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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)
#-------------------------------------------------------------------------------------------------------
import string
from . import lib
from . import calculator as calculate
from .lib import pka_print
def interactionMatrix(interaction):
"""
printing out all information in resInfo
"""
keys = ["COO", "CYS", "TYR", "HIS", "N+ ", "LYS", "ARG", "ROH", "AMD", "TRP"]
pka_print("interaction matrix:")
for key1 in keys:
str = "%6s:" % (key1)
for key2 in keys:
do_pair, iterative = interaction[key1][key2]
if do_pair == True and iterative == True:
str += "%3s" % ("I")
elif do_pair == True and iterative == False:
str += "%3s" % ("N")
else:
str += "%3s" % ("-")
pka_print(str)
def printResInfo(resInfo):
"""
printing out all information in resInfo
"""
pka_print("in resInfo:")
for key1 in list(resInfo.keys()):
pka_print(" --- %s ---" % (key1))
for key2 in list(resInfo[key1].keys()):
pka_print(key2, resInfo[key1][key2])
def printCooArgAtomDistances(residue_coo, residue_arg):
"""
printing out all COO and ARG distances for debugging, picking closest + runner-up
"""
for atom_coo in residue_coo.makeDeterminantAtomList(residue_arg.resName):
for atom_arg in residue_arg.makeDeterminantAtomList(residue_coo.resName):
distance = calculate.InterAtomDistance(atom_coo, atom_arg)
pka_print("%3s %3s %6.2lf" % (atom_coo.name, atom_arg.name, distance))
def printBackBoneAtoms(list):
"""
Prints out determinant information for debugging
"""
pka_print(" --- debug back-bone atom list --- ")
for atoms in list:
label1 = "%s%4d%2s" % (atoms[0].resName, atoms[0].resNumb, atoms[0].chainID)
label2 = "%s%4d%2s" % (atoms[1].resName, atoms[1].resNumb, atoms[1].chainID)
pka_print("%s - %s" % (label1, label2))
def printResidues(residue_list):
"""
Prints out determinant information for debugging
"""
pka_print(" --- debug residue list --- ")
for residue in residue_list:
residue.printLabel()
def printIterativeDeterminants(all_determinants):
"""
Prints out determinant information for debugging
"""
if True:
pka_print(" --- Iterative determinants ---")
pka_print("%28s%8s" % ("H-bond", "Coulomb") )
for determinant in all_determinants:
pair = determinant[0]
values = determinant[1]
annihilation = determinant[2]
residue1 = pair[0]
residue2 = pair[1]
str = ""
str += " %s %s" % (residue1.label, residue2.label)
str += " %6.2lf %6.2lf" % (values[0], values[1])
pka_print(str)
else:
# priting out ALL types of determinants - mainly debugging
pka_print(" --- debug iterative determinants --- ")
pka_print("len(sidechain_determinants) = %d" % (len(all_determinants[0])))
pka_print("len(backbone_determinants) = %d" % (len(all_determinants[1])))
pka_print("len(coulomb_determinants) = %d" % (len(all_determinants[2])))
sidechain_determinants = all_determinants[0]
backbone_determinants = all_determinants[1]
coulomb_determinants = all_determinants[2]
if True:
for type in range(0,3):
determinants = all_determinants[type]
if type == 0:
pka_print("Iterative side-chain interactions:")
elif type == 1:
pka_print("Iterative back-bone interactions:")
elif type == 2:
pka_print("Iterative Coulomb interactions:")
for determinant in determinants:
pair = determinant[0]
values = determinant[1]
pair = determinant[0]
value = determinant[1]
residue1 = pair[0]
residue2 = pair[1]
str = ""
str += "'%s' '%s'" % (residue1.label, residue2.label)
str += " "
str += "%6.2lf %6.2lf" % (value, value)
pka_print(str)
def printAlignment(alignment):
"""
Prints out alignment information for debugging
"""
for key in list(alignment.keys()):
pka_print( " --- %s ---" % (key) )
for key2 in list(alignment[key].keys()):
pka_print("%s %5d%2s" % (alignment[key][key2]["name"], alignment[key][key2]["resNumb"], alignment[key][key2]["chainID"]))
pka_print("%s\n" % (alignment[key][key2]["sequence"]))
def printAllAtoms(protein):
"""
Prints out determinant information for debugging
"""
pka_print("Not implemented yet")
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