Scoring Functions (dockerasmus.score)

Generalized Scoring Function

class dockerasmus.score.ScoringFunction(*components, **kwargs)

The generalisation of a scoring function

The ScoringFunction will first fetch dynamically the requirements that must be pre-computed before calling each scoring component: for instance, since both components.Coulomb and components.LennardJones require the atom-wise distance matrix between the two proteins, this matrix will be created only once. This magic behaviour is obtained by matching the names of the arguments of each scoring component with an actual function in the requirements module.

components

list – the list of individual components that are used independently to compute the final score.

requirements

Set displays – a set of arguments that must be preprocessed to compute the score, based on the requirements of the individual scoring components.

Examples

Non-bound terms of Cornell’s scoring function:

>>> f = ScoringFunction(LennardJones, Coulomb)
>>> f(barnase, barstar)
-84.9...

Using weights on individual components:

>>> g = ScoringFunction(LennardJones, Fabiola, weights=[1, 3])
>>> g(barnase, barstar)
-118.54...

Components (dockerasmus.score.components)

class dockerasmus.score.components.LennardJones(force_backend=None)

A scoring component modeling Van der Waals interactions.

Reference:

Jones, J. E. “On the Determination of Molecular Fields. II. From the Equation of State of a Gas”. Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences 106, 463–477 (1924).

class dockerasmus.score.components.Coulomb(force_backend=None)

A scoring component modeling electrostatic forces.

Reference:

Coulomb, C. A. “Premier mémoire sur l’électricité et le magnétisme”. Histoire de l’Académie Royale des Sciences, 569-577 (1785).

class dockerasmus.score.components.Fabiola(force_backend=None)

A scoring component modeling hydrogen bonds.

Reference:

Fabiola, F., Bertram, R., Korostelev, A. & Chapman, M. S. “An improved hydrogen bond potential: Impact on medium resolution protein structures”. Protein Sci 11, 1415–1423 (2002).

class dockerasmus.score.components.ScreenedCoulomb(force_backend=None)

A scoring component modeling screened electrostatic forces.

Reference:

Mehler, E. L., and G. Eichele. “Electrostatic Effects in Water-Accessible Regions of Proteins.” Biochemistry 23, no. 17 (August 1, 1984): 3887–91. doi:10.1021/bi00312a015.

Requirements (dockerasmus.score.requirements)

dockerasmus.score.requirements.potential_well_depth(protein1, protein2)

The \(\epsilon\) of the atoms of protein1 and protein2.

dockerasmus.score.requirements.vdw_radius(protein1, protein2)

The Van der Waals radius of the atoms of protein1 and protein2.

dockerasmus.score.requirements.charge(protein1, protein2)

The charge of the atoms of protein1 and protein2.

dockerasmus.score.requirements.ocn_atoms_positions(protein1, protein2)

The positions of O, C and N atoms in protein1 and protein2.

dockerasmus.score.requirements.distance(protein1, protein2)

The euclidean distances of protein1 atoms to protein2 atoms.

Hint

If available, the distance matrix will be computed using scipy.spatial.distance.cdist. Speedup is substantial !