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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

typedef utility::pointer::access_ptr< RemodelConstraintGenerator > protocols::forge::remodel::RemodelConstraintGeneratorAP

Definition at line 31 of file RemodelConstraintGenerator.fwd.hh.

typedef utility::pointer::access_ptr< RemodelConstraintGenerator const > protocols::forge::remodel::RemodelConstraintGeneratorCAP

Definition at line 32 of file RemodelConstraintGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< RemodelConstraintGenerator const > protocols::forge::remodel::RemodelConstraintGeneratorCOP

Definition at line 30 of file RemodelConstraintGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< RemodelConstraintGenerator > protocols::forge::remodel::RemodelConstraintGeneratorOP

Definition at line 28 of file RemodelConstraintGenerator.fwd.hh.

typedef utility::pointer::owning_ptr< RemodelEnzdesCstModule > protocols::forge::remodel::RemodelEnzdesCstModuleOP

Definition at line 25 of file RemodelEnzdesCstModule.fwd.hh.

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

access pointer for RemodelLoopMover

Definition at line 30 of file RemodelLoopMover.fwd.hh.

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

const access pointer for RemodelLoopMover

Definition at line 38 of file RemodelLoopMover.fwd.hh.

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

const owning pointer for RemodelLoopMover

Definition at line 46 of file RemodelLoopMover.fwd.hh.

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

owning pointer for RemodelLoopMover

Definition at line 42 of file RemodelLoopMover.fwd.hh.

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

RemodelMover access pointer.

Definition at line 40 of file RemodelMover.fwd.hh.

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

RemodelMover const access pointer.

Definition at line 44 of file RemodelMover.fwd.hh.

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

RemodelMover const owning pointer.

Definition at line 36 of file RemodelMover.fwd.hh.

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

RemodelMover owning pointer.

Definition at line 28 of file RemodelMover.fwd.hh.

typedef utility::pointer::owning_ptr< RemodelRotamerLinks > protocols::forge::remodel::RemodelRotamerLinksOP

Definition at line 19 of file RemodelRotamerLinks.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueVicinityInfo const > protocols::forge::remodel::ResidueVicinityInfoCOP

Definition at line 45 of file ResidueVicinityRCG.hh.

typedef utility::pointer::owning_ptr< ResidueVicinityInfo > protocols::forge::remodel::ResidueVicinityInfoOP

Definition at line 43 of file ResidueVicinityRCG.hh.

typedef utility::pointer::access_ptr< ResidueVicinityRCG const > protocols::forge::remodel::ResidueVicinityRCGCAP

Definition at line 41 of file ResidueVicinityRCG.hh.

typedef utility::pointer::owning_ptr< ResidueVicinityRCG > protocols::forge::remodel::ResidueVicinityRCGOP

Definition at line 38 of file ResidueVicinityRCG.hh.

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 
)

Definition at line 1302 of file RemodelLoopMover.cc.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::lj_wdepth(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

static numeric::random::RandomGenerator protocols::forge::remodel::RG ( 2342342  )
static

Referenced by protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelLoopMover::determine_loops_to_model(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::parse_my_tag(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

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 
)

Definition at line 255 of file RemodelDesignMover.cc.

References core::sequence::end, core::pose::Pose::metric(), and core::pose::Pose::total_residue().

Referenced by protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::forge::remodel::RemodelDesignMover::mode1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode2_packertask(), protocols::forge::remodel::RemodelDesignMover::mode3_packertask(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), and protocols::forge::remodel::RemodelDesignMover::reduce_task().

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

Referenced by protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), and protocols::forge::remodel::RemodelData::updateWithDsspAssignment().

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