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protocols::abinitio::abscript Namespace Reference

Classes

class  AbscriptLoopCloserCM
 
class  AbscriptLoopCloserCMCreator
 
class  AbscriptMover
 
class  AbscriptMoverCreator
 
class  AbscriptStageMover
 
class  AtomPack
 
class  ConstraintPreparer
 
class  ConstraintPreparerCreator
 
class  FragmentCM
 
class  FragmentCMCreator
 
class  FragmentJumpCM
 
class  FragmentJumpCMCreator
 
class  JumpSampleData
 
class  JumpSampleDataCreator
 
class  ResidueChunkSelection
 
class  RigidChunkCM
 
class  RigidChunkCMCreator
 
class  StagePreparer
 
class  StructPerturberCM
 
class  StructPerturberCMCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< AbscriptLoopCloserCM
AbscriptLoopCloserCMOP
 
typedef
utility::pointer::shared_ptr
< AbscriptLoopCloserCM const > 
AbscriptLoopCloserCMCOP
 
typedef
utility::pointer::shared_ptr
< AbscriptMover
AbscriptMoverOP
 
typedef
utility::pointer::shared_ptr
< AbscriptMover const > 
AbscriptMoverCOP
 
typedef
utility::pointer::shared_ptr
< AbscriptStageMover
AbscriptStageMoverOP
 
typedef
utility::pointer::shared_ptr
< AbscriptStageMover const > 
AbscriptStageMoverCOP
 
typedef
utility::pointer::shared_ptr
< ConstraintPreparer
ConstraintPreparerOP
 
typedef
utility::pointer::shared_ptr
< ConstraintPreparer const > 
ConstraintPreparerCOP
 
typedef
utility::pointer::shared_ptr
< FragmentCM
FragmentCMOP
 
typedef
utility::pointer::shared_ptr
< FragmentCM const > 
FragmentCMCOP
 
typedef
utility::pointer::shared_ptr
< FragmentJumpCM
FragmentJumpCMOP
 
typedef
utility::pointer::shared_ptr
< FragmentJumpCM const > 
FragmentJumpCMCOP
 
typedef
utility::pointer::shared_ptr
< JumpSampleData
JumpSampleDataOP
 
typedef
utility::pointer::shared_ptr
< JumpSampleData const > 
JumpSampleDataCOP
 
typedef
utility::pointer::shared_ptr
< RigidChunkCM
RigidChunkCMOP
 
typedef
utility::pointer::shared_ptr
< RigidChunkCM const > 
RigidChunkCMCOP
 
typedef utility::vector1< StageIDStageIDs
 
typedef
utility::pointer::shared_ptr
< StagePreparer
StagePreparerOP
 
typedef
utility::pointer::shared_ptr
< StagePreparer const > 
StagePreparerCOP
 
typedef
utility::pointer::shared_ptr
< StructPerturberCM
StructPerturberCMOP
 
typedef
utility::pointer::shared_ptr
< StructPerturberCM const > 
StructPerturberCMCOP
 

Enumerations

enum  StageID {
  I = 1, II, IIIa, IIIb,
  IVa, IVb, END
}
 

Functions

core::Real angle_diff (core::Real const &a, core::Real const &b)
 
bool angle_cpy (core::pose::Pose &target, core::pose::Pose const &source, core::id::TorsionID t_id)
 
StageIDincrement_stageid (StageID &id)
 
core::scoring::ScoreFunctionOP setup_score (std::string const &scorename, basic::options::FileVectorOptionKey optkey)
 
void verify_stage_ID (std::map< std::string, StageID > const &id_map, std::string const &id)
 
core::Real score_cst (core::pose::Pose &pose, core::scoring::ScoreFunction const &scfxn)
 
bool loop_stop_comp (loops::Loop const &lhs, loops::Loop const &rhs)
 
core::Size determine_frag_size (std::string const &file)
 
loops::Loops read_rigid_core (std::string const &file)
 
core::Size find_disulfide_partner (core::pose::Pose const &pose, core::Size const resid)
 
void fix_internal_coords_of_siblings (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::id::AtomID atom, core::id::AtomID ref_atom)
 
void fix_mainchain_connect (core::pose::Pose &pose, core::Size global_upper, core::pose::Pose const &ref_pose, core::Size local_upper)
 

Variables

core::Real const DEFAULT_TEMP = 2.0
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AbscriptMover const > protocols::abinitio::abscript::AbscriptMoverCOP
typedef utility::pointer::shared_ptr< AbscriptMover > protocols::abinitio::abscript::AbscriptMoverOP
typedef utility::pointer::shared_ptr< AbscriptStageMover const > protocols::abinitio::abscript::AbscriptStageMoverCOP
typedef utility::pointer::shared_ptr< ConstraintPreparer const > protocols::abinitio::abscript::ConstraintPreparerCOP
typedef utility::pointer::shared_ptr< FragmentCM const > protocols::abinitio::abscript::FragmentCMCOP
typedef utility::pointer::shared_ptr< FragmentCM > protocols::abinitio::abscript::FragmentCMOP
typedef utility::pointer::shared_ptr< FragmentJumpCM const > protocols::abinitio::abscript::FragmentJumpCMCOP
typedef utility::pointer::shared_ptr< FragmentJumpCM > protocols::abinitio::abscript::FragmentJumpCMOP
typedef utility::pointer::shared_ptr< JumpSampleData const > protocols::abinitio::abscript::JumpSampleDataCOP
typedef utility::pointer::shared_ptr< JumpSampleData > protocols::abinitio::abscript::JumpSampleDataOP
typedef utility::pointer::shared_ptr< RigidChunkCM const > protocols::abinitio::abscript::RigidChunkCMCOP
typedef utility::pointer::shared_ptr< RigidChunkCM > protocols::abinitio::abscript::RigidChunkCMOP
typedef utility::vector1< StageID > protocols::abinitio::abscript::StageIDs
typedef utility::pointer::shared_ptr< StagePreparer const > protocols::abinitio::abscript::StagePreparerCOP
typedef utility::pointer::shared_ptr< StagePreparer > protocols::abinitio::abscript::StagePreparerOP
typedef utility::pointer::shared_ptr< StructPerturberCM const > protocols::abinitio::abscript::StructPerturberCMCOP

Enumeration Type Documentation

Enumerator
II 
IIIa 
IIIb 
IVa 
IVb 
END 

Function Documentation

bool protocols::abinitio::abscript::angle_cpy ( core::pose::Pose target,
core::pose::Pose const &  source,
core::id::TorsionID  t_id 
)
core::Real protocols::abinitio::abscript::angle_diff ( core::Real const &  a,
core::Real const &  b 
)
core::Size protocols::abinitio::abscript::determine_frag_size ( std::string const &  file)
core::Size protocols::abinitio::abscript::find_disulfide_partner ( core::pose::Pose const &  pose,
core::Size const  resid 
)
void protocols::abinitio::abscript::fix_internal_coords_of_siblings ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose,
core::id::AtomID  atom,
core::id::AtomID  ref_atom 
)
void protocols::abinitio::abscript::fix_mainchain_connect ( core::pose::Pose pose,
core::Size  global_upper,
core::pose::Pose const &  ref_pose,
core::Size  local_upper 
)
StageID& protocols::abinitio::abscript::increment_stageid ( StageID &  id)
bool protocols::abinitio::abscript::loop_stop_comp ( loops::Loop const &  lhs,
loops::Loop const &  rhs 
)
loops::Loops protocols::abinitio::abscript::read_rigid_core ( std::string const &  file)
core::Real protocols::abinitio::abscript::score_cst ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  scfxn 
)
core::scoring::ScoreFunctionOP protocols::abinitio::abscript::setup_score ( std::string const &  scorename,
basic::options::FileVectorOptionKey  optkey 
)
void protocols::abinitio::abscript::verify_stage_ID ( std::map< std::string, StageID > const &  id_map,
std::string const &  id 
)

Variable Documentation

core::Real const protocols::abinitio::abscript::DEFAULT_TEMP = 2.0