protocols::dna::DnaInterfaceFinder Class Reference

#include <DnaInterfaceFinder.hh>

Inheritance diagram for protocols::dna::DnaInterfaceFinder:

Collaboration diagram for protocols::dna::DnaInterfaceFinder:

Public Member Functions
	DnaInterfaceFinder (core::Real close_threshold=10 *10, core::Real contact_threshold=3.7 *3.7, core::Real z_cutoff=10., bool base_only=false)
virtual	~DnaInterfaceFinder ()
DnaInterfaceFinderOP	clone () const
void	determine_protein_interface (core::pose::Pose const &pose)
void	determine_interface (core::pose::Pose const &pose, utility::vector1< core::Size > const &protein_positions, utility::vector1< core::Size > const &dna_positions)
void	determine_interface (core::pose::Pose const &pose)
void	determine_protein_interface (core::pose::Pose const &pose, utility::vector1< core::Size > const &protein_positions, utility::vector1< core::Size > const &dna_positions)
void	determine_dna_interface (core::pose::Pose const &pose, utility::vector1< core::Size > const &protein_positions, utility::vector1< core::Size > const &dna_positions)
bool	initialized () const
DnaNeighbors const &	protein_neighbors () const
DnaNeighbors const &	dna_neighbors () const

Private Attributes
core::Real	close_threshold_
core::Real	contact_threshold_
core::Real	z_cutoff_
bool	base_only_
bool	initialized_
DnaNeighbors	protein_neighbors_
DnaNeighbors	dna_neighbors_

Detailed Description

Definition at line 45 of file DnaInterfaceFinder.hh.

Constructor & Destructor Documentation

protocols::dna::DnaInterfaceFinder::DnaInterfaceFinder ( core::Real  close_threshold = 10 * 10, core::Real  contact_threshold = 3.7 * 3.7, core::Real  z_cutoff = 10., bool  base_only = false  )

inline

Definition at line 48 of file DnaInterfaceFinder.hh.

Referenced by clone().

virtual protocols::dna::DnaInterfaceFinder::~DnaInterfaceFinder ( )

inlinevirtual

Definition at line 61 of file DnaInterfaceFinder.hh.

Member Function Documentation

DnaInterfaceFinderOP protocols::dna::DnaInterfaceFinder::clone ( ) const

inline

Definition at line 63 of file DnaInterfaceFinder.hh.

References DnaInterfaceFinder().

void protocols::dna::DnaInterfaceFinder::determine_dna_interface	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	protein_positions,
		utility::vector1< core::Size > const &	dna_positions
	)

Definition at line 106 of file DnaInterfaceFinder.cc.

References protocols::dna::argrot_dna_dis2(), protocols::dna::DnaNeighbor::close(), protocols::dna::close_to_dna(), protocols::dna::DnaNeighbor::contact(), core::sequence::end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and protocols::dna::z_axis_dist().

Referenced by protocols::motifs::MotifSearch::protein_DNA_motif_target_positions_JA(), and protocols::motifs::LigandMotifSearch::protein_DNA_motif_target_positions_JA().

void protocols::dna::DnaInterfaceFinder::determine_interface	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	protein_positions,
		utility::vector1< core::Size > const &	dna_positions
	)

Definition at line 59 of file DnaInterfaceFinder.cc.

void protocols::dna::DnaInterfaceFinder::determine_interface

(

core::pose::Pose const &

pose)

Definition at line 33 of file DnaInterfaceFinder.cc.

References core::sequence::end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void protocols::dna::DnaInterfaceFinder::determine_protein_interface

(

core::pose::Pose const &

pose)

Definition at line 46 of file DnaInterfaceFinder.cc.

References core::sequence::end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::dna::PDBOutput::output_hbond_info(), protocols::motifs::MotifSearch::protein_DNA_motif_build_positions_JA(), and protocols::motifs::LigandMotifSearch::protein_DNA_motif_build_positions_JA().

void protocols::dna::DnaInterfaceFinder::determine_protein_interface	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	protein_positions,
		utility::vector1< core::Size > const &	dna_positions
	)

Definition at line 70 of file DnaInterfaceFinder.cc.

References protocols::dna::argrot_dna_dis2(), protocols::dna::DnaNeighbor::close(), protocols::dna::close_to_dna(), protocols::dna::DnaNeighbor::contact(), core::sequence::end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and protocols::dna::z_axis_dist().

DnaNeighbors const & protocols::dna::DnaInterfaceFinder::dna_neighbors

(

)

const

Definition at line 149 of file DnaInterfaceFinder.cc.

bool protocols::dna::DnaInterfaceFinder::initialized ( ) const

inline

Definition at line 91 of file DnaInterfaceFinder.hh.

References initialized_.

DnaNeighbors const & protocols::dna::DnaInterfaceFinder::protein_neighbors

(

)

const

Definition at line 142 of file DnaInterfaceFinder.cc.

Member Data Documentation

bool protocols::dna::DnaInterfaceFinder::base_only_

private

Definition at line 98 of file DnaInterfaceFinder.hh.

core::Real protocols::dna::DnaInterfaceFinder::close_threshold_

private

Definition at line 97 of file DnaInterfaceFinder.hh.

core::Real protocols::dna::DnaInterfaceFinder::contact_threshold_

private

Definition at line 97 of file DnaInterfaceFinder.hh.

DnaNeighbors protocols::dna::DnaInterfaceFinder::dna_neighbors_

private

Definition at line 101 of file DnaInterfaceFinder.hh.

bool protocols::dna::DnaInterfaceFinder::initialized_

private

Definition at line 99 of file DnaInterfaceFinder.hh.

Referenced by initialized().

DnaNeighbors protocols::dna::DnaInterfaceFinder::protein_neighbors_

private

Definition at line 100 of file DnaInterfaceFinder.hh.

core::Real protocols::dna::DnaInterfaceFinder::z_cutoff_

private

Definition at line 97 of file DnaInterfaceFinder.hh.

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

• src/protocols/dna/DnaInterfaceFinder.hh
• src/protocols/dna/DnaInterfaceFinder.cc