protocols::pockets::NonPlaidFingerprint Class Reference

#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, core::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, core::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, core::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 VirtualBase. 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

NonPlaidFingerprint()

protocols::pockets::NonPlaidFingerprint::NonPlaidFingerprint

(

)

~NonPlaidFingerprint()

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

override

Member Function Documentation

calculate_protein_CoM()

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().

change_CoM_to_ligandCoM()

void protocols::pockets::NonPlaidFingerprint::change_CoM_to_ligandCoM

(

numeric::xyzVector< core::Real > const &

ligandCoM

)

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

choose_origin_with_lowest_eggshell_ruggedness()

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_().

combine_xyz_lists()

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().

convert_cart_to_spherical_and_round()

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.

convert_spherical_list_to_cartesian_list()

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_.

get_electrostatics_energy()

core::Real protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy

(

core::pose::Pose const &

ligand_pose

)

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

get_interpolated_esp_energy()

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.

get_interpolated_esp_energy_with_type()

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.

get_nearest_neighbour_esp_energy()

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

get_pose_resnum()

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().

get_Rvalue()

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

get_surface_esp()

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().

include_eggshell_points_based_on_known_ligand()

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

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

Referenced by setup_from_PocketGrid_and_known_ligand().

place_origin_point()

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().

remove_duplicate_phi_psi()

std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::remove_duplicate_phi_psi

(

std::list< spherical_coor_triplet > const &

rounded_triplet

)

References protocols::cluster::calibur::aa, and protocols::pockets::spherical_coor_triplet::rho.

set_multiple_origin()

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().

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().

set_origin_away_from_eggshell()

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_().

set_origin_away_from_eggshell_plane()

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,
		core::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_().

set_origin_away_from_protein_center()

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_().

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,
		core::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().

set_origin_from_residue()

void protocols::pockets::NonPlaidFingerprint::set_origin_from_residue

(

core::pose::Pose const &

protein_pose

)

References core::conformation::Residue::atom(), protocols::pockets::FingerprintBase::CoM_, get_pose_resnum(), core::conformation::Residue::nheavyatoms(), protocols::pockets::FingerprintBase::origin_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by set_origin_from_option_().

set_rho_to_zero()

std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::set_rho_to_zero

(

std::list< spherical_coor_triplet > const &

rounded_triplet

)

References protocols::cluster::calibur::aa, and protocols::pockets::spherical_coor_triplet::rho.

setup_from_ConnollySurface()

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

References protocols::pockets::FingerprintBase::CoM_, combine_xyz_lists(), protocols::pockets::PocketGrid::dim_, egg_and_ext_list_, protocols::pockets::EggshellGrid::eggshell_CoM_, protocols::pockets::EggshellGrid::eggshell_coord_list(), eggshell_list_, protocols::pockets::EggshellGrid::extra_coord_list(), extshell_list_, protocols::pockets::PocketGrid::mid_, protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::pocketGrid_dim_, protocols::pockets::FingerprintBase::pocketGrid_mid_, protocols::pockets::FingerprintBase::pocketGrid_spacing_, set_origin(), setup_from_EggshellGrid(), and protocols::pockets::PocketGrid::spacing_.

setup_from_eggshell_pdb_file()

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_.

setup_from_eggshell_triplet_file()

void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file

(

std::string const &

input_filename

)

References protocols::pockets::FingerprintBase::CoM_, protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::num_origins_, protocols::pockets::spherical_coor_triplet::ori, protocols::pockets::FingerprintBase::origin_, protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::FingerprintBase::pocketGrid_dim_, protocols::pockets::FingerprintBase::pocketGrid_mid_, protocols::pockets::FingerprintBase::pocketGrid_spacing_, protocols::pockets::spherical_coor_triplet::psi, protocols::pockets::spherical_coor_triplet::rho, and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

setup_from_EggshellGrid()

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().

setup_from_espGrid()

