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#
# * This library is free software; you can redistribute it and/or
# * modify it under the terms of the GNU Lesser General Public
# * License as published by the Free Software Foundation; either
# * version 2.1 of the License, or (at your option) any later version.
# *
# * This library is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# * Lesser General Public License for more details.
#
#propka3.0, revision 182 2011-08-09
#-------------------------------------------------------------------------------------------------------
#-- --
#-- PROPKA: A PROTEIN PKA PREDICTOR --
#-- --
#-- VERSION 3.0, 01/01/2011, COPENHAGEN --
#-- BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD --
#-- --
#-------------------------------------------------------------------------------------------------------
#
#
#-------------------------------------------------------------------------------------------------------
# References:
#
# Very Fast Empirical Prediction and Rationalization of Protein pKa Values
# Hui Li, Andrew D. Robertson and Jan H. Jensen
# PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)
#
# Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes
# Delphine C. Bas, David M. Rogers and Jan H. Jensen
# PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)
#
# PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions
# Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen
# Journal of Chemical Theory and Computation, 7, 525-537 (2011)
#-------------------------------------------------------------------------------------------------------
from .lib import pka_print
def resName2Type(resName=None):
"""
definition of which parameter-group each residues belongs to
"""
resType = {'C- ': "COO",
'ASP': "COO",
'GLU': "COO",
'HIS': "HIS",
'CYS': "CYS",
'TYR': "TYR",
'LYS': "LYS",
'ARG': "ARG",
'N+ ': "N+ ",
'SER': "ROH",
'THR': "ROH",
'ASN': "AMD",
'GLN': "AMD",
'TRP': "TRP"}
if resName in resType:
return resType[resName]
else:
return resType
def getQs(resName=None):
"""
Returns a dictionary with residue charges
"""
Q = {'COO': -1.0,
'ASP': -1.0,
'GLU': -1.0,
'C- ': -1.0,
'TYR': -1.0,
'CYS': -1.0,
'HIS': 1.0,
'LYS': 1.0,
'ARG': 1.0,
'N+ ': 1.0}
if resName in Q:
return Q[resName]
else:
return Q
def pKa_mod(resName=None):
"""
returns a dictionary with model/water pKa values
"""
pKa_mod = {'C- ': 3.20,
'ASP': 3.80,
'GLU': 4.50,
'HIS': 6.50,
'CYS': 9.00,
'TYR': 10.00,
'LYS': 10.50,
'ARG': 12.50,
'N+ ': 8.00}
if resName == None:
return pKa_mod
elif resName in pKa_mod:
return pKa_mod[resName]
else:
# generic value for 'uninteresting' residues, e.g. ASN, GLN
return 20.00
def getInteraction():
"""
matrix for propka interactions; Note that only the LOWER part of the matrix is used!
'N' non-iterative interaction
'I' iterative interaction
'-' no interaction
"""
# COO CYS TYR HIS N+ LYS ARG
side_chain = {'COO': ["I", "I", "N", "N", "N", "N", "N"],
