From 5129e91d4aee364414504237d170c8850f10cf17 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Thu, 5 Jul 2012 09:41:32 +0200
Subject: [PATCH] provide better usage description
---
tools/molck/main.cc | 21 ++++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index bcc35ea54..bf1576138 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -83,7 +83,22 @@ CompoundLibPtr load_compound_lib()
void usage()
{
- std::cerr << "usage: molck file1.pdb [file2.pdb [...]]" << std::endl;
+ std::cerr << "usage: molck [options] file1.pdb [file2.pdb [...]]" << std::endl;
+ std::cerr << "options" << 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;
+ std::cerr << " oxt - Remove terminal oxygens" << std::endl;
+ std::cerr << " nonstd - Remove all residues not " << std::endl
+ << " one of the 20 standard amino acids" << std::endl;
+ std::cerr << " unk - Remove unknown atoms and atoms that " << std::endl
+ << " 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 files to stdout" << 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
+ << " acid, e.g. MSE -> MET, SEP -> SER." << std::endl;
exit(0);
}
@@ -114,7 +129,7 @@ int main(int argc, char *argv[])
("files", po::value< std::vector<String> >(), "input file(s)")
("stdout", "write cleaned structure to stdout")
("map-nonstd", "map non standard residues back to standard ones (e.g.: MSE->MET,SEP->SER,etc.)")
- ("assign-elem", "insert element")
+ ("fix-ele", "insert element")
;
po::positional_options_description p;
p.add("files", -1);
@@ -143,7 +158,7 @@ int main(int argc, char *argv[])
if (vm.count("map-nonstd")) {
map_nonstd_res = true;
}
- if (vm.count("assign-elem")) {
+ if (vm.count("fix-ele")) {
assign_elem = true;
}
--
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