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Merge pull request #29 from Electrostatics/master

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* Replace PROPKA pickle with JSON.
* Replace optionparser with argparse.
* Fix tests for Ubuntu WSL.
* Fix verbosity/logging.
This commit is contained in:
Nathan Baker
2020-05-16 17:09:52 -07:00
committed by GitHub
parent 91925bb920 0fbaa6711f
commit 6ae2908c4b
9 changed files with 163 additions and 656 deletions
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16
Tests/pkacalc_test.py
View File

@@ -4,6 +4,13 @@ import re
from subprocess import call
import sys
import unittest
import logging
# This error tolerance was chosen to make Ubuntu 18.04 pass under Windows
# Subsystem Linux.
ACCEPTABLE_ERROR = 0.001
# Setting this up as a direct translation of the original runtest.py script
# that will be run as part of 'python setup.py test'. This takes on the
@@ -53,16 +60,21 @@ class SystemTest(unittest.TestCase):
expected_value = float(ref.readline())
value = float(m.group(0))
value_error = (value-expected_value)/expected_value
if(value != expected_value):
if abs(value_error) > ACCEPTABLE_ERROR:
logging.error(value_error)
identity = line[:m.start()].strip()
errors.append("%12s %8.2f %8.2f" %
(identity, expected_value, value))
os.remove("%s.pka" % pdb)
os.remove("%s.propka_input" % pdb)
ref.close()
output.close()
if errors:
error_header = " Group Expected Calculated\n"
self.Fail("Unexpected pKa values:\n" + error_header +
self.fail("Unexpected pKa values:\n" + error_header +
"\n".join(errors))

21
propka/__init__.py
View File

@@ -1,5 +1,20 @@
# propka 3.1
# (Module renamed from original Source to propka to facilitate setuptools installation)
"""PROPKA 3.1
__all__ = ['coupled_residues', 'lib', 'parameters', 'residue', 'bonds', 'debug', 'ligand', 'pdb', 'calculator', 'determinants', 'mutate', 'protein', 'chain', 'iterative', 'output', 'protonate']
See https://github.com/jensengroup/propka-3.1 for more information.
Please cite these PROPKA references in publications:
* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen.
"Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and
Rationalization of pKa Values." Journal of Chemical Theory and Computation 7,
no. 7 (2011): 2284-2295.
* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen.
"PROPKA3: consistent treatment of internal and surface residues in empirical pKa
predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.
"""
__all__ = ["atom", "bonds", "calculations", "conformation_container",
"coupled_groups", "determinant", "determinants", "group",
"hybrid36", "iterative", "lib", "ligand_pka_values", "ligand",
"molecular_container", "output", "parameters", "pdb", "protonate",
"run", "vector_algebra", "version"]

9
propka/bonds.py
View File

@@ -3,6 +3,7 @@ from __future__ import division
from __future__ import print_function
import pickle,sys,os,math,propka.calculations
import json
import pkg_resources
from propka.lib import info, warning
@@ -28,11 +29,9 @@ class bondmaker:
self.max_sq_distance = max(list(self.distances_squared.values())+[self.default_dist_squared])
# protein bonding data
self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.dat')
data = open(self.data_file_name,'rb')
self.protein_bonds = pickle.load(data)
data.close()
self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.json')
with open(self.data_file_name,'rt') as json_file:
self.protein_bonds = json.load(json_file)
self.intra_residue_backbone_bonds = {'N': ['CA'],

