From 8fa9251703e3f2b9a751edd20b7be83c35f48a57 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Sat, 14 Jul 2012 02:39:27 +0200
Subject: [PATCH] Fixes to usage string
---
tools/molck/main.cc | 24 +++++++++++++-----------
1 file changed, 13 insertions(+), 11 deletions(-)
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 3ae8c9a94..07baf9496 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -95,13 +95,13 @@ void usage()
{
std::cerr << "usage: molck [options] file1.pdb [file2.pdb [...]]" << std::endl;
std::cerr << "options" << std::endl;
- std::cerr << " --complib location of the compound library file" << std::endl;
- std::cerr << " If not provided, the following locations are searched" << std::endl;
- std::cerr << " in this order:" << std::endl;
- std::cerr << " 1. Working directory" << std::endl;
- std::cerr << " 2. OpenStructure standard library location" << std::endl;
- std::cerr << " (if the executable is part of a standard" << std::endl;
- std::cerr << " OpenStructure installation)" << std::endl;
+ std::cerr << " --complib=path location of the compound library file" << std::endl;
+ std::cerr << " If not provided, the following locations are searched" << std::endl;
+ std::cerr << " in this order:" << std::endl;
+ std::cerr << " 1. Working directory" << std::endl;
+ std::cerr << " 2. OpenStructure standard library location" << std::endl;
+ std::cerr << " (if the executable is part of a standard" << std::endl;
+ std::cerr << " OpenStructure installation)" << std::endl;
std::cerr << " --rm=<a>,<b> remove atoms and residues matching some criteria" << std::endl;
std::cerr << " zeroocc - Remove atoms with zero occupancy" << std::endl;
std::cerr << " hyd - Remove hydrogen atoms" << std::endl;
@@ -112,10 +112,12 @@ void usage()
<< " are not supposed to be part of a residue" << std::endl;
std::cerr << " --fix-ele clean up element column" << std::endl;
std::cerr << " --stdout write cleaned file(s) to stdout" << std::endl;
- std::cerr << " --fileout=blueprint write cleaned file(s) to disk." << std::endl;
- std::cerr << " The blueprint is used to generate the output path and" << std::endl;
- std::cerr << " filemane, substituting % with the original file name" << std::endl;
- std::cerr << " minus the extension" << std::endl;
+ std::cerr << " --fileout=blueprint write cleaned file(s) to disk" << std::endl;
+ std::cerr << " The blueprint string, which must contain a % character," << std::endl;
+ std::cerr << " is used to generate the output filename and path" << std::endl;
+ std::cerr << " by replacing % with the input file name without" << std::endl;
+ std::cerr << " the extension. Output files automatically add" << std::endl;
+ std::cerr << " '.pdb' extension" << std::endl;
std::cerr << " --color=auto|on|off " << std::endl
<< " whether output should be colored" << std::endl;
std::cerr << " --map-nonstd maps modified residues back to the parent amino " << std::endl
--
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