#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::NonPlaidFingerprint:

Public Member Functions
	NonPlaidFingerprint ()

	~NonPlaidFingerprint () override

void	change_CoM_to_ligandCoM (numeric::xyzVector< core::Real > const &ligandCoM)

void	setup_from_espGrid (std::string const &input_filename, core::pose::Pose const &protein_pose, bool delphi)

void	setup_from_PocketGrid (core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid)

void	setup_from_PocketGrid (core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, PocketGrid const &grid_for_extshell)

void	setup_from_PocketGrid_and_known_ligand (core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, PocketGrid const &grid_for_extshell, core::pose::Pose const &known_ligand_pose, core::Real const &trim_dist)

void	setup_from_PocketGrid_using_bound_ligand (core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, PocketGrid const &grid_for_extshell, core::pose::Pose const &known_ligand_pose)

void	setup_from_EggshellGrid ()

void	setup_from_ConnollySurface (core::pose::Pose const &protein_pose, PocketGrid const &pocket_grid, PocketGrid const &grid_for_extshell)

void	write_eggshell_to_pdb_file (std::string const &output_eggshell_name) const

void	setup_from_eggshell_pdb_file (std::string const &input_filename)

void	trim_based_on_known_ligand (core::pose::Pose const &known_ligand_pose)

void	include_eggshell_points_based_on_known_ligand (core::pose::Pose const &known_ligand_pose, core::Real const &trim_dist)

void	setup_from_eggshell_triplet_file (std::string const &input_filename)

void	setup_from_PlaidFingerprint (PlaidFingerprint const &pfp)

void	choose_origin_with_lowest_eggshell_ruggedness (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell)

void	set_origin (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell)

void	set_origin_from_option_ (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell, Size const &set_origin_option)

void	set_multiple_origin (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell)

numeric::xyzVector< core::Real >	place_origin_point (core::Real const &angle)

void	set_origin_away_from_protein_center (core::pose::Pose const &protein_pose)

void	set_origin_from_residue (core::pose::Pose const &protein_pose)

core::Size	get_pose_resnum (int const pdbnum, char const pdbchn, core::pose::Pose const &ps)

void	set_origin_away_from_eggshell (std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell, core::pose::Pose const &protein_pose)

void	set_origin_away_from_eggshell_plane (std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell, core::pose::Pose const &protein_pose, Size const &set_origin_option)

core::Real	get_Rvalue (core::pose::Pose const &protein_pose, std::list< numeric::xyzVector< core::Real > > const &egg_and_extra_shell, Size const &set_origin_option)

numeric::xyzVector< core::Real >	calculate_protein_CoM (core::pose::Pose const &protein_pose)

std::list< numeric::xyzVector < core::Real > >	combine_xyz_lists (std::list< numeric::xyzVector< core::Real > > const &xyz_list_1, std::list< numeric::xyzVector< core::Real > > const &xyz_list_2)

std::list< spherical_coor_triplet >	remove_duplicate_phi_psi (std::list< spherical_coor_triplet > const &rounded_triplet)

std::list< spherical_coor_triplet >	convert_cart_to_spherical_and_round (std::list< numeric::xyzVector< core::Real > > const &xyz_list)

std::list< numeric::xyzVector < core::Real > >	convert_spherical_list_to_cartesian_list (std::list< spherical_coor_triplet > const &unique_triplet)

std::list< spherical_coor_triplet >	set_rho_to_zero (std::list< spherical_coor_triplet > const &rounded_triplet)

core::Real	get_electrostatics_energy (core::pose::Pose const &ligand_pose)

core::Real	get_nearest_neighbour_esp_energy (numeric::xyzVector< core::Real > const &ligand_atom, core::Real const &atom_charge)

core::Real	get_interpolated_esp_energy (numeric::xyzVector< core::Real > const &ligand_atom, core::Real const &atom_charge)

core::Real	get_interpolated_esp_energy_with_type (numeric::xyzVector< core::Real > const &ligand_atom, core::Real const &atom_charge)

core::Real	get_surface_esp (std::list< numeric::xyzVector< core::Real > > const &surfacePoints_list, std::string const &inp_espGrid_fname)