165
propka/lib.py
View File

@@ -4,6 +4,8 @@ from __future__ import print_function
import sys
import pkg_resources
import logging
import argparse
logger = logging.getLogger("propka")
stdout_handler = logging.StreamHandler(sys.stdout)
@@ -136,81 +138,107 @@ def parse_res_string(res_str):
return chain, resnum, inscode
def build_parser(parser=None):
"""Build an argument parser for PROPKA.
Args:
parser_: existing parser. If this is not None, then the PROPKA parser will
be created as a subparser to this existing parser. Otherwise, a
new parser will be created.
Returns:
ArgumentParser object.
"""
if parser is not None:
group = parser.add_argument_group(title="PROPKA invoation options")
else:
parser = argparse.ArgumentParser(description=("PROPKA predicts the pKa values of ionizable "
"groups in proteins and protein-ligand "
"complexes based in the 3D structure"),
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# This is duck-typing at its finest
group = parser
group.add_argument("input_pdb", help="read data from <filename>")
group.add_argument("-f", "--file", action="append", dest="filenames", default=[],
help="read data from <filename>, i.e. <filename> is added to arguments")
group.add_argument("-r", "--reference", dest="reference", default="neutral",
help=("setting which reference to use for stability calculations "
"[neutral/low-pH]"))
group.add_argument("-c", "--chain", action="append", dest="chains",
help=('creating the protein with only a specified chain. Specify '
'" " for chains without ID [all]'))
group.add_argument("-i", "--titrate_only", dest="titrate_only",
help=('Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for example: '
'-i "A:10,A:11"'))
group.add_argument("-t", "--thermophile", action="append", dest="thermophiles",
help=("defining a thermophile filename; usually used in "
"'alignment-mutations'"))
group.add_argument("-a", "--alignment", action="append", dest="alignment",
help=("alignment file connecting <filename> and <thermophile> "
"[<thermophile>.pir]"))
group.add_argument("-m", "--mutation", action="append", dest="mutations",
help=("specifying mutation labels which is used to modify "
"<filename> according to, e.g. N25R/N181D"))
group.add_argument("-v", "--version", dest="version_label", default="Jan15",
help="specifying the sub-version of propka [Jan15/Dec19]")
group.add_argument("-p", "--parameters", dest="parameters",
default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%(default)s]")
group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
help="logging level verbosity", default="INFO")
group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0,
help="setting pH-value used in e.g. stability calculations [7.0]")
group.add_argument("-w", "--window", dest="window", nargs=3, type=float,
default=(0.0, 14.0, 1.0),
help=("setting the pH-window to show e.g. stability profiles "
"[0.0, 14.0, 1.0]"))
group.add_argument("-g", "--grid", dest="grid", nargs=3, type=float,
default=(0.0, 14.0, 0.1),
help=("setting the pH-grid to calculate e.g. stability "
"related properties [0.0, 14.0, 0.1]"))
group.add_argument("--mutator", dest="mutator",
help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
group.add_argument("--mutator-option", dest="mutator_options", action="append",
help="setting property for mutator [e.g. type=\"side-chain\"]")
group.add_argument("-d", "--display-coupled-residues", dest="display_coupled_residues",
action="store_true", help=("Displays alternative pKa values due "
"to coupling of titratable groups"))
group.add_argument("-l", "--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file",
action="store_true", default=False,
help=("Reuses the ligand mol2 files allowing the user to alter "
"ligand bond orders"))
group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true",
help="Keep protons in input file", default=False)
group.add_argument("--protonate-all", dest="protonate_all", action="store_true",
help="Protonate all atoms (will not influence pKa calculation)",
default=False)
return parser
def loadOptions(*args):
"""
Load the arguments parser with options. Note that verbosity is set as soon as this function is invoked.
"""
from optparse import OptionParser
Load the arguments parser with options. Note that verbosity is set as soon
as this function is invoked.
Returns:
argparse namespace
"""
