Package lib :: Module physical_constants
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Module physical_constants

source code

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

Functions [hide private]
 
dipolar_constant(gx, gh, r)
Calculate the dipolar constant.
source code
 
pcs_constant(T, Bo, r)
Calculate the pseudocontact shift constant.
source code
float
return_gyromagnetic_ratio(nucleus=None)
Return the gyromagnetic ratio for the given nucleus type.
source code
float
return_atomic_mass(element=None)
Return the atomic mass for the given element type.
source code
str
element_from_isotope(isotope)
Determine and return the element name for the given isotope.
source code
int
number_from_isotope(isotope)
Determine and return the isotope number for the given isotope.
source code
Variables [hide private]
  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__ = 'lib'

Imports: pi, ascii_letters, digits, nan, RelaxError


Function Details [hide private]

dipolar_constant(gx, gh, r)

source code 

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)

source code 

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)

source code 

Return the gyromagnetic ratio for the given nucleus type.

Parameters:
  • nucleus (str) - The nucleus type.
Returns: float
The desired gyromagnetic ratio.
Raises:

return_atomic_mass(element=None)

source code 

Return the atomic mass for the given element type.

Parameters:
  • element (str) - The element type.
Returns: float
The desired atomic mass.
Raises:

element_from_isotope(isotope)

source code 

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)

source code 

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 [hide private]

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