biometal.hydrophobicity

Contains functions for examining hydrophobicity.

biometal.hydrophobicity.solvation(model, x, y, z, radius, pc=False, het=True, metal=True)[source]

Determines the average solvation within a given sphere of an atomium model. By default, all atoms within the radius will be considered, but you can opt to exlcude heteroatoms (atoms not part of a chain residue) if you so desire.

Parameters:
  • model (Model) – The atomium model to examine.
  • x – The x-coordinate of the centre of the sphere.
  • y – The y-coordinate of the centre of the sphere.
  • z – The z-coordinate of the centre of the sphere.
  • radius – The radius of the sphere.
  • pc (bool) – If True, atomic partial charges will be used instead of atomic solvation parameters (squared).
  • het (bool) – If False, only atoms that have a residue will be considered.
  • metal (bool) – If False, only non-metal atoms will be considered.
Raises:
  • TypeError – if the model is not an atomium model object.
  • TypeError – if the coordinates are not numeric.
  • TypeError – if the radius is not numeric.
  • ValueError – if the radius is negative.
Return type:

float

biometal.hydrophobicity.atom_solvation(atom)[source]

Returns the atomic solvation parameter of an atomium atom. The atomic solvation parameters are taken from Yamashita et al (1990).

Parameters:atom (Atom) – an atomium atom object.
Return type:float
biometal.hydrophobicity.atom_partial_charge(atom)[source]

Returns the atomic partial charge of an atomium atom.

Parameters:atom (Atom) – an atomium atom object.
Return type:float
biometal.hydrophobicity.hydrophobic_contrast(model, x, y, z, radius, pc=False, het=True, metal=True)[source]

Determines the hydrophobic contrast within a sphere - a measure of how heterogenous the hydrophobicity is within the sphere.

A homogeneous sphere will evaluate to zero, a sphere with a region of high hydrophilic atoms enclosed within a region of high hydrophobic regions will have a high positive value, and the converse will have a high negative value.

Parameters:
  • model (Model) – The atomium model to examine.
  • x – The x-coordinate of the centre of the sphere.
  • y – The y-coordinate of the centre of the sphere.
  • z – The z-coordinate of the centre of the sphere.
  • radius – The radius of the sphere.
  • het (bool) – If False, only atoms that have a residue will be considered.
  • metal (bool) – If False, only non-metal atoms will be considered.
Raises:
  • TypeError – if the model is not an atomium model object.
  • TypeError – if the coordinates are not numeric.
  • TypeError – if the radius is not numeric.
  • ValueError – if the radius is negative.
Return type:

float