'CYS': ["I", "I", "N", "I", "N", "N", "N"],
'TYR': ["N", "N", "I", "I", "I", "I", "N"],
'HIS': ["I", "I", "I", "I", "N", "N", "N"],
'N+ ': ["N", "N", "I", "N", "I", "N", "N"],
'LYS': ["N", "N", "I", "N", "N", "I", "N"],
'ARG': ["N", "N", "N", "N", "N", "N", "I"],
'ROH': ["N", "N", "N", "-", "-", "-", "-"],
'AMD': ["N", "N", "N", "N", "-", "-", "-"],
'TRP': ["N", "N", "N", "-", "-", "-", "-"]}
return side_chain
# ------- Coulomb parameters --------- #
def getCoulombParameters(label=None):
"""
storage of Coulomb default parameters
"""
CoulombParameters = {}
CoulombParameters['Linear'] = {'cutoff': [4.0, 7.0],
'max_dpka': 2.40,
'scaled': True,
}
CoulombParameters['Coulomb'] = {'cutoff': [4.0, 10.0],
'diel': 80.00,
'scaled': True,
}
if label in CoulombParameters:
return CoulombParameters[label]
else:
return CoulombParameters
# ------- Desolvation parameters --------- #
def getDesolvationParameters(label=None):
"""
storage of desolvation default parameters
"""
DesolvationParameters = {}
DesolvationParameters['propka2'] = {'allowance': 400.00,
'prefactor': -0.01,
'local': -0.07,
'radii': getLocalRadii(),
}
DesolvationParameters['ContactModel'] = {'allowance': 400.00,
'prefactor': -0.01,
'local': -0.07,
'radii': getLocalRadii(),
}
DesolvationParameters['VolumeModel'] = {'allowance': 0.00,
'prefactor': -13.50,
'surface': 0.25,
'volume': getVanDerWaalsVolumes(),
}
DesolvationParameters['ScaledVolumeModel'] = {'allowance': 0.00,
'prefactor': -13.50,
'surface': 0.00,
'volume': getVanDerWaalsVolumes(),
}
if label in DesolvationParameters:
return DesolvationParameters[label]
else:
return DesolvationParameters
def getVanDerWaalsVolumes():
"""
storing relative Van der Waals volumes for volume desolvation models
"""
# relative tabulated
VanDerWaalsVolume = {'C': 1.40, # 20.58 all 'C' and 'CA' atoms
'C4': 2.64, # 38.79 hydrodphobic carbon atoms + unidentified atoms
'N': 1.06, # 15.60 all nitrogen atoms
'O': 1.00, # 14.71 all oxygen atoms
'S': 1.66, # 24.43 all sulphur atoms
}
return VanDerWaalsVolume
def getLocalRadii():
"""
local radii used in the 'propka2' and 'contact' desolvation models
"""
local_radius = {'ASP': 4.5,
'GLU': 4.5,
'HIS': 4.5,
'CYS': 3.5,
'TYR': 3.5,
'LYS': 4.5,
'ARG': 5.0,
'C- ': 4.5,
'N+ ': 4.5}
return local_radius
# ------- hydrogen-bond parameters --------- #
def getHydrogenBondParameters(type=None):
"""
definitions of default back-bone or side-chain interaction parameters
IMPORTANT: parameters with assigned to 'None' are given by the reverse
(e.g. CYS-COO is given by COO-CYS) generated at the end.
"""
if type == "back-bone":
# --- old 'propka1' back-bone parameter set ---
# parameters determining the interaction with back-bone NH or CO groups
parameters = {"COO": [-1.20, [2.00, 3.50]],
"CYS": [-2.40, [3.50, 4.50]],
"TYR": [-1.20, [3.50, 4.50]],
"HIS": [ 1.20, [2.00, 3.50]],
"N+ ": [ 1.20, [2.00, 3.50]],
"LYS": [ 1.20, [2.00, 3.50]],
"ARG": [ 1.20, [2.00, 3.50]]}
elif type == "side-chain":
