#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::NonPlaidFingerprint:

Collaboration diagram for protocols::pockets::NonPlaidFingerprint:

Classes
struct	float4

Public Member Functions
	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_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	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_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)

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

virtual	~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

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_

float4	atom_ [ATOMS_ARRAY]

float4	atom_maxmin_phipsi_ [ATOMS_ARRAY]

float4	ligand_maxmin_phipsi_ [NUMBER_OF_PARTICLES]

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_

Detailed Description

Definition at line 91 of file Fingerprint.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 93 of file Fingerprint.hh.

Member Function Documentation

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

Definition at line 772 of file Fingerprint.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), 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().

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
	)

Definition at line 1680 of file Fingerprint.cc.

Referenced by setup_from_PocketGrid().

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
	)

Definition at line 186 of file Fingerprint.cc.

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 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
	)

Definition at line 163 of file Fingerprint.cc.

References get_Rvalue(), and set_origin_from_option_().

Referenced by setup_from_PocketGrid().

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
	)

Definition at line 731 of file Fingerprint.cc.

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
	)

Definition at line 631 of file Fingerprint.cc.

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)

Definition at line 761 of file Fingerprint.cc.

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
	)

Definition at line 213 of file Fingerprint.cc.

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

Referenced by get_Rvalue(), and set_origin().

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

Definition at line 413 of file Fingerprint.cc.

References protocols::loops::chainID, 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)

Definition at line 515 of file Fingerprint.cc.

References protocols::pockets::FingerprintBase::CoM_, protocols::pockets::FingerprintBase::origin_, 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_.

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

Definition at line 234 of file Fingerprint.cc.

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

Referenced by setup_from_PocketGrid().

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

Definition at line 109 of file Fingerprint.cc.

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
	)

Definition at line 117 of file Fingerprint.cc.

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

Definition at line 125 of file Fingerprint.cc.

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)

Definition at line 596 of file Fingerprint.cc.

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

Definition at line 146 of file Fingerprint.cc.

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

Member Data Documentation

float4 protocols::pockets::NonPlaidFingerprint::atom_[ATOMS_ARRAY]

Definition at line 148 of file Fingerprint.hh.

float4 protocols::pockets::NonPlaidFingerprint::atom_maxmin_phipsi_[ATOMS_ARRAY]

Definition at line 149 of file Fingerprint.hh.

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

Definition at line 93 of file Fingerprint.hh.

Referenced by setup_from_PocketGrid().

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

Definition at line 96 of file Fingerprint.hh.

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

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

Definition at line 97 of file Fingerprint.hh.

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

float4 protocols::pockets::NonPlaidFingerprint::ligand_maxmin_phipsi_[NUMBER_OF_PARTICLES]

Definition at line 150 of file Fingerprint.hh.

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

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

Classes

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation