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Public Member Functions | Public Attributes | Protected Attributes | Friends | List of all members
protocols::pockets::FingerprintBase Class Reference

#include <Fingerprint.hh>

Inheritance diagram for protocols::pockets::FingerprintBase:
Inheritance graph
[legend]

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

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

References CoM_, and origin_.

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

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

References 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_().

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_().

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

References num_origins_.

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

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(), protocols::pockets::PlaidFingerprint::select_conf_and_move_ligand_(), and protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint().

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_.

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().

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_.

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::setup_from_PlaidFingerprint(), protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand(), and protocols::pockets::PlaidFingerprint::update_rhos_().

Friends And Related Function Documentation

friend class DarcParticleSwarmMinimizer
friend
friend class FingerprintMultifunc
friend

Member Data Documentation

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().

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_().

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_().

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().

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().

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().

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().

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_().

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