Skip to content
Snippets Groups Projects
Commit 3ca3e4d9 authored by Gerardo Tauriello's avatar Gerardo Tauriello
Browse files

Reduce width of molck usage code.

parent ec7ca9da
No related branches found
No related tags found
No related merge requests found
.. Note on large code blocks: keep max. width to 100 or it will look bad
on webpage!
========================= =========================
Molecular Checker (Molck) Molecular Checker (Molck)
========================= =========================
...@@ -37,23 +40,23 @@ please find them following: ...@@ -37,23 +40,23 @@ please find them following:
.. code-block:: bash .. code-block:: bash
usage: molck [options] file1.pdb [file2.pdb [...]] usage: molck [options] file1.pdb [file2.pdb [...]]
options options
--complib=path location of the compound library file. If not provided, the --complib=path location of the compound library file. If not provided, the
following locations are searched in this order: following locations are searched in this order:
1. Working directory, 1. Working directory,
2. OpenStructure standard library location (if the 2. OpenStructure standard library location (if the
executable is part of a standard OpenStructure installation) executable is part of a standard OpenStructure installation)
--rm=<a>,<b> remove atoms and residues matching some criteria: --rm=<a>,<b> remove atoms and residues matching some criteria:
- zeroocc - Remove atoms with zero occupancy - zeroocc - Remove atoms with zero occupancy
- hyd - Remove hydrogen atoms - hyd - Remove hydrogen atoms
- oxt - Remove terminal oxygens - oxt - Remove terminal oxygens
- nonstd - Remove all residues not one of the 20 standard amino acids - nonstd - Remove all residues not one of the 20 standard amino acids
- unk - Remove unknown and atoms not following the nomenclature - unk - Remove unknown and atoms not following the nomenclature
--fix-ele clean up element column --fix-ele clean up element column
--stdout write cleaned file(s) to stdout --stdout write cleaned file(s) to stdout
--out=filename write cleaned file(s) to disk. % characters in the filename are --out=filename write cleaned file(s) to disk. % characters in the filename are
replaced with the basename of the input file without extension. replaced with the basename of the input file without extension.
Default: %-molcked.pdb Default: %-molcked.pdb
--color=auto|on|off whether output should be colored --color=auto|on|off whether output should be colored
--map-nonstd maps modified residues back to the parent amino acid, for example --map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER. MSE -> MET, SEP -> SER.
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment