1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176
|
#
# * 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")
|