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
|
.. -*- coding: utf-8 -*-
.. _propka3-command:
============================
:program:`propka3` command
============================
PROPKA predicts the pKa values of ionizable groups in proteins and
protein-ligand complexes based in the 3D structure. The
:program:`propka3` command has the following options::
propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS] [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT] [-m MUTATIONS]
[-v VERSION_LABEL] [-p PARAMETERS] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH] [-w WINDOW WINDOW WINDOW]
[-g GRID GRID GRID] [--mutator MUTATOR] [--mutator-option MUTATOR_OPTIONS] [-d] [-l] [-k] [-q] [--protonate-all]
input_pdb
.. program:: propka3
.. option:: input_pdb
read data from file <input_pdb>
.. option:: -h, --help
show this help message and exit
.. option:: -f FILENAMES, --file FILENAMES
read data from <filename>, i.e. <filename> is added to
arguments (default: [])
.. option:: -r REFERENCE, --reference REFERENCE
setting which reference to use for stability calculations
[neutral/low-pH] (default: neutral)
.. option:: -c CHAINS, --chain CHAINS
creating the protein with only a specified chain. Specify
" " for chains without ID [all] (default: None)
.. option:: -i TITRATE_ONLY, --titrate_only TITRATE_ONLY
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"`` (default: None)
.. option:: -t THERMOPHILES, --thermophile THERMOPHILES
defining a thermophile filename; usually used in
'alignment-mutations' (default: None)
.. option:: -a ALIGNMENT, --alignment ALIGNMENT
alignment file connecting <filename> and <thermophile>
[<thermophile>.pir] (default: None)
.. option:: -m MUTATIONS, --mutation MUTATIONS
specifying mutation labels which is used to modify
<filename> according to, e.g. N25R/N181D (default: None)
.. option:: --version
show program's version number and exit
.. option:: -p PARAMETERS, --parameters PARAMETERS
set the parameter file (default:
<installation_directory>/propka/propka/propka.cfg)
.. option:: --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
logging level verbosity (default: INFO)
.. option:: -o PH, --pH PH
setting pH-value used in e.g. stability calculations
(default: 7.0)
.. option:: -w WINDOW WINDOW WINDOW, --window WINDOW WINDOW WINDOW
setting the pH-window to show e.g. stability profiles
(default: (0.0, 14.0, 1.0))
.. option:: -g GRID GRID GRID, --grid GRID GRID GRID
setting the pH-grid to calculate e.g. stability related
properties (default: (0.0, 14.0, 0.1))
.. option:: --mutator MUTATOR
setting approach for mutating <filename>
[alignment/scwrl/jackal] (default: None)
.. option:: --mutator-option MUTATOR_OPTIONS
setting property for mutator [e.g. type="side-chain"]
(default: None)
.. option:: -d, --display-coupled-residues
Displays alternative pKa values due to coupling of
titratable groups (default: False)
.. option:: -l, --reuse-ligand-mol2-files
Reuses the ligand mol2 files allowing the user to alter
ligand bond orders (default: False)
.. option:: -k, --keep-protons
Keep protons in input file (default: False)
.. option:: -q, --quiet
suppress non-warning messages (default: None)
.. option:: --protonate-all
Protonate all atoms (will not influence pKa calculation)
(default: False)
|
