schrodinger.protein.protassign.pka_prediction module¶
Module containing pKa predictor classes for ProtAssign and associated functions.
Copyright Schrodinger, LLC. All rights reserved.
- schrodinger.protein.protassign.pka_prediction.get_annotated_atom(residue)¶
Returns annotated atom of residue _StructureAtom or None
- schrodinger.protein.protassign.pka_prediction.get_annotated_atom_property(residue)¶
Returns property dict of annotated atom or an empty dict if atom is not present
- schrodinger.protein.protassign.pka_prediction.get_pka(residue)¶
Return predicted pKa of residue
- schrodinger.protein.protassign.pka_prediction.set_pka(residue, pka)¶
Set predicted pKa of residue
- schrodinger.protein.protassign.pka_prediction.shift_pka(residue, amount)¶
Shift the predicted pKa of residue
- schrodinger.protein.protassign.pka_prediction.get_interaction_label(label, suffix)¶
Create property label for a given interaction.
- schrodinger.protein.protassign.pka_prediction.set_interaction_label(residue, label, suffix=None)¶
Set a label of the annoted atom of residue to True
- schrodinger.protein.protassign.pka_prediction.has_interaction_label(residue, label, suffix=None)¶
Check if the annotated atom of the residue has a label
- schrodinger.protein.protassign.pka_prediction.residue_to_label(residue_or_atom)¶
Create string from residue or atom.
- schrodinger.protein.protassign.pka_prediction.log_interaction(residue1, residue2, name, distance=None, angle=None)¶
Log the interaction between two residues and its distance and angle optionally
- schrodinger.protein.protassign.pka_prediction.get_carboxyl_atoms(residue)¶
Get carboxyl atom groups from residue. Returns multiple groups if multiple are present. The first atom will be the carbon. It specifically adds Glu and Asp even if they are protonated and uses a SMARTS pattern otherwise to extract the carboxyl group.
- schrodinger.protein.protassign.pka_prediction.get_residue_neighborhoods(st, residues, distance_cell)¶
- schrodinger.protein.protassign.pka_prediction.protonate_histidine(histidine)¶
- class schrodinger.protein.protassign.pka_prediction.HistidinepKaPredictor¶
Bases:
object
Empirical histidine pKa predictor
- INTERNAL_PKA = 6.5¶
- METAL_PKA_SHIFT = -4.0¶
- STATIC_DONOR_PKA_SHIFT = -3.0¶
- FORCED_ACCEPTOR_PKA_SHIFT = -3.0¶
- PI_CATION_PKA_SHIFT = -1.0¶
- PI_PI_PKA_SHIFT = 1.0¶
- CARBOXYLIC_ACID_PKA_SHIFT = 1.0¶
- DOUBLE_SIDED_HBOND_PKA_SHIFT = 1.0¶
- MAX_STATIC_DONOR_INTERACTION_DISTANCE = 3.0¶
- MIN_STATIC_DONOR_INTERACTION_ANGLE = 120¶
- MAX_STATIC_ACCEPTOR_INTERACTION_DISTANCE = 2.5¶
- MIN_STATIC_ACCEPTOR_INTERACTION_ANGLE = 120¶
- MAX_METAL_INTERACTION_DISTANCE = 3.5¶
- MAX_PI_PI_INTERACTION_DISTANCE = 4.5¶
- MAX_PI_PI_INTERACTION_ANGLE = 30¶
- MAX_PI_CATION_INTERACTION_DISTANCE = 4.5¶
- MAX_PI_CATION_INTERACTION_ANGLE = 30¶
- MAX_PI_ARG_INTERACTION_DISTANCE = 5.5¶
- MAX_CARBOXYLIC_ACID_INTERACTION_DISTANCE = 3.8¶
- MIN_CARBOXYLIC_ACID_INTERACTION_ANGLE = 140¶
- NITROGEN_PDBNAMES = {' ND1', ' NE2'}¶
- CARBON_PDBNAMES = {' CD2', ' CE1'}¶
- SIDECHAINS_PDBNAMES = {' CD2', ' CE1', ' CG ', ' ND1', ' NE2'}¶
- predict(st, protassign=None, flip=False)¶
Predict histidine pKa with empirical rules. Currently this requires the structure being annotated by ProtAssign.
- Parameters
st (Structure) – ProtAssign annotated structure
protassign (schrodinger.protein.assignment.ProtAssign) – ProtAssign instance to calculate forced acceptor interactions
flip (bool) – Calculate pKa of flipped version of histidne
Returns None but annotates ANNOTATED_ATOM of each histidine with found interactions and predicted pKa
- metal_interactions()¶
- cation_pi_interactions()¶
- arginine_interactions()¶
- pi_pi_interactions()¶
Check if histidine is involved in pi-pi interaction
- carboxyl_interactions()¶
Check if histidine is interacting with a carboxyl group.
- static_donor_interactions()¶
Check if histidine is interacting with a static donor
- identify_forced_amide_states()¶
Identify amide residues that are forced in a state due to them interacting with a static donor. This is done in a single pass and not iteratively.
- static_acceptor_interactions()¶
Check if histidine is interacting with a static acceptor
- class schrodinger.protein.protassign.pka_prediction.AsparticAcidpKaPredictor¶
Bases:
schrodinger.protein.protassign.pka_prediction._CarboxylicAcidpKaPredictor
Aspartic acid emperical pKa predictor
- INTERNAL_PKA = 3.4¶
- PDBRES_NAMES = {'ASH ', 'ASP '}¶
- CARBON_PDBNAME = ' CG '¶
- OXYGEN_PDBNAMES = [' OD1', ' OD2']¶
- SIDECHAIN_PDBNAMES = [' OD1', ' OD2', ' CG ']¶
- class schrodinger.protein.protassign.pka_prediction.GlutamicAcidpKaPredictor¶
Bases:
schrodinger.protein.protassign.pka_prediction._CarboxylicAcidpKaPredictor
Glutamic acid emperical pKa predictor
- INTERNAL_PKA = 4.2¶
- PDBRES_NAMES = {'GLH ', 'GLU '}¶
- CARBON_PDBNAME = ' CD '¶
- OXYGEN_PDBNAMES = [' OE1', ' OE2']¶
- SIDECHAIN_PDBNAMES = [' OE1', ' OE2', ' CD ']¶