Public Member Functions inherited from protocols::pockets::FingerprintBase
	FingerprintBase ()

void	print_to_file (std::string const &output_filename) const

void	print_to_pdb (std::string const &output_pdbname) const

void	print_to_pdb (std::string const &output_pdbname, numeric::xyzVector< core::Real > const &translation) const

core::Size	num_origins () const

numeric::xyzVector< core::Real >	origin () const

utility::vector1 < numeric::xyzVector < core::Real > >	multi_origin_list () const

numeric::xyzVector< core::Real >	CoM () const

void	CHEAT_CoM (numeric::xyzVector< core::Real > const &inp_CoM)

std::list < spherical_coor_triplet > const &	triplet_fingerprint_data () const

	~FingerprintBase () override
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

Public Attributes
numeric::xyzVector< core::Real >	pocket_CoM_

std::list< numeric::xyzVector < core::Real > >	egg_and_ext_list_

std::list< numeric::xyzVector < core::Real > >	eggshell_list_

std::list< numeric::xyzVector < core::Real > >	extshell_list_

std::vector< std::vector < std::vector< core::Real > > >	espGrid_

std::vector< std::vector < std::vector < ElectrostaticpotentialGrid::PtType > > >	typGrid_

core::Real	esp_spacing_

numeric::xyzVector< core::Real >	esp_mid_

numeric::xyzVector< core::Size >	esp_dim_

Public Attributes inherited from protocols::pockets::FingerprintBase
numeric::xyzVector< core::Real >	pocketGrid_mid_

numeric::xyzVector< core::Real >	pocketGrid_dim_

core::Real	pocketGrid_spacing_

Additional Inherited Members
Protected Attributes inherited from protocols::pockets::FingerprintBase
core::Size	num_origins_

numeric::xyzVector< core::Real >	origin_

utility::vector1 < numeric::xyzVector < core::Real > >	multi_origin_list_

numeric::xyzVector< core::Real >	CoM_

std::list< spherical_coor_triplet >	triplet_fingerprint_data_

Constructor & Destructor Documentation

protocols::pockets::NonPlaidFingerprint::NonPlaidFingerprint ( )

protocols::pockets::NonPlaidFingerprint::~NonPlaidFingerprint ( )

override

Member Function Documentation

numeric::xyzVector< core::Real > protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM ( core::pose::Pose const & protein_pose )

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by set_origin_away_from_eggshell(), set_origin_away_from_eggshell_plane(), and set_origin_away_from_protein_center().

void protocols::pockets::NonPlaidFingerprint::change_CoM_to_ligandCoM ( numeric::xyzVector< core::Real > const & ligandCoM )

References protocols::pockets::FingerprintBase::CoM_.

void protocols::pockets::NonPlaidFingerprint::choose_origin_with_lowest_eggshell_ruggedness	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell
	)

References get_Rvalue(), and set_origin_from_option_().

Referenced by set_origin_from_option_().

std::list< numeric::xyzVector< core::Real > > protocols::pockets::NonPlaidFingerprint::combine_xyz_lists	(	std::list< numeric::xyzVector< core::Real > > const &	xyz_list_1,
		std::list< numeric::xyzVector< core::Real > > const &	xyz_list_2
	)

Referenced by setup_from_ConnollySurface(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), and setup_from_PocketGrid_using_bound_ligand().

std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::convert_cart_to_spherical_and_round ( std::list< numeric::xyzVector< core::Real > > const & xyz_list )

References protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), protocols::pockets::FingerprintBase::origin_, protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, and protocols::pockets::spherical_coor_triplet::rho.

std::list< numeric::xyzVector< core::Real > > protocols::pockets::NonPlaidFingerprint::convert_spherical_list_to_cartesian_list ( std::list< spherical_coor_triplet > const & unique_triplet )

References protocols::pockets::convert_spherical_coor_triplet_to_cartesian(), and protocols::pockets::FingerprintBase::origin_.

core::Real protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy ( core::pose::Pose const & ligand_pose )

References core::conformation::Residue::is_protein(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

core::Real protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy	(	numeric::xyzVector< core::Real > const &	ligand_atom,
		core::Real const &	atom_charge
	)

References core::chemical::element::C, protocols::pockets::convert_cartesian_to_grid(), protocols::comparative_modeling::features::X, and core::chemical::element::Y.

core::Real protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy_with_type	(	numeric::xyzVector< core::Real > const &	ligand_atom,
		core::Real const &	atom_charge
	)

References core::chemical::element::C, protocols::pockets::convert_cartesian_to_grid(), protocols::pockets::ElectrostaticpotentialGrid::PROTEIN, protocols::comparative_modeling::features::X, and core::chemical::element::Y.

core::Real protocols::pockets::NonPlaidFingerprint::get_nearest_neighbour_esp_energy	(	numeric::xyzVector< core::Real > const &	ligand_atom,
		core::Real const &	atom_charge
	)

core::Size protocols::pockets::NonPlaidFingerprint::get_pose_resnum	(	int const	pdbnum,
		char const	pdbchn,
		core::pose::Pose const &	ps
	)

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

Referenced by set_origin_from_residue().

core::Real protocols::pockets::NonPlaidFingerprint::get_Rvalue	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell,
		Size const &	set_origin_option
	)

References protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), protocols::pockets::FingerprintBase::origin_, protocols::pockets::spherical_coor_triplet::rho, and set_origin_from_option_().

Referenced by choose_origin_with_lowest_eggshell_ruggedness().

core::Real protocols::pockets::NonPlaidFingerprint::get_surface_esp	(	std::list< numeric::xyzVector< core::Real > > const &	surfacePoints_list,
		std::string const &	inp_espGrid_fname
	)

References protocols::pockets::ElectrostaticpotentialGrid::espGrid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_dim_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_mid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_spacing_, and protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values().

void protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand	(	core::pose::Pose const &	known_ligand_pose,
		core::Real const &	trim_dist
	)

References core::conformation::Residue::atom(), core::pose::Pose::conformation(), eggshell_list_, core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by setup_from_PocketGrid_and_known_ligand().

numeric::xyzVector< core::Real > protocols::pockets::NonPlaidFingerprint::place_origin_point ( core::Real const & angle )

References protocols::pockets::FingerprintBase::CoM_, protocols::pockets::FingerprintBase::origin_, and core::pack::dunbrack::product().

std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::remove_duplicate_phi_psi ( std::list< spherical_coor_triplet > const & rounded_triplet )

References protocols::pockets::spherical_coor_triplet::rho.

void protocols::pockets::NonPlaidFingerprint::set_multiple_origin	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell
	)

References protocols::pockets::FingerprintBase::CoM_, protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::origin_, core::pack::dunbrack::product(), and set_origin_from_option_().

Referenced by set_origin().

void protocols::pockets::NonPlaidFingerprint::set_origin	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell
	)

References protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::origin_, set_multiple_origin(), and set_origin_from_option_().

Referenced by setup_from_ConnollySurface(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), and setup_from_PocketGrid_using_bound_ligand().

void protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell	(	std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell,
		core::pose::Pose const &	protein_pose
	)

References calculate_protein_CoM(), protocols::pockets::FingerprintBase::CoM_, and protocols::pockets::FingerprintBase::origin_.

Referenced by set_origin_from_option_().

void protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell_plane	(	std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell,
		core::pose::Pose const &	protein_pose,
		Size const &	set_origin_option
	)

References protocols::comparative_modeling::features::A, protocols::match::upstream::b, calculate_protein_CoM(), protocols::pockets::FingerprintBase::CoM_, and protocols::pockets::FingerprintBase::origin_.

Referenced by set_origin_from_option_().

void protocols::pockets::NonPlaidFingerprint::set_origin_away_from_protein_center ( core::pose::Pose const & protein_pose )

References calculate_protein_CoM(), protocols::pockets::FingerprintBase::CoM_, and protocols::pockets::FingerprintBase::origin_.

Referenced by set_origin_from_option_().

void protocols::pockets::NonPlaidFingerprint::set_origin_from_option_	(	core::pose::Pose const &	protein_pose,
		std::list< numeric::xyzVector< core::Real > > const &	egg_and_extra_shell,
		Size const &	set_origin_option
	)

References choose_origin_with_lowest_eggshell_ruggedness(), set_origin_away_from_eggshell(), set_origin_away_from_eggshell_plane(), set_origin_away_from_protein_center(), and set_origin_from_residue().

Referenced by choose_origin_with_lowest_eggshell_ruggedness(), get_Rvalue(), set_multiple_origin(), and set_origin().

void protocols::pockets::NonPlaidFingerprint::set_origin_from_residue ( core::pose::Pose const & protein_pose )

References protocols::pockets::FingerprintBase::CoM_, get_pose_resnum(), protocols::pockets::FingerprintBase::origin_, and core::pose::Pose::residue().

Referenced by set_origin_from_option_().

std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::set_rho_to_zero ( std::list< spherical_coor_triplet > const & rounded_triplet )

References protocols::pockets::spherical_coor_triplet::rho.

void protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface	(	core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid,
		PocketGrid const &	grid_for_extshell
	)

void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file ( std::string const & input_filename )

References protocols::pockets::FingerprintBase::CoM_, protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), protocols::pockets::FingerprintBase::origin_, protocols::pockets::spherical_coor_triplet::rho, and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file ( std::string const & input_filename )

void protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid ( )

References protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), eggshell_list_, extshell_list_, protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, protocols::pockets::spherical_coor_triplet::rho, and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

Referenced by setup_from_ConnollySurface(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), and setup_from_PocketGrid_using_bound_ligand().

void protocols::pockets::NonPlaidFingerprint::setup_from_espGrid	(	std::string const &	input_filename,
		core::pose::Pose const &	protein_pose,
		bool	delphi
	)

void protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint ( PlaidFingerprint const & pfp )

References protocols::pockets::FingerprintBase::origin(), protocols::pockets::FingerprintBase::origin_, protocols::pockets::FingerprintBase::triplet_fingerprint_data(), and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

void protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid	(	core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid
	)

void protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid	(	core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid,
		PocketGrid const &	grid_for_extshell
	)

void protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand	(	core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid,
		PocketGrid const &	grid_for_extshell,
		core::pose::Pose const &	known_ligand_pose,
		core::Real const &	trim_dist
	)

void protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand	(	core::pose::Pose const &	protein_pose,
		PocketGrid const &	pocket_grid,
		PocketGrid const &	grid_for_extshell,
		core::pose::Pose const &	known_ligand_pose
	)

void protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand ( core::pose::Pose const & known_ligand_pose )

References protocols::pockets::FingerprintBase::CoM_, protocols::pockets::convert_spherical_coor_triplet_to_cartesian(), protocols::pockets::FingerprintBase::origin_, protocols::pockets::FingerprintBase::triplet_fingerprint_data(), and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

void protocols::pockets::NonPlaidFingerprint::write_eggshell_to_pdb_file ( std::string const & output_eggshell_name ) const

References protocols::pockets::FingerprintBase::CoM_, eggshell_list_, extshell_list_, and protocols::pockets::FingerprintBase::origin_.

Member Data Documentation

std::list< numeric::xyzVector<core::Real> > protocols::pockets::NonPlaidFingerprint::egg_and_ext_list_

Referenced by setup_from_ConnollySurface(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), and setup_from_PocketGrid_using_bound_ligand().

std::list< numeric::xyzVector<core::Real> > protocols::pockets::NonPlaidFingerprint::eggshell_list_

Referenced by include_eggshell_points_based_on_known_ligand(), setup_from_ConnollySurface(), setup_from_EggshellGrid(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), setup_from_PocketGrid_using_bound_ligand(), and write_eggshell_to_pdb_file().

numeric::xyzVector<core::Size> protocols::pockets::NonPlaidFingerprint::esp_dim_

Referenced by setup_from_espGrid().

numeric::xyzVector<core::Real> protocols::pockets::NonPlaidFingerprint::esp_mid_

Referenced by setup_from_espGrid().

core::Real protocols::pockets::NonPlaidFingerprint::esp_spacing_

Referenced by setup_from_espGrid().

std::vector< std::vector < std::vector <core::Real> > > protocols::pockets::NonPlaidFingerprint::espGrid_

Referenced by setup_from_espGrid().

std::list< numeric::xyzVector<core::Real> > protocols::pockets::NonPlaidFingerprint::extshell_list_

Referenced by setup_from_ConnollySurface(), setup_from_EggshellGrid(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), setup_from_PocketGrid_using_bound_ligand(), and write_eggshell_to_pdb_file().

numeric::xyzVector<core::Real> protocols::pockets::NonPlaidFingerprint::pocket_CoM_

Referenced by setup_from_PocketGrid().

std::vector< std::vector < std::vector <ElectrostaticpotentialGrid::PtType> > > protocols::pockets::NonPlaidFingerprint::typGrid_

Referenced by setup_from_espGrid().

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

src/protocols/pockets/Fingerprint.hh
src/protocols/pockets/Fingerprint.cc

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation