#include <Interface.hh>

Inheritance diagram for protocols::scoring::Interface:

Public Types
typedef core::pack::task::PackerTaskOP	PackerTaskOP

typedef core::Real	Real

Public Member Functions
	Interface ()

	Interface (core::Size const jump_number_in)

	Interface (ObjexxFCL::FArray1D_bool partner)

void	jump (core::Size const jump_number)

core::Size	jump_id () const

void	calculate (core::pose::Pose const &pose)
	base for calculating the interface More...

void	print (core::pose::Pose const &pose)
	print out the interface information More...

void	show (core::pose::Pose const &pose)

void	show (std::ostream &out, core::pose::Pose const &pose)

void	set_pack (core::pose::Pose const &pose, PackerTaskOP task)
	sets up which residues are to be packed More...

core::Size	closest_interface_residue (core::pose::Pose const &pose, core::Size src_rsd, core::Real &distance)
	find the nearest residue at the interface to a given residue More...

void	distance (Real const distance_in)

core::Vector	center (core::pose::Pose const &pose)
	calculates the center of mass of interface residues More...

bool	is_interface (core::conformation::Residue const &rsd) const

bool	is_interface (core::Size const position) const

core::Size	interface_nres ()
	returns the total number of residues on both sides of the interface for a given jump More...

bool	is_pair (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2)
	returns whether the rsd1 and rsd2 are considered a contact pair based on contact_list_ array More...

void	set_symmetric_pack (core::pose::Pose const &pose, PackerTaskOP task)

utility::vector1< utility::vector1_int >	pair_list ()
	Get two lists containing the residues on each side of the interface. More...

utility::vector1< utility::vector1_size >	contact_list ()
	The contact_list is pose.size() long, each element (contact_list_[i]) contains a list of residues from the other partner that interacts with residue i. This is calculated in protein_calculate, and used by Interface.is_pair() function as well as the interchain_vdw, interchain_env, and interchain_pair scoring components. More...

Private Member Functions
void	protein_calculate (core::pose::Pose const &pose)
	calculate the protein-protien interface More...

void	ligand_calculate (core::pose::Pose const &pose)

void	NA_calculate (core::pose::Pose const &)

void	symmetric_protein_calculate (core::pose::Pose const &pose)

Private Attributes
core::Size	jump_number_

Real	distance_squared_

ObjexxFCL::FArray1D_bool	partner_

ObjexxFCL::FArray1D_bool	is_interface_

utility::vector1< utility::vector1_int >	pair_list_

utility::vector1< utility::vector1_size >	contact_list_

bool	use_input_partners_

Member Typedef Documentation

◆ PackerTaskOP

typedef core::pack::task::PackerTaskOP protocols::scoring::Interface::PackerTaskOP

◆ Real

typedef core::Real protocols::scoring::Interface::Real

Constructor & Destructor Documentation

◆ Interface() [1/3]

protocols::scoring::Interface::Interface ( )

inline

◆ Interface() [2/3]

protocols::scoring::Interface::Interface ( core::Size const jump_number_in )

inline

◆ Interface() [3/3]

protocols::scoring::Interface::Interface ( ObjexxFCL::FArray1D_bool partner )

inline

Member Function Documentation

◆ calculate()

void protocols::scoring::Interface::calculate ( core::pose::Pose const & pose )

base for calculating the interface

decide which type of an interface calculation to use

Author: Monica Berrondo October 19 2007

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::energies(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_NA(), core::conformation::symmetry::is_symmetric(), core::conformation::Residue::is_virtual_residue(), protocols::scoring::max_interchain_sites(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::kinematics::FoldTree::upstream_jump_residue().

◆ center()

core::Vector protocols::scoring::Interface::center ( core::pose::Pose const & pose )

calculates the center of mass of interface residues

calculate the center of mass of the interface loops over all residues at the interface and gets the xyz coordinates for the c-alpha atom of that residue

References: pose_docking_calc_interface from pose_docking.cc

Author: Monica Berrondo June 14 2007

References core::conformation::membrane::center, core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ closest_interface_residue()

core::Size protocols::scoring::Interface::closest_interface_residue	(	core::pose::Pose const &	pose,
		core::Size	src_rsd,
		core::Real &	distance
	)

find the nearest residue at the interface to a given residue

Author: Monica Berrondo November 18, 2010

References core::kinematics::distance(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ contact_list()

utility::vector1< utility::vector1_size > protocols::scoring::Interface::contact_list ( )

inline

The contact_list is pose.size() long, each element (contact_list_[i]) contains a list of residues from the other partner that interacts with residue i. This is calculated in protein_calculate, and used by Interface.is_pair() function as well as the interchain_vdw, interchain_env, and interchain_pair scoring components.

◆ distance()

void protocols::scoring::Interface::distance ( Real const distance_in )

Referenced by protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::symmetric_docking::SymRestrictTaskForDocking::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::geometry::centroids_by_jump_int(), protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges(), protocols::ub_e2c::ubi_e2c_modeler::CSP_fraction(), protocols::ddG_main(), protocols::seeded_abinitio::define_movemap_chains(), protocols::docking::EllipsoidalRandomizationMover::get_interface_residues(), protocols::ub_e2c::ubi_e2c_modeler::monoub_CSP_fraction(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::enzdes::LigInterfaceEnergyFilter::report(), protocols::simple_ddg::AlaScan::report(), protocols::simple_ddg::AlaScan::report_symmetry(), and protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap().

◆ interface_nres()

core::Size protocols::scoring::Interface::interface_nres ( )

returns the total number of residues on both sides of the interface for a given jump

◆ is_interface() [1/2]

bool protocols::scoring::Interface::is_interface ( core::conformation::Residue const & rsd ) const

References core::conformation::Residue::seqpos().

Referenced by protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::membrane::MPFindInterfaceMover::calculate_interface_SASA(), protocols::geometry::centroids_by_jump_int(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::compute(), protocols::ub_e2c::ubi_e2c_modeler::CSP_fraction(), protocols::ddG_main(), protocols::seeded_abinitio::define_movemap_chains(), protocols::docking::membrane::MPFindInterfaceMover::fractions_small_residues(), protocols::docking::EllipsoidalRandomizationMover::get_interface_residues(), protocols::ub_e2c::ubi_e2c_modeler::monoub_CSP_fraction(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::enzdes::LigInterfaceEnergyFilter::report(), protocols::simple_ddg::AlaScan::report(), protocols::simple_ddg::AlaScan::report_symmetry(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::ddg::ddGMover::setup_packer_task_for_mutations(), and protocols::docking::ConformerSwitchMover::switch_conformer().

◆ is_interface() [2/2]

bool protocols::scoring::Interface::is_interface ( core::Size const position ) const

◆ is_pair()

bool protocols::scoring::Interface::is_pair	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2
	)

returns whether the rsd1 and rsd2 are considered a contact pair based on contact_list_ array

Function to determine whether two residues are a "pair" for docking-type scoring calculations, such as vdw and pair across an interface

References core::conformation::Residue::seqpos().

Referenced by protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges(), protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions().

◆ jump()

void protocols::scoring::Interface::jump ( core::Size const jump_number )

Referenced by protocols::protein_interface_design::movers::LoopFinder::apply(), and protocols::simple_ddg::AlaScan::report().

◆ jump_id()

core::Size protocols::scoring::Interface::jump_id ( ) const

inline

◆ ligand_calculate()

void protocols::scoring::Interface::ligand_calculate ( core::pose::Pose const & pose )

private

References core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

◆ NA_calculate()

void protocols::scoring::Interface::NA_calculate ( core::pose::Pose const & pose )

private

◆ pair_list()

utility::vector1< utility::vector1_int > protocols::scoring::Interface::pair_list ( )

inline

Get two lists containing the residues on each side of the interface.

You might expect something called pair_list() to output pairs or somehow relate to the is_pair function, but it does not. It returns a two element list.

The first element is a list of all residues on the lower partner of the interface.
The second element is a list of all the residues in the interface on the upper partner. Both lists are sorted by residue number, so the indices of one list have no relationship to the other list.
Todo:
rename this to something more logical & give it a better return type

make a function that returns a vector1<pair<core::Size,Size> > containing all interacting pairs. This would be easy to implement.

Referenced by protocols::protein_interface_design::movers::DisulfideMover::disulfide_list().

◆ print()

void protocols::scoring::Interface::print ( core::pose::Pose const & pose )

print out the interface information

Author: Monica Berrondo November 07 2007

Referenced by protocols::ddG_main().

◆ protein_calculate()

void protocols::scoring::Interface::protein_calculate ( core::pose::Pose const & pose )

private

calculate the protein-protien interface

decide which type of an interface calculation to use calculate the residues that are at the interface this uses the CAlpha class (at least for now) which gets the distances between c-alpha atoms Returns a vector of bools, true if at interface, false otherwise

This uses partition_by_jump to determine which residues belong to each partner those on one side of the jump are set to 0, the others are set to 1 A residue is at the interface if it is within 8A radius of the residue in question on the other partner

References: pose_docking_calc_interface from pose_docking.cc

Author: Monica Berrondo June 14 2007

References core::sequence::end, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::conformation::Residue::is_water(), and core::pose::Pose::residue().

◆ set_pack()

void protocols::scoring::Interface::set_pack	(	core::pose::Pose const &	pose,
		PackerTaskOP	task
	)

sets up which residues are to be packed

References: pose_docking_repack from pose_docking.cc

Author: Monica Berrondo June 14 2007

References core::kinematics::FoldTree::cutpoint_by_jump(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ set_symmetric_pack()

void protocols::scoring::Interface::set_symmetric_pack	(	core::pose::Pose const &	pose,
		PackerTaskOP	task
	)

References core::pose::Pose::conformation(), and core::pose::Pose::size().

Referenced by protocols::symmetric_docking::SymRestrictTaskForDocking::apply().

◆ show() [1/2]

void protocols::scoring::Interface::show ( core::pose::Pose const & pose )

References TR().

◆ show() [2/2]

void protocols::scoring::Interface::show	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)

References core::conformation::Residue::aa(), protocols::scoring::max_interchain_sites(), core::conformation::membrane::out, core::pose::Pose::residue(), and core::conformation::Residue::seqpos().

◆ symmetric_protein_calculate()

void protocols::scoring::Interface::symmetric_protein_calculate ( core::pose::Pose const & pose )

private

References core::pose::Pose::conformation(), core::sequence::end, core::pose::Pose::energies(), and core::pose::Pose::size().

Member Data Documentation

◆ contact_list_

utility::vector1< utility::vector1_size > protocols::scoring::Interface::contact_list_

private

◆ distance_squared_

Real protocols::scoring::Interface::distance_squared_

private

◆ is_interface_

ObjexxFCL::FArray1D_bool protocols::scoring::Interface::is_interface_

private

◆ jump_number_

core::Size protocols::scoring::Interface::jump_number_

private

◆ pair_list_

utility::vector1< utility::vector1_int > protocols::scoring::Interface::pair_list_

private

◆ partner_

ObjexxFCL::FArray1D_bool protocols::scoring::Interface::partner_

private

◆ use_input_partners_

bool protocols::scoring::Interface::use_input_partners_

private

The documentation for this class was generated from the following files:

src/protocols/scoring/Interface.hh
src/protocols/scoring/Interface.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ PackerTaskOP

◆ Real

Constructor & Destructor Documentation

◆ Interface() [1/3]

◆ Interface() [2/3]

◆ Interface() [3/3]

Member Function Documentation

◆ calculate()

◆ center()

◆ closest_interface_residue()

◆ contact_list()

◆ distance()

◆ interface_nres()

◆ is_interface() [1/2]

◆ is_interface() [2/2]

◆ is_pair()

◆ jump()

◆ jump_id()

◆ ligand_calculate()

◆ NA_calculate()

◆ pair_list()

◆ print()

◆ protein_calculate()

◆ set_pack()

◆ set_symmetric_pack()

◆ show() [1/2]

◆ show() [2/2]

◆ symmetric_protein_calculate()

Member Data Documentation

◆ contact_list_

◆ distance_squared_

◆ is_interface_

◆ jump_number_

◆ pair_list_

◆ partner_

◆ use_input_partners_