Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Functions
protocols::forge::remodel Namespace Reference

Classes

class  EXCN_RemoveCstsFailed
 
class  GenericRemodelConstraintGenerator
 generic remodel constraint generator for use with arbitrary ConstraintGenerators More...
 
struct  LineObject
 
class  RemodelAccumulator
 
class  RemodelConstraintGenerator
 pure virtual base class More...
 
class  RemodelData
 
class  RemodelDesignMover
 
class  RemodelEnzdesCstModule
 
class  RemodelGlobalFrame
 
class  RemodelLigandHandler
 
class  RemodelLoopMover
 Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...
 
class  RemodelMover
 
class  RemodelMoverCreator
 
class  RemodelRotamerLinks
 
class  RemodelRotamerLinksCreator
 
class  RemodelWorkingSet
 
class  ResidueVicinityCstGeneratorCreator
 
class  ResidueVicinityInfo
 small helper class for the ResidueVicinityRCG More...
 
class  ResidueVicinityRCG
 a RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions More...
 
class  Segment
 

Typedefs

typedef
utility::pointer::shared_ptr
< RemodelConstraintGenerator
RemodelConstraintGeneratorOP
 
typedef
utility::pointer::shared_ptr
< RemodelConstraintGenerator
const > 
RemodelConstraintGeneratorCOP
 
typedef
utility::pointer::weak_ptr
< RemodelConstraintGenerator
RemodelConstraintGeneratorAP
 
typedef
utility::pointer::weak_ptr
< RemodelConstraintGenerator
const > 
RemodelConstraintGeneratorCAP
 
typedef
utility::pointer::shared_ptr
< GenericRemodelConstraintGenerator
GenericRemodelConstraintGeneratorOP
 
typedef
utility::pointer::shared_ptr
< GenericRemodelConstraintGenerator
const > 
GenericRemodelConstraintGeneratorCOP
 
typedef
utility::pointer::shared_ptr
< RemodelEnzdesCstModule
RemodelEnzdesCstModuleOP
 
typedef
utility::pointer::shared_ptr
< RemodelGlobalFrame
RemodelGlobalFrame_OP
 RemodelGlobalFrame owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelGlobalFrame const > 
RemodelGlobalFrame_COP
 RemodelGlobalFrame const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelGlobalFrame
RemodelGlobalFrame_AP
 RemodelGlobalFrame access pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelGlobalFrame const > 
RemodelGlobalFrame_CAP
 RemodelGlobalFrame const access pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelLigandHandler
RemodelLigandHandler_OP
 RemodelLigandHandler owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelLigandHandler const > 
RemodelLigandHandler_COP
 RemodelLigandHandler const owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelLigandHandler
RemodelLigandHandler_AP
 RemodelLigandHandler access pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelLigandHandler const > 
RemodelLigandHandler_CAP
 RemodelLigandHandler const access pointer. More...
 
typedef
utility::pointer::weak_ptr
< RemodelLoopMover
RemodelLoopMoverAP
 access pointer for RemodelLoopMover More...
 
typedef
utility::pointer::weak_ptr
< RemodelLoopMover const > 
RemodelLoopMoverCAP
 const access pointer for RemodelLoopMover More...
 
typedef
utility::pointer::shared_ptr
< RemodelLoopMover
RemodelLoopMoverOP
 owning pointer for RemodelLoopMover More...
 
typedef
utility::pointer::shared_ptr
< RemodelLoopMover const > 
RemodelLoopMoverCOP
 const owning pointer for RemodelLoopMover More...
 
typedef
utility::pointer::shared_ptr
< RemodelMover
RemodelMover_OP
 RemodelMover owning pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelMover const > 
RemodelMover_COP
 RemodelMover const owning pointer. More...
 
typedef
utility::pointer::weak_ptr
< RemodelMover
RemodelMover_AP
 RemodelMover access pointer. More...
 
typedef
utility::pointer::weak_ptr
< RemodelMover const > 
RemodelMover_CAP
 RemodelMover const access pointer. More...
 
typedef
utility::pointer::shared_ptr
< RemodelRotamerLinks
RemodelRotamerLinksOP
 
typedef
utility::pointer::shared_ptr
< ResidueVicinityRCG
ResidueVicinityRCGOP
 
typedef
utility::pointer::weak_ptr
< ResidueVicinityRCG const > 
ResidueVicinityRCGCAP
 
typedef
utility::pointer::shared_ptr
< ResidueVicinityInfo
ResidueVicinityInfoOP
 
typedef
utility::pointer::shared_ptr
< ResidueVicinityInfo const > 
ResidueVicinityInfoCOP
 

Functions

static basic::Tracer TR ("protocols.forge.remodel.RemodelAccumulator")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelDesignMover")
 
core::Real build_and_score_disulfide (core::pose::Pose &blank_pose, core::scoring::ScoreFunctionOP sfxn, const bool relax_bb, core::Size const res1, core::Size const res2)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelEnzdesCstModule")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelGlobalFrame")
 
numeric::xyzVector< core::Realcompute_center_of_mass (core::pose::Pose const &pose, core::Size range_start, core::Size range_stop)
 
Matrix3f rot_mat (MatrixXf &A, MatrixXf &B)
 
MatrixXf ideal_COMs (core::Real rise, core::Real radius, core::Real omega, int unitn)
 
core::Real get_RMSD (MatrixXf &A, MatrixXf &B)
 
core::Real get_RMSD (Eigen::MatrixXf &A, Eigen::MatrixXf &B)
 
