protocols::cyclic_peptide::crosslinker Namespace Reference

Classes
class	One_Four_BBMB_Helper
	A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,4-bis(bromomethyl)benzene (BBMB) cross-linker. More...
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	Thioether_Helper
	A CrosslinkerMoverHelper for placing a terminal (or lariat-style) thioether linkage. 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< One_Four_BBMB_Helper >	One_Four_BBMB_HelperOP
typedef utility::pointer::shared_ptr< One_Four_BBMB_Helper const >	One_Four_BBMB_HelperCOP
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
using	Thioether_HelperOP = utility::pointer::shared_ptr< Thioether_Helper >
using	Thioether_HelperCOP = utility::pointer::shared_ptr< Thioether_Helper const >
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...

Functions
void	set_up_thioether_variants (core::pose::Pose &pose, core::Size const ntermres, core::Size const sidechainres)
	Given a pose and two residues, set up the thioether variant types. More...
void	set_up_thioether_bond_mover (protocols::simple_moves::DeclareBond &termini, core::pose::Pose const &pose, core::Size const ntermres, core::Size const sidechainres)
	Set up the mover that creates thioether lariat bonds. More...
void	correct_thioether_virtuals (core::pose::Pose &pose, core::Size const ntermres, core::Size const sidechainres)
	Correct the bond angles and bond lenghts for virtual atoms at thioether bonds. More...
void	set_up_thioether_constraints (core::pose::Pose &pose, core::Size const ntermres, core::Size const sidechainres)
	Given a pose and two residues to constrain (the first being the residue with the modified N-terminus, and the second being the one with the thiol-containing sidechain), add constraints for a thioether linkage. More...

Variables
constexpr core::Real	THIOETHER_UTIL_THIOETHER_BOND_LENGTH = 1.827
constexpr core::Real	THIOETHER_UTIL_THIOETHER_BOND_C_ANGLE = 1.781
constexpr core::Real	THIOETHER_UTIL_THIOETHER_BOND_N_ANGLE = 1.960

Typedef Documentation

CrosslinkerMoverHelperCOP

typedef utility::pointer::shared_ptr< CrosslinkerMoverHelper const > protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelperCOP

CrosslinkerMoverHelperOP

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

Metal_HelperBaseCOP

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

Metal_HelperBaseOP

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

OctahedralMetal_HelperCOP

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

OctahedralMetal_HelperOP

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

One_Four_BBMB_HelperCOP

typedef utility::pointer::shared_ptr< One_Four_BBMB_Helper const > protocols::cyclic_peptide::crosslinker::One_Four_BBMB_HelperCOP

One_Four_BBMB_HelperOP

typedef utility::pointer::shared_ptr< One_Four_BBMB_Helper > protocols::cyclic_peptide::crosslinker::One_Four_BBMB_HelperOP

SquarePlanarMetal_HelperCOP

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

SquarePlanarMetal_HelperOP

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

SquarePyramidalMetal_HelperCOP

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

SquarePyramidalMetal_HelperOP

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

TBMB_HelperCOP

typedef utility::pointer::shared_ptr< TBMB_Helper const > protocols::cyclic_peptide::crosslinker::TBMB_HelperCOP

TBMB_HelperOP

typedef utility::pointer::shared_ptr< TBMB_Helper > protocols::cyclic_peptide::crosslinker::TBMB_HelperOP

TetrahedralMetal_HelperCOP

typedef utility::pointer::shared_ptr< TetrahedralMetal_Helper const > protocols::cyclic_peptide::crosslinker::TetrahedralMetal_HelperCOP

TetrahedralMetal_HelperOP

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

Thioether_HelperCOP

using protocols::cyclic_peptide::crosslinker::Thioether_HelperCOP = typedef utility::pointer::shared_ptr< Thioether_Helper const >

Thioether_HelperOP

using protocols::cyclic_peptide::crosslinker::Thioether_HelperOP = typedef utility::pointer::shared_ptr< Thioether_Helper >

TMA_HelperCOP

typedef utility::pointer::shared_ptr< TMA_Helper const > protocols::cyclic_peptide::crosslinker::TMA_HelperCOP

TMA_HelperOP

typedef utility::pointer::shared_ptr< TMA_Helper > protocols::cyclic_peptide::crosslinker::TMA_HelperOP

TrigonalPlanarMetal_HelperCOP

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

TrigonalPlanarMetal_HelperOP

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

TrigonalPyramidalMetal_HelperCOP

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

TrigonalPyramidalMetal_HelperOP

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

Enumeration Type Documentation

Metal_HelperBase_Metal

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

Metal_HelperBase_MetalLigand

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

Function Documentation

correct_thioether_virtuals()

void protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals	(	core::pose::Pose &	pose,
		core::Size const	ntermres,
		core::Size const	sidechainres
	)

Correct the bond angles and bond lenghts for virtual atoms at thioether bonds.

References core::chemical::ResidueType::atom_index(), core::chemical::ICoorAtomID::atomno(), core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::chemical::ResidueType::icoor(), core::pose::Pose::residue_type(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), THIOETHER_UTIL_THIOETHER_BOND_C_ANGLE, THIOETHER_UTIL_THIOETHER_BOND_LENGTH, THIOETHER_UTIL_THIOETHER_BOND_N_ANGLE, and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_native().

set_up_thioether_bond_mover()

void protocols::cyclic_peptide::crosslinker::set_up_thioether_bond_mover	(	protocols::simple_moves::DeclareBond &	termini,
		core::pose::Pose const &	pose,
		core::Size const	ntermres,
		core::Size const	sidechainres
	)

Set up the mover that creates thioether lariat bonds.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::residue_connect_atom_index(), core::pose::Pose::residue_type(), protocols::simple_moves::DeclareBond::set(), and protocols::cyclic_peptide::TR().

Referenced by protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_asymmetric(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_thioether_lariat_cyclization_mover().

set_up_thioether_constraints()

void protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints	(	core::pose::Pose &	pose,
		core::Size const	ntermres,
		core::Size const	sidechainres
	)

Given a pose and two residues to constrain (the first being the residue with the modified N-terminus, and the second being the one with the thiol-containing sidechain), add constraints for a thioether linkage.

References core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_name(), core::chemical::ICoorAtomID::atomno(), core::id::AtomID::atomno(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::n_possible_residue_connections(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connect_atom_index(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), core::chemical::AtomICoor::stub_atom1(), THIOETHER_UTIL_THIOETHER_BOND_C_ANGLE, THIOETHER_UTIL_THIOETHER_BOND_LENGTH, THIOETHER_UTIL_THIOETHER_BOND_N_ANGLE, and protocols::cyclic_peptide::TR().

Referenced by protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_constraints_asymmetric(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_thioether_lariat_cyclic_constraints().

set_up_thioether_variants()

void protocols::cyclic_peptide::crosslinker::set_up_thioether_variants	(	core::pose::Pose &	pose,
		core::Size const	ntermres,
		core::Size const	sidechainres
	)

Given a pose and two residues, set up the thioether variant types.

Sidechainres gets SIDECHAIN_CONJUGATION; ntermres gets ACETYLATED_NTERMINUS_CONNECTION_VARIANT. The pose is modified by this operation.

References core::chemical::ACETYLATED_NTERMINUS_CONNECTION_VARIANT, core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueTypeBase::base_name(), core::chemical::AtomICoor::build(), core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_lower(), core::chemical::ResidueType::has(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_sidechain_thiol(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), core::chemical::SIDECHAIN_CONJUGATION, core::id::to_string(), protocols::cyclic_peptide::TR(), core::conformation::Conformation::update_polymeric_connection(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_asymmetric(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_thioether_lariat_variants().

Variable Documentation

THIOETHER_UTIL_THIOETHER_BOND_C_ANGLE

constexpr core::Real protocols::cyclic_peptide::crosslinker::THIOETHER_UTIL_THIOETHER_BOND_C_ANGLE = 1.781

constexpr

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_thioether_lariat(), correct_thioether_virtuals(), and set_up_thioether_constraints().

THIOETHER_UTIL_THIOETHER_BOND_LENGTH

constexpr core::Real protocols::cyclic_peptide::crosslinker::THIOETHER_UTIL_THIOETHER_BOND_LENGTH = 1.827

constexpr

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_thioether_lariat(), correct_thioether_virtuals(), and set_up_thioether_constraints().

THIOETHER_UTIL_THIOETHER_BOND_N_ANGLE

constexpr core::Real protocols::cyclic_peptide::crosslinker::THIOETHER_UTIL_THIOETHER_BOND_N_ANGLE = 1.960

constexpr

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_thioether_lariat(), correct_thioether_virtuals(), and set_up_thioether_constraints().