# defining a 'usage' message
usage = "usage: %prog [options] filename"
# creating a parser
parser = OptionParser(usage)
# loading the parser
parser.add_option("-f", "--file", action="append", dest="filenames",
help="read data from <filename>, i.e. <filename> is added to arguments")
parser.add_option("-r", "--reference", dest="reference", default="neutral",
help="setting which reference to use for stability calculations [neutral/low-pH]")
parser.add_option("-c", "--chain", action="append", dest="chains",
help='creating the protein with only a specified chain. Specify " " for chains without ID [all]')
parser.add_option("-i", "--titrate_only", dest="titrate_only",
help='Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for example: '
'-i "A:10,A:11"')
parser.add_option("-t", "--thermophile", action="append", dest="thermophiles",
help="defining a thermophile filename; usually used in 'alignment-mutations'")
parser.add_option("-a", "--alignment", action="append", dest="alignment",
help="alignment file connecting <filename> and <thermophile> [<thermophile>.pir]")
parser.add_option("-m", "--mutation", action="append", dest="mutations",
help="specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D")
parser.add_option("-v", "--version", dest="version_label", default="Jan15",
help="specifying the sub-version of propka [Jan15/Dec19]")
parser.add_option("-p", "--parameters",dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%default]")
parser.add_option("-z", "--verbose", dest="verbosity", action="store_const", const=2,
help="output debugging information")
parser.add_option("-q", "--quiet", dest="verbosity", action="store_const", const=0, default=1,
help="inhibit printing to stdout")
parser.add_option("-o", "--pH", dest="pH", type="float", default=7.0,
help="setting pH-value used in e.g. stability calculations [7.0]")
parser.add_option("-w", "--window", dest="window", nargs=3, type="float", default=(0.0, 14.0, 1.0),
help="setting the pH-window to show e.g. stability profiles [0.0, 14.0, 1.0]")
parser.add_option("-g", "--grid", dest="grid", nargs=3, type="float", default=(0.0, 14.0, 0.1),
help="setting the pH-grid to calculate e.g. stability related properties [0.0, 14.0, 0.1]")
parser.add_option("--mutator", dest="mutator",
help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
parser.add_option("--mutator-option", dest="mutator_options", action="append",
help="setting property for mutator [e.g. type=\"side-chain\"]")
parser.add_option("-d","--display-coupled-residues", dest="display_coupled_residues", action="store_true",
help="Displays alternative pKa values due to coupling of titratable groups")
parser.add_option("-l","--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file", action="store_true",
help="Reuses the ligand mol2 files allowing the user to alter ligand bond orders", default=False)
parser.add_option("-k","--keep-protons", dest="keep_protons", action="store_true",
help="Keep protons in input file", default=False)
parser.add_option("--protonate-all", dest="protonate_all", action="store_true",
help="Protonate all atoms (will not influence pKa calculation)", default=False)
parser = build_parser()
# parsing and returning options and arguments
if len(args) == 0:
# command line
options, args = parser.parse_args()
options = parser.parse_args()
else:
options, args = parser.parse_args(list(args))
options = parser.parse_args(list(args))
# adding specified filenames to arguments
if options.filenames:
for filename in options.filenames:
args.append(filename)
# checking at early stage that there is at least one pdbfile to work with. The error message is misleading
# if one is using the python interface via Molecular_container.
if len(args) == 0:
info("No pdbfile provided")
#sys.exit(9)
options.filenames.append(options.input_pdb)
# Convert titrate_only string to a list of (chain, resnum) items:
if options.titrate_only is not None:
@@ -226,20 +254,11 @@ def loadOptions(*args):
# Set the no-print variable
if options.verbosity == 0:
logger.setLevel(logging.CRITICAL)
elif options.verbosity == 1:
logger.setLevel(logging.INFO)
elif options.verbosity == 2:
logger.setLevel(logging.DEBUG)
else:
logger.warning("Invalid verbosity level, using default")
level = getattr(logging, options.log_level)
logger.setLevel(level)
# done!
return options, args
return options
def makeTidyAtomLabel(name,element):

568
propka/protein_bonds.dat
View File

@@ -1,568 +0,0 @@
(dp0
S'CYS'
p1
(dp2
S'CB'
p3
(lp4
S'CA'
p5
aS'SG'
p6
asg5
(lp7
g3
asg6
(lp8
g3
aS'SG'
p9
assS'GLN'
p10
(dp11
S'CB'
p12
(lp13
S'CA'
p14
aS'CG'
p15
asg14
(lp16
g12
asg15
(lp17
g12
aS'CD'
p18
asg18
(lp19
g15
aS'OE1'
p20
aS'NE2'
p21
asg21
(lp22
g18
asg20
(lp23
g18
assS'HIS'
p24
(dp25
S'CD2'
p26
(lp27
S'CG'
p28
aS'NE2'
p29
asS'CB'
p30
(lp31
S'CA'
p32
ag28
asg32
(lp33
g30
asg28
(lp34
g30
aS'ND1'
p35
ag26
asS'CE1'
p36
(lp37
g35
ag29
asg35
(lp38
g28
ag36
asg29
(lp39
g26
ag36
assS'ASN'
p40
(dp41
S'CB'
p42
(lp43
S'CA'
p44
aS'CG'
p45
asg44
(lp46
g42
asS'ND2'
p47
(lp48
g45
asg45
(lp49
g42
aS'OD1'
p50
ag47
asg50
(lp51
g45
assS'VAL'
p52
(dp53
S'CG1'
p54
(lp55
S'CB'
p56
asg56
(lp57
S'CA'
p58
ag54
aS'CG2'
p59
asg58
(lp60
g56
asg59
(lp61
g56
assS'LYS'
p62
(dp63
S'CB'
p64
(lp65
S'CA'
p66
aS'CG'
p67
asg66
(lp68
g64
asg67
(lp69
g64
aS'CD'
p70
asS'CE'
p71
(lp72
g70
aS'NZ'
p73
asg70
(lp74
g67
ag71
asg73
(lp75
g71
assS'ILE'
p76
(dp77
S'CG1'
p78
(lp79
S'CB'
p80
aS'CD1'
p81
asg80
(lp82
S'CA'
p83
ag78
aS'CG2'
p84
asg83
(lp85
g80
asg84
(lp86
g80
asg81
(lp87
g78
assS'PRO'
p88
(dp89
S'CB'
p90
(lp91
S'CA'
p92
aS'CG'
p93
asg92
(lp94
g90
asS'CD'
p95
(lp96
S'N'
p97
ag93
asg93
(lp98
g90
ag95
asg97
(lp99
g95
assS'THR'
p100
(dp101
S'CB'
p102
(lp103
S'CA'
p104
aS'OG1'
p105
aS'CG2'
p106
asg104
(lp107
g102
asg106
(lp108
g102
asg105
(lp109
g102
assS'PHE'
p110
(dp111
S'CD2'
p112
(lp113
S'CG'
p114
aS'CE2'
p115
asS'CB'
p116
(lp117
S'CA'
p118
ag114
asg118
(lp119
g116
asg114
(lp120
g116
aS'CD1'
p121
ag112
asS'CZ'
p122
(lp123
S'CE1'
p124
ag115
asg121
(lp125
g114
ag124
asg124
(lp126
g121
ag122
asg115
(lp127
g112
ag122
assS'ALA'
p128
(dp129
S'CB'
p130
(lp131
S'CA'
p132
asg132
(lp133
g130
assS'MET'
p134
(dp135
S'CB'
p136
(lp137
S'CA'
p138
aS'CG'
p139
asg138
(lp140
g136
asg139
(lp141
g136
aS'SD'
p142
asS'CE'
p143
(lp144
g142
asg142
(lp145
g139
ag143
assS'ASP'
p146
(dp147
S'CB'
p148
(lp149
S'CA'
p150
aS'CG'
p151
asg150
(lp152
g148
asg151
(lp153
g148
aS'OD1'
p154
aS'OD2'
p155
asg155
(lp156
g151
asg154
(lp157
g151
assS'LEU'
p158
(dp159
S'CB'
p160
(lp161
S'CA'
p162
aS'CG'
p163
asg162
(lp164
g160
asg163
(lp165
g160
aS'CD1'
p166
aS'CD2'
p167
asg166
(lp168
g163
asg167
(lp169
g163
assS'ARG'
p170
(dp171
S'CB'
p172
(lp173
S'CA'
p174
aS'CG'
p175
asg174
(lp176
g172
asg175
(lp177
g172
aS'CD'
p178
asS'NE'
p179
(lp180
g178
aS'CZ'
p181
asg178
(lp182
g175
ag179
asg181
(lp183
g179
aS'NH1'
p184
aS'NH2'
p185
asg184
(lp186
g181
asg185
(lp187
g181
assS'TRP'
p188
(dp189
S'CZ2'
p190
(lp191
S'CE2'
p192
aS'CH2'
p193
asS'CB'
p194
(lp195
S'CA'
p196
aS'CG'
p197
asg196
(lp198
g194
asg197
(lp199
g194
aS'CD1'
p200
aS'CD2'
p201
asg193
(lp202
g190
aS'CZ3'
p203
asg192
(lp204
g201
aS'NE1'
p205
ag190
asS'CE3'
p206
(lp207
g201
ag203
asg200
(lp208
g197
ag205
asg201
(lp209
g197
ag192
ag206
asg203
(lp210
g206
ag193
asg205
(lp211
g200
ag192
assS'GLU'
p212
(dp213
S'OE2'
p214
(lp215
S'CD'
p216
asS'CA'
p217
(lp218
S'CB'
p219
asS'CG'
p220
(lp221
g219
ag216
asg216
(lp222
g220
aS'OE1'
p223
ag214
asg219
(lp224
g217
ag220
asg223
(lp225
g216
assS'TYR'
p226
(dp227
S'CD2'
p228
(lp229
S'CG'
p230
aS'CE2'
p231
asS'OH'
p232
(lp233
S'CZ'
p234
asS'CB'
p235
(lp236
S'CA'
p237
ag230
asg237
(lp238
g235
asg230
(lp239
g235
aS'CD1'
p240
ag228
asg234
(lp241
S'CE1'
p242
ag231
ag232
asg240
(lp243
g230
ag242
asg242
(lp244
g240
ag234
asg231
(lp245
g228
ag234
assS'SER'
p246
(dp247
S'OG'
p248
(lp249
S'CB'
p250
asg250
(lp251
S'CA'
p252
ag248
asg252
(lp253
g250
ass.

