protocols::abinitio::TemplateJumpSetup Class Reference

#include <TemplateJumpSetup.hh>

Inheritance diagram for protocols::abinitio::TemplateJumpSetup:

Public Member Functions
	TemplateJumpSetup (TemplatesCOP templates, core::fragment::SecondaryStructureCOP secstruct, PairingStatisticsCOP, core::scoring::dssp::PairingList const &helix_pairings)
	~TemplateJumpSetup () override
std::string	type_name () const override
jumping::JumpSample	create_jump_sample () const override
jumping::JumpSample	clean_jumps (jumping::JumpSample const &) const override
	take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample() More...
core::fragment::FragSetOP	generate_jump_frags (jumping::JumpSample const &, core::kinematics::MoveMap const &) const override
	returns an ordered FragSet that is compatible with the JumpSample default: generate jumps from ss-library according to JumpSample More...
bool	is_helix_jump (core::scoring::dssp::Pairing const &p) const
Public Member Functions inherited from protocols::jumping::BaseJumpSetup
	~BaseJumpSetup () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

Private Attributes
TemplatesCOP	templates_
core::fragment::SecondaryStructureCOP	secstruct_
PairingStatisticsCOP	strand_stats_
core::scoring::dssp::PairingList	helix_pairings_

Constructor & Destructor Documentation

TemplateJumpSetup()

protocols::abinitio::TemplateJumpSetup::TemplateJumpSetup	(	TemplatesCOP	templates,
		core::fragment::SecondaryStructureCOP	secstruct,
		PairingStatisticsCOP	strand_stats,
		core::scoring::dssp::PairingList const &	helix_pairings
	)

~TemplateJumpSetup()

protocols::abinitio::TemplateJumpSetup::~TemplateJumpSetup ( )

overridedefault

Member Function Documentation

clean_jumps()

jumping::JumpSample protocols::abinitio::TemplateJumpSetup::clean_jumps ( jumping::JumpSample const &  ) const

overridevirtual

take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample()

Implements protocols::jumping::BaseJumpSetup.

References protocols::jumping::JumpSample::generate_jump_frames(), protocols::jumping::JumpSample::get_pairing(), secstruct_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_jump(), and strand_stats_.

create_jump_sample()

JumpSample protocols::abinitio::TemplateJumpSetup::create_jump_sample ( ) const

overridevirtual

Implements protocols::jumping::BaseJumpSetup.

Reimplemented in protocols::abinitio::FixTemplateJumpSetup.

References core::scoring::dssp::StrandPairing::get_beta_pairs(), helix_pairings_, protocols::mean_field::min(), core::scoring::rg, secstruct_, core::scoring::dssp::StrandPairing::size(), core::scoring::dssp::StrandPairingSet::size(), core::scoring::dssp::StrandPairingSet::strand_pairing(), strand_stats_, templates_, and tr().

generate_jump_frags()

core::fragment::FragSetOP protocols::abinitio::TemplateJumpSetup::generate_jump_frags ( jumping::JumpSample const &  target_jumps, core::kinematics::MoveMap const &  mm  ) const

overridevirtual

returns an ordered FragSet that is compatible with the JumpSample default: generate jumps from ss-library according to JumpSample

Reimplemented from protocols::jumping::BaseJumpSetup.

References protocols::jumping::JumpSample::generate_jump_frames(), protocols::jumping::JumpSample::get_pairing(), is_helix_jump(), strand_stats_, templates_, and tr().

is_helix_jump()

bool protocols::abinitio::TemplