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protocols::swa::protein Namespace Reference

Classes

class  MainChainTorsionSet
 
class  StepWiseBetaAntiParallelJumpSampleGenerator
 
class  StepWiseProteinCCD_Closer
 
class  StepWiseProteinFilterer
 
class  StepWiseProteinFragmentSampleGenerator
 
class  StepWiseProteinJumpSampleGenerator
 
class  StepWiseProteinLoopBridger
 
class  StepWiseProteinMainChainSampleGenerator
 
class  StepWiseProteinPacker
 
class  StepWiseProteinPoseMinimizer
 
class  StepWiseProteinPoseSetup
 
class  StepWiseProteinResidueSampler
 
class  StepWiseProteinScreener
 

Typedefs

typedef utility::vector1
< MainChainTorsionSet > 		MainChainTorsionSetList
 
typedef std::map< std::string,
core::pose::PoseOP > 		PoseList
 
typedef std::map< core::Size,
core::Size > 		ResMap
 

Functions

 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 do_set_xyz (pose::Pose const &pose, Size const i, pose::Pose &scratch_pose, Size const i_scratch, core::kinematics::Stub const &stub)
 
void generate_beta_database_test ()
 
void fix_end_phi_psi (pose::Pose &pose, pose::Pose &start_pose, Size const &start_res, Size const &end_res)
 
void reinstate_side_chain_angles (pose::Pose &pose, pose::Pose const &src_pose)
 
Real get_rotamer_angle (core::Size const &i, core::Size const &N_SAMPLE)
 
void output_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const &silent_file, std::string const &tag, core::io::silent::SilentFileDataOP sfd_in)
 
void output_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const &silent_file, std::string const &tag, core::io::silent::SilentFileDataOP sfd_in, utility::vector1< core::Size > const &calc_rms_res)
 
void remove_end_variants (core::pose::Pose &pose)
 
Real get_pretend_psi_explicit (core::pose::Pose const &pose, Size const &res)
 
Real get_pretend_phi_explicit (core::pose::Pose const &pose, Size const &res)
 
void setup_protein_CA_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, Size const base_res, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)
 
void setup_protein_backbone_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, Size const base_res, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)
 
void setup_protein_backbone_atom_id_map (core::pose::Pose const &pose_1, core::pose::Pose const &pose_2, Size const base_res, Size const base_res2, core::id::AtomID_Map< core::id::AtomID > &atom_ID_map)
 
void fragment_set_slice (core::fragment::ConstantLengthFragSetOP &fragset, utility::vector1< core::Size > const &slice_res)
 

Typedef Documentation

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

Definition at line 54 of file MainChainTorsionClasses.hh.

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

Definition at line 36 of file StepWiseProteinPoseSetup.hh.

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

Definition at line 39 of file StepWiseProteinScreener.hh.

Function Documentation

void protocols::swa::protein::do_set_xyz ( pose::Pose const &  pose,
Size const  i,
pose::Pose &  scratch_pose,
Size const  i_scratch,
core::kinematics::Stub const &  stub 
)

Definition at line 72 of file StepWiseBetaAntiParallelUtil.cc.

References core::kinematics::Stub::global2local(), core::chemical::ResidueType::has(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by generate_beta_database_test().

void protocols::swa::protein::fix_end_phi_psi ( pose::Pose &  pose,
pose::Pose &  start_pose,
Size const &  start_res,
Size const &  end_res 
)

Definition at line 98 of file StepWiseProteinPoseSetup.cc.

References get_pretend_phi_explicit(), get_pretend_psi_explicit(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

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

void protocols::swa::protein::fragment_set_slice ( core::fragment::ConstantLengthFragSetOP &  fragset,
utility::vector1< core::Size > const &  slice_res 
)

Definition at line 256 of file StepWiseProteinUtil.cc.

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

void protocols::swa::protein::generate_beta_database_test ( )

Definition at line 109 of file StepWiseBetaAntiParallelUtil.cc.

References protocols::swa::StepWiseClusterer::cluster(), protocols::swa::StepWiseClusterer::clustered_pose_list(), do_set_xyz(), core::scoring::hbonds::HBond::don_res(), core::chemical::FA_STANDARD, core::scoring::hbonds::fill_hbond_set(), protocols::swa::get_file_name(), core::chemical::ChemicalManager::get_instance(), core::scoring::getScoreFunction(), protocols::swa::load_s_and_l(), core::chemical::LOWER_TERMINUS, core::pose::make_pose_from_sequence(), core::kinematics::FoldTree::new_jump(), protocols::swa::StepWiseClusterer::output_silent_file(), core::import_pose::pose_from_pdb(), core::pose::remove_variant_type_from_pose_residue(), core::chemical::ChemicalManager::residue_type_set(), protocols::swa::StepWiseClusterer::set_calc_rms_res(), protocols::swa::StepWiseClusterer::set_cluster_radius(), protocols::swa::StepWiseClusterer::set_max_decoys(), protocols::swa::StepWiseClusterer::set_rename_tags(), protocols::swa::StepWiseClusterer::set_score_diff_cut(), and core::chemical::UPPER_TERMINUS.

core::Real protocols::swa::protein::get_pretend_phi_explicit ( core::pose::Pose const &  pose,
Size const &  res 
)

Definition at line 159 of file StepWiseProteinUtil.cc.

References core::conformation::Residue::has(), phi(), core::pose::Pose::residue(), and core::pose::Pose::xyz().

