basic usage for propka3 command

docs/source/command.rst

@@ -0,0 +1,129 @@
+.. -*- coding: utf-8 -*-
+
+================================
+ The :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] [--generate-propka-input]
+         [--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::  -v VERSION_LABEL, --version VERSION_LABEL
+	     
+             specifying the sub-version of propka [Jan15/Dec19]
+	     (default: Jan15)
+	     
+.. 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::  --generate-propka-input
+	     
+             Generate a PROPKA input file (default: False)
+	     
+.. option::  --protonate-all
+
+	     Protonate all atoms (will not influence pKa calculation)
+	     (default: False)
+	     

docs/source/index.rst

@@ -84,6 +84,7 @@ Indices and tables
 
    installation
    quickstart
+   command
    api
    references
 

docs/source/quickstart.rst

@@ -181,7 +181,7 @@ Getting help
 
 A brief list of available options can be obtained by running PROPKA
 with no options. A longer list of options and descriptions is
-available using the :option:`--help` option:
+available using the :option:`propka3 --help` option:
 
 .. code-block:: bash