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Commit 3ca3e4d9 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Reduce width of molck usage code.

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.. 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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