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

References esp_dim_, esp_mid_, esp_spacing_, espGrid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_dim_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_mid_, protocols::pockets::ElectrostaticpotentialGrid::espGrid_spacing_, protocols::pockets::ElectrostaticpotentialGrid::get_DELPHI_espGrid_values(), protocols::pockets::ElectrostaticpotentialGrid::get_ZAP_espGrid_values_with_type(), typGrid_, protocols::pockets::ElectrostaticpotentialGrid::typGrid_, and protocols::pockets::ElectrostaticpotentialGrid::write_espGrid_to_pdb().

setup_from_PlaidFingerprint()

void protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint

(

PlaidFingerprint const &

pfp

)

References protocols::pockets::FingerprintBase::origin_, and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

setup_from_PocketGrid() [1/2]

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

setup_from_PocketGrid() [2/2]

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

References protocols::pockets::FingerprintBase::CoM_, combine_xyz_lists(), protocols::pockets::PocketGrid::dim_, egg_and_ext_list_, protocols::pockets::EggshellGrid::eggshell_CoM_, protocols::pockets::EggshellGrid::eggshell_coord_list(), eggshell_list_, protocols::pockets::EggshellGrid::extra_coord_list(), extshell_list_, protocols::pockets::PocketGrid::mid_, protocols::pockets::FingerprintBase::multi_origin_list_, pocket_CoM_, protocols::pockets::FingerprintBase::pocketGrid_dim_, protocols::pockets::FingerprintBase::pocketGrid_mid_, protocols::pockets::FingerprintBase::pocketGrid_spacing_, set_origin(), setup_from_EggshellGrid(), and protocols::pockets::PocketGrid::spacing_.

setup_from_PocketGrid_and_known_ligand()

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
	)

References protocols::pockets::FingerprintBase::CoM_, combine_xyz_lists(), protocols::pockets::PocketGrid::dim_, egg_and_ext_list_, protocols::pockets::EggshellGrid::eggshell_CoM_, protocols::pockets::EggshellGrid::eggshell_coord_list(), eggshell_list_, protocols::pockets::EggshellGrid::extra_coord_list(), extshell_list_, include_eggshell_points_based_on_known_ligand(), protocols::pockets::PocketGrid::mid_, protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::pocketGrid_dim_, protocols::pockets::FingerprintBase::pocketGrid_mid_, protocols::pockets::FingerprintBase::pocketGrid_spacing_, set_origin(), setup_from_EggshellGrid(), and protocols::pockets::PocketGrid::spacing_.

setup_from_PocketGrid_using_bound_ligand()

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
	)

References protocols::pockets::FingerprintBase::CoM_, combine_xyz_lists(), protocols::pockets::PocketGrid::dim_, egg_and_ext_list_, protocols::pockets::EggshellGrid::eggshell_CoM_, protocols::pockets::EggshellGrid::eggshell_coord_list(), eggshell_list_, protocols::pockets::EggshellGrid::extra_coord_list(), extshell_list_, protocols::pockets::PocketGrid::mid_, protocols::pockets::FingerprintBase::multi_origin_list_, protocols::pockets::FingerprintBase::pocketGrid_dim_, protocols::pockets::FingerprintBase::pocketGrid_mid_, protocols::pockets::FingerprintBase::pocketGrid_spacing_, set_origin(), setup_from_EggshellGrid(), and protocols::pockets::PocketGrid::spacing_.

trim_based_on_known_ligand()

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_, core::conformation::membrane::out, protocols::pockets::FingerprintBase::triplet_fingerprint_data(), and protocols::pockets::FingerprintBase::triplet_fingerprint_data_.

write_eggshell_to_pdb_file()

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_, protocols::pockets::FingerprintBase::origin_, and core::conformation::membrane::out.

Member Data Documentation

egg_and_ext_list_

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().

eggshell_list_

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().

esp_dim_

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

Referenced by setup_from_espGrid().

esp_mid_

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

Referenced by setup_from_espGrid().

esp_spacing_

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

Referenced by setup_from_espGrid().

espGrid_

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

Referenced by setup_from_espGrid().

extshell_list_

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().

pocket_CoM_

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

Referenced by setup_from_PocketGrid().

typGrid_

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

Referenced by setup_from_espGrid().

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

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