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Public Member Functions | Private Attributes | List of all members
core::scoring::packing::PoseBalls Class Reference

#include <PoseBalls.hh>

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Public Member Functions

virtual ~PoseBalls ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 
 PoseBalls (core::pose::Pose const &pose, core::Size Hmode=0, bool ignore_water=true)
 
core::Size const & nballs () const
 
core::Size const & id_to_index (core::id::AtomID const &aid) const
 
core::id::AtomID const & index_to_id (core::Size const &index) const
 
Ball const & ball (core::Size const &index) const
 
Ball const & ball (core::id::AtomID const &id) const
 
Ball & ball (core::Size const &index)
 
Ball & ball (core::id::AtomID const &id)
 
std::string const & atom_name (core::Size const &index) const
 
core::Size const & atom_num (core::Size const &index) const
 
core::Size const & atom_type (core::Size const &index) const
 
std::string const & res_name (core::Size const &index) const
 
core::Size const & res_num (core::Size const &index) const
 
void reset_surf ()
 
void set_surf (core::Size const &index, core::Size const &ialpha, Real const &val)
 
Real const & surf (core::Size const &index, core::Size const &ialpha)
 
utility::vector1< Ball > const & balls () const
 
utility::vector1
< core::id::AtomID > const & 		atomids () const
 
char const & secstruct (core::Size const &i) const
 
core::Real const & smooth_nb (core::Size const &i) const
 
core::Real const & bfac (core::Size const &i) const
 
bool havesurf (core::Size const &i) const
 
bool is_heavy (core::Size const &i) const
 
uint nbhist (core::Size atype, core::Size bin)
 
void output_pdb (std::ostream &out) const
 
void compute_smooth_nb ()
 

Private Attributes

core::Size nballs_
 
core::id::AtomID_Map< Size > id_to_index_
 
utility::vector1
< core::id::AtomID > 		index_to_id_
 
utility::vector1< Ball > balls_
 
utility::vector1< std::string > atom_name_
 
utility::vector1< core::Size > atom_num_
 
utility::vector1< std::string > res_name_
 
utility::vector1< core::Size > res_num_
 
utility::vector1< core::Size > atom_type_
 
utility::vector1< core::Size > atom_parent_
 
utility::vector1< core::Real > smooth_nb_
 
utility::vector1< core::Real > bfac_
 
utility::vector1< bool > is_heavy_
 
utility::vector1< char > secstruct_
 
utility::vector1
< utility::vector1< Real > > 		surf_
 
utility::vector1
< utility::vector1< uint > > 		nbhist_
 

Detailed Description

Definition at line 32 of file PoseBalls.hh.

Constructor & Destructor Documentation

core::scoring::packing::PoseBalls::~PoseBalls ( )
virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 40 of file PoseBalls.cc.

core::scoring::packing::PoseBalls::PoseBalls ( core::pose::Pose const &  pose,
core::Size  Hmode = 0,
bool  ignore_water = true 
)

Definition at line 72 of file PoseBalls.cc.

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::initialize_atomid_map(), core::chemical::AtomType::is_heavyatom(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::is_virtual(), core::chemical::AtomType::lj_radius(), core::pose::Pose::n_residue(), core::chemical::AtomType::name(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Member Function Documentation

std::string const& core::scoring::packing::PoseBalls::atom_name ( core::Size const &  index) const
inline

Definition at line 66 of file PoseBalls.hh.

References atom_name_.

core::Size const& core::scoring::packing::PoseBalls::atom_num ( core::Size const &  index) const
inline

Definition at line 70 of file PoseBalls.hh.

References atom_num_.

Referenced by core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), and core::scoring::packing::initialize_AtomID_Map().

core::Size const& core::scoring::packing::PoseBalls::atom_type ( core::Size const &  index) const
inline

Definition at line 74 of file PoseBalls.hh.

References atom_type_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), and core::scoring::packing::compute_smooth_nb_deriv().

utility::vector1<core::id::AtomID> const& core::scoring::packing::PoseBalls::atomids ( ) const
inline

Definition at line 107 of file PoseBalls.hh.

References index_to_id_.

Ball const& core::scoring::packing::PoseBalls::ball ( core::Size const &  index) const
inline

Definition at line 55 of file PoseBalls.hh.

References balls_.

Referenced by core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), core::scoring::packing::compute_holes_surfs(), core::scoring::packing::compute_smooth_nb_deriv(), and core::scoring::packing::get_surf_vol_deriv().

Ball const& core::scoring::packing::PoseBalls::ball ( core::id::AtomID const &  id) const
inline

Definition at line 59 of file PoseBalls.hh.

References balls_, and id_to_index_.

Ball& core::scoring::packing::PoseBalls::ball ( core::Size const &  index)
inline

Definition at line 63 of file PoseBalls.hh.

References balls_.

Ball& core::scoring::packing::PoseBalls::ball ( core::id::AtomID const &  id)
inline

Definition at line 64 of file PoseBalls.hh.

References balls_, and id_to_index_.

utility::vector1<Ball> const& core::scoring::packing::PoseBalls::balls ( ) const
inline

Definition at line 103 of file PoseBalls.hh.

References balls_.

core::Real const& core::scoring::packing::PoseBalls::bfac ( core::Size const &  i) const
inline

Definition at line 117 of file PoseBalls.hh.

References bfac_.

void core::scoring::packing::PoseBalls::compute_smooth_nb ( )

Definition at line 201 of file PoseBalls.cc.

References core::scoring::packing::sigmoidish_neighbor(), and protocols::kinmatch::xyz().

bool core::scoring::packing::PoseBalls::havesurf ( core::Size const &  i) const
inline

Definition at line 120 of file PoseBalls.hh.

References atom_parent_.

core::Size const& core::scoring::packing::PoseBalls::id_to_index ( core::id::AtomID const &  aid) const
inline

Definition at line 47 of file PoseBalls.hh.

References id_to_index_.

core::id::AtomID const& core::scoring::packing::PoseBalls::index_to_id ( core::Size const &  index) const
inline

Definition at line 51 of file PoseBalls.hh.

References index_to_id_.

Referenced by core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), core::scoring::packing::compute_smooth_nb_deriv(), and core::scoring::packing::get_surf_vol_deriv().

bool core::scoring::packing::PoseBalls::is_heavy ( core::Size const &  i) const
inline

Definition at line 124 of file PoseBalls.hh.

References is_heavy_.

Referenced by core::scoring::packing::compute_smooth_nb_deriv().

core::Size const& core::scoring::packing::PoseBalls::nballs ( ) const
inline

Definition at line 43 of file PoseBalls.hh.

References nballs_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_holes_score_res(), core::scoring::packing::compute_holes_surfs(), core::scoring::packing::compute_rosettaholes_score(), core::scoring::packing::compute_smooth_nb_deriv(), core::scoring::packing::HolesEnergy::finalize_total_energy(), core::scoring::packing::get_surf_vol_deriv(), and core::scoring::packing::initialize_AtomID_Map().

uint core::scoring::packing::PoseBalls::nbhist ( core::Size  atype,
core::Size  bin 
)
inline

Definition at line 128 of file PoseBalls.hh.

References nbhist_.

void core::scoring::packing::PoseBalls::output_pdb ( std::ostream &  out) const

Definition at line 247 of file PoseBalls.cc.

std::string const& core::scoring::packing::PoseBalls::res_name ( core::Size const &  index) const
inline

Definition at line 78 of file PoseBalls.hh.

References res_name_.

Referenced by core::scoring::packing::compute_holes_deriv_res(), and core::scoring::packing::compute_holes_score_res().

core::Size const& core::scoring::packing::PoseBalls::res_num ( core::Size const &  index) const
inline

Definition at line 82 of file PoseBalls.hh.

References res_num_.

Referenced by core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), and core::scoring::packing::initialize_AtomID_Map().

void core::scoring::packing::PoseBalls::reset_surf ( )
inline

Definition at line 86 of file PoseBalls.hh.

References nballs_, and surf_.

