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#!/usr/bin/env python
#
# * 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, sys, copy, math
def getCatchAllCompareWithExperiment(argv):
"""
returns mutation label
"""
import mats
if "mutation" in argv:
mutation = argv['mutation']
if mutation.upper() == "NONE" or mutation.upper() == "ALL":
mutation = None
else:
mutation = None
if mutation == None:
return "ALL"
else:
return mats.makeLabelFromMutationTag(mutation)
def getExperiment(fullname):
"""
return experimental values
"""
name = fullname[:4]
if name == "1pga":
# B1_ProteinG
experiment = {
"GLU 15 A": 4.40,
"GLU 19 A": 3.70,
"ASP 22 A": 2.90,
"GLU 27 A": 4.50,
"ASP 36 A": 3.80,
"ASP 40 A": 4.00,
"GLU 42 A": 4.40,
"ASP 46 A": 3.60,
"ASP 47 A": 3.40,
"GLU 56 A": 4.00,
}
elif name == "1igd":
# B2_ProteinG
experiment = {
"GLU 20 A": 4.30,
"ASP 27 A": 2.90,
"GLU 29 A": 4.20,
"GLU 32 A": 4.60,
"ASP 41 A": 3.90,
"ASP 45 A": 4.40,
"ASP 51 A": 3.60,
"ASP 52 A": 3.40,
"GLU 61 A": 4.20,
}
elif name == "1a2p":
# Barnase
experiment = {
"ASP 8 A": 2.90,
"ASP 12 A": 3.80,
"ASP 22 A": 3.30,
"GLU 29 A": 3.80,
"ASP 44 A": 3.40,
# "ASP 54 A": 2.20, # <= 2.2
"GLU 60 A": 3.00,
# "GLU 73 A": 2.10, # <= 2.1
# "ASP 75 A": 3.10, # difficult barnase pi-stacking
"ASP 86 A": 4.20,
# "ASP 93 A": 2.00, # < 2.0
# "ASP 101 A": 2.00, # <= 2
}
elif name == "1rnz":
# Bovine_RNase
experiment = {
"GLU 2 A": 2.70,
"GLU 9 A": 4.00,
# "ASP 14 A": 1.80, # < 2.0
"ASP 38 A": 2.80,
"GLU 49 A": 4.50,
"ASP 53 A": 3.80,
"ASP 83 A": 3.40,
"GLU 86 A": 4.05,
"GLU 111 A": 3.50,
"ASP 121 A": 3.05,
}
elif name == "4icb":
# Calbindin
experiment = {
"GLU 4 A": 3.80,
"GLU 5 A": 3.40,
"GLU 11 A": 4.70,
"GLU 17 A": 3.60,
"GLU 26 A": 4.10,
"ASP 47 A": 3.00,
"GLU 48 A": 4.60,
"GLU 64 A": 3.80,
}
elif name == "1kxi":
# Cardiotoxin
experiment = {
"GLU 17 A": 4.00,
"ASP 42 A": 3.20,
# "ASP 59 A": 2.30, # < 2.3
"GLU 17 B": 4.00,
"ASP 42 B": 3.20,
# "ASP 59 B": 2.30, # < 2.3
}
elif name == "1kxi_A":
# Cardiotoxin
experiment = {"GLU 17 A": 4.00,
"ASP 42 A": 3.20,
"ASP 59 A": 2.30}
elif name == "1kxi_B":
# Cardiotoxin
experiment = {"GLU 17 B": 4.00,
"ASP 42 B": 3.20,
"ASP 59 B": 2.30}
elif name == "1cdc":
# CD2d1
experiment = {
"ASP 25 A": 3.50,
"ASP 26 A": 3.60,
"ASP 28 A": 3.60,
"GLU 29 A": 4.40,
"GLU 33 A": 4.20,
"GLU 41 A": 6.70,
"GLU 56 A": 3.90,
"ASP 62 A": 4.20,
"ASP 71 A": 3.20,
"ASP 72 A": 4.10,
"ASP 94 A": 3.90,
"GLU 99 A": 4.20,
"ASP 25 B": 3.50,
"ASP 26 B": 3.60,
"ASP 28 B": 3.60,
"GLU 29 B": 4.40,
"GLU 33 B": 4.20,
"GLU 41 B": 6.70,
"GLU 56 B": 3.90,
"ASP 62 B": 4.20,
"ASP 71 B": 3.20,
"ASP 72 B": 4.10,
"ASP 94 B": 3.90,
"GLU 99 B": 4.20,
}
elif name == "1beo":
# Cryptogein
experiment = {
"ASP 21 A": 2.50,
"ASP 30 A": 2.50,
"ASP 72 A": 2.60,
}
elif name == "1hpx":
# HIV_protease, note, homodimer, B is assumed to be A
experiment = {