21
propka/protein_bonds.json Normal file
View File

@@ -0,0 +1,21 @@
{
"CYS": { "CB": [ "CA", "SG" ], "CA": [ "CB" ], "SG": [ "CB", "SG" ] },
"GLN": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "CD": [ "CG", "OE1", "NE2" ], "NE2": [ "CD" ], "OE1": [ "CD" ] },
"HIS": { "CD2": [ "CG", "NE2" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "ND1", "CD2" ], "CE1": [ "ND1", "NE2" ], "ND1": [ "CG", "CE1" ], "NE2": [ "CD2", "CE1" ] },
"ASN": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "ND2": [ "CG" ], "CG": [ "CB", "OD1", "ND2" ], "OD1": [ "CG" ] },
"VAL": { "CG1": [ "CB" ], "CB": [ "CA", "CG1", "CG2" ], "CA": [ "CB" ], "CG2": [ "CB" ] },
"LYS": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "CE": [ "CD", "NZ" ], "CD": [ "CG", "CE" ], "NZ": [ "CE" ] },
"ILE": { "CG1": [ "CB", "CD1" ], "CB": [ "CA", "CG1", "CG2" ], "CA": [ "CB" ], "CG2": [ "CB" ], "CD1": [ "CG1" ] },
"PRO": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CD": [ "N", "CG" ], "CG": [ "CB", "CD" ], "N": [ "CD" ] },
"THR": { "CB": [ "CA", "OG1", "CG2" ], "CA": [ "CB" ], "CG2": [ "CB" ], "OG1": [ "CB" ] },
"PHE": { "CD2": [ "CG", "CE2" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CZ": [ "CE1", "CE2" ], "CD1": [ "CG", "CE1" ], "CE1": [ "CD1", "CZ" ], "CE2": [ "CD2", "CZ" ] },
"ALA": { "CB": [ "CA" ], "CA": [ "CB" ] },
"MET": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "SD" ], "CE": [ "SD" ], "SD": [ "CG", "CE" ] },
"ASP": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "OD1", "OD2" ], "OD2": [ "CG" ], "OD1": [ "CG" ] },
"LEU": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CD1": [ "CG" ], "CD2": [ "CG" ] },
"ARG": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "NE": [ "CD", "CZ" ], "CD": [ "CG", "NE" ], "CZ": [ "NE", "NH1", "NH2" ], "NH1": [ "CZ" ], "NH2": [ "CZ" ] },
"TRP": { "CZ2": [ "CE2", "CH2" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CH2": [ "CZ2", "CZ3" ], "CE2": [ "CD2", "NE1", "CZ2" ], "CE3": [ "CD2", "CZ3" ], "CD1": [ "CG", "NE1" ], "CD2": [ "CG", "CE2", "CE3" ], "CZ3": [ "CE3", "CH2" ], "NE1": [ "CD1", "CE2" ] },
"GLU": { "OE2": [ "CD" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "CD": [ "CG", "OE1", "OE2" ], "CB": [ "CA", "CG" ], "OE1": [ "CD" ] },
"TYR": { "CD2": [ "CG", "CE2" ], "OH": [ "CZ" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CZ": [ "CE1", "CE2", "OH" ], "CD1": [ "CG", "CE1" ], "CE1": [ "CD1", "CZ" ], "CE2": [ "CD2", "CZ" ] },
"SER": { "OG": [ "CB" ], "CB": [ "CA", "OG" ], "CA": [ "CB" ] }
}

14
propka/run.py
View File

@@ -1,13 +1,18 @@
# entry point for propka script
import logging
import propka.lib, propka.molecular_container
_LOGGER = logging.getLogger("PROPKA")
def main():
"""
Reads in structure files, calculates pKa values, and prints pKa files
"""
# loading options, flaggs and arguments
options, pdbfiles = propka.lib.loadOptions()
options = propka.lib.loadOptions()
pdbfiles = options.filenames
for pdbfile in pdbfiles:
my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
@@ -25,7 +30,10 @@ def single(pdbfile, optargs=None):
single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
"""
optargs = optargs if optargs is not None else []
options, ignored_pdbfiles = propka.lib.loadOptions(*optargs)
options = propka.lib.loadOptions(*optargs)
pdbfile = options.filenames.pop(0)
if len(options.filenames) > 0:
_LOGGER.warning("Ignoring filenames: %s", options.filenames)
my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
my_molecule.calculate_pka()

3
scripts/propka31.py
View File

@@ -16,7 +16,8 @@ def main():
Reads in structure files, calculates pKa values, and prints pKa files
"""
# loading options, flaggs and arguments
options, pdbfiles = propka.lib.loadOptions()
options = propka.lib.loadOptions()
pdbfiles = options.filenames
for pdbfile in pdbfiles:
my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)

2
setup.py
View File

@@ -6,7 +6,7 @@
from setuptools import setup, find_packages
VERSION = "3.1.0"
VERSION = "3.1.1"
setup(name="PROPKA",
version=VERSION,