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protocols::mpi_refinement Namespace Reference

Classes

class  Clusterer
 
struct  MethodParams
 
class  MPI_Refine_Emperor
 
class  MPI_Refine_Master
 
class  MPI_Refinement
 
class  MultiObjective
 
class  Scheduler
 
class  Serial_Refine
 
class  StructAvrgMover
 
class  WorkUnit_bbGauss
 
class  WorkUnit_CombinePose
 
class  WorkUnit_FragInsert
 
class  WorkUnit_KicCloser
 
class  WorkUnit_LoopHash
 
class  WorkUnit_MD
 
class  WorkUnit_NormalMode
 
class  WorkUnit_PartialAbinitio
 
class  WorkUnit_RamaPerturber
 
class  WorkUnit_Relax
 
class  WorkUnit_Sampler
 

Typedefs

typedef
utility::pointer::shared_ptr
< MultiObjective
MultiObjectiveOP
 
typedef
utility::pointer::shared_ptr
< MultiObjective const > 
MultiObjectiveCOP
 
typedef
utility::pointer::shared_ptr
< WorkUnit_Sampler
WorkUnit_SamplerOP
 
typedef
utility::pointer::shared_ptr
< WorkUnit_Sampler const > 
WorkUnit_SamplerCOP
 

Functions

static basic::Tracer TR ("MPI.LHR.C")
 
static basic::Tracer TR ("MPI.LHR.E")
 
static basic::Tracer TR ("MPI.LHR.M")
 
static basic::Tracer TR ("MPI.LHR.A")
 
static basic::Tracer TR ("MPI.LHR.O")
 
static basic::Tracer TR ("MPI.LHR.S")
 
static basic::Tracer TR ("protocols.mpi_refinement.SerialRefine")
 
static basic::Tracer TR ("MPI.LHR.StructAvrger")
 
utility::vector1< std::pair
< core::Size, core::Size > > 
get_loop_info_full (core::io::silent::SilentStructOP ss, utility::vector1< bool > &is_terminus, std::string const &mode)
 
void get_loop_info (core::io::silent::SilentStructOP ss, core::Size &res1, core::Size &res2, bool &is_terminus)
 
void constrain_residue (core::pose::Pose &pose, core::Size const resno, utility::vector1< core::Size > exclres, std::string const &cst_type, core::Real const stdev)
 
utility::vector1< core::Sizeget_touched_res (core::pose::Pose const pose, utility::vector1< core::Size > const loopres, core::Real dist_cut)
 
protocols::minimization_packing::PackRotamersMoverOP setup_packer (core::pose::Pose const &pose, core::kinematics::MoveMap const mm, core::scoring::ScoreFunctionCOP sfxn)
 
void add_movemap_from_loopres (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const loopres, bool const nonideal)
 
void ramp_minpack_loop (core::pose::Pose &pose, utility::vector1< core::Size > const loopres, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal, bool const ramp, bool const efficient, bool const envmin)
 
void ramp_minpack_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal, bool const ramp)
 
void add_poseinfo_to_ss (core::io::silent::SilentStruct &ss, core::pose::Pose const &ref_pose, std::string const &suffix)
 
core::Real Zscore_to_library (core::Real const score, core::Real const mean, core::Real const stdev, core::Real const maxval, core::Real const minval)
 
utility::vector1< core::Sizeloopstring_to_loopvector (std::string const &loopstr, core::Size const ext)
 
utility::vector1
< utility::vector1< core::Size > > 
loopstring_to_loopregions (std::string const &loopstr)
 
void copy_pose_crd (core::pose::Pose const pose_frame, core::pose::Pose &pose_work, utility::vector1< utility::vector1< core::Size > > const loopregions)
 
void mean_and_stdev (utility::vector1< core::Real > values, core::Real const frac, core::Real &shave_cut, core::Real &mean, core::Real &stdev)
 
void superimpose_all (core::io::silent::SilentStructCOP ss_ref, protocols::wum::SilentStructStore &structs, utility::vector1< std::string > const columns_copy)
 
core::Real CA_Sscore (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, core::Real &rmsd, utility::vector1< core::Size > const &loopres, bool const superimpose, core::Real const dbase)
 
core::Real CA_Sscore (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, core::Real &rmsd, bool const superimpose, core::Real const dbase)
 
core::Real distance (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, std::string const &similarity_measure, bool const superimpose)
 
void add_init_dev_penalty (core::io::silent::SilentStructOP ss, ObjexxFCL::FArray2D< core::Real > const init_xyz, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
 
void add_init_dev_penalty (core::io::silent::SilentStructOP ss, core::pose::Pose pose0, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
 
void add_init_dev_penalty (protocols::wum::SilentStructStore &structs, core::pose::Pose const pose0, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
 
std::map< core::Size,
utility::vector1< core::Real > > 
read_ss2 (std::string ssfile)
 
static basic::Tracer TR ("WorkUnit_Sampler.AggressiveType")
 
static basic::Tracer TR ("WorkUnit_Sampler.LoopType")
 
static basic::Tracer TR ("WorkUnit_Sampler.Relax")
 
static basic::Tracer TR ("WorkUnit_Sampler")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< MultiObjective const > protocols::mpi_refinement::MultiObjectiveCOP
typedef utility::pointer::shared_ptr< MultiObjective > protocols::mpi_refinement::MultiObjectiveOP
typedef utility::pointer::shared_ptr< WorkUnit_Sampler const > protocols::mpi_refinement::WorkUnit_SamplerCOP
typedef utility::pointer::shared_ptr< WorkUnit_Sampler > protocols::mpi_refinement::WorkUnit_SamplerOP

