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

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.

__package__ = 'lib'

Imports: pi, ascii_letters, digits, nan

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.

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