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protocols::fldsgn::topology::BB_Pos Class Reference

#include <BB_Pos.hh>

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Public Member Functions

void resize (Size const nres)
 
void clear ()
 
void take_coordinates_from_pose (Pose const &pose)
 
Vector const & N (Size const i) const
 
Vector const & CA (Size const i) const
 
Vector const & CB (Size const i) const
 
Vector const & C (Size const i) const
 
Vector const & O (Size const i) const
 
Size size () const
 @ More...
 

Private Types

typedef core::Size Size
 
typedef core::Vector Vector
 
typedef core::pose::Pose Pose
 

Private Member Functions

bool bbindices_up_to_date (Pose const &pose) const
 
void update_indices (Pose const &pose)
 

Private Attributes

utility::vector1< Vector > N_
 
utility::vector1< Vector > CA_
 
utility::vector1< Vector > CB_
 
utility::vector1< Vector > C_
 
utility::vector1< Vector > O_
 
utility::vector1
< core::chemical::ResidueType
const * > 		residue_types_
 
utility::vector1< Size > N_index_
 
utility::vector1< Size > CA_index_
 
utility::vector1< Size > CB_index_
 
utility::vector1< Size > C_index_
 
utility::vector1< Size > O_index_
 

Detailed Description

Definition at line 39 of file BB_Pos.hh.

Member Typedef Documentation

typedef core::pose::Pose protocols::fldsgn::topology::BB_Pos::Pose
private

Definition at line 44 of file BB_Pos.hh.

typedef core::Size protocols::fldsgn::topology::BB_Pos::Size
private

Definition at line 42 of file BB_Pos.hh.

typedef core::Vector protocols::fldsgn::topology::BB_Pos::Vector
private

Definition at line 43 of file BB_Pos.hh.

Member Function Documentation

bool protocols::fldsgn::topology::BB_Pos::bbindices_up_to_date ( Pose const &  pose) const
private

Definition at line 106 of file BB_Pos.cc.

References N_, core::pose::Pose::residue_type(), residue_types_, and core::pose::Pose::total_residue().

Referenced by take_coordinates_from_pose().

Vector const& protocols::fldsgn::topology::BB_Pos::C ( Size const  i) const
inline

accessor for C's coordinate on residue i, requires take_coordinates_from_pose have been recently called.

Definition at line 82 of file BB_Pos.hh.

References C_.

Referenced by protocols::fldsgn::topology::Strand::calc_geometry(), protocols::fldsgn::topology::Helix::calc_geometry(), protocols::fldsgn::potentials::sspot::HSPairPotential::helix_end(), protocols::fldsgn::potentials::sspot::SSPairPotential::pair_dp(), and protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::pair_dp().

Vector const& protocols::fldsgn::topology::BB_Pos::CA ( Size const  i) const
inline

accessor for CA's coordinate on residue i, requires take_coordinates_from_pose have been recently called.

Definition at line 67 of file BB_Pos.hh.

References CA_.

Referenced by protocols::fldsgn::topology::Helix::calc_geometry(), and protocols::fldsgn::potentials::sspot::HSPairPotential::helix_end().

Vector const& protocols::fldsgn::topology::BB_Pos::CB ( Size const  i) const
inline

accessor for CB's coordinate on residue i, requires take_coordinates_from_pose have been recently called.

Definition at line 74 of file BB_Pos.hh.

References CB_.

void protocols::fldsgn::topology::BB_Pos::clear ( )

. After a change in size, the residue types and the integer indices are all wrong. Erase the old information.

Definition at line 53 of file BB_Pos.cc.

References C_, C_index_, CA_, CA_index_, CB_, CB_index_, N_, N_index_, O_, O_index_, and residue_types_.

Referenced by protocols::fldsgn::topology::SS_Info2::clear_data().

Vector const& protocols::fldsgn::topology::BB_Pos::N ( Size const  i) const
inline

accessor for N's coordinate on residue i, requires take_coordinates_from_pose have been recently called.

Definition at line 60 of file BB_Pos.hh.

References N_.

Referenced by protocols::fldsgn::topology::Strand::calc_geometry(), protocols::fldsgn::topology::Helix::calc_geometry(), and protocols::fldsgn::potentials::sspot::HSPairPotential::helix_end().

Vector const& protocols::fldsgn::topology::BB_Pos::O ( Size const  i) const
inline

accessor for O's coordinate on residue i, requires take_coordinates_from_pose have been recently called.

