protocols::swa Namespace Reference

Namespaces
	monte_carlo
	protein
	rna

Classes
class	InputStreamWithResidueInfo
class	MainChainTorsionSet
class	PoseFilter
class	PoseFilter_RMSD_Screen
class	RigidBodySampler
class	StepWiseClusterer
class	StepWiseCombineSampleGenerator
class	StepWiseDoNothingSampleGenerator
class	StepWiseFilterer
class	StepWiseIdentitySampleGenerator
class	StepWiseJobParameters
class	StepWisePoseCombineSampleGenerator
class	StepWisePoseSampleGenerator
class	StepWisePoseSetup
class	StepWiseResidueSampler
class	StepWiseScreener

Typedefs
typedef utility::pointer::owning_ptr < InputStreamWithResidueInfo >	InputStreamWithResidueInfoOP
typedef utility::pointer::owning_ptr < InputStreamWithResidueInfo const >	InputStreamWithResidueInfoCOP
typedef utility::vector1 < MainChainTorsionSet >	MainChainTorsionSetList
typedef utility::pointer::owning_ptr < PoseFilter >	PoseFilterOP
typedef utility::pointer::owning_ptr < PoseFilter const >	PoseFilterCOP
typedef utility::pointer::owning_ptr < RigidBodySampler >	RigidBodySamplerOP
typedef utility::pointer::owning_ptr < RigidBodySampler const >	RigidBodySamplerCOP
typedef utility::pointer::owning_ptr < StepWiseClusterer >	StepWiseClustererOP
typedef utility::pointer::owning_ptr < StepWiseClusterer const >	StepWiseClustererCOP
typedef std::map< std::string, core::pose::PoseOP >	PoseList
typedef utility::pointer::owning_ptr < StepWiseJobParameters >	StepWiseJobParametersOP
typedef utility::pointer::owning_ptr < StepWiseJobParameters const >	StepWiseJobParametersCOP
typedef utility::pointer::owning_ptr < StepWisePoseSampleGenerator >	StepWisePoseSampleGeneratorOP
typedef utility::pointer::owning_ptr < StepWisePoseSampleGenerator const >	StepWisePoseSampleGeneratorCOP
typedef utility::pointer::owning_ptr < StepWisePoseSetup >	StepWisePoseSetupOP
typedef utility::pointer::owning_ptr < StepWisePoseSetup const >	StepWisePoseSetupCOP
typedef std::map< core::Size, core::Size >	ResMap

Functions
core::import_pose::pose_stream::PoseInputStreamOP	setup_pose_input_stream (utility::options::StringVectorOption const &option_s1, utility::options::StringVectorOption const &option_silent1, utility::options::StringVectorOption const &option_tags1)
void	initialize_input_streams (utility::vector1< protocols::swa::InputStreamWithResidueInfoOP > &input_streams)
void	initialize_input_streams_with_residue_info (utility::vector1< InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< std::string > const &pdb_tags, utility::vector1< std::string > const &silent_files_in, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &input_res2)
	MainChainTorsionSet (core::Real const &phi, core::Real const &psi, core::Real const &omega)
	MainChainTorsionSet (core::Real const &phi, core::Real const &psi)
	~MainChainTorsionSet ()
core::Real const	phi () const
core::Real const	psi () const
core::Real const	omega () const
void	virtualize_o2star (pose::Pose &pose)
bool	in_vector (Size const &i, utility::vector1< Size > const &vec)
Size	make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)
bool	Is_close_chain_break (pose::Pose const &pose)
bool	Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
void	Output_boolean (std::string const &tag, bool boolean)
void	Output_boolean (bool boolean)
void	Output_movemap (kinematics::MoveMap const &mm, Size const total_residue)
void	Figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const &fixed_res, bool const move_takeoff_torsions, bool const move_jumps_between_chains)
void	pdbslice (core::pose::Pose &new_pose, core::pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)
void	pdbslice (core::pose::Pose &pose, utility::vector1< core::Size > const &slice_res)
id::AtomID_Map< id::AtomID >	create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &superimpose_res)
id::AtomID_Map< id::AtomID >	create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)
utility::vector1< Size > const	convert_to_working_res (utility::vector1< Size > const &res_vector, utility::vector1< Size > const &working_res)
core::scoring::constraints::ConstraintSetOP	constraint_set_slice (core::scoring::constraints::ConstraintSetOP &cst_set, utility::vector1< core::Size > const &slice_res, pose::Pose const &pose, pose::Pose const &full_pose)
utility::vector1< std::string >	load_s_and_l ()
std::string	get_file_name (std::string const &silent_file, std::string const &tag)
void	check_scorefxn_has_constraint_terms_if_pose_has_constraints (pose::Pose const &pose, core::scoring::ScoreFunctionOP &scorefxn)
utility::vector1< Size >	merge_vectors (utility::vector1< Size > const &vec1, utility::vector1< Size > const &vec2)
void	create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)
void	create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)
void	get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)
void	translate (pose::Pose &pose, Vector const shift, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
void	rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res, Vector const &centroid)
void	rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)
void	get_base_centroid_and_rotation_matrix (pose::Pose const &pose, Size const i, Vector &centroid, Matrix &M)
void	translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i, utility::vector1< Size > const moving_res, bool const do_not_rotate)
void	translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i)