#"ASP 25 B": 6.20, # > 6.2
"ASP 29 B": 3.20,
"ASP 30 B": 3.90,
"ASP 60 B": 3.00,
#"ASP 25 A": 2.50, # < 2.5
"ASP 29 A": 3.70,
"ASP 30 A": 3.80,
"ASP 60 A": 3.00,
}
elif name == "1lys":
# Hen lysozyme
experiment = {
"GLU 7 A": 2.90,
"ASP 18 A": 2.70,
"GLU 35 A": 6.20,
# "ASP 48 A": 2.50, # < 2.5
"ASP 52 A": 3.70,
# "ASP 66 A": 2.00, # < 2.5
"ASP 87 A": 2.10,
"ASP 101 A": 4.10,
"ASP 119 A": 3.20,
}
elif name == "135l":
# Turkey lysozyme
experiment = {
"GLU 7 A": 2.70,
"ASP 18 A": 2.70,
"GLU 35 A": 6.10,
# "ASP 48 A": 2.50, # < 2.5
"ASP 52 A": 3.80,
# "ASP 66 A": 2.00, # < 2.5
"ASP 87 A": 2.10,
"ASP 119 A": 3.40,
}
elif name == "2rn2":
# Ribonuclease H1
experiment = {
"GLU 6 A": 4.50,
"ASP 10 A": 6.10,
"GLU 32 A": 3.60,
"GLU 48 A": 4.40,
"GLU 57 A": 3.20,
"GLU 61 A": 3.90,
"GLU 64 A": 4.40,
"ASP 70 A": 2.60,
"ASP 94 A": 3.20,
# "ASP 102 A": 2.00, # < 2
"ASP 108 A": 3.20,
"GLU 119 A": 4.10,
"GLU 129 A": 3.60,
"GLU 131 A": 4.30,
"ASP 134 A": 4.10,
"GLU 135 A": 4.30,
"GLU 147 A": 4.20,
# "ASP 148 A": 2.00, # < 2
"GLU 154 A": 4.40,
}
elif name == "2ovo":
# Ovomucoid3Dom
experiment = {
"ASP 7 A": 2.50,
"GLU 10 A": 4.10,
"GLU 19 A": 3.20,
"ASP 27 A": 2.20,
"GLU 43 A": 4.80,
}
elif name == "1xnb":
# Xylanase
experiment = {
"ASP 4 A": 3.00,
"ASP 11 A": 2.50,
"GLU 78 A": 4.60,
# "ASP 83 A": 2.00, # < 2
# "ASP 101 A": 2.00, # < 2
"ASP 106 A": 2.70,
"ASP 119 A": 3.20,
"ASP 121 A": 3.60,
"GLU 172 A": 6.70,
}
elif name == "1de3":
# Sarcin
experiment = {
"ASP 9 A": 3.90,
"GLU 19 A": 4.60,
"GLU 31 A": 4.60,
# "ASP 41 A": 3.00, # < 3
"ASP 57 A": 4.30,
"ASP 59 A": 4.10,
"ASP 75 A": 3.90,
# "ASP 77 A": 3.00, # < 3
"ASP 85 A": 3.80,
# "ASP 91 A": 3.00, # < 3
"GLU 96 A": 5.10,
# "ASP 102 A": 3.00, # < 3
# "ASP 105 A": 3.00, # < 3
"ASP 109 A": 3.70,
"GLU 115 A": 4.90,
"GLU 140 A": 4.30,
"GLU 144 A": 4.30,
}
elif name == "2bus":
# BullSeminalInhibitor
experiment = {
"ASP 6 A": 4.00,
"GLU 9 A": 4.30,
"ASP 12 A": 3.60,
"GLU 20 A": 4.10,
}
elif name == "1egf":
# Epidermal Growthfactor
experiment = {
"ASP 11 A": 3.90,
"GLU 24 A": 4.10,
"ASP 27 A": 4.00,
"ASP 40 A": 3.60,
"ASP 46 A": 3.80,
"GLU 51 A": 4.00,
}
elif name == "1mhi":
# Insulin
experiment = {
"GLU 4 A": 2.60,
# "GLU 17 A": 3.70, # > 3.7
"ASP 9 B": 2.60,
"GLU 13 B": 2.20,
"GLU 21 B": 3.70,
}
else:
print("could not find experimental data for \"%s\"" % (name))
sys.exit(9)
return experiment
def makeErrorPlot(points):
"""
do patented error graph data
"""
error_list = []
for i in range(0, 41):
error_list.append(0.00)
for point in points:
abs_diff = abs(point)
i = 0
while abs_diff > float(i)/10.0 and i < 41:
error_list[i] += 1.0
i += 1
number_of_points = float(len(points))
for i in range(0, 41):
error = float(i)/10.0
fraction = error_list[i]/number_of_points
print("%6.2lf%6.2lf" % (error, fraction))
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