flexibleLoopDesign.cc File Reference

#include <basic/options/util.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/dwkulp.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/TaskOperations.fwd.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/CCDLoopClosureMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/loops/kinematic_closure/KinematicMover.hh>
#include <protocols/moves/kinematic_closure/KinematicPerturber.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <numeric/random/random.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/rms_util.hh>
#include <basic/MetricValue.hh>
#include <basic/Tracer.hh>
#include <protocols/frag_picker/FragmentPicker.hh>
#include <protocols/frag_picker/FragmentPicker.fwd.hh>
#include <protocols/frag_picker/VallProvider.hh>
#include <protocols/frag_picker/VallProvider.fwd.hh>
#include <protocols/frag_picker/VallChunk.hh>
#include <protocols/frag_picker/VallResidue.hh>
#include <protocols/frag_picker/FragmentCandidate.hh>
#include <protocols/frag_picker/FragmentCandidate.fwd.hh>
#include <protocols/frag_picker/FragmentSelectingRule.hh>
#include <protocols/frag_picker/VallChunkFilter.hh>
#include <protocols/frag_picker/BoundedCollector.hh>
#include <protocols/frag_picker/BestTotalScoreSelector.hh>
#include <protocols/frag_picker/DiversifyCrmsdByClustering.hh>
#include <protocols/frag_picker/scores/FragmentScoringMethod.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/loops/ccd_closure.hh>
#include <protocols/moves/Mover.hh>
#include <utility/excn/Exceptions.hh>
#include <core/import_pose/import_pose.hh>
#include <iostream>
#include <fstream>
#include <numeric>
#include <functional>

Functions
double	annealTemperature (double initialTemp, double finalTemp, int step, int totalsteps, int numAnnealCycles)
void	setup_fragment_mover (core::pose::Pose &_pose, protocols::loops::Loop &_loop, vector< vector< protocols::moves::MoverOP > > &_bbMovers, string _polyAminoAcidOverride)
unsigned int	hd (const std::string &s1, const std::string &s2)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("flexibleLoopDesign")

Function Documentation

annealTemperature()

double annealTemperature	(	double	initialTemp,
		double	finalTemp,
		int	step,
		int	totalsteps,
		int	numAnnealCycles
	)

References enumerate_junctions::int, and test_mm_lj::step.

Referenced by main().

hd()

unsigned int hd	(	const std::string &	s1,
		const std::string &	s2
	)

References numeric::inner_product(), basic::options::OptionKeys::stepwise::s1, and basic::options::OptionKeys::stepwise::s2.

Referenced by main(), run(), run_tyr_his(), and run_zn2his().

main()

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

References annealTemperature(), argv, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::io::ocstream::clear(), utility::io::oc::cout, dist(), test.T009_Exceptions::e, basic::options::OptionKeys::packing::ex1::ex1, basic::options::OptionKeys::packing::ex2::ex2, basic::options::OptionKeys::packing::extrachi_cutoff, fold_tree_from_loops(), basic::options::OptionKeys::dwkulp::forcePolyAAfragments, val2thr::fout, test.T020_Pose_Bindings::ft, hd(), create_a3b_hbs::i, basic::init(), enumerate_junctions::int, create_a3b_hbs::j, extract_by_sidechain_sasa_score::l, mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, loops::my_loops, basic::options::option, options, test.Workshop6test::pack_mover, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::r, numeric::random::RandomGenerator::random_range(), basic::options::OptionKeys::packing::resfile, numeric::random::rg(), average_rmsds::rmsd, oop_conformations::scorefxn, setup_fragment_mover(), subloop_histogram::size, basic::options::start_file(), vancomycin::task, local::temperature, TR, basic::options::OptionKeys::packing::use_input_sc, and basic::options::OptionKeys::inout::dbms::user.

setup_fragment_mover()

void setup_fragment_mover	(	core::pose::Pose &	_pose,
		protocols::loops::Loop &	_loop,
		vector< vector< protocols::moves::MoverOP > > &	_bbMovers,
		string	_polyAminoAcidOverride
	)

References basic::options::OptionKeys::nonlocal::chunks, basic::options::OptionKeys::frags::scoring::config, utility::io::oc::cout, create_a3b_hbs::j, basic::options::option, secstruct(), basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::in::file::vall.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("flexibleLoopDesign") ( "flexibleLoopDesign"  )

static

Referenced by main().