From 3ca3e4d9dda1666f24ff3fea81e71cc15615e661 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 12 Aug 2019 18:50:20 +0200
Subject: [PATCH] Reduce width of molck usage code.
---
modules/mol/alg/doc/molck.rst | 33 ++++++++++++++++++---------------
1 file changed, 18 insertions(+), 15 deletions(-)
diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 1dfaf6add..7ffd414ae 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -1,3 +1,6 @@
+.. Note on large code blocks: keep max. width to 100 or it will look bad
+ on webpage!
+
=========================
Molecular Checker (Molck)
=========================
@@ -37,23 +40,23 @@ please find them following:
.. code-block:: bash
usage: molck [options] file1.pdb [file2.pdb [...]]
- options
- --complib=path location of the compound library file. If not provided, the
- following locations are searched in this order:
- 1. Working directory,
- 2. OpenStructure standard library location (if the
- executable is part of a standard OpenStructure installation)
+ options
+ --complib=path location of the compound library file. If not provided, the
+ following locations are searched in this order:
+ 1. Working directory,
+ 2. OpenStructure standard library location (if the
+ executable is part of a standard OpenStructure installation)
--rm=<a>,<b> remove atoms and residues matching some criteria:
- - zeroocc - Remove atoms with zero occupancy
- - hyd - Remove hydrogen atoms
- - oxt - Remove terminal oxygens
- - nonstd - Remove all residues not one of the 20 standard amino acids
- - unk - Remove unknown and atoms not following the nomenclature
+ - zeroocc - Remove atoms with zero occupancy
+ - hyd - Remove hydrogen atoms
+ - oxt - Remove terminal oxygens
+ - nonstd - Remove all residues not one of the 20 standard amino acids
+ - unk - Remove unknown and atoms not following the nomenclature
--fix-ele clean up element column
- --stdout write cleaned file(s) to stdout
- --out=filename write cleaned file(s) to disk. % characters in the filename are
- replaced with the basename of the input file without extension.
- Default: %-molcked.pdb
+ --stdout write cleaned file(s) to stdout
+ --out=filename write cleaned file(s) to disk. % characters in the filename are
+ replaced with the basename of the input file without extension.
+ Default: %-molcked.pdb
--color=auto|on|off whether output should be colored
--map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER.
--
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