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Classes | Typedefs | Enumerations
protocols::cyclic_peptide::crosslinker Namespace Reference

Classes

class  CrosslinkerMoverHelper
 A base class for helper objects that the CrosslinkerMover uses to set up specific types of linkers. More...
 
class  Metal_HelperBase
 A base class for setting up metals. This is a pure virtual class that must be subclassed for specific metal geometries.. More...
 
class  OctahedralMetal_Helper
 A helper class for setting up octahedrally-coordinated metals. More...
 
class  SquarePlanarMetal_Helper
 A helper class for setting up square planarly-coordinated metals like Ni. More...
 
class  SquarePyramidalMetal_Helper
 A helper class for setting up square pyramidally-coordinated metals like Ni. More...
 
class  TBMB_Helper
 A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,3,5-tris(bromomethyl)benzene (TBMB) cross-linker. More...
 
class  TetrahedralMetal_Helper
 A helper class for setting up tetrahedrally-coordinated metals like Zn or Cu. More...
 
class  TMA_Helper
 A derived class of the CrosslinkerMoverHelper base class, used to set up the trimesic acid (TMA) cross-linker. More...
 
class  TrigonalPlanarMetal_Helper
 A helper class for setting up trigonal planarly-coordinated metals like Zn or Cu. More...
 
class  TrigonalPyramidalMetal_Helper
 A helper class for setting up trigonal pyramidally-coordinated metals like Zn or Cu. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< CrosslinkerMoverHelper
CrosslinkerMoverHelperOP
 
typedef
utility::pointer::shared_ptr
< CrosslinkerMoverHelper const > 
CrosslinkerMoverHelperCOP
 
typedef
utility::pointer::shared_ptr
< Metal_HelperBase
Metal_HelperBaseOP
 
typedef
utility::pointer::shared_ptr
< Metal_HelperBase const > 
Metal_HelperBaseCOP
 
typedef
utility::pointer::shared_ptr
< OctahedralMetal_Helper
OctahedralMetal_HelperOP
 
typedef
utility::pointer::shared_ptr
< OctahedralMetal_Helper const > 
OctahedralMetal_HelperCOP
 
typedef
utility::pointer::shared_ptr
< SquarePlanarMetal_Helper
SquarePlanarMetal_HelperOP
 
typedef
utility::pointer::shared_ptr
< SquarePlanarMetal_Helper
const > 
SquarePlanarMetal_HelperCOP
 
typedef
utility::pointer::shared_ptr
< SquarePyramidalMetal_Helper
SquarePyramidalMetal_HelperOP
 
typedef
utility::pointer::shared_ptr
< SquarePyramidalMetal_Helper
const > 
SquarePyramidalMetal_HelperCOP
 
typedef
utility::pointer::shared_ptr
< TBMB_Helper
TBMB_HelperOP
 
typedef
utility::pointer::shared_ptr
< TBMB_Helper const > 
TBMB_HelperCOP
 
typedef
utility::pointer::shared_ptr
< TetrahedralMetal_Helper
TetrahedralMetal_HelperOP
 
typedef
utility::pointer::shared_ptr
< TetrahedralMetal_Helper
const > 
TetrahedralMetal_HelperCOP
 
typedef
utility::pointer::shared_ptr
< TMA_Helper
TMA_HelperOP
 
typedef
utility::pointer::shared_ptr
< TMA_Helper const > 
TMA_HelperCOP
 
typedef
utility::pointer::shared_ptr
< TrigonalPlanarMetal_Helper
TrigonalPlanarMetal_HelperOP
 
typedef
utility::pointer::shared_ptr
< TrigonalPlanarMetal_Helper
const > 
TrigonalPlanarMetal_HelperCOP
 
typedef
utility::pointer::shared_ptr
< TrigonalPyramidalMetal_Helper
TrigonalPyramidalMetal_HelperOP
 
typedef
utility::pointer::shared_ptr
< TrigonalPyramidalMetal_Helper
const > 
TrigonalPyramidalMetal_HelperCOP
 

Enumerations

enum  Metal_HelperBase_Metal {
  MH_Zn = 1, MH_Fe2, MH_Ni2, MH_unknown_metal,
  MH_end_of_list = MH_unknown_metal
}
 Metal types compatible with this helper. More...
 
enum  Metal_HelperBase_MetalLigand {
  MHLigand_Nd_histidine = 1, MHLigand_Ne_histidine, MHLigand_O_carboxyl, MHLigand_N_pyridine,
  MHLigand_S_cysteine, MHLigand_unknown_ligand, MHLigand_end_of_list = MHLigand_unknown_ligand
}
 Metal-liganding atom types compatible with this helper. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< TBMB_Helper const > protocols::cyclic_peptide::crosslinker::TBMB_HelperCOP
typedef utility::pointer::shared_ptr< TBMB_Helper > protocols::cyclic_peptide::crosslinker::TBMB_HelperOP
typedef utility::pointer::shared_ptr< TMA_Helper const > protocols::cyclic_peptide::crosslinker::TMA_HelperCOP
typedef utility::pointer::shared_ptr< TMA_Helper > protocols::cyclic_peptide::crosslinker::TMA_HelperOP

Enumeration Type Documentation

Metal types compatible with this helper.

If you add to this list, you need to add entries to the switch statement in metal_type_string_from_enum(), as well as the map in ideal_bond_length().

Enumerator
MH_Zn 
MH_Fe2 
MH_Ni2 
MH_unknown_metal 
MH_end_of_list 

Metal-liganding atom types compatible with this helper.

If you add to this list, you need to add entries to the map in ideal_bond_length().

Enumerator
MHLigand_Nd_histidine 
MHLigand_Ne_histidine 
MHLigand_O_carboxyl 
MHLigand_N_pyridine 
MHLigand_S_cysteine 
MHLigand_unknown_ligand 
MHLigand_end_of_list