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Remove some unused code

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- Remove all code which was previously marked with
  `NotImplementedError("unused")`.
- Remove unsued command line arguments
This commit is contained in:
Thomas Holder
2023-12-21 22:24:29 +01:00
parent 6ee0df8e6d
commit 9ea6d8815d
9 changed files with 17 additions and 370 deletions
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29
docs/source/command.rst
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@@ -10,9 +10,9 @@ 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]
propka3 [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS] [-i TITRATE_ONLY]
[-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]
[-g GRID GRID GRID] [-d] [-l] [-k] [-q] [--protonate-all]
input_pdb
@@ -47,21 +47,6 @@ protein-ligand complexes based in the 3D structure. The
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
@@ -90,16 +75,6 @@ protein-ligand complexes based in the 3D structure. The
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