protocols::pockets::FingerprintBase Class Reference

#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::FingerprintBase:

Public Member Functions
	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 >	pocketGrid_mid_
numeric::xyzVector< core::Real >	pocketGrid_dim_
core::Real	pocketGrid_spacing_

Protected Attributes
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_

Friends
class	FingerprintMultifunc
class	DarcParticleSwarmMinimizer

Constructor & Destructor Documentation

FingerprintBase()

protocols::pockets::FingerprintBase::FingerprintBase

(

)

References CoM_, and origin_.

~FingerprintBase()

protocols::pockets::FingerprintBase::~FingerprintBase ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

CHEAT_CoM()

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

inline

References CoM_.

CoM()

numeric::xyzVector<core::Real> protocols::pockets::FingerprintBase::CoM ( ) const

inline

References CoM_.

Referenced by protocols::pockets::PlaidFingerprint::get_oriented_pose(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), and protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_().

multi_origin_list()

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

inline

References multi_origin_list_.

Referenced by protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_().

num_origins()

core::Size protocols::pockets::FingerprintBase::num_origins ( ) const

inline

References num_origins_.

Referenced by protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_().

origin()

numeric::xyzVector<core::Real> protocols::pockets::FingerprintBase::origin ( ) const

inline

References origin_.

Referenced by protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::pockets::PlaidFingerprint::get_oriented_pose(), and protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_().

print_to_file()

void protocols::pockets::FingerprintBase::print_to_file

(

std::string const &

output_filename

)

const

References CoM_, multi_origin_list_, core::conformation::membrane::out, pocketGrid_dim_, pocketGrid_mid_, pocketGrid_spacing_, and triplet_fingerprint_data_.

print_to_pdb() [1/2]

void protocols::pockets::FingerprintBase::print_to_pdb

(

std::string const &

output_pdbname

)

const

Referenced by protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb().

print_to_pdb() [2/2]

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

References CoM_, protocols::pockets::convert_spherical_coor_triplet_to_cartesian(), multi_origin_list_, core::conformation::membrane::out, core::id::to_string(), and triplet_fingerprint_data_.

triplet_fingerprint_data()

std::list< spherical_coor_triplet > const& protocols::pockets::FingerprintBase::triplet_fingerprint_data ( ) const

inline

References triplet_fingerprint_data_.

Referenced by protocols::pockets::PlaidFingerprint::fp_compare(), protocols::pockets::PlaidFingerprint::fp_compare_deriv(), protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand(), and protocols::pockets::PlaidFingerprint::update_rhos_().

Friends And Related Function Documentation

DarcParticleSwarmMinimizer

friend class DarcParticleSwarmMinimizer

friend

FingerprintMultifunc

friend class FingerprintMultifunc

friend

Member Data Documentation

CoM_

numeric::xyzVector<core::Real> protocols::pockets::FingerprintBase::CoM_

protected

Referenced by protocols::pockets::NonPlaidFingerprint::change_CoM_to_ligandCoM(), CHEAT_CoM(), CoM(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), FingerprintBase(), protocols::pockets::PlaidFingerprint::get_oriented_pose(), protocols::pockets::NonPlaidFingerprint::place_origin_point(), print_to_file(), print_to_pdb(), protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_(), protocols::pockets::NonPlaidFingerprint::set_multiple_origin(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell_plane(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_protein_center(), protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand(), protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand(), and protocols::pockets::NonPlaidFingerprint::write_eggshell_to_pdb_file().

multi_origin_list_

utility::vector1< numeric::xyzVector<core::Real> > protocols::pockets::FingerprintBase::multi_origin_list_

protected

Referenced by multi_origin_list(), print_to_file(), print_to_pdb(), protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_(), protocols::pockets::NonPlaidFingerprint::set_multiple_origin(), protocols::pockets::NonPlaidFingerprint::set_origin(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand(), and protocols::pockets::PlaidFingerprint::update_rhos_().

num_origins_

core::Size protocols::pockets::FingerprintBase::num_origins_

protected

Referenced by num_origins(), protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), and protocols::pockets::PlaidFingerprint::update_rhos_().

origin_

numeric::xyzVector<core::Real> protocols::pockets::FingerprintBase::origin_

protected

Referenced by protocols::pockets::NonPlaidFingerprint::convert_cart_to_spherical_and_round(), protocols::pockets::NonPlaidFingerprint::convert_spherical_list_to_cartesian_list(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), FingerprintBase(), protocols::pockets::PlaidFingerprint::get_oriented_pose(), protocols::pockets::NonPlaidFingerprint::get_Rvalue(), origin(), protocols::pockets::NonPlaidFingerprint::place_origin_point(), protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_(), protocols::pockets::NonPlaidFingerprint::set_multiple_origin(), protocols::pockets::NonPlaidFingerprint::set_origin(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell_plane(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_protein_center(), protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint(), protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand(), and protocols::pockets::NonPlaidFingerprint::write_eggshell_to_pdb_file().

pocketGrid_dim_

numeric::xyzVector<core::Real> protocols::pockets::FingerprintBase::pocketGrid_dim_

Referenced by print_to_file(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

pocketGrid_mid_

numeric::xyzVector<core::Real> protocols::pockets::FingerprintBase::pocketGrid_mid_

Referenced by print_to_file(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

pocketGrid_spacing_

core::Real protocols::pockets::FingerprintBase::pocketGrid_spacing_

Referenced by print_to_file(), protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_and_known_ligand(), and protocols::pockets::NonPlaidFingerprint::setup_from_PocketGrid_using_bound_ligand().

triplet_fingerprint_data_

std::list< spherical_coor_triplet > protocols::pockets::FingerprintBase::triplet_fingerprint_data_

protected

Referenced by protocols::pockets::PlaidFingerprint::fp_compare(), protocols::pockets::PlaidFingerprint::fp_compare_deriv(), print_to_file(), print_to_pdb(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file(), protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint(), protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand(), triplet_fingerprint_data(), and protocols::pockets::PlaidFingerprint::update_rhos_().

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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