Definition at line 89 of file BB_Pos.hh.

References O_.

Referenced by protocols::fldsgn::potentials::sspot::SSPairPotential::pair_dp(), and protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::pair_dp().

void protocols::fldsgn::topology::BB_Pos::resize ( Size const  nres)

. After a change in size, the residue types and the integer indices are all wrong. Erase the old information.

Definition at line 31 of file BB_Pos.cc.

References C_, C_index_, CA_, CA_index_, CB_, CB_index_, N_, N_index_, O_, O_index_, and residue_types_.

Referenced by protocols::fldsgn::topology::SS_Info2::resize(), and update_indices().

Size protocols::fldsgn::topology::BB_Pos::size ( ) const
inline

@

Definition at line 95 of file BB_Pos.hh.

References residue_types_.

Referenced by protocols::fldsgn::topology::SS_Info2::set_SSorient().

void protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose ( Pose const &  pose)

: Optimize the common case where the sequence of the pose is not changing from score function evaluation to evaluation (e.g. abinitio!)

Definition at line 71 of file BB_Pos.cc.

References core::chemical::aa_gly, bbindices_up_to_date(), C_, C_index_, CA_, CA_index_, CB_, CB_index_, N_, N_index_, O_, O_index_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and update_indices().

Referenced by protocols::fldsgn::topology::SS_Info2::initialize(), and protocols::fldsgn::topology::SS_Info2::set_SSorient().

void protocols::fldsgn::topology::BB_Pos::update_indices ( Pose const &  pose)
private

Definition at line 117 of file BB_Pos.cc.

References core::chemical::aa_gly, C_index_, CA_index_, CB_index_, N_index_, O_index_, core::pose::Pose::residue(), residue_types_, resize(), and core::pose::Pose::total_residue().

Referenced by take_coordinates_from_pose().

Member Data Documentation

utility::vector1< Vector > protocols::fldsgn::topology::BB_Pos::C_
private

Definition at line 110 of file BB_Pos.hh.

Referenced by C(), clear(), resize(), and take_coordinates_from_pose().

utility::vector1< Size > protocols::fldsgn::topology::BB_Pos::C_index_
private

Definition at line 119 of file BB_Pos.hh.

Referenced by clear(), resize(), take_coordinates_from_pose(), and update_indices().

utility::vector1< Vector > protocols::fldsgn::topology::BB_Pos::CA_
private

Definition at line 108 of file BB_Pos.hh.

Referenced by CA(), clear(), resize(), and take_coordinates_from_pose().

utility::vector1< Size > protocols::fldsgn::topology::BB_Pos::CA_index_
private

Definition at line 117 of file BB_Pos.hh.

Referenced by clear(), resize(), take_coordinates_from_pose(), and update_indices().

utility::vector1< Vector > protocols::fldsgn::topology::BB_Pos::CB_
private

Definition at line 109 of file BB_Pos.hh.

Referenced by CB(), clear(), resize(), and take_coordinates_from_pose().

utility::vector1< Size > protocols::fldsgn::topology::BB_Pos::CB_index_
private

Definition at line 118 of file BB_Pos.hh.

Referenced by clear(), resize(), take_coordinates_from_pose(), and update_indices().

utility::vector1< Vector > protocols::fldsgn::topology::BB_Pos::N_
private

Definition at line 107 of file BB_Pos.hh.

Referenced by bbindices_up_to_date(), clear(), N(), resize(), and take_coordinates_from_pose().

utility::vector1< Size > protocols::fldsgn::topology::BB_Pos::N_index_
private

Definition at line 116 of file BB_Pos.hh.

Referenced by clear(), resize(), take_coordinates_from_pose(), and update_indices().

utility::vector1< Vector > protocols::fldsgn::topology::BB_Pos::O_
private

Definition at line 111 of file BB_Pos.hh.

Referenced by clear(), O(), resize(), and take_coordinates_from_pose().

utility::vector1< Size > protocols::fldsgn::topology::BB_Pos::O_index_
private

Definition at line 120 of file BB_Pos.hh.

Referenced by clear(), resize(), take_coordinates_from_pose(), and update_indices().

utility::vector1< core::chemical::ResidueType const * > protocols::fldsgn::topology::BB_Pos::residue_types_
private

Residue types must match those of the pose for the indices to match.

Definition at line 115 of file BB_Pos.hh.

Referenced by bbindices_up_to_date(), clear(), resize(), size(), and update_indices().

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