Rosetta Protocols  2014.35
Public Member Functions | Public Attributes | List of all members
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::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)
 
- 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::Realorigin () const
 
numeric::xyzVector< core::RealCoM () 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::Realorigin_
 
std::list< spherical_coor_triplettriplet_fingerprint_data_
 
numeric::xyzVector< core::RealCoM_
 

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)
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_Rvalue ( core::pose::Pose const &  protein_pose,
std::list< numeric::xyzVector< core::Real > > const &  egg_and_extra_shell,
Size const &  set_origin_option 
)
void protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand ( core::pose::Pose const &  known_ligand_pose,
core::Real const &  trim_dist 
)
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_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,
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,
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_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_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_
std::list< numeric::xyzVector<core::Real> > protocols::pockets::NonPlaidFingerprint::extshell_list_

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