diff --git a/modules/mol/alg/doc/molck.rst b/modules/mol/alg/doc/molck.rst
index 7ffd414ae95c5f2f10c6cb739398dd164718792b..286127b2882447ee370230c2345b013fff8db30a 100644
--- a/modules/mol/alg/doc/molck.rst
+++ b/modules/mol/alg/doc/molck.rst
@@ -37,29 +37,33 @@ All Options
The molck executable supports several other command line options,
please find them following:
-.. code-block:: bash
+.. 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:
+ 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)
- --rm=<a>,<b> remove atoms and residues matching some criteria:
+ 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
- --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
- --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.
+ - nonstd - Remove all residues not one of the
+ 20 standard amino acids
+ - unk - Remove unknown and atoms not following
+ the nomenclature
+ Default: hyd
+ --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
+ --color=auto|on|off Whether output should be colored. Delault: auto
+ --map-nonstd Maps modified residues back to the parent amino acid,
+ for example: MSE -> MET, SEP -> SER.
================
Molck Python API
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 2016019cf472acfd14c1812be73433ff61bd5b85..53ff93f4dbe8f10d3782e70ac8842f285c43bee5 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -23,28 +23,32 @@ namespace po=boost::program_options;
namespace fs=boost::filesystem;
const char* USAGE=
-"this is molck - the molecule checker\n"
-"usage: molck [options] file1.pdb [file2.pdb [...]]\n"
-"options \n"
-" --complib=path location of the compound library file. If not provided, the \n"
-" following locations are searched in this order: \n"
-" 1. Working directory, 2. OpenStructure standard library location (if the \n"
-" executable is part of a standard OpenStructure installation) \n"
-" --rm=<a>,<b> remove atoms and residues matching some criteria \n"
-" zeroocc - Remove atoms with zero occupancy \n"
-" hyd - Remove hydrogen atoms \n"
-" oxt - Remove terminal oxygens \n"
-" nonstd - Remove all residues not one of the 20 standard amino acids \n"
-" unk - Remove unknown and atoms not following the nomenclature\n"
-" --fix-ele clean up element column\n"
-" --stdout write cleaned file(s) to stdout \n"
-" --out=filename write cleaned file(s) to disk. % characters in the filename are \n"
-" replaced with the basename of the input file without extension. \n"
-" Default: %-molcked.pdb \n"
-" --color=auto|on|off \n"
-" whether output should be colored\n"
-" --map-nonstd maps modified residues back to the parent amino acid, for example\n"
-" MSE -> MET, SEP -> SER.\n";
+"This is molck - the molecule checker\n"
+"Usage: molck [options] file1.pdb [file2.pdb [...]]\n"
+"Options\n"
+" --complib=path Location of the compound library file. If not provided,\n"
+" the following locations are searched in this order:\n"
+" 1. Working directory,\n"
+" 2. OpenStructure standard library location (if the\n"
+" executable is part of a standard OpenStructure\n"
+" installation)\n"
+" --rm=<a>,<b> Remove atoms and residues matching some criteria:\n"
+" - zeroocc - Remove atoms with zero occupancy\n"
+" - hyd - Remove hydrogen atoms\n"
+" - oxt - Remove terminal oxygens\n"
+" - nonstd - Remove all residues not one of the\n"
+" 20 standard amino acids\n"
+" - unk - Remove unknown and atoms not following\n"
+" the nomenclature\n"
+" Default: hyd\n"
+" --fix-ele Clean up element column\n"
+" --stdout Write cleaned file(s) to stdout\n"
+" --out=filename Write cleaned file(s) to disk. % characters in the\n"
+" filename are replaced with the basename of the input\n"
+" file without extension. Default: %-molcked.pdb\n"
+" --color=auto|on|off Whether output should be colored. Delault: auto\n"
+" --map-nonstd Maps modified residues back to the parent amino acid,\n"
+" for example: MSE -> MET, SEP -> SER.\n";
void usage()
{
@@ -139,8 +143,10 @@ int main(int argc, char *argv[])
usage();
}
IOProfile prof;
- prof.fault_tolerant=true;
- ost::mol::alg::MolckSettings settings;
+ prof.fault_tolerant = true;
+ // set all settings to false by default (set to true if args given)
+ ost::mol::alg::MolckSettings settings(false, false, false, false, false,
+ false, false, false);
String rm;
String color;
@@ -152,15 +158,15 @@ int main(int argc, char *argv[])
po::options_description desc("Options");
desc.add_options()
("rm", po::value<String>(&rm)->default_value("hyd"), "atoms to be removed")
- ("color", po::value<String>(&color)->default_value("auto"),
+ ("color", po::value<String>(&color)->default_value("auto"),
"whether the output should be colored.")
("files", po::value< std::vector<String> >(), "input file(s)")
("stdout", "write cleaned file(s) to stdout")
- ("out,o", po::value<String>(&output_blueprint_string)->default_value("%-molcked.pdb"),
+ ("out,o", po::value<String>(&output_blueprint_string)->default_value("%-molcked.pdb"),
"write cleaned file to output using blueprint to determine path")
("map-nonstd", "map non standard residues back to standard ones (e.g.: MSE->MET,SEP->SER,etc.)")
- ("fix-ele", "insert element")
- ("complib", po::value<String>(&custom_path)->default_value(""),"location of the compound library file")
+ ("fix-ele", "insert element")
+ ("complib", po::value<String>(&custom_path)->default_value(""),"location of the compound library file")
;
po::positional_options_description p;
p.add("files", -1);