capri15_scoring.hh File Reference

#include <devel/dna/protocols.hh>
#include <devel/dna/util.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/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 <iosfwd>
#include <sstream>
#include <string>
#include <set>
#include <cstdlib>
#include <math.h>
#include <basic/Tracer.hh>

Classes
class	CapriData
class	CapriTwoBodyEnergy
class	CapriTotalEnergy

Typedefs
typedef utility::pointer::owning_ptr< CapriData >	CapriDataOP

Enumerations
enum	CapriScoreType {   BLUE = 1 , CYAN , PINK , RED ,   n_experimental_constraint_scores = RED }

Functions
id::AtomID	pid (std::string const &name, Size const seqpos, pose::Pose const &pose)
CapriData const &	retrieve_capri_data_from_pose (pose::Pose const &pose)
void	setup_capri_data (pose::Pose &pose, std::string const &pssm_file, id::SequenceMapping const &fasta2pose)

Typedef Documentation

CapriDataOP

typedef utility::pointer::owning_ptr< CapriData > CapriDataOP

Enumeration Type Documentation

CapriScoreType

enum CapriScoreType

Enumerator
BLUE
CYAN
PINK
RED
n_experimental_constraint_scores

Function Documentation

pid()

id::AtomID pid	(	std::string const &	name,
		Size const	seqpos,
		pose::Pose const &	pose
	)

Helper for the constraints setup below

References name, and beta_nonlocal::pose.

Referenced by capri_t033_trim_dock_test(), basic::execute(), utility::options::OptionCollection::find_key_cl(), basic::get_usage_from_procfilesystem(), main(), CapriTotalEnergy::setup_rna_atoms_for_pose(), and setup_sam_constraints().

retrieve_capri_data_from_pose()

CapriData const& retrieve_capri_data_from_pose ( pose::Pose const &  pose )

inline

References beta_nonlocal::pose.

Referenced by CapriTotalEnergy::finalize_total_energy(), and sample_rna_dofs_new().

setup_capri_data()

void setup_capri_data	(	pose::Pose &	pose,
		std::string const &	pssm_file,
		id::SequenceMapping const &	fasta2pose
	)

References data, getline(), create_a3b_hbs::i, extract_by_sidechain_sasa_score::l, line, beta_nonlocal::pose, beta_sc_scan::seq, tag, and utility_exit_with_message.

Referenced by capri_t033_centroid_trim_dock_test(), centroid_rescore_test(), rebuild_trimmed_loops(), relax_test(), trim_dock_rebuild_relax_test(), and trim_dock_rebuild_relax_test_rhiju().