Referenced by core::scoring::packing::compute_holes_surfs().

char const& core::scoring::packing::PoseBalls::secstruct ( core::Size const &  i) const
inline

Definition at line 111 of file PoseBalls.hh.

References secstruct_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), and core::scoring::packing::compute_smooth_nb_deriv().

void core::scoring::packing::PoseBalls::set_surf ( core::Size const &  index,
core::Size const &  ialpha,
Real const &  val 
)
inline

Definition at line 94 of file PoseBalls.hh.

References atom_parent_, and surf_.

Referenced by core::scoring::packing::compute_holes_surfs().

core::Real const& core::scoring::packing::PoseBalls::smooth_nb ( core::Size const &  i) const
inline

Definition at line 114 of file PoseBalls.hh.

References smooth_nb_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), and core::scoring::packing::compute_rosettaholes_score().

Real const& core::scoring::packing::PoseBalls::surf ( core::Size const &  index,
core::Size const &  ialpha 
)
inline

Definition at line 99 of file PoseBalls.hh.

References surf_.

Referenced by core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_score(), and core::scoring::packing::compute_rosettaholes_score().

Member Data Documentation

utility::vector1<std::string> core::scoring::packing::PoseBalls::atom_name_
private

Definition at line 143 of file PoseBalls.hh.

Referenced by atom_name().

utility::vector1<core::Size> core::scoring::packing::PoseBalls::atom_num_
private

Definition at line 144 of file PoseBalls.hh.

Referenced by atom_num().

utility::vector1<core::Size> core::scoring::packing::PoseBalls::atom_parent_
private

Definition at line 148 of file PoseBalls.hh.

Referenced by havesurf(), and set_surf().

utility::vector1<core::Size> core::scoring::packing::PoseBalls::atom_type_
private

Definition at line 147 of file PoseBalls.hh.

Referenced by atom_type().

utility::vector1<Ball> core::scoring::packing::PoseBalls::balls_
private

Definition at line 142 of file PoseBalls.hh.

Referenced by ball(), and balls().

utility::vector1<core::Real> core::scoring::packing::PoseBalls::bfac_
private

Definition at line 150 of file PoseBalls.hh.

Referenced by bfac().

core::id::AtomID_Map<Size> core::scoring::packing::PoseBalls::id_to_index_
private

Definition at line 140 of file PoseBalls.hh.

Referenced by ball(), and id_to_index().

utility::vector1<core::id::AtomID> core::scoring::packing::PoseBalls::index_to_id_
private

Definition at line 141 of file PoseBalls.hh.

Referenced by atomids(), and index_to_id().

utility::vector1<bool> core::scoring::packing::PoseBalls::is_heavy_
private

Definition at line 151 of file PoseBalls.hh.

Referenced by is_heavy().

core::Size core::scoring::packing::PoseBalls::nballs_
private

Definition at line 139 of file PoseBalls.hh.

Referenced by nballs(), and reset_surf().

utility::vector1<utility::vector1<uint> > core::scoring::packing::PoseBalls::nbhist_
private

Definition at line 154 of file PoseBalls.hh.

Referenced by nbhist().

utility::vector1<std::string> core::scoring::packing::PoseBalls::res_name_
private

Definition at line 145 of file PoseBalls.hh.

Referenced by res_name().

utility::vector1<core::Size> core::scoring::packing::PoseBalls::res_num_
private

Definition at line 146 of file PoseBalls.hh.

Referenced by res_num().

utility::vector1<char> core::scoring::packing::PoseBalls::secstruct_
private

Definition at line 152 of file PoseBalls.hh.

Referenced by secstruct().

utility::vector1<core::Real> core::scoring::packing::PoseBalls::smooth_nb_
private

Definition at line 149 of file PoseBalls.hh.

Referenced by smooth_nb().

utility::vector1<utility::vector1<Real> > core::scoring::packing::PoseBalls::surf_
private

Definition at line 153 of file PoseBalls.hh.

Referenced by reset_surf(), set_surf(), and surf().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:30:15 for Rosetta 3.5 by   doxygen 1.8.4