# --- old 'propka1' side-chain parameter set ---
# parameters determining the interaction with side-chain NH or CO groups
# IMPORTANT: parameters with assigned to 'None' are given by the reverse
# (e.g. CYS-COO is given by COO-CYS) generated at the end.
parameters = {}
parameters["COO"] = {"COO": [-0.80, [ 2.50, 3.50]],
"CYS": [-0.80, [ 3.00, 4.00]],
"TYR": [-0.80, [ 3.00, 4.00]],
"HIS": [-0.80, [ 2.00, 3.00]],
"N+ ": [-1.20, [ 3.00, 4.50]],
"LYS": [-0.80, [ 3.00, 4.00]],
"ARG": [-0.80, [ 2.00, 4.00]],
"ROH": [-0.80, [ 3.00, 4.00]],
"AMD": [-0.80, [ 2.00, 3.00]],
"TRP": [-0.80, [ 2.00, 3.00]]}
parameters["CYS"] = {"COO": None,
"CYS": [-1.60, [ 3.00, 5.00]],
"TYR": [-0.80, [ 3.50, 4.50]],
"HIS": [-1.60, [ 3.00, 4.00]],
"N+ ": [-2.40, [ 3.00, 4.50]],
"LYS": [-1.60, [ 3.00, 4.00]],
"ARG": [-1.60, [ 2.50, 4.00]],
"ROH": [-1.60, [ 3.50, 4.50]],
"AMD": [-1.60, [ 2.50, 3.50]],
"TRP": [-1.60, [ 2.50, 3.50]]}
parameters["TYR"] = {"COO": None,
"CYS": None,
"TYR": [ 0.80, [ 3.50, 4.50]],
"HIS": [-0.80, [ 2.00, 3.00]],
"N+ ": [-1.20, [ 3.00, 4.50]],
"LYS": [-0.80, [ 3.00, 4.00]],
"ARG": [-0.80, [ 2.50, 4.00]],
"ROH": [-0.80, [ 3.50, 4.50]],
"AMD": [-0.80, [ 2.50, 3.50]],
"TRP": [-0.80, [ 2.50, 3.50]]}
parameters["HIS"] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": [ 0.00, [ 0.00, 0.00]],
"N+ ": [ 0.00, [ 0.00, 0.00]],
"LYS": [ 0.00, [ 0.00, 0.00]],
"ARG": [ 0.00, [ 0.00, 0.00]],
"ROH": [ 0.00, [ 0.00, 0.00]],
"AMD": [ 0.80, [ 2.00, 3.00]],
"TRP": [ 0.00, [ 0.00, 0.00]]}
parameters["N+ "] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": None,
"N+ ": [ 0.00, [ 0.00, 0.00]],
"LYS": [ 0.00, [ 0.00, 0.00]],
"ARG": [ 0.00, [ 0.00, 0.00]],
"ROH": [ 0.00, [ 0.00, 0.00]],
"AMD": [ 0.00, [ 0.00, 0.00]],
"TRP": [ 0.00, [ 0.00, 0.00]]}
parameters["LYS"] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": None,
"N+ ": None,
"LYS": [ 0.00, [ 0.00, 0.00]],
"ARG": [ 0.00, [ 0.00, 0.00]],
"ROH": [ 0.00, [ 0.00, 0.00]],
"AMD": [ 0.00, [ 0.00, 0.00]],
"TRP": [ 0.00, [ 0.00, 0.00]]}
parameters["ARG"] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": None,
"N+ ": None,
"LYS": None,
"ARG": [ 0.00, [ 0.00, 0.00]],
"ROH": [ 0.00, [ 0.00, 0.00]],
"AMD": [ 0.00, [ 0.00, 0.00]],
"TRP": [ 0.00, [ 0.00, 0.00]]}
parameters["ROH"] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": None,
"N+ ": None,
"LYS": None,
"ARG": None,
"ROH": [ 0.00, [ 0.00, 0.00]],
"AMD": [ 0.00, [ 0.00, 0.00]],
"TRP": [ 0.00, [ 0.00, 0.00]]}
parameters["AMD"] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": None,
"N+ ": None,
"LYS": None,
"ARG": None,
"ROH": None,
"AMD": [ 0.00, [ 0.00, 0.00]],
"TRP": [ 0.00, [ 0.00, 0.00]]}
parameters["TRP"] = {"COO": None,
"CYS": None,
"TYR": None,
"HIS": None,
"N+ ": None,
"LYS": None,
"ARG": None,
"ROH": None,
"AMD": None,
"TRP": [ 0.00, [ 0.00, 0.00]]}
# updating side-chain parameter matrix to full matrix
keys = list(parameters.keys())
for key1 in keys:
for key2 in keys:
if key2 not in parameters[key1]:
parameters[key1][key2] == [ 0.00, [ 0.00, 0.00]]
elif parameters[key1][key2] == None:
parameters[key1][key2] = parameters[key2][key1]
else:
pka_print("cannot determine what type of hydrogen-bonding interactions you want type=\"%s\" ['back-bone', 'side-chain']" % (label))
sys.exit(9)
return parameters
|
