schrodinger.application.bioluminate.tap.charge module

Utility functions for calculating TAP charge-based metrics.

TAP defines patches of surface hydrophobicity (PSH), patches of positive charge (PPC), patches of negative charge (PNC), and the structural Fv charge symmetry parameter (SFvCSP).

From the TAP paper: The following charges were assigned by sequence: aspartic acid, -1; glutamic acid, -1; lysine, +1; arginine, +1; histidine, +0.1 (Henderson-Hasselbalch equation applied: pKa 6, pH 7.4, and rounded up to one decimal place). Tyrosine hydroxyl deprotonation was not considered. Salt-bridge residues were assigned a charge of 0.

The PPC and PNC metrics are analogous in form to PSH, with H(R,S) substituted for abs(Q(R)), the absolute value of the charge assigned to residue R. SFvCSP values were calculated as [sum<RH> Q(RH)]*[sum<RL> Q(RL)], where RH and RL are surface-exposed VH and VL residues, respectively.

The released TAP/TNP implementation has an inconsistency: salt-bridge residues are assigned glycine hydrophobicity, but the charge-based scores effectively keep the sequence-assigned charges. The patch matrices read lower-case charge properties that the salt-bridge block does not clear, and the Fv chain-charge totals are accumulated before salt bridges are applied. We follow that behavior because it reproduces TAP-server output for the published examples.

schrodinger.application.bioluminate.tap.charge.get_res_pnc_contribution(residue: Residue) → float

Get the contribution of a given residue to the PNC metric, which is either the absolute value of the charge if negative, otherwise 0.

Parameters:

residue – The amino acid residue.

Returns:

The contribution of the given residue to the PNC metric.

schrodinger.application.bioluminate.tap.charge.get_res_ppc_contribution(residue: Residue) → float

Get the contribution of a given residue to the PPC metric, which is either the charge if positive, otherwise 0.

Parameters:

residue – The amino acid residue.

Returns:

The contribution of the given residue to the PPC metric.

schrodinger.application.bioluminate.tap.charge.get_res_sfvcsp_contribution(residue: Residue) → float

Get the contribution of a given residue to the SFvCSP metric, which is simply its charge

Parameters:

residue – The amino acid residue.

Returns:

The contribution of the given residue to the SFvCSP metric.