Typedef Documentation

typedef utility::pointer::owning_ptr< InputStreamWithResidueInfo const > protocols::swa::InputStreamWithResidueInfoCOP

Definition at line 24 of file InputStreamWithResidueInfo.fwd.hh.

typedef utility::pointer::owning_ptr< InputStreamWithResidueInfo > protocols::swa::InputStreamWithResidueInfoOP

Definition at line 22 of file InputStreamWithResidueInfo.fwd.hh.

typedef utility::vector1< MainChainTorsionSet > protocols::swa::MainChainTorsionSetList

Definition at line 53 of file MainChainTorsionClasses.hh.

typedef utility::pointer::owning_ptr< PoseFilter const > protocols::swa::PoseFilterCOP

Definition at line 24 of file PoseFilter.fwd.hh.

typedef utility::pointer::owning_ptr< PoseFilter > protocols::swa::PoseFilterOP

Definition at line 22 of file PoseFilter.fwd.hh.

typedef std::map< std::string, pose::PoseOP > protocols::swa::PoseList

Definition at line 35 of file StepWiseFilterer.hh.

typedef std::map< core::Size, core::Size > protocols::swa::ResMap

Definition at line 39 of file StepWiseScreener.hh.

typedef utility::pointer::owning_ptr< RigidBodySampler const > protocols::swa::RigidBodySamplerCOP

Definition at line 24 of file RigidBodySampler.fwd.hh.

typedef utility::pointer::owning_ptr< RigidBodySampler > protocols::swa::RigidBodySamplerOP

Definition at line 22 of file RigidBodySampler.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseClusterer const > protocols::swa::StepWiseClustererCOP

Definition at line 24 of file StepWiseClusterer.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseClusterer > protocols::swa::StepWiseClustererOP

Definition at line 22 of file StepWiseClusterer.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseJobParameters const > protocols::swa::StepWiseJobParametersCOP

Definition at line 24 of file StepWiseJobParameters.fwd.hh.

typedef utility::pointer::owning_ptr< StepWiseJobParameters > protocols::swa::StepWiseJobParametersOP

Definition at line 22 of file StepWiseJobParameters.fwd.hh.

typedef utility::pointer::owning_ptr< StepWisePoseSampleGenerator const > protocols::swa::StepWisePoseSampleGeneratorCOP

Definition at line 24 of file StepWisePoseSampleGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< StepWisePoseSampleGenerator > protocols::swa::StepWisePoseSampleGeneratorOP

Definition at line 22 of file StepWisePoseSampleGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< StepWisePoseSetup const > protocols::swa::StepWisePoseSetupCOP

Definition at line 24 of file StepWisePoseSetup.fwd.hh.

typedef utility::pointer::owning_ptr< StepWisePoseSetup > protocols::swa::StepWisePoseSetupOP

Definition at line 22 of file StepWisePoseSetup.fwd.hh.

Function Documentation

void protocols::swa::check_scorefxn_has_constraint_terms_if_pose_has_constraints	(	pose::Pose const &	pose,
		core::scoring::ScoreFunctionOP &	scorefxn
	)

Definition at line 527 of file StepWiseUtil.cc.

References core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), and core::scoring::coordinate_constraint.

scoring::constraints::ConstraintSetOP protocols::swa::constraint_set_slice	(	core::scoring::constraints::ConstraintSetOP &	cst_set,
		utility::vector1< core::Size > const &	slice_res,
		pose::Pose const &	pose,
		pose::Pose const &	full_pose
	)

Definition at line 397 of file StepWiseUtil.cc.

References core::pose::Pose::total_residue().

Referenced by protocols::swa::StepWisePoseSetup::setup_constraints().

bool protocols::swa::Contain_seq_num	(	Size const &	seq_num,
		utility::vector1< core::Size > const &	residue_list
	)

Definition at line 100 of file StepWiseUtil.cc.

Referenced by protocols::swa::StepWisePoseSetup::check_superimpose_res(), and protocols::swa::StepWisePoseSetup::figure_out_jump_partners().

utility::vector1< Size > const protocols::swa::convert_to_working_res	(	utility::vector1< Size > const &	res_vector,
		utility::vector1< Size > const &	working_res
	)

Definition at line 368 of file StepWiseUtil.cc.

id::AtomID_Map< id::AtomID > protocols::swa::create_alignment_id_map	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		utility::vector1< core::Size > const &	superimpose_res
	)

Definition at line 316 of file StepWiseUtil.cc.

References core::scoring::rna::chemical_shift::Contain_seq_num(), protocols::swa::rna::create_alignment_id_map(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::RNA_DeNovoProtocol::align_and_output_to_silent_file(), protocols::swa::StepWisePoseSetup::align_poses(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::align_VDW_rep_screen_pose(), and protocols::swa::InputStreamWithResidueInfo::copy_next_pose_segment().

id::AtomID_Map< id::AtomID > protocols::swa::create_alignment_id_map	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::Size, core::Size >	res_map
	)

Definition at line 336 of file StepWiseUtil.cc.

References core::id::BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), protocols::swa::protein::setup_protein_backbone_atom_id_map(), protocols::swa::rna::setup_suite_atom_id_map(), and core::pose::Pose::total_residue().

void protocols::swa::create_euler_rotation	(	Matrix &	M,
		Real const &	alpha,
		Real const &	beta,
		Real const &	gamma,
		Vector const &	,
		Vector const &	axis2,
		Vector const &	axis3
	)

Definition at line 561 of file StepWiseUtil.cc.

Referenced by protocols::swa::RigidBodySampler::apply_rigid_body_settings(), create_euler_rotation(), get_euler_angles(), and protocols::swa::RigidBodySampler::search_rotations_and_translations().

void protocols::swa::create_euler_rotation	(	Matrix &	M,
		Real const &	alpha,
		Real const &	beta,
		Real const &	gamma
	)

Definition at line 581 of file StepWiseUtil.cc.

References create_euler_rotation().

void protocols::swa::Figure_out_moving_residues	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	fixed_res,
		bool const	move_takeoff_torsions,
		bool const	move_jumps_between_chains
	)

Definition at line 172 of file StepWiseUtil.cc.

References core::id::BB, core::id::CHI, core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_lower_terminus(), core::conformation::Residue::mainchain_torsions(), core::chemical::N_ACETYLATION, core::conformation::Residue::nchi(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::swa::protein::StepWiseProteinPoseMinimizer::apply().

void protocols::swa::get_base_centroid_and_rotation_matrix	(	pose::Pose const &	pose,
		Size const	i,
		Vector &	centroid,
		Matrix &	M
	)

Definition at line 716 of file StepWiseUtil.cc.

References core::pose::Pose::residue().

Referenced by translate_and_rotate_residue_to_origin().

void protocols::swa::get_euler_angles	(	Real &	alpha,
		Real &	beta,
		Real &	gamma,
		Matrix	M1,
		Matrix	M2,
		bool const	verbose
	)

Definition at line 595 of file StepWiseUtil.cc.

References create_euler_rotation().

std::string protocols::swa::get_file_name	(	std::string const &	silent_file,
		std::string const &	tag
	)

Definition at line 516 of file StepWiseUtil.cc.

Referenced by protocols::swa::protein::generate_beta_database_test().

bool protocols::swa::in_vector	(	Size const &	i,
		utility::vector1< Size > const &	vec
	)

Definition at line 540 of file RigidBodySampler.cc.

Referenced by protocols::swa::RigidBodySampler::check_num_hbonds().

void protocols::swa::initialize_input_streams

(

utility::vector1< protocols::swa::InputStreamWithResidueInfoOP > &

input_streams)

Definition at line 95 of file InputStreamWithResidueInfo.cc.

References initialize_input_streams_with_residue_info(), and setup_pose_input_stream().

void protocols::swa::initialize_input_streams_with_residue_info	(	utility::vector1< InputStreamWithResidueInfoOP > &	input_streams_with_residue_info,
		utility::vector1< std::string > const &	pdb_tags,
		utility::vector1< std::string > const &	silent_files_in,
		utility::vector1< core::Size > const &	input_res,
		utility::vector1< core::Size > const &	input_res2
	)

Definition at line 349 of file InputStreamWithResidueInfo.cc.

References protocols::swa::InputStreamWithResidueInfo::InputStreamWithResidueInfo().

Referenced by initialize_input_streams().

bool protocols::swa::Is_close_chain_break

(

pose::Pose const &

pose)

Definition at line 86 of file StepWiseUtil.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::StepWisePoseSetup::check_close_chain_break().

utility::vector1< std::string > protocols::swa::load_s_and_l

(

)

Definition at line 474 of file StepWiseUtil.cc.

References protocols::abinitio::filename().

Referenced by protocols::swa::protein::generate_beta_database_test().

protocols::swa::MainChainTorsionSet	(	core::Real const &	phi,
		core::Real const &	psi,
		core::Real const &	omega
	)

Definition at line 47 of file MainChainTorsionClasses.cc.

Referenced by protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_coarse(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_full(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only(), and protocols::swa::StepWiseScreener::StepWiseScreener().

protocols::swa::MainChainTorsionSet	(	core::Real const &	phi,
		core::Real const &	psi
	)

Definition at line 53 of file MainChainTorsionClasses.cc.

Size protocols::swa::make_cut_at_moving_suite	(	pose::Pose &	pose,
		Size const &	moving_suite
	)

Definition at line 66 of file StepWiseUtil.cc.

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::new_jump().

utility::vector1< Size > protocols::swa::merge_vectors	(	utility::vector1< Size > const &	vec1,
		utility::vector1< Size > const &	vec2
	)

Definition at line 544 of file StepWiseUtil.cc.

core::Real const protocols::swa::omega

(

)

const

Definition at line 63 of file MainChainTorsionClasses.cc.

void protocols::swa::Output_boolean	(	std::string const &	tag,
		bool	boolean
	)

Definition at line 111 of file StepWiseUtil.cc.

References protocols::comparative_modeling::features::A.

void protocols::swa::Output_boolean

(

bool

boolean)

Definition at line 126 of file StepWiseUtil.cc.

References protocols::comparative_modeling::features::A.

void protocols::swa::Output_movemap	(	kinematics::MoveMap const &	mm,
		Size const	total_residue
	)

Definition at line 140 of file StepWiseUtil.cc.

References protocols::comparative_modeling::features::A, core::id::BB, core::id::CHI, core::kinematics::MoveMap::get(), and protocols::swa::rna::Output_boolean().

void protocols::swa::pdbslice	(	core::pose::Pose &	new_pose,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	slice_res
	)

Definition at line 261 of file StepWiseUtil.cc.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::scoring::rna::chi1_torsion_atom(), core::pose::Pose::clear(), core::conformation::Residue::clone(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Referenced by protocols::swa::StepWiseClusterer::do_some_clustering(), protocols::swa::StepWisePoseSetup::make_pose(), and pdbslice().

void protocols::swa::pdbslice	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	slice_res
	)

Definition at line 305 of file StepWiseUtil.cc.

References pdbslice().

core::Real const protocols::swa::phi

(

)

const

Definition at line 61 of file MainChainTorsionClasses.cc.

Referenced by protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::movers::Splice::apply(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), protocols::frag_picker::scores::MidPhiOut::cached_score(), core::chemical::ResidueType::calculate_icoor(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), core::pose::copy_dofs(), protocols::frag_picker::scores::ProlinePhiScore::describe_score(), protocols::frag_picker::scores::RamaScore::do_caching(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::cartesian::MolecularDynamics::doDihedralDerivatives(), protocols::sic_dock::dump_loophash_linkers(), protocols::MakeRotLib::dunbrack_print(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsions_derivatives(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbind(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::swa::StepWiseScreener::filter_native_BIG_BINS(), core::scoring::rna::fix_sugar_coords(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::frags::VallData::get_frags(), protocols::frags::RMSVallData::get_frags(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_full(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only(), core::scoring::get_orientation(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::sic_dock::get_xform_stats(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::sparta::Sparta::SpartaLib::getResInfo(), core::scoring::hbonds::hb_energy_deriv_u2(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), core::io::silent::ProteinSilentStruct_Template< T >::operator=(), OPT_1GRP_KEY(), core::scoring::P_AA::P_AA_pp_energy(), core::chemical::patch_operation_from_patch_file_line(), core::io::silent::ProteinSilentStruct_Template< T >::print_conformation(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::geometry::random_reorientation_matrix(), core::kinematics::Jump::random_trans(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_bbdep_continuous_minimization_data(), protocols::frags::VallData::read_file(), protocols::frags::RMSVallData::read_file(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), protocols::antibody2::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), core::scoring::P_AA::read_P_AA_pp(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotameric_data(), protocols::frag_picker::FragmentPicker::read_spine_x(), core::scoring::OmegaTether::read_table_from_stream(), core::chemical::read_topology_file(), protocols::protein_interface_design::movers::Splice::read_torsion_database(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::frag_picker::scores::ProlinePhiScore::score(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::cartesian::MolecularDynamics::setDihedralDerivatives(), protocols::comparative_modeling::features::TorsionFeature::values_from_pose(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema(), protocols::features::ProteinBackboneTorsionAngleFeatures::write_protein_backbone_torsion_angles_table_schema(), core::chemical::ResidueDatabaseIO::write_residue_type_icoor_table_schema(), protocols::features::ProteinResidueConformationFeatures::write_schema_to_db(), and protocols::features::ResidueConformationFeatures::write_schema_to_db().

core::Real const protocols::swa::psi

(

)

const

Definition at line 62 of file MainChainTorsionClasses.cc.

Referenced by protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::movers::Splice::apply(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), protocols::frag_picker::scores::MidPsiOut::cached_score(), core::util::ABEGO::check_rama(), protocols::frag_picker::scores::RamaScore::do_caching(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::sic_dock::dump_loophash_linkers(), protocols::MakeRotLib::dunbrack_print(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbind(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::swa::StepWiseScreener::filter_native_BIG_BINS(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::frags::VallData::get_frags(), protocols::frags::RMSVallData::get_frags(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_full(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::sic_dock::get_xform_stats(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::sparta::Sparta::SpartaLib::getResInfo(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), core::io::silent::ProteinSilentStruct_Template< T >::operator=(), OPT_1GRP_KEY(), core::scoring::P_AA::P_AA_pp_energy(), core::io::silent::ProteinSilentStruct_Template< T >::print_conformation(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::geometry::random_reorientation_matrix(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_bbdep_continuous_minimization_data(), protocols::frags::VallData::read_file(), protocols::frags::RMSVallData::read_file(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), protocols::antibody2::H3CterInsert::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), core::scoring::P_AA::read_P_AA_pp(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotameric_data(), protocols::frag_picker::FragmentPicker::read_spine_x(), core::scoring::OmegaTether::read_table_from_stream(), protocols::protein_interface_design::movers::Splice::read_torsion_database(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::SaltBridgeFeatures::report_features(), protocols::frag_picker::scores::ProlinePhiScore::score(), core::util::ABEGOManager::torsion2index_level2(), core::util::ABEGOManager::torsion2index_level3(), core::util::ABEGOManager::torsion2index_level4(), protocols::comparative_modeling::features::TorsionFeature::values_from_pose(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::verify_phipsi_bins(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_table_schema(), protocols::features::LoopAnchorFeatures::write_loop_anchor_transforms_three_res_table_schema(), protocols::features::ProteinBackboneTorsionAngleFeatures::write_protein_backbone_torsion_angles_table_schema(), protocols::features::SaltBridgeFeatures::write_salt_bridges_table_schema(), protocols::features::ProteinResidueConformationFeatures::write_schema_to_db(), and protocols::features::ResidueConformationFeatures::write_schema_to_db().

void protocols::swa::rotate	(	pose::Pose &	pose,
		Matrix const	M,
		pose::Pose const &	ref_pose,
		utility::vector1< Size > const &	moving_res,
		Vector const &	centroid
	)

Definition at line 686 of file StepWiseUtil.cc.

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::ligand_docking::Rotates::apply(), protocols::swa::RigidBodySampler::apply_rigid_body_settings(), core::chemical::read_topology_file(), rotate(), protocols::swa::RigidBodySampler::search_rotations_and_translations(), and translate_and_rotate_residue_to_origin().

void protocols::swa::rotate	(	pose::Pose &	pose,
		Matrix const	M,
		pose::Pose const &	ref_pose,
		utility::vector1< Size > const &	moving_res
	)

Definition at line 706 of file StepWiseUtil.cc.

References rotate().

core::import_pose::pose_stream::PoseInputStreamOP protocols::swa::setup_pose_input_stream	(	utility::options::StringVectorOption const &	option_s1,
		utility::options::StringVectorOption const &	option_silent1,
		utility::options::StringVectorOption const &	option_tags1
	)

Definition at line 60 of file InputStreamWithResidueInfo.cc.

Referenced by initialize_input_streams().

void protocols::swa::translate	(	pose::Pose &	pose,
		Vector const	shift,
		pose::Pose const &	ref_pose,
		utility::vector1< Size > const &	moving_res
	)

Definition at line 666 of file StepWiseUtil.cc.

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::ligand_docking::CompoundTranslate::apply(), protocols::swa::RigidBodySampler::apply_rigid_body_settings(), protocols::simple_moves::ddG::calculate(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::swa::RigidBodySampler::figure_out_reference_energy(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::simple_moves::ddG::no_repack_ddG(), protocols::ligand_docking::CompoundTranslate::parse_my_tag(), protocols::protein_interface_design::movers::part_complex(), protocols::hybridization::DomainAssembly::run(), protocols::swa::RigidBodySampler::search_translations(), protocols::simple_moves::ddG::symm_ddG(), and translate_and_rotate_residue_to_origin().

void protocols::swa::translate_and_rotate_residue_to_origin	(	pose::Pose &	pose,
		Size const	i,
		utility::vector1< Size > const	moving_res,
		bool const	do_not_rotate
	)

Definition at line 729 of file StepWiseUtil.cc.

References get_base_centroid_and_rotation_matrix(), rotate(), and translate().

Referenced by translate_and_rotate_residue_to_origin().

void protocols::swa::translate_and_rotate_residue_to_origin	(	pose::Pose &	pose,
		Size const	i
	)

Definition at line 743 of file StepWiseUtil.cc.

References translate_and_rotate_residue_to_origin().

void protocols::swa::virtualize_o2star

(

pose::Pose &

pose)

Definition at line 210 of file RigidBodySampler.cc.

References core::pose::add_variant_type_to_pose_residue(), and core::pose::Pose::total_residue().

Referenced by protocols::swa::RigidBodySampler::search_translations().

protocols::swa::~MainChainTorsionSet

(

)

Definition at line 59 of file MainChainTorsionClasses.cc.