Rosetta 3.4
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protocols::swa Namespace Reference

Namespaces

namespace  protein
namespace  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 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)
bool possible_root (core::kinematics::FoldTree const &f, Size const &n)
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::AtomIDcreate_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &superimpose_res)
id::AtomID_Map< id::AtomIDcreate_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< Sizemerge_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 std::map< std::string, pose::PoseOP > protocols::swa::PoseList

Function Documentation

void protocols::swa::check_scorefxn_has_constraint_terms_if_pose_has_constraints ( pose::Pose const &  pose,
core::scoring::ScoreFunctionOP scorefxn 
)
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 
)
bool protocols::swa::Contain_seq_num ( Size const &  seq_num,
utility::vector1< core::Size > const &  residue_list 
)
utility::vector1< Size > const protocols::swa::convert_to_working_res ( utility::vector1< Size > const &  res_vector,
utility::vector1< Size > const &  working_res 
)
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 
)
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 
)
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 
)
void protocols::swa::create_euler_rotation ( Matrix M,
Real const &  alpha,
Real const &  beta,
Real const &  gamma 
)
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 
)
void protocols::swa::get_base_centroid_and_rotation_matrix ( pose::Pose const &  pose,
Size const  i,
Vector centroid,
Matrix M 
)
void protocols::swa::get_euler_angles ( Real alpha,
Real beta,
Real gamma,
Matrix  M1,
Matrix  M2,
bool const  verbose 
)
std::string protocols::swa::get_file_name ( std::string const &  silent_file,
std::string const &  tag 
)
bool protocols::swa::in_vector ( Size const &  i,
utility::vector1< Size > const &  vec 
)
void protocols::swa::initialize_input_streams ( utility::vector1< protocols::swa::InputStreamWithResidueInfoOP > &  input_streams)
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 
)
bool protocols::swa::Is_close_chain_break ( pose::Pose const &  pose)
utility::vector1< std::string > protocols::swa::load_s_and_l ( )
protocols::swa::MainChainTorsionSet ( core::Real const &  phi,
core::Real const &  psi 
)
protocols::swa::MainChainTorsionSet ( core::Real const &  phi,
core::Real const &  psi,
core::Real const &  omega 
)
Size protocols::swa::make_cut_at_moving_suite ( pose::Pose pose,
Size const &  moving_suite 
)
utility::vector1< Size > protocols::swa::merge_vectors ( utility::vector1< Size > const &  vec1,
utility::vector1< Size > const &  vec2 
)
core::Real const protocols::swa::omega ( ) const
void protocols::swa::Output_boolean ( std::string const &  tag,
bool  boolean 
)
void protocols::swa::Output_boolean ( bool  boolean)
void protocols::swa::Output_movemap ( kinematics::MoveMap const &  mm,
Size const  total_residue 
)
void protocols::swa::pdbslice ( core::pose::Pose new_pose,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  slice_res 
)
void protocols::swa::pdbslice ( core::pose::Pose pose,
utility::vector1< core::Size > const &  slice_res 
)

References pdbslice().

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

Referenced by protocols::protein_interface_design::filters::Torsion::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(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), protocols::loophash::LoopHashSampler::build_structures(), protocols::frag_picker::scores::MidPhiOut::cached_score(), core::chemical::ResidueType::calculate_icoor(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), core::optimization::cartesian_collect_torsional_deriv(), core::pose::copy_dofs(), protocols::pockets::correct_phi_psi(), protocols::frag_picker::scores::ProlinePhiScore::describe_score(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::frag_picker::scores::RamaScore::do_caching(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::MakeRotLib::dunbrack_print(), core::scoring::methods::CartesianBondedEnergy::eval_atom_derivative(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::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(), 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(), core::scoring::get_orientation(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::frag_picker::FragmentPicker::getFragSet(), core::scoring::hbonds::hb_energy_deriv_u2(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), protocols::features::ResidueConformationFeatures::load_conformation(), 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(), 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::Ab_H3_cter_insert_mover::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), protocols::frag_picker::FragmentPicker::read_spine_x(), core::chemical::read_topology_file(), protocols::frag_picker::scores::ProlinePhiScore::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), and protocols::comparative_modeling::features::TorsionFeature::values_from_pose().

bool protocols::swa::possible_root ( core::kinematics::FoldTree const &  f,
Size const &  n 
)
core::Real const protocols::swa::psi ( ) const

Referenced by protocols::protein_interface_design::filters::Torsion::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(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), protocols::loophash::LoopHashSampler::build_structures(), protocols::frag_picker::scores::MidPsiOut::cached_score(), core::util::ABEGO::check_rama(), protocols::frag_picker::scores::TorsionBinSimilarity::do_caching(), protocols::frag_picker::scores::RamaScore::do_caching(), protocols::frag_picker::scores::LAMBEGO_Similarity::do_caching(), protocols::MakeRotLib::dunbrack_print(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::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::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::frags::VallData::get_frags(), protocols::frags::RMSVallData::get_frags(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::frag_picker::FragmentPicker::getFragSet(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), protocols::features::ResidueConformationFeatures::load_conformation(), 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(), 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::Ab_H3_cter_insert_mover::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), protocols::frag_picker::FragmentPicker::read_spine_x(), protocols::frag_picker::scores::ProlinePhiScore::score(), core::util::ABEGOManager::torsion2index_level2(), core::util::ABEGOManager::torsion2index_level3(), and protocols::comparative_modeling::features::TorsionFeature::values_from_pose().

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

References rotate().

void protocols::swa::rotate ( pose::Pose pose,
Matrix const  M,
pose::Pose const &  ref_pose,
utility::vector1< Size > const &  moving_res,
Vector const &  centroid 
)
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 
)
void protocols::swa::translate ( pose::Pose pose,
Vector const  shift,
pose::Pose const &  ref_pose,
utility::vector1< Size > const &  moving_res 
)
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 
)
void protocols::swa::translate_and_rotate_residue_to_origin ( pose::Pose pose,
Size const  i 
)
void protocols::swa::virtualize_o2star ( pose::Pose pose)
protocols::swa::~MainChainTorsionSet ( )
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