Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Functions
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 std::map< std::string, core::pose::PoseOP > protocols::swa::protein::PoseList

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 
)
void protocols::swa::protein::fix_end_phi_psi ( pose::Pose pose,
pose::Pose start_pose,
Size const &  start_res,
Size const &  end_res 
)
void protocols::swa::protein::fragment_set_slice ( core::fragment::ConstantLengthFragSetOP fragset,
utility::vector1< core::Size > const &  slice_res 
)
void protocols::swa::protein::generate_beta_database_test ( )
core::Real protocols::swa::protein::get_pretend_phi_explicit ( core::pose::Pose const &  pose,
Size const &  res 
)
core::Real protocols::swa::protein::get_pretend_psi_explicit ( core::pose::Pose const &  pose,
Size const &  res 
)
core::Real protocols::swa::protein::get_rotamer_angle ( core::Size const &  i,
core::Size const &  N_SAMPLE 
)
protocols::swa::protein::MainChainTorsionSet ( core::Real const &  phi,
core::Real const &  psi,
core::Real const &  omega 
)
core::Real const protocols::swa::protein::omega ( ) const
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 
)
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 
)
core::Real const protocols::swa::protein::phi ( ) const
core::Real const protocols::swa::protein::psi ( ) const
void protocols::swa::protein::reinstate_side_chain_angles ( pose::Pose pose,
pose::Pose const &  src_pose 
)
void protocols::swa::protein::remove_end_variants ( core::pose::Pose pose)
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 
)
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 
)
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 
)
protocols::swa::protein::~MainChainTorsionSet ( )