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

#include <BB_Pos.hh>

Public Member Functions
void	resize (core::Size const nres)
void	clear ()
void	take_coordinates_from_pose (Pose const &pose)
Vector const &	N (core::Size const i) const
Vector const &	CA (core::Size const i) const
Vector const &	CB (core::Size const i) const
Vector const &	C (core::Size const i) const
Vector const &	O (core::Size const i) const
core::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::ResidueTypeCOP >	residue_types_
utility::vector1< core::Size >	N_index_
utility::vector1< core::Size >	CA_index_
utility::vector1< core::Size >	CB_index_
utility::vector1< core::Size >	C_index_
utility::vector1< core::Size >	O_index_

Member Typedef Documentation

Pose

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

private

Size

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

private

Vector

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

private

Member Function Documentation

bbindices_up_to_date()

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

private

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

Referenced by take_coordinates_from_pose().

C()

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

inline

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

References C_.

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

CA()

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

inline

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

References CA_.

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

CB()

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

inline

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

References CB_.

Referenced by protocols::fldsgn::topology::Sheet::calc_geometry(), protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_helix_cycle(), and protocols::fldsgn::topology::BetaAlphaBetaMotif::calc_inout().

clear()

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.

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().

N()

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

inline

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

References N_.

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

O()

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

inline

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

References O_.

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

resize()

void protocols::fldsgn::topology::BB_Pos::resize

(

core::Size const

nres

)

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

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()

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

inline

@

References residue_types_.

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

take_coordinates_from_pose()

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!)

References core::conformation::Residue::aa(), core::chemical::aa_gly, bbindices_up_to_date(), C_, C_index_, CA_, CA_index_, CB_, CB_index_, core::conformation::Residue::is_protein(), N_, N_index_, O_, O_index_, core::pose::Pose::residue(), core::pose::Pose::size(), update_indices(), and core::conformation::Residue::xyz().

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

update_indices()

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

private

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::conformation::Residue::atom_index(), C_index_, CA_index_, CB_index_, core::conformation::Residue::is_protein(), N_index_, O_index_, core::pose::Pose::residue(), residue_types_, resize(), core::pose::Pose::size(), and core::conformation::Residue::type_ptr().

Referenced by take_coordinates_from_pose().

Member Data Documentation

C_

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

private

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

C_index_

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

private

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

CA_

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

private

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

CA_index_

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

private

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

CB_

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

private

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

CB_index_

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

private

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

N_

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

private

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

N_index_

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

private

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

O_

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

private

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

O_index_

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

private

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

residue_types_

utility::vector1< core::chemical::ResidueTypeCOP > protocols::fldsgn::topology::BB_Pos::residue_types_

private

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

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

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

• src/protocols/fldsgn/topology/BB_Pos.hh
• src/protocols/fldsgn/topology/BB_Pos.cc