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< CrosslinkerMoverHelper const > protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP

typedef utility::pointer::shared_ptr< CrosslinkerMoverHelper > protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperOP

typedef utility::pointer::shared_ptr< Metal_HelperBase const > protocols::cyclic_peptide::crosslinker::Metal_HelperBaseCOP

typedef utility::pointer::shared_ptr< Metal_HelperBase > protocols::cyclic_peptide::crosslinker::Metal_HelperBaseOP

typedef utility::pointer::shared_ptr< OctahedralMetal_Helper const > protocols::cyclic_peptide::crosslinker::OctahedralMetal_HelperCOP

typedef utility::pointer::shared_ptr< OctahedralMetal_Helper > protocols::cyclic_peptide::crosslinker::OctahedralMetal_HelperOP

typedef utility::pointer::shared_ptr< SquarePlanarMetal_Helper const > protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_HelperCOP

typedef utility::pointer::shared_ptr< SquarePlanarMetal_Helper > protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_HelperOP

typedef utility::pointer::shared_ptr< SquarePyramidalMetal_Helper const > protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_HelperCOP

typedef utility::pointer::shared_ptr< SquarePyramidalMetal_Helper > protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_HelperOP

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< TetrahedralMetal_Helper const > protocols::cyclic_peptide::crosslinker::TetrahedralMetal_HelperCOP

typedef utility::pointer::shared_ptr< TetrahedralMetal_Helper > protocols::cyclic_peptide::crosslinker::TetrahedralMetal_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

typedef utility::pointer::shared_ptr< TrigonalPlanarMetal_Helper const > protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_HelperCOP

typedef utility::pointer::shared_ptr< TrigonalPlanarMetal_Helper > protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_HelperOP

typedef utility::pointer::shared_ptr< TrigonalPyramidalMetal_Helper const > protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_HelperCOP

typedef utility::pointer::shared_ptr< TrigonalPyramidalMetal_Helper > protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_HelperOP

Enumeration Type Documentation

enum protocols::cyclic_peptide::crosslinker::Metal_HelperBase_Metal

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

enum protocols::cyclic_peptide::crosslinker::Metal_HelperBase_MetalLigand

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