loop_model.hh File Reference

#include <devel/dna/protocols.hh>
#include <devel/dna/util.hh>
#include <protocols/frags/VallData.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/frags/TorsionFragment.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/rigid_body_moves.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/dna/DNA_BasePotential.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/AtomVDW.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/energy_methods/FA_ElecEnergy.hh>
#include <core/scoring/etable/count_pair/CountPairAll.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/scoring/etable/count_pair/CountPairFactory.hh>
#include <core/types.hh>
#include <core/chemical/ResidueSelector.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/util.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rotamer_set/WaterPackingInfo.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/visualize.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/prof.hh>
#include <basic/basic.hh>
#include <core/id/SequenceMapping.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <iosfwd>
#include <string>
#include <set>
#include <cstdlib>
#include <math.h>
#include <basic/options/keys/loops.OptionKeys.gen.hh>

Typedefs
typedef utility::vector1< std::pair< std::string, Size > >	SS_Quotas

Functions
void	setup_loops_from_mapping (pose::Pose &pose, id::SequenceMapping const &mapping, protocols::loops::Loops &loops, bool const start_extended)
void	setup_loops_fragment_libraries_with_ss (std::string const target_seq, protocols::loops::Loops const &loops, std::map< Size, protocols::frags::TorsionFragmentLibraryOP > &frag_libs, std::map< Size, bool > &frag_libs_init, SS_Quotas const &ss_quotas, std::map< Size, Real > const &ss_weight)
void	setup_frags_from_vall (pose::Pose const &pose, protocols::loops::Loops const &loops, std::map< Size, protocols::frags::TorsionFragmentLibraryOP > &frag_libs, std::map< Size, bool > &frag_libs_init, SS_Quotas const &ss_quotas=empty_ss_quotas, bool const pick_6mers=false)
void	full_protein_repack (pose::Pose &pose, ScoreFunction const &scorefxn)

Variables
static SS_Quotas const	empty_ss_quotas

Typedef Documentation

SS_Quotas

typedef utility::vector1< std::pair< std::string, Size > > SS_Quotas

Function Documentation

full_protein_repack()

void full_protein_repack	(	pose::Pose &	pose,
		ScoreFunction const &	scorefxn
	)

References create_a3b_hbs::ii, basic::options::OptionKeys::dna::specificity::nloop, beta_nonlocal::pose, oop_conformations::scorefxn, and vancomycin::task.

Referenced by capri_t033_loop_test(), capri_t033_trim_dock_test(), juke_sam_pos(), and sample_rna_dofs_new().

setup_frags_from_vall()

void setup_frags_from_vall	(	pose::Pose const &	pose,
		protocols::loops::Loops const &	loops,
		std::map< Size, protocols::frags::TorsionFragmentLibraryOP > &	frag_libs,
		std::map< Size, bool > &	frag_libs_init,
		SS_Quotas const &	ss_quotas = empty_ss_quotas,
		bool const	pick_6mers = false
	)

fragment setup:

1. pick 3mer library from vall
2. derive 1mer libary from 3mers

References usec::frag_size, basic::options::OptionKeys::frags::frags, beta_nonlocal::pose, and setup_loops_fragment_libraries_with_ss().

Referenced by capri_t033_loop_test(), diversify_sam_loop_test(), and rebuild_trimmed_loops().

setup_loops_fragment_libraries_with_ss()

void setup_loops_fragment_libraries_with_ss	(	std::string const	target_seq,
		protocols::loops::Loops const &	loops,
		std::map< Size, protocols::frags::TorsionFragmentLibraryOP > &	frag_libs,
		std::map< Size, bool > &	frag_libs_init,
		SS_Quotas const &	ss_quotas,
		std::map< Size, Real > const &	ss_weight
	)

References usec::frag_size, create_a3b_hbs::i, subloop_histogram::iterator, demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, name, basic::options::OptionKeys::ddg::nfrags, create_a3b_hbs::nres, option, secstruct(), basic::options::OptionKeys::in::file::vall, and basic::options::OptionKeys::loops::vall_file.

Referenced by setup_frags_from_vall().

setup_loops_from_mapping()

void setup_loops_from_mapping	(	pose::Pose &	pose,
		id::SequenceMapping const &	mapping,
		protocols::loops::Loops &	loops,
		bool const	start_extended
	)

stochastic – choose cutpoints, may update pose foldtree

Note

mapping goes from the source pdb to the target sequence, and has already been extended and applied, ie the sequence of pose is the target sequence and pose.size() == mapping.size2()

CURRENTLY SKIPS TERMINAL LOOPS FOR HISTORICAL REASONS!!!

References loops::cutpoint, create_a3b_hbs::i, demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, beta_nonlocal::pose, numeric::random::uniform(), and utility_exit_with_message.

Referenced by capri_t033_loop_test(), rebuild_trimmed_loops(), and relax_test().

Variable Documentation

empty_ss_quotas

SS_Quotas const empty_ss_quotas

static