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- Remove all code which was previously marked with
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101 lines
3.0 KiB
ReStructuredText
101 lines
3.0 KiB
ReStructuredText
.. -*- coding: utf-8 -*-
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.. _propka3-command:
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============================
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:program:`propka3` command
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============================
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PROPKA predicts the pKa values of ionizable groups in proteins and
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protein-ligand complexes based in the 3D structure. The
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:program:`propka3` command has the following options::
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propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS] [-i TITRATE_ONLY]
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[-v VERSION_LABEL] [-p PARAMETERS] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH] [-w WINDOW WINDOW WINDOW]
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[-g GRID GRID GRID] [-d] [-l] [-k] [-q] [--protonate-all]
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input_pdb
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.. program:: propka3
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.. option:: input_pdb
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read data from file <input_pdb>
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.. option:: -h, --help
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show this help message and exit
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.. option:: -f FILENAMES, --file FILENAMES
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read data from <filename>, i.e. <filename> is added to
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arguments (default: [])
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.. option:: -r REFERENCE, --reference REFERENCE
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setting which reference to use for stability calculations
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[neutral/low-pH] (default: neutral)
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.. option:: -c CHAINS, --chain CHAINS
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creating the protein with only a specified chain. Specify
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" " for chains without ID [all] (default: None)
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.. option:: -i TITRATE_ONLY, --titrate_only TITRATE_ONLY
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Treat only the specified residues as titratable. Value
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should be a comma-separated list of "chain:resnum"
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values; for example: ``-i "A:10,A:11"`` (default: None)
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.. option:: --version
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show program's version number and exit
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.. option:: -p PARAMETERS, --parameters PARAMETERS
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set the parameter file (default:
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<installation_directory>/propka/propka/propka.cfg)
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.. option:: --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
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logging level verbosity (default: INFO)
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.. option:: -o PH, --pH PH
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setting pH-value used in e.g. stability calculations
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(default: 7.0)
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.. option:: -w WINDOW WINDOW WINDOW, --window WINDOW WINDOW WINDOW
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setting the pH-window to show e.g. stability profiles
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(default: (0.0, 14.0, 1.0))
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.. option:: -g GRID GRID GRID, --grid GRID GRID GRID
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setting the pH-grid to calculate e.g. stability related
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properties (default: (0.0, 14.0, 0.1))
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.. option:: -d, --display-coupled-residues
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Displays alternative pKa values due to coupling of
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titratable groups (default: False)
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.. option:: -l, --reuse-ligand-mol2-files
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Reuses the ligand mol2 files allowing the user to alter
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ligand bond orders (default: False)
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.. option:: -k, --keep-protons
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Keep protons in input file (default: False)
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.. option:: -q, --quiet
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suppress non-warning messages (default: None)
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.. option:: --protonate-all
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Protonate all atoms (will not influence pKa calculation)
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(default: False)
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