Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::forge::remodel Namespace Reference

Classes

struct  LineObject
 
class  RemodelAccumulator
 
class  RemodelConstraintGenerator
 pure virtual base class More...
 
class  RemodelData
 
class  RemodelDesignMover
 
class  RemodelEnzdesCstModule
 
class  RemodelGlobalFrame
 
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  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::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::owning_ptr
< RemodelGlobalFrame
RemodelGlobalFrame_OP
 RemodelGlobalFrame owning pointer. More...
 
typedef
utility::pointer::owning_ptr
< RemodelGlobalFrame const > 
RemodelGlobalFrame_COP
 RemodelGlobalFrame const owning pointer. More...
 
typedef
utility::pointer::access_ptr
< RemodelGlobalFrame
RemodelGlobalFrame_AP
 RemodelGlobalFrame access pointer. More...
 
typedef
utility::pointer::access_ptr
< RemodelGlobalFrame const > 
RemodelGlobalFrame_CAP
 RemodelGlobalFrame const access pointer. More...
 
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

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 (double rise, double radius, double omega, int unitn)
 
double get_RMSD (MatrixXf &A, MatrixXf &B)
 
bool fast_clash_check (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const check_atids, core::Real const clash_dist_cut)
 
utility::vector1
< utility::vector1< std::pair
< Size, Size > > > 
recursive_multiple_disulfide_former (utility::vector1< std::pair< Size, Size > > &disulfides_formed, utility::vector1< std::pair< Size, Size > > &disulfides_possible, Size const &max_disulfides)
 Function for recursively creating multiple disulfides. More...
 

Variables

static basic::Tracer TR ("protocols.forge.remodel.RemodelAccumulator")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelDesignMover")
 
static
numeric::random::RandomGenerator 
RG (2342342)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelEnzdesCstModule")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelGlobalFrame")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelLoopMover")
 
static
numeric::random::RandomGenerator 
RG (9788221)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelMover")
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelRotamerLinks", t_info)
 
static basic::Tracer TR ("protocols.forge.remodel.RemodelWorkingSet")
 

Typedef Documentation

RemodelGlobalFrame access pointer.

RemodelGlobalFrame const access pointer.

RemodelGlobalFrame const owning pointer.

RemodelGlobalFrame owning pointer.

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

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 
)
double protocols::forge::remodel::get_RMSD ( MatrixXf &  A,
MatrixXf &  B 
)

References rmsd.

MatrixXf protocols::forge::remodel::ideal_COMs ( double  rise,
double  radius,
double  omega,
int  unitn 
)
utility::vector1< utility::vector1< std::pair<Size,Size> > > protocols::forge::remodel::recursive_multiple_disulfide_former ( utility::vector1< std::pair< Size, Size > > &  disulfides_formed,
utility::vector1< std::pair< Size, Size > > &  disulfides_possible,
Size const &  max_disulfides 
)

Function for recursively creating multiple disulfides.

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

Matrix3f protocols::forge::remodel::rot_mat ( MatrixXf &  A,
MatrixXf &  B 
)

Variable Documentation

numeric::random::RandomGenerator protocols::forge::remodel::RG(2342342)
static
numeric::random::RandomGenerator protocols::forge::remodel::RG(9788221)
static
basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelRotamerLinks", t_info)
static
basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelEnzdesCstModule")
static
basic::Tracer protocols::forge::remodel::TR("protocols.forge.remodel.RemodelDesignMover")
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::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

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