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protocols::forge::remodel Namespace Reference

Classes

class  RemodelAccumulator
 
class  RemodelConstraintGenerator
 pure virtual base class More...
 
struct  LineObject
 
class  RemodelData
 
class  RemodelDesignMover
 
class  RemodelEnzdesCstModule
 
class  RemodelLoopMover
 Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...
 
class  RemodelLoopMoverCreator
 
class  RemodelMover
 
class  RemodelMoverCreator
 
class  RemodelRotamerLinks
 
class  RemodelRotamerLinksCreator
 
class  WorkingRemodelSet
 
class  Segment
 
class  ResidueVicinityCstGeneratorCreator
 
class  ResidueVicinityInfo
 small helper class for the ResidueVicinityRCG More...
 
class  ResidueVicinityRCG
 a RemodelConstraintGenerator that creates AmbiguousMultiConstraints for all positions More...
 

Typedefs

typedef
utility::pointer::owning_ptr
< RemodelConstraintGenerator
RemodelConstraintGeneratorOP
 
typedef
utility::pointer::owning_ptr
< RemodelConstraintGenerator
const > 
RemodelConstraintGeneratorCOP
 
typedef
utility::pointer::access_ptr
< RemodelConstraintGenerator
RemodelConstraintGeneratorAP
 
typedef
utility::pointer::access_ptr
< RemodelConstraintGenerator
const > 
RemodelConstraintGeneratorCAP
 
typedef
utility::pointer::owning_ptr
< RemodelEnzdesCstModule
RemodelEnzdesCstModuleOP
 
typedef
utility::pointer::access_ptr
< RemodelLoopMover
RemodelLoopMoverAP
 access pointer for RemodelLoopMover More...
 
typedef
utility::pointer::access_ptr
< RemodelLoopMover const > 
RemodelLoopMoverCAP
 const access pointer for RemodelLoopMover More...
 
typedef
utility::pointer::owning_ptr
< RemodelLoopMover
RemodelLoopMoverOP
 owning pointer for RemodelLoopMover More...
 
typedef
utility::pointer::owning_ptr
< RemodelLoopMover const > 
RemodelLoopMoverCOP
 const owning pointer for RemodelLoopMover More...
 
typedef
utility::pointer::owning_ptr
< RemodelMover
RemodelMover_OP
 RemodelMover owning pointer. More...
 
typedef
utility::pointer::owning_ptr
< RemodelMover const > 
RemodelMover_COP
 RemodelMover const owning pointer. More...
 
typedef
utility::pointer::access_ptr
< RemodelMover
RemodelMover_AP
 RemodelMover access pointer. More...
 
typedef
utility::pointer::access_ptr
< RemodelMover const > 
RemodelMover_CAP
 RemodelMover const access pointer. More...
 
typedef
utility::pointer::owning_ptr
< RemodelRotamerLinks
RemodelRotamerLinksOP
 
typedef
utility::pointer::owning_ptr
< ResidueVicinityRCG
ResidueVicinityRCGOP
 
typedef
utility::pointer::access_ptr
< ResidueVicinityRCG const > 
ResidueVicinityRCGCAP
 
typedef
utility::pointer::owning_ptr
< ResidueVicinityInfo
ResidueVicinityInfoOP
 
typedef
utility::pointer::owning_ptr
< ResidueVicinityInfo const > 
ResidueVicinityInfoCOP
 

Functions

static basic::Tracer TR ("protocols.forge.remodel.RemodelAccumulator")
 
static basic::Tracer TR_REMODEL ("REMODELd")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelDesignMover")
 
static
numeric::random::RandomGenerator 
RG (2342342)
 
void run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelEnzdesCstModule")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelLoopMover")
 
static
numeric::random::RandomGenerator 
RG (9788221)
 
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")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelRotamerLinks", t_info)
 
static basic::Tracer TR ("REMODELw")
 

Typedef Documentation

access pointer for RemodelLoopMover

const access pointer for RemodelLoopMover

const owning pointer for RemodelLoopMover

owning pointer for RemodelLoopMover

RemodelMover access pointer.

RemodelMover const access pointer.

RemodelMover const owning pointer.

RemodelMover owning pointer.

Function Documentation

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 
)
static numeric::random::RandomGenerator protocols::forge::remodel::RG ( 2342342  )
static
static numeric::random::RandomGenerator protocols::forge::remodel::RG ( 9788221  )
static
void protocols::forge::remodel::run_calculator ( core::pose::Pose const &  pose,
std::string const &  calculator,
std::string const &  calculation,
utility::vector1_bool &  residues 
)
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelRotamerLinks"  ,
t_info   
)
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelEnzdesCstModule"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelAccumulator"  )
static

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelDesignMover::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::RemodelDesignMover::check_state(), 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_seq_relax(), protocols::forge::remodel::RemodelEnzdesCstModule::enable_constraint_scoreterms(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::mode1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode2_packertask(), protocols::forge::remodel::RemodelDesignMover::mode3_packertask(), protocols::forge::remodel::RemodelDesignMover::mode4_packertask(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::forge::remodel::RemodelDesignMover::mode6_packertask(), protocols::forge::remodel::RemodelConstraintGenerator::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), protocols::forge::remodel::RemodelMover::register_user_options(), protocols::forge::remodel::RemodelMover::RemodelMover(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), and protocols::forge::remodel::WorkingRemodelSet::workingSetGen().

static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelDesignMover"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelLoopMover"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "REMODELw"  )
static
static basic::Tracer protocols::forge::remodel::TR ( "protocols.forge.remodel.RemodelMover"  )
static
static basic::Tracer protocols::forge::remodel::TR_REMODEL ( "REMODELd"  )
static