Package rosetta :: Package core :: Package pack :: Package dunbrack :: Module _core_pack_dunbrack_
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Module _core_pack_dunbrack_

Classes [hide private]
  BBDepNRChiSample_T_double_T
P for precision
  BBDepNRChiSample_T_double_TAP
  BBDepNRChiSample_T_double_TCAP
  BBDepNRChiSample_T_float_T
P for precision
  BBDepNRChiSample_T_float_TAP
  BBDepNRChiSample_T_float_TCAP
  BBIndNRChiSample_T_float_T
core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.hh:77
  BBIndNRChiSample_T_float_TAP
  BBIndNRChiSample_T_float_TCAP
  ChiSet
core/pack/dunbrack/ChiSet.hh:33
  ChiSetAP
  ChiSetCAP
  DunbrackConstraint
core/pack/dunbrack/DunbrackConstraint.hh:29
  DunbrackConstraintAP
  DunbrackConstraintCAP
  DunbrackConstraintCreator
Mover creator for the DunbrackConstraint constraint
  DunbrackConstraintCreatorAP
  DunbrackConstraintCreatorCAP
  DunbrackEnergy
core/pack/dunbrack/DunbrackEnergy.hh:39
  DunbrackEnergyAP
  DunbrackEnergyCAP
  DunbrackEnergyCreator
core/pack/dunbrack/DunbrackEnergyCreator.hh:30
  DunbrackEnergyCreatorAP
  DunbrackEnergyCreatorCAP
  DunbrackRotamerSampleData
core/pack/dunbrack/DunbrackRotamer.hh:346
  DunbrackRotamerSampleDataAP
  DunbrackRotamerSampleDataCAP
  ProbSortClass
core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.hh:184
  ProbSortClassAP
  ProbSortClassCAP
  RotamerBuildingData
a simple class for passing data around in virtual function calls of the rotamer creating process.
  RotamerBuildingDataAP
  RotamerBuildingDataCAP
  RotamerConstraint
This class favors a particular rotamer at a particular position by reducing its Dunbrack energy.
  RotamerConstraintAP
  RotamerConstraintCAP
  RotamerLibrary
////////////////////////////////////////////////////////////////////////////
  RotamerLibraryAP
  RotamerLibraryCAP
  RotamerLibraryScratchSpace
core/pack/dunbrack/RotamerLibraryScratchSpace.hh:35
  RotamerLibraryScratchSpaceAP
  RotamerLibraryScratchSpaceCAP
  SingleLigandRotamerLibrary
A fixed library of conformations for some residue type (doesn't have to be a ligand).
  SingleLigandRotamerLibraryAP
  SingleLigandRotamerLibraryCAP
  SingleResidueDunbrackLibrary
core/pack/dunbrack/SingleResidueDunbrackLibrary.hh:42
  SingleResidueDunbrackLibraryAP
  SingleResidueDunbrackLibraryCAP
  SingleResiduePeptoidLibrary
core/pack/dunbrack/SingleResiduePeptoidLibrary.hh:38
  SingleResiduePeptoidLibraryAP
  SingleResiduePeptoidLibraryCAP
  SingleResidueRotamerLibrary
SingleResidueRotamerLibrary pure virtual base class
  SingleResidueRotamerLibraryAP
  SingleResidueRotamerLibraryCAP
  SingletonBase_T_core_chemical_ChemicalManager_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_core_chemical_ChemicalManager_TAP
  SingletonBase_T_core_chemical_ChemicalManager_TCAP
  SingletonBase_T_core_pack_dunbrack_RotamerLibrary_T
SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way.
  SingletonBase_T_core_pack_dunbrack_RotamerLibrary_TAP
  SingletonBase_T_core_pack_dunbrack_RotamerLibrary_TCAP
  __CPP_DunbrackConstraintCreator__
  __CPP_DunbrackConstraint__
  __CPP_DunbrackEnergyCreator__
  __CPP_DunbrackEnergy__
  __CPP_RotamerConstraint__
  __CPP_SingleLigandRotamerLibrary__
  __CPP_SingleResidueRotamerLibrary__
Functions [hide private]
 
bicubic_interpolation(...)
bicubic_interpolation( (float)v00, (float)d2dx200, (float)d2dy200, (float)d4dx2y200, (float)v01, (float)d2dx201, (float)d2dy201, (float)d4dx2y201, (float)v10, (float)d2dx210, (float)d2dy210, (float)d4dx2y210, (float)v11, (float)d2dx211, (float)d2dy211, (float)d4dx2y211, (float)dxp, (float)dyp, (float)binwx, (float)binwy, (float)val, (float)dvaldx, (float)dvaldy) -> None : core/pack/dunbrack/DunbrackRotamer.hh:433
 
bit_is_set(...)
bit_is_set( (int)num, (int)num_len, (int)pos) -> bool : core/pack/dunbrack/DunbrackRotamer.hh:57
 
expand_proton_chi(...)
expand_proton_chi( (ExtraRotSample)ex_samp_level, (ResidueType)concrete_residue, (int)proton_chi, (object)chi_set_vector) -> None : Should this be here?
 
load_unboundrot(...)
load_unboundrot( (Pose)pose, (object)unboundrot_poses) -> None : Convenience function adds constraints to the supplied pose based on the list of provided poses.
 
positive_pow(...)
positive_pow( (int)mantissa, (int)exponent) -> int : core/pack/dunbrack/DunbrackRotamer.hh:50
 
psc_compare(...)
psc_compare( (ProbSortClass)left, (ProbSortClass)right) -> bool : core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.hh:191
 
read_dunbrack_library(...)
read_dunbrack_library( (RotamerLibrary)rotamer_library) -> None : core/pack/dunbrack/RotamerLibrary.hh:423
 
rotamer_from_chi(...)
rotamer_from_chi( (ResidueType)rsd_type, (vector1_Real)chi, (vector1_Size)rot) -> None : core/pack/dunbrack/RotamerLibrary.hh:76
 
rotamer_from_chi_02(...)
rotamer_from_chi_02( (object)chi, (AA)res, (int)nchi, (object)rot) -> None : core/pack/dunbrack/RotamerLibrary.hh:95
 
subtract_chi_angles(...)
subtract_chi_angles( (float)chi1, (float)chi2, (AA)aa, (int)chino) -> float : Find the difference in angles between two chi values using hard-coded symmetry information for the symmetric amino acids.
Variables [hide private]
  __package__ = None
Function Details [hide private]

bicubic_interpolation(...)

 

bicubic_interpolation( (float)v00, (float)d2dx200, (float)d2dy200, (float)d4dx2y200, (float)v01, (float)d2dx201, (float)d2dy201, (float)d4dx2y201, (float)v10, (float)d2dx210, (float)d2dy210, (float)d4dx2y210, (float)v11, (float)d2dx211, (float)d2dy211, (float)d4dx2y211, (float)dxp, (float)dyp, (float)binwx, (float)binwy, (float)val, (float)dvaldx, (float)dvaldy) -> None :
    core/pack/dunbrack/DunbrackRotamer.hh:433

    C++ signature :
        void bicubic_interpolation(double,double,double,double,double,double,double,double,double,double,double,double,double,double,double,double,double,double,double,double,double {lvalue},double {lvalue},double {lvalue})

bit_is_set(...)

 

bit_is_set( (int)num, (int)num_len, (int)pos) -> bool :
    core/pack/dunbrack/DunbrackRotamer.hh:57

    C++ signature :
        bool bit_is_set(unsigned long,unsigned long,unsigned long)

expand_proton_chi(...)

 

expand_proton_chi( (ExtraRotSample)ex_samp_level, (ResidueType)concrete_residue, (int)proton_chi, (object)chi_set_vector) -> None :
    Should this be here?
    

    C++ signature :
        void expand_proton_chi(core::pack::task::ExtraRotSample,boost::shared_ptr<core::chemical::ResidueType const>,unsigned long,utility::vector1<boost::shared_ptr<core::pack::dunbrack::ChiSet>, std::allocator<boost::shared_ptr<core::pack::dunbrack::ChiSet> > > {lvalue})

load_unboundrot(...)

 

load_unboundrot( (Pose)pose, (object)unboundrot_poses) -> None :
    Convenience function adds constraints to the supplied pose based on
    the list of provided poses.
    

    C++ signature :
        void load_unboundrot(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose const>, std::allocator<boost::shared_ptr<core::pose::Pose const> > >)

load_unboundrot( (Pose)pose) -> None :
    Convenience function adds constraints to the supplied pose based on
    the -unboundrot command line flag.
    

    C++ signature :
        void load_unboundrot(core::pose::Pose {lvalue})

positive_pow(...)

 

positive_pow( (int)mantissa, (int)exponent) -> int :
    core/pack/dunbrack/DunbrackRotamer.hh:50

    C++ signature :
        unsigned long positive_pow(unsigned long,unsigned long)

psc_compare(...)

 

psc_compare( (ProbSortClass)left, (ProbSortClass)right) -> bool :
    core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.hh:191

    C++ signature :
        bool psc_compare(core::pack::dunbrack::ProbSortClass,core::pack::dunbrack::ProbSortClass)

read_dunbrack_library(...)

 

read_dunbrack_library( (RotamerLibrary)rotamer_library) -> None :
    core/pack/dunbrack/RotamerLibrary.hh:423

    C++ signature :
        void read_dunbrack_library(core::pack::dunbrack::RotamerLibrary {lvalue})

rotamer_from_chi(...)

 

rotamer_from_chi( (ResidueType)rsd_type, (vector1_Real)chi, (vector1_Size)rot) -> None :
    core/pack/dunbrack/RotamerLibrary.hh:76

    C++ signature :
        void rotamer_from_chi(core::chemical::ResidueType,utility::vector1<double, std::allocator<double> >,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

rotamer_from_chi( (Residue)rsd, (vector1_Size)rot) -> None :
    core/pack/dunbrack/RotamerLibrary.hh:69

    C++ signature :
        void rotamer_from_chi(core::conformation::Residue,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

rotamer_from_chi_02(...)

 

rotamer_from_chi_02( (object)chi, (AA)res, (int)nchi, (object)rot) -> None :
    core/pack/dunbrack/RotamerLibrary.hh:95

    C++ signature :
        void rotamer_from_chi_02(utility::fixedsizearray1<double, 4ul>,core::chemical::AA,unsigned long,utility::fixedsizearray1<unsigned long, 4ul> {lvalue})

rotamer_from_chi_02( (vector1_Real)chi, (AA)res, (vector1_Size)rot) -> None :
    Do not bother calling this function if you're interested in staying
    up to date with changes in the rotamer library.  Call rotamer_from_chi instead.
    It will eventually call this function iff dun10 is not set to true.
    

    C++ signature :
        void rotamer_from_chi_02(utility::vector1<double, std::allocator<double> >,core::chemical::AA,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})

subtract_chi_angles(...)

 

subtract_chi_angles( (float)chi1, (float)chi2, (AA)aa, (int)chino) -> float :
    Find the difference in angles between two chi values using hard-coded
    symmetry information for the symmetric amino acids.  Disappears for 2010 library.
    

    C++ signature :
        double subtract_chi_angles(double,double,core::chemical::AA,int)