protocols::pockets::NonPlaidFingerprint Class Reference

#include <Fingerprint.hh>

Public Member Functions
	NonPlaidFingerprint ()
	~NonPlaidFingerprint ()
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	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	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_origin_away_from_protein_center (core::pose::Pose const &protein_pose)
void	set_origin_from_residue (core::pose::Pose const &protein_pose)
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)
Public Member Functions inherited from protocols::pockets::FingerprintBase
	FingerprintBase ()
virtual	~FingerprintBase ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
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
numeric::xyzVector< core::Real >	origin () const
numeric::xyzVector< core::Real >	CoM () const
std::list < spherical_coor_triplet > const &	triplet_fingerprint_data () const
void	CHEAT_CoM (numeric::xyzVector< core::Real > const &inp_CoM)

Public Attributes
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_

Additional Inherited Members
Protected Attributes inherited from protocols::pockets::FingerprintBase
numeric::xyzVector< core::Real >	origin_
std::list< spherical_coor_triplet >	triplet_fingerprint_data_
numeric::xyzVector< core::Real >	CoM_

Constructor & Destructor Documentation

protocols::pockets::NonPlaidFingerprint::NonPlaidFingerprint

(

)

protocols::pockets::NonPlaidFingerprint::~NonPlaidFingerprint

(

)

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::total_residue(), numeric::xyzVector< class >::x(), core::conformation::Atom::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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

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_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.

Referenced by setup_from_EggshellGrid().

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_.

Referenced by setup_from_EggshellGrid().

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(), cos_of(), num_points, protocols::pockets::FingerprintBase::origin_, protocols::pockets::spherical_coor_triplet::rho, and set_origin_from_option_().

Referenced by set_origin().

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(), numeric::xyzVector< class >::distance(), eggshell_list_, exit, core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::pose::Pose::total_residue(), numeric::xyzVector< class >::x(), core::conformation::Atom::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by setup_from_PocketGrid_and_known_ligand().

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.

Referenced by setup_from_EggshellGrid().

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

References get_Rvalue(), option, and set_origin_from_option_().

Referenced by 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_, numeric::xyzVector< class >::distance(), numeric::xyzVector< class >::normalize(), protocols::pockets::FingerprintBase::origin_, and numeric::xyzVector< class >::zero().

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::match::upstream::b, calculate_protein_CoM(), protocols::pockets::FingerprintBase::CoM_, cross_product(), numeric::xyzVector< class >::distance(), inverse(), numeric::xyzVector< class >::normalize(), protocols::pockets::FingerprintBase::origin_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), numeric::xyzVector< class >::z(), and numeric::xyzVector< class >::zero().

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_, numeric::xyzVector< class >::normalize(), 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 exit, set_origin_away_from_eggshell(), set_origin_away_from_eggshell_plane(), set_origin_away_from_protein_center(), and set_origin_from_residue().

Referenced by get_Rvalue(), and set_origin().

void protocols::pockets::NonPlaidFingerprint::set_origin_from_residue

(

core::pose::Pose const &

protein_pose

)

References protocols::pockets::FingerprintBase::CoM_, numeric::xyzVector< class >::normalize(), option, protocols::pockets::FingerprintBase::origin_, core::pose::Pose::residue(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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.

Referenced by setup_from_EggshellGrid().

void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file

(

std::string const &

input_filename

)

References protocols::loops::chainID, protocols::pockets::FingerprintBase::CoM_, protocols::pockets::convert_cartesian_to_spherical_coor_triplet(), exit, protocols::pockets::FingerprintBase::origin_, restype, protocols::pockets::spherical_coor_triplet::rho, protocols::pockets::FingerprintBase::triplet_fingerprint_data_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file

(

std::string const &

input_filename

)

References protocols::pockets::FingerprintBase::CoM_, exit, protocols::pockets::FingerprintBase::origin_, protocols::pockets::spherical_coor_triplet::phi, protocols::pockets::spherical_coor_triplet::psi, protocols::pockets::spherical_coor_triplet::rho, protocols::pockets::FingerprintBase::triplet_fingerprint_data_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid

(

)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::FingerprintBase::CoM_, convert_cart_to_spherical_and_round(), protocols::pockets::convert_spherical_coor_triplet_to_cartesian(), convert_spherical_list_to_cartesian_list(), eggshell_list_, extshell_list_, utility::io::ozstream::open(), protocols::pockets::FingerprintBase::origin_, remove_duplicate_phi_psi(), set_rho_to_zero(), protocols::pockets::FingerprintBase::triplet_fingerprint_data_, write_eggshell_to_pdb_file(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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

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
	)

References protocols::pockets::FingerprintBase::CoM_, combine_xyz_lists(), 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_, set_origin(), and setup_from_EggshellGrid().

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(), 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(), set_origin(), and setup_from_EggshellGrid().

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(), 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_, set_origin(), and setup_from_EggshellGrid().

void protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand

(

core::pose::Pose const &

known_ligand_pose

)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::FingerprintBase::CoM_, protocols::pockets::convert_spherical_coor_triplet_to_cartesian(), utility::io::ozstream::open(), protocols::pockets::FingerprintBase::origin_, protocols::pockets::FingerprintBase::triplet_fingerprint_data(), protocols::pockets::FingerprintBase::triplet_fingerprint_data_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::pockets::NonPlaidFingerprint::write_eggshell_to_pdb_file

(

std::string const &

output_eggshell_name

)

const

References utility::io::ozstream::clear(), utility::io::ozstream::close(), protocols::pockets::FingerprintBase::CoM_, eggshell_list_, extshell_list_, utility::io::ozstream::open(), protocols::pockets::FingerprintBase::origin_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by setup_from_EggshellGrid().

Member Data Documentation

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

Referenced by 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_EggshellGrid(), setup_from_PocketGrid(), setup_from_PocketGrid_and_known_ligand(), setup_from_PocketGrid_using_bound_ligand(), and write_eggshell_to_pdb_file().

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

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

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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