schrodinger.application.bioluminate.tap.hydrophobicity module

Utilities for calculating hydrophobicity-based TAP values.

The symbols and 1-2 normalization below follow the TAP paper; the paper does not provide a separate rationale for choosing that normalized range.

From the TAP paper:

Where R_1 and R_2 are two surface-exposed residues with a closest heavy-atom distance, r_12, 7.5 Å and H(R,S) is the normalized hydrophobicity score (between 1 and 2) for residue R in scheme S, the PSH metric can be calculated as sum<R_1,R_2> H(R_1,S)*H(R_2,S) / r_12^2. […] Salt-bridge residues were assigned the same value as glycine in each hydrophobicity scale.

schrodinger.application.bioluminate.tap.hydrophobicity.get_normalized_hydrophobicity_dict()

Get the Kyte-Doolittle hydrophobicity scores normalized to a 1-2 range, as used in the TAP paper for PSH calculation.

Returns:

A dictionary mapping each amino acid residue to its normalized Kyte-Doolittle hydrophobicity score.

schrodinger.application.bioluminate.tap.hydrophobicity.get_res_psh_contribution(residue) → float

Get the Kyte-Doolittle hydrophobicity score for a given amino acid residue.

Parameters:

residue – The amino acid residue.

Returns:

The Kyte-Doolittle hydrophobicity score for the given residue. Salt-bridge residues are assigned the same value as glycine. Non-standard amino acids are assigned a score of 0.0.