Merge pull request #29 from Electrostatics/master

* Replace PROPKA pickle with JSON.
* Replace optionparser with argparse.
* Fix tests for Ubuntu WSL.
* Fix verbosity/logging.

Tests/pkacalc_test.py

@@ -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))

propka/__init__.py

@@ -1,5 +1,20 @@
-# propka 3.1
+"""PROPKA 3.1
-# (Module renamed from original Source to propka to facilitate setuptools installation)
 
-__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"]

propka/bonds.py

@@ -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')
+        self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.json')
-
+        with open(self.data_file_name,'rt') as json_file:
-        data = open(self.data_file_name,'rb')
+            self.protein_bonds = json.load(json_file)
-        self.protein_bonds = pickle.load(data)
-        data.close()
 
 
         self.intra_residue_backbone_bonds = {'N': ['CA'],

propka/lib.py

@@ -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.
+    Load the arguments parser with options. Note that verbosity is set as soon
-    """
+    as this function is invoked.
-    from optparse import OptionParser
 
+    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",
+    parser = build_parser()
-           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)
-
 
     # 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:
+    options.filenames.append(options.input_pdb)
-      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)
 
     # 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:
+    level = getattr(logging, options.log_level)
-        logger.setLevel(logging.CRITICAL)
+    logger.setLevel(level)
-    elif options.verbosity == 1:
-        logger.setLevel(logging.INFO)
-    elif options.verbosity == 2:
-        logger.setLevel(logging.DEBUG)
-    else:
-        logger.warning("Invalid verbosity level, using default")
 
     # done!
-    return options, args
+    return options
-
-
-
 
 
 def makeTidyAtomLabel(name,element):

propka/protein_bonds.dat

@@ -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.

propka/protein_bonds.json

@@ -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" ] }
+}

propka/run.py

@@ -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()

scripts/propka31.py

@@ -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)

setup.py

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