.

float return_atomic_mass(element=None)
Return the atomic mass for the given element type.

str element_from_isotope(isotope)
Determine and return the element name for the given isotope.

int number_from_isotope(isotope)
Determine and return the isotope number for the given isotope.

Variables

h = 6.62606876e-34
Planck's constant.

h_bar = 1.05457159642e-34
Dirac's constant.

mu0 = 1.25663706144e-06
The magnetic constant or the permeability of vacuum.

kB = 1.380650424e-23
Boltzmann's constant in SI units of J.K^-1 (the last 2 digits of '24' are within the measured error limits).

N15_CSA = -0.000172
The 15N CSA in the NH bond (default value).

NH_BOND_LENGTH = 1.02e-10
The length of the NH bond (default value).

NH_BOND_LENGTH_RDC = 1.041e-10
The length of the NH bond for RDCs (from Ottiger, M.

CA_HA_BOND_LENGTH_RDC = 1.118e-10
The length of the C_alpha-H_alpha bond for RDCs (from Ottiger, M.

CA_C_BOND_LENGTH_RDC = 1.526e-10
The length of the C_alpha-C_prime bond for RDCs (from Ottiger, M.

C_N_BOND_LENGTH_RDC = 1.329e-10
The length of the C_prime-N bond for RDCs (from Ottiger, M.

C_HN_BOND_LENGTH_RDC = 2.067e-10
The length of the C_prime-HN bond for RDCs (from Ottiger, M.

g13C = 67280000.0
The 13C gyromagnetic ratio.

g1H = 267522212.0
The 1H gyromagnetic ratio.

g15N = -27126000.0
The 15N gyromagnetic ratio.

g17O = -36280000.0
The 17O gyromagnetic ratio.

g31P = 108410000.0
The 31P gyromagnetic ratio.

ArH = 1.00794
Proton atomic mass.

ArC = 12.0107
Carbon atomic mass.

ArN = 14.0067
Nitrogen atomic mass.

ArO = 15.9994
Oxygen atomic mass.

ArS = 32.065
Sulphur atomic mass.

ArCa = 40.078
Calcium atomic mass.

__package__ = None
hash(x)

Imports: pi, ascii_letters, digits, upper, nan, RelaxError

Function Details

dipolar_constant(gx, gh, r)

Calculate the dipolar constant.

The dipolar constant is defined as:

         mu0 gI.gS.h_bar
   d = - --- ----------- ,
         4pi    r**3

where:

• mu0 is the permeability of free space,
• gI and gS are the gyromagnetic ratios of the I and S spins,
• h_bar is Dirac's constant which is equal to Planck's constant divided by 2pi,
• r is the distance between the two spins.

Parameters:

• gx (float) - The gyromagnetic ratio of the heteronucleus (or first spin).
• gh (float) - The gyromagnetic ratio of the proton (or second spin).
• r (float) - The distance between the two nuclei.

pcs_constant(T, Bo, r)

Calculate the pseudocontact shift constant.

The pseudocontact shift constant is defined as:

       mu0 15kT   1
   d = --- ----- ---- ,
       4pi Bo**2 r**3

where:

• mu0 is the permeability of free space,
• k is Boltzmann's constant,
• T is the absolute temperature,
• Bo is the magnetic field strength,
• r is the distance between the paramagnetic centre (electron spin) and the nuclear spin.

Parameters:

• T (float) - The temperature in kelvin.
• Bo (float) - The magnetic field strength.
• r (float) - The distance between the two nuclei.

return_gyromagnetic_ratio(nucleus=None)

Return the gyromagnetic ratio for the given nucleus type.

Parameters:

• nucleus (str) - The nucleus type.

Returns: float

The desired gyromagnetic ratio.

Raises:

• RelaxError - If the nucleus type is unknown.

return_atomic_mass(element=None)

Return the atomic mass for the given element type.

Parameters:

• element (str) - The element type.

Returns: float

The desired atomic mass.

Raises:

• RelaxError - If the element type is unknown.

element_from_isotope(isotope)

Determine and return the element name for the given isotope.

Parameters:

• isotope (str) - The isotope name, such as '1H', '15N'.

Returns: str

The element name.

number_from_isotope(isotope)

Determine and return the isotope number for the given isotope.

Parameters:

• isotope (str) - The isotope name, such as '1H', '15N'.

Returns: int

The isotope number.

Variables Details

NH_BOND_LENGTH_RDC

The length of the NH bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).

Value:

1.041e-10

CA_HA_BOND_LENGTH_RDC

The length of the C_alpha-H_alpha bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).

Value:

1.118e-10

CA_C_BOND_LENGTH_RDC

The length of the C_alpha-C_prime bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).

Value:

1.526e-10

C_N_BOND_LENGTH_RDC

The length of the C_prime-N bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).

Value:

1.329e-10

C_HN_BOND_LENGTH_RDC

The length of the C_prime-HN bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).

Value:

2.067e-10