Function Documentation

void protocols::mpi_refinement::add_init_dev_penalty ( core::io::silent::SilentStructOP  ss,
ObjexxFCL::FArray2D< core::Real > const  init_xyz,
std::string const &  mode,
core::Real const  iha_cut,
core::Real const  iha_penalty_slope 
)
void protocols::mpi_refinement::add_init_dev_penalty ( core::io::silent::SilentStructOP  ss,
core::pose::Pose  pose0,
std::string const &  mode,
core::Real const  iha_cut,
core::Real const  iha_penalty_slope 
)
void protocols::mpi_refinement::add_init_dev_penalty ( protocols::wum::SilentStructStore structs,
core::pose::Pose const  pose0,
std::string const &  mode,
core::Real const  iha_cut,
core::Real const  iha_penalty_slope 
)
void protocols::mpi_refinement::add_movemap_from_loopres ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const  loopres,
bool const  nonideal 
)
void protocols::mpi_refinement::add_poseinfo_to_ss ( core::io::silent::SilentStruct ss,
core::pose::Pose const &  ref_pose,
std::string const &  suffix 
)
core::Real protocols::mpi_refinement::CA_Sscore ( core::io::silent::SilentStructOP  ss1,
core::io::silent::SilentStructOP  ss2,
core::Real rmsd,
utility::vector1< core::Size > const &  loopres,
bool const  superimpose,
core::Real const  dbase 
)
core::Real protocols::mpi_refinement::CA_Sscore ( core::io::silent::SilentStructOP  ss1,
core::io::silent::SilentStructOP  ss2,
core::Real rmsd,
bool const  superimpose,
core::Real const  dbase 
)

References CA_Sscore().

void protocols::mpi_refinement::constrain_residue ( core::pose::Pose pose,
core::Size const  resno,
utility::vector1< core::Size exclres,
std::string const &  cst_type,
core::Real const  stdev 
)
void protocols::mpi_refinement::copy_pose_crd ( core::pose::Pose const  pose_frame,
core::pose::Pose pose_work,
utility::vector1< utility::vector1< core::Size > > const  loopregions 
)
core::Real protocols::mpi_refinement::distance ( core::io::silent::SilentStructOP  ss1,
core::io::silent::SilentStructOP  ss2,
std::string const &  similarity_measure,
bool const  superimpose 
)
void protocols::mpi_refinement::get_loop_info ( core::io::silent::SilentStructOP  ss,
core::Size res1,
core::Size res2,
bool is_terminus 
)
utility::vector1< std::pair< core::Size, core::Size > > protocols::mpi_refinement::get_loop_info_full ( core::io::silent::SilentStructOP  ss,
utility::vector1< bool > &  is_terminus,
std::string const &  mode 
)
utility::vector1< core::Size > protocols::mpi_refinement::get_touched_res ( core::pose::Pose const  pose,
utility::vector1< core::Size > const  loopres,
core::Real  dist_cut 
)
utility::vector1< utility::vector1< core::Size > > protocols::mpi_refinement::loopstring_to_loopregions ( std::string const &  loopstr)
utility::vector1< core::Size > protocols::mpi_refinement::loopstring_to_loopvector ( std::string const &  loopstr,
core::Size const  ext 
)
void protocols::mpi_refinement::mean_and_stdev ( utility::vector1< core::Real values,
core::Real const  frac,
core::Real shave_cut,
core::Real mean,
core::Real stdev 
)
void protocols::mpi_refinement::ramp_minpack_loop ( core::pose::Pose pose,
utility::vector1< core::Size > const  loopres,
core::scoring::ScoreFunctionCOP  sfxn,
bool const  nonideal,
bool const  ramp,
bool const  efficient,
bool const  envmin 
)
void protocols::mpi_refinement::ramp_minpack_pose ( core::pose::Pose pose,
core::scoring::ScoreFunctionCOP  sfxn,
bool const  nonideal,
bool const  ramp 
)
std::map< core::Size, utility::vector1< core::Real > > protocols::mpi_refinement::read_ss2 ( std::string  ssfile)
protocols::minimization_packing::PackRotamersMoverOP protocols::mpi_refinement::setup_packer ( core::pose::Pose const &  pose,
core::kinematics::MoveMap const  mm,
core::scoring::ScoreFunctionCOP  sfxn 
)
void protocols::mpi_refinement::superimpose_all ( core::io::silent::SilentStructCOP  ss_ref,
protocols::wum::SilentStructStore structs,
utility::vector1< std::string > const  columns_copy 
)
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.S"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.C"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.StructAvrger"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.E"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.O"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "protocols.mpi_refinement.SerialRefine"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.A"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler.AggressiveType"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.M"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler.LoopType"  )
static
static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler.Relax"  )
static
core::Real protocols::mpi_refinement::Zscore_to_library ( core::Real const  score,
core::Real const  mean,
core::Real const  stdev,
core::Real const  maxval,
core::Real const  minval 
)