Eigen::Matrix3f rot_mat (Eigen::MatrixXf &A, Eigen::MatrixXf &B)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelLigandHandler")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelMover")
 
bool fast_clash_check (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const check_atids, core::Real const clash_dist_cut)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelMover")
 
utility::vector1
< utility::vector1< std::pair
< core::Size, Size > > > 
recursive_multiple_disulfide_former (utility::vector1< std::pair< core::Size, Size > > &disulfides_formed, utility::vector1< std::pair< core::Size, Size > > &disulfides_possible, core::Size const &max_disulfides)
 Function for recursively creating multiple disulfides. More...
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelRotamerLinks", t_info)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelWorkingSet")
 

Typedef Documentation

RemodelGlobalFrame access pointer.

typedef utility::pointer::shared_ptr< RemodelGlobalFrame const > protocols::forge::remodel::RemodelGlobalFrame_CAP

RemodelGlobalFrame const access pointer.

typedef utility::pointer::shared_ptr< RemodelGlobalFrame const > protocols::forge::remodel::RemodelGlobalFrame_COP

RemodelGlobalFrame const owning pointer.

RemodelGlobalFrame owning pointer.

RemodelLigandHandler access pointer.

typedef utility::pointer::shared_ptr< RemodelLigandHandler const > protocols::forge::remodel::RemodelLigandHandler_CAP

RemodelLigandHandler const access pointer.

typedef utility::pointer::shared_ptr< RemodelLigandHandler const > protocols::forge::remodel::RemodelLigandHandler_COP

RemodelLigandHandler const owning pointer.

RemodelLigandHandler owning pointer.

typedef utility::pointer::weak_ptr< RemodelLoopMover > protocols::forge::remodel::RemodelLoopMoverAP

access pointer for RemodelLoopMover

typedef utility::pointer::weak_ptr< RemodelLoopMover const > protocols::forge::remodel::RemodelLoopMoverCAP

const access pointer for RemodelLoopMover

typedef utility::pointer::shared_ptr< RemodelLoopMover const > protocols::forge::remodel::RemodelLoopMoverCOP

const owning pointer for RemodelLoopMover

typedef utility::pointer::shared_ptr< RemodelLoopMover > protocols::forge::remodel::RemodelLoopMoverOP

owning pointer for RemodelLoopMover

typedef utility::pointer::weak_ptr< RemodelMover > protocols::forge::remodel::RemodelMover_AP

RemodelMover access pointer.

typedef utility::pointer::weak_ptr< RemodelMover const > protocols::forge::remodel::RemodelMover_CAP

RemodelMover const access pointer.

typedef utility::pointer::shared_ptr< RemodelMover const > protocols::forge::remodel::RemodelMover_COP

RemodelMover const owning pointer.

typedef utility::pointer::shared_ptr< RemodelMover > protocols::forge::remodel::RemodelMover_OP

RemodelMover owning pointer.

typedef utility::pointer::shared_ptr< ResidueVicinityInfo const > protocols::forge::remodel::ResidueVicinityInfoCOP
typedef utility::pointer::weak_ptr< ResidueVicinityRCG const > protocols::forge::remodel::ResidueVicinityRCGCAP

Function Documentation

core::Real protocols::forge::remodel::build_and_score_disulfide ( core::pose::Pose blank_pose,
core::scoring::ScoreFunctionOP  sfxn,
const bool  relax_bb,
core::Size const  res1,
core::Size const  res2 
)
numeric::xyzVector< core::Real > protocols::forge::remodel::compute_center_of_mass ( core::pose::Pose const &  pose,
core::Size  range_start,
core::Size  range_stop 
)
bool protocols::forge::remodel::fast_clash_check ( core::pose::Pose const &  pose,
utility::vector1< core::id::AtomID > const  check_atids,
core::Real const  clash_dist_cut 
)
core::Real protocols::forge::remodel::get_RMSD ( Eigen::MatrixXf &  A,
Eigen::MatrixXf &  B 
)
core::Real protocols::forge::remodel::get_RMSD ( MatrixXf &  A,
MatrixXf &  B 
)
Eigen::MatrixXf protocols::forge::remodel::ideal_COMs ( core::Real  rise,
core::Real  radius,
core::Real  omega,
int  unitn 
)
utility::vector1< utility::vector1< std::pair<core::Size,Size> > > protocols::forge::remodel::recursive_multiple_disulfide_former ( utility::vector1< std::pair< core::Size, Size > > &  disulfides_formed,
utility::vector1< std::pair< core::Size, Size > > &  disulfides_possible,
core::Size const &  max_disulfides 
)

Function for recursively creating multiple disulfides.

References core::sequence::end.

Referenced by protocols::forge::remodel::RemodelMover::apply().

Eigen::Matrix3f protocols::forge::remodel::rot_mat ( Eigen::MatrixXf &  A,
Eigen::MatrixXf &  B 
)
Matrix3f protocols::forge::remodel::rot_mat ( MatrixXf &  A,
MatrixXf &  B 
)
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelEnzdesCstModule"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelRotamerLinks"  ,
t_info   
)
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelAccumulator"  )
static

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::remodel::RemodelLoopMover::check_closure_criteria(), protocols::forge::remodel::RemodelConstraintGenerator::clear_stored_constraints(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::forge::remodel::RemodelEnzdesCstModule::enable_constraint_scoreterms(), protocols::forge::remodel::RemodelLoopMover::fa_relax_stage(), protocols::forge::remodel::RemodelLoopMover::generate_ncs_csts(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag(), protocols::forge::remodel::RemodelMover::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::forge::remodel::RemodelMover::register_user_options(), protocols::forge::remodel::RemodelMover::RemodelMover(), protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::forge::remodel::RemodelLoopMover::set_ideal_helices(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::forge::remodel::RemodelMover::setup_remodel_data_for_loop_btw_parametric_components(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelDesignMover"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelWorkingSet"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelLigandHandler"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelGlobalFrame"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelMover"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelMover"  )
static