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/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/NoOutputJobOutputter.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 <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <string>
#include <core/import_pose/import_pose.hh>
#include <utility/excn/Exceptions.hh>

Classes
class	RmsfMover
class	FitMover

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

Functions
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...

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

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

FitMoverOP

using FitMoverOP = utility::pointer::shared_ptr<FitMover>

RmsfMoverCOP

using RmsfMoverCOP = utility::pointer::shared_ptr<const RmsfMover>

RmsfMoverOP

using RmsfMoverOP = utility::pointer::shared_ptr<RmsfMover>

Function Documentation

main()

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

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

References argv, test.T009_Exceptions::e, basic::init(), register_options(), and run().

read_input_weights()

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

References create_a3b_hbs::i, basic::options::OptionKeys::in::in, natoms(), option, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and weights().

Referenced by run().

read_structures()

void read_structures

(

RmsfMoverOP

rmsf_tool

)

References sfd.

Referenced by run().

register_options()

void register_options

(

)

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

Referenced by main().

round()

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

References create_a3b_hbs::i.

Referenced by LoopHashRelax_Sampler::apply(), pyrosetta.toolbox.cleaning::cleanCRYS(), mp_ddG::compute_ddG(), fill_input_poses_based_on_possible_checkpoints(), filterNonCore(), get_ang_samp(), get_vallfrags(), best_ifaceE::main(), prune_atdiff_top5pct::main(), main(), perturb(), mp_ddG::print_ddG_breakdown(), read_sphere(), utility::round(), run(), show_accuracy_report(), and ui::ui_protocols::helical_bundle::HelixOptionWidget::update_slider_spinner_values().

run()

void run

(

)

References extract_by_sidechain_sasa_score::cutoff, PREcst::fname, BundlePairRmsdCalculator::fraction, create_a3b_hbs::i, basic::Tracer::Info, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, option, erraser_single_res_analysis::out, out::pdb(), pyrosetta.distributed.io::pose_from_file, read_input_weights(), read_structures(), basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::rigid::rigid, average_rmsds::rmsd, round(), superimpose(), tr, basic::options::OptionKeys::inout::dbms::user, weights(), and xx.

Referenced by main().

superimpose()

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

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

Referenced by automorph_rmsd(), chain_rmsd(), and run().

Variable Documentation

tr

basic::Tracer tr("main") ( "main"  )

static

Referenced by run().