#include <Sheet.hh>
Public Types | |
| typedef core::Size | Size |
| typedef core::Real | Real |
| typedef core::Vector | Vector |
| typedef core::pose::Pose | Pose |
| typedef utility::vector1< core::Size > | VecSize |
| typedef utility::vector1< int > | VecInt |
| typedef utility::vector1< Real > | VecReal |
| typedef protocols::fldsgn::topology::SS_Info2_COP | SS_Info2_COP |
Public Member Functions | |
| Sheet () | |
| default constructor More... | |
| Sheet (VecSize const &order_strands, VecInt const &orient_strands, bool is_barrel) | |
| value constructor More... | |
| Sheet (Sheet const &s) | |
| copy constructor More... | |
| ~Sheet () override | |
| default destructor More... | |
| SheetOP | clone () |
| clone this object More... | |
| void | initialize () |
| intialize this class More... | |
| core::Size | num_strands () const |
| the number strands inclued in More... | |
| bool | is_barrel () const |
| is this barrel ? More... | |
| VecSize | order_strands () const |
| core::Size | order_strand (core::Size const s) const |
| VecInt | orient_strands () const |
| int | orient_strand (core::Size const s) const |
| core::Size | strand_order (core::Size const s) |
| VecInt | ca_cb_orients () const |
| int | ca_cb_orient (core::Size const s) const |
| int | which_side (Vector const &vec) const |
| utility::vector1< Real > | calc_sasa_bothsides (Pose const &pose, SS_Info2_COP const ssinfo, Real pore_radius=1.5) |
| calc surface areas only with beta-sheet More... | |
| void | calc_geometry (SS_Info2_COP const ssinfo) |
| calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_ More... | |
| bool | is_member (core::Size const s) |
| whether the given strand number belongs to this sheet or not More... | |
Private Attributes | |
| core::Size | num_strands_ |
| bool | is_barrel_ |
| VecSize | order_strands_ |
| order of strand in sheet -> id of strand More... | |
| VecInt | orient_strands_ |
| order of strand in sheet -> id of strand More... | |
| std::map< core::Size, core::Size > | strand_order_ |
| id of strand -> order of strand in sheet More... | |
| Vector | sheet_plane_ |
| vector defining sheet plane More... | |
| Vector | sheet_center_ |
| "center" of sheet More... | |
| VecInt | ca_cb_orients_ |
| bool | is_geometry_initialized_ |
| geometries was calculated or not More... | |
Friends | |
| std::ostream & | operator<< (std::ostream &out, const Sheet &s) |
| return strand pairing More... | |
Member Typedef Documentation
◆ Pose
◆ Real
◆ Size
◆ SS_Info2_COP
◆ VecInt
| typedef utility::vector1< int > protocols::fldsgn::topology::Sheet::VecInt |
◆ VecReal
| typedef utility::vector1< Real > protocols::fldsgn::topology::Sheet::VecReal |
◆ VecSize
| typedef utility::vector1< core::Size > protocols::fldsgn::topology::Sheet::VecSize |
◆ Vector
Constructor & Destructor Documentation
◆ Sheet() [1/3]
| protocols::fldsgn::topology::Sheet::Sheet | ( | ) |
default constructor
References initialize().
◆ Sheet() [2/3]
| protocols::fldsgn::topology::Sheet::Sheet | ( | VecSize const & | order_strands, |
| VecInt const & | orient_strands, | ||
| bool | is_barrel | ||
| ) |
value constructor
References initialize(), order_strands(), and orient_strands().
◆ Sheet() [3/3]
| protocols::fldsgn::topology::Sheet::Sheet | ( | Sheet const & | s | ) |
copy constructor
◆ ~Sheet()
|
overridedefault |
default destructor
Member Function Documentation
◆ ca_cb_orient()
|
inline |
References ca_cb_orients_.
Referenced by calc_sasa_bothsides().
◆ ca_cb_orients()
|
inline |
References ca_cb_orients_.
◆ calc_geometry()
| void protocols::fldsgn::topology::Sheet::calc_geometry | ( | SS_Info2_COP const | ssinfo | ) |
calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_
calc geometry
References protocols::fldsgn::topology::BB_Pos::CA(), ca_cb_orients_, protocols::fldsgn::topology::BB_Pos::CB(), core::sequence::end, is_geometry_initialized_, num_strands_, order_strands_, orient_strands_, sheet_center_, sheet_plane_, and protocols::fldsgn::topology::BB_Pos::size().
◆ calc_sasa_bothsides()
| utility::vector1< Real > protocols::fldsgn::topology::Sheet::calc_sasa_bothsides | ( | Pose const & | pose, |
| SS_Info2_COP const | ssinfo, | ||
| Real | pore_radius = 1.5 |
||
| ) |
calc surface areas only with beta-sheet
References ca_cb_orient(), core::scoring::calc_per_atom_sasa(), core::sequence::end, core::pose::initialize_atomid_map(), is_geometry_initialized_, order_strands_, core::id::AtomID_Map< T >::set(), and core::pose::Pose::size().
◆ clone()
|
inline |
clone this object
◆ initialize()
| void protocols::fldsgn::topology::Sheet::initialize | ( | ) |
intialize this class
initialize this class
References num_strands_, order_strands_, and strand_order_.
Referenced by Sheet().
◆ is_barrel()
|
inline |
is this barrel ?
References is_barrel_.
◆ is_member()
| bool protocols::fldsgn::topology::Sheet::is_member | ( | core::Size const | s | ) |
whether the given strand number belongs to this sheet or not
References order_strands_.
◆ num_strands()
|
inline |
the number strands inclued in
References num_strands_.
◆ order_strand()
|
inline |
References order_strands_.
◆ order_strands()
|
inline |
References order_strands_.
Referenced by Sheet().
◆ orient_strand()
|
inline |
References orient_strands_.
◆ orient_strands()
|
inline |
References orient_strands_.
Referenced by Sheet().
◆ strand_order()
|
inline |
References strand_order_.
◆ which_side()
| int protocols::fldsgn::topology::Sheet::which_side | ( | Vector const & | vec | ) | const |
References sheet_center_, and sheet_plane_.
Friends And Related Function Documentation
◆ operator<<
|
friend |
return strand pairing
Member Data Documentation
◆ ca_cb_orients_
|
private |
Referenced by ca_cb_orient(), ca_cb_orients(), and calc_geometry().
◆ is_barrel_
|
private |
Referenced by is_barrel().
◆ is_geometry_initialized_
|
private |
geometries was calculated or not
Referenced by calc_geometry(), and calc_sasa_bothsides().
◆ num_strands_
|
private |
Referenced by calc_geometry(), initialize(), and num_strands().
◆ order_strands_
|
private |
order of strand in sheet -> id of strand
Referenced by calc_geometry(), calc_sasa_bothsides(), initialize(), is_member(), order_strand(), and order_strands().
◆ orient_strands_
|
private |
order of strand in sheet -> id of strand
Referenced by calc_geometry(), orient_strand(), and orient_strands().
◆ sheet_center_
|
private |
"center" of sheet
Referenced by calc_geometry(), and which_side().
◆ sheet_plane_
|
private |
vector defining sheet plane
Referenced by calc_geometry(), and which_side().
◆ strand_order_
|
private |
id of strand -> order of strand in sheet
Referenced by initialize(), and strand_order().
The documentation for this class was generated from the following files:
