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Public Member Functions | Public Attributes | List of all members
protocols::pockets::NonPlaidFingerprint Class Reference

#include <Fingerprint.hh>

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

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::Realplace_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::Realcalculate_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_tripletremove_duplicate_phi_psi (std::list< spherical_coor_triplet > const &rounded_triplet)
 
std::list< spherical_coor_tripletconvert_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_tripletset_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::Realorigin () const
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
multi_origin_list () const
 
numeric::xyzVector< core::RealCoM () 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::Realpocket_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::Realesp_mid_
 
numeric::xyzVector< core::Sizeesp_dim_
 
- Public Attributes inherited from protocols::pockets::FingerprintBase
numeric::xyzVector< core::RealpocketGrid_mid_
 
numeric::xyzVector< core::RealpocketGrid_dim_
 
core::Real pocketGrid_spacing_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::pockets::FingerprintBase
core::Size num_origins_
 
numeric::xyzVector< core::Realorigin_
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
multi_origin_list_
 
numeric::xyzVector< core::RealCoM_
 
std::list< spherical_coor_triplettriplet_fingerprint_data_
 

Constructor & Destructor Documentation

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

Member Function Documentation

numeric::xyzVector< core::Real > protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM ( core::pose::Pose const &  protein_pose)
void protocols::pockets::NonPlaidFingerprint::change_CoM_to_ligandCoM ( numeric::xyzVector< core::Real > const &  ligandCoM)
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 
)
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 
)
std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::convert_cart_to_spherical_and_round ( std::list< numeric::xyzVector< core::Real > > const &  xyz_list)
std::list< numeric::xyzVector< core::Real > > protocols::pockets::NonPlaidFingerprint::convert_spherical_list_to_cartesian_list ( std::list< spherical_coor_triplet > const &  unique_triplet)
core::Real protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy ( core::pose::Pose const &  ligand_pose)
core::Real protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy ( numeric::xyzVector< core::Real > const &  ligand_atom,
core::Real const &  atom_charge 
)
core::Real protocols::pockets::NonPlaidFingerprint::get_interpolated_esp_energy_with_type ( numeric::xyzVector< core::Real > const &  ligand_atom,
core::Real const &  atom_charge 
)
core::Real protocols::pockets::NonPlaidFingerprint::get_nearest_neighbour_esp_energy ( numeric::xyzVector< core::Real > const &  ligand_atom,
core::Real const &  atom_charge 
)
core::Size protocols::pockets::NonPlaidFingerprint::get_pose_resnum ( int const  pdbnum,
char const  pdbchn,
core::pose::Pose const &  ps 
)
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 
)
core::Real protocols::pockets::NonPlaidFingerprint::get_surface_esp ( std::list< numeric::xyzVector< core::Real > > const &  surfacePoints_list,
std::string const &  inp_espGrid_fname 
)
void protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand ( core::pose::Pose const &  known_ligand_pose,
core::Real const &  trim_dist 
)
numeric::xyzVector< core::Real > protocols::pockets::NonPlaidFingerprint::place_origin_point ( core::Real const &  angle)
std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::remove_duplicate_phi_psi ( std::list< spherical_coor_triplet > const &  rounded_triplet)
void protocols::pockets::NonPlaidFingerprint::set_multiple_origin ( core::pose::Pose const &  protein_pose,
std::list< numeric::xyzVector< core::Real > > const &  egg_and_extra_shell 
)
void protocols::pockets::NonPlaidFingerprint::set_origin ( core::pose::Pose const &  protein_pose,
std::list< numeric::xyzVector< core::Real > > const &  egg_and_extra_shell 
)
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 
)
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 
)
void protocols::pockets::NonPlaidFingerprint::set_origin_away_from_protein_center ( core::pose::Pose const &  protein_pose)
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 
)
void protocols::pockets::NonPlaidFingerprint::set_origin_from_residue ( core::pose::Pose const &  protein_pose)
std::list< spherical_coor_triplet > protocols::pockets::NonPlaidFingerprint::set_rho_to_zero ( std::list< spherical_coor_triplet > const &  rounded_triplet)
void protocols::pockets::NonPlaidFingerprint::setup_from_ConnollySurface ( core::pose::Pose const &  protein_pose,
PocketGrid const &  pocket_grid,
PocketGrid const &  grid_for_extshell 
)
void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_pdb_file ( std::string const &  input_filename)
void protocols::pockets::NonPlaidFingerprint::setup_from_eggshell_triplet_file ( std::string const &  input_filename)
void protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid ( )
void protocols::pockets::NonPlaidFingerprint::setup_from_espGrid ( std::string const &  input_filename,
core::pose::Pose const &  protein_pose,
bool  delphi 
)
void protocols::pockets::NonPlaidFingerprint::setup_from_PlaidFingerprint ( PlaidFingerprint const &  pfp)
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 
)
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 
)
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 
)
void protocols::pockets::NonPlaidFingerprint::trim_based_on_known_ligand ( core::pose::Pose const &  known_ligand_pose)
void protocols::pockets::NonPlaidFingerprint::write_eggshell_to_pdb_file ( std::string const &  output_eggshell_name) const

Member Data Documentation

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

Referenced by setup_from_espGrid().

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

Referenced by setup_from_espGrid().

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

Referenced by setup_from_espGrid().

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

Referenced by setup_from_espGrid().

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

Referenced by setup_from_PocketGrid().

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

Referenced by setup_from_espGrid().


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