Referenced by fix_end_phi_psi(), protocols::swa::StepWisePoseSetup::fix_phi_psi_offsets(), protocols::swa::StepWisePoseSetup::initialize_phi_psi_offsets(), and protocols::swa::StepWisePoseSetup::save_phi_psi_offsets().

core::Real protocols::swa::protein::get_pretend_psi_explicit ( core::pose::Pose const &  pose,
Size const &  res 
)

Definition at line 140 of file StepWiseProteinUtil.cc.

References psi(), and core::pose::Pose::xyz().

Referenced by fix_end_phi_psi(), protocols::swa::StepWisePoseSetup::fix_phi_psi_offsets(), protocols::swa::StepWisePoseSetup::initialize_phi_psi_offsets(), and protocols::swa::StepWisePoseSetup::save_phi_psi_offsets().

core::Real protocols::swa::protein::get_rotamer_angle ( core::Size const &  i,
core::Size const &  N_SAMPLE 
)

Definition at line 60 of file StepWiseProteinUtil.cc.

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

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

Definition at line 48 of file MainChainTorsionClasses.cc.

Referenced by protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_coarse(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_full(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::swa::protein::StepWiseProteinScreener::sample_cis_omega(), and protocols::swa::protein::StepWiseProteinScreener::setup_torsion_sets().

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

Definition at line 54 of file MainChainTorsionClasses.cc.

core::Real const protocols::swa::protein::omega ( ) const

Definition at line 64 of file MainChainTorsionClasses.cc.

Referenced by protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists_real().

void protocols::swa::protein::output_silent_struct ( core::pose::Pose const &  pose,
core::pose::PoseCOP const &  native_pose_op,
std::string const &  silent_file,
std::string const &  tag,
core::io::silent::SilentFileDataOP  sfd_in 
)

Definition at line 67 of file StepWiseProteinUtil.cc.

Referenced by protocols::swa::protein::StepWiseProteinPoseMinimizer::apply(), protocols::swa::StepWiseScreener::filter_and_output(), protocols::swa::protein::StepWiseProteinScreener::filter_and_output(), protocols::swa::StepWiseResidueSampler::sample_residues(), protocols::swa::protein::StepWiseProteinPacker::sample_residues(), and protocols::swa::protein::StepWiseProteinResidueSampler::sample_residues().

void protocols::swa::protein::output_silent_struct ( core::pose::Pose const &  pose,
core::pose::PoseCOP const &  native_pose_op,
std::string const &  silent_file,
std::string const &  tag,
core::io::silent::SilentFileDataOP  sfd_in,
utility::vector1< core::Size > const &  calc_rms_res 
)

Definition at line 77 of file StepWiseProteinUtil.cc.

References core::io::silent::SilentStruct::add_energy(), core::scoring::rms_at_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms_no_super(), core::scoring::setup_matching_CA_atoms(), core::scoring::setup_matching_heavy_atoms(), core::scoring::setup_matching_protein_backbone_heavy_atoms(), and core::io::silent::SilentFileData::write_silent_struct().

core::Real const protocols::swa::protein::phi ( ) const

Definition at line 62 of file MainChainTorsionClasses.cc.

Referenced by protocols::swa::protein::StepWiseProteinScreener::filter_big_bin(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_full(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only(), get_pretend_phi_explicit(), protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists_real(), and protocols::swa::protein::StepWiseProteinScreener::sample_cis_omega().

core::Real const protocols::swa::protein::psi ( ) const

Definition at line 63 of file MainChainTorsionClasses.cc.

Referenced by protocols::swa::protein::StepWiseProteinScreener::filter_big_bin(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_full(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only(), get_pretend_psi_explicit(), protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists_real(), and protocols::swa::protein::StepWiseProteinScreener::sample_cis_omega().

void protocols::swa::protein::reinstate_side_chain_angles ( pose::Pose &  pose,
pose::Pose const &  src_pose 
)

Definition at line 374 of file StepWiseProteinResidueSampler.cc.

References core::pose::Pose::chi(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue_type(), core::pose::Pose::set_chi(), and core::pose::Pose::total_residue().

void protocols::swa::protein::remove_end_variants ( core::pose::Pose &  pose)

Definition at line 126 of file StepWiseProteinUtil.cc.

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

void protocols::swa::protein::setup_protein_backbone_atom_id_map ( core::pose::Pose const &  pose_1,
core::pose::Pose const &  pose_2,
Size const  base_res,
core::id::AtomID_Map< core::id::AtomID > &  atom_ID_map 
)

Definition at line 207 of file StepWiseProteinUtil.cc.

Referenced by protocols::swa::create_alignment_id_map().

void protocols::swa::protein::setup_protein_backbone_atom_id_map ( core::pose::Pose const &  pose_1,
core::pose::Pose const &  pose_2,
Size const  base_res,
Size const  base_res2,
core::id::AtomID_Map< core::id::AtomID > &  atom_ID_map 
)

Definition at line 216 of file StepWiseProteinUtil.cc.

References core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_protein(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::set().

void protocols::swa::protein::setup_protein_CA_atom_id_map ( core::pose::Pose const &  pose_1,
core::pose::Pose const &  pose_2,
Size const  base_res,
core::id::AtomID_Map< core::id::AtomID > &  atom_ID_map 
)

Definition at line 189 of file StepWiseProteinUtil.cc.

References core::chemical::ResidueType::is_protein(), core::pose::named_atom_id_to_atom_id(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::set().

protocols::swa::protein::~MainChainTorsionSet ( )

Definition at line 60 of file MainChainTorsionClasses.cc.

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