ensemble_analysis.cc File Reference

analyse sets of structures More...

#include <protocols/moves/Mover.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/NoOutputJobOutputter.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <protocols/jd2/SilentFileJobInputter.hh>
#include <protocols/toolbox/DecoySetEvaluation.hh>
#include <protocols/toolbox/superimpose.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/LoopsFileIO.hh>
#include <basic/options/option_macros.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ostream>
#include <algorithm>
#include <string>
#include <core/import_pose/import_pose.hh>
#include <utility/excn/EXCN_Base.hh>

Classes
class	RmsfMover
class	FitMover

Typedefs
typedef utility::pointer::shared_ptr < RmsfMover >	RmsfMoverOP
typedef utility::pointer::shared_ptr < RmsfMover const >	RmsfMoverCOP
typedef utility::pointer::shared_ptr < FitMover >	FitMoverOP

Functions
static thread_local basic::Tracer	tr ("main")
void	register_options ()
void	read_structures (RmsfMoverOP rmsf_tool)
core::Size	read_input_weights (FArray1D_double &weights, Size natoms)
Size	superimpose (DecoySetEvaluation &eval, utility::vector1< Real > &rmsf_result, FArray1D_double &weights)
core::Real	round (core::Real d, core::Size digits)
void	run ()
int	main (int argc, char *argv[])
	=============================== MAIN ============================================================ More...

Detailed Description

analyse sets of structures

This tool allows to superimpose structures using the wRMSD method [ Damm&Carlson, Biophys J (2006) 90:4558-4573 ]

Superimposed structures can be written as output pdbs and the converged residues can be determined

Author

Oliver Lange

Typedef Documentation

typedef utility::pointer::shared_ptr< FitMover > FitMoverOP

typedef utility::pointer::shared_ptr< RmsfMover const > RmsfMoverCOP

typedef utility::pointer::shared_ptr< RmsfMover > RmsfMoverOP

Function Documentation

int main	(	int	argc,
		char *	argv[]
	)

=============================== MAIN ============================================================

References utility::io::oc::cerr, utility::io::oc::cout, devel::init(), utility::excn::EXCN_Base::msg(), register_options(), run(), and utility::excn::EXCN_Base::show().

core::Size read_input_weights	(	FArray1D_double &	weights,
		Size	natoms
	)

References basic::options::OptionKeys::in::in, basic::options::OptionKeys::cluster::loops, name, option, basic::options::OptionKeys::rigid::rigid, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::optE::weights.

Referenced by run().

void read_structures

(

RmsfMoverOP

rmsf_tool

)

Referenced by run().

void register_options

(

)

References basic::options::OptionKeys::cp::cutoff, basic::options::OptionKeys::in::in, in::file::native(), NEW_OPT, OPT, options, basic::options::OptionKeys::canonical_sampling::out::out, out::pdb(), basic::options::OptionKeys::AnchoredDesign::rmsd, in::file::s(), in::file::silent(), and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by main().

core::Real round	(	core::Real	d,
		core::Size	digits
	)

Referenced by toolbox.cleaning::cleanCRYS(), toolbox::cleanCRYS(), predict_ddG::compute_ddG(), mp_ddG::compute_ddG(), app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis::get_top_scoring_by_percent(), best_ifaceE::main(), prune_atdiff_top5pct::main(), src::output_scorefile(), mp_ddG::print_ddG_breakdown(), predict_ddG::print_ddG_breakdown(), utility::round(), and run().

void run

(

)

References basic::options::OptionKeys::cp::cutoff, basic::Tracer::Info, basic::options::OptionKeys::jd2::jd2, basic::options::OptionKeys::cluster::loops, in::file::native(), test.Workshop7test::native_pose, option, options, basic::options::OptionKeys::canonical_sampling::out::out, out::pdb(), read_input_weights(), read_structures(), basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::rigid::rigid, basic::options::OptionKeys::AnchoredDesign::rmsd, round(), superimpose(), tr(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::optE::weights.

Referenced by main().

Size superimpose	(	DecoySetEvaluation &	eval,
		utility::vector1< Real > &	rmsf_result,
		FArray1D_double &	weights
	)

References option, and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by run().

static thread_local basic::Tracer tr ( "main"  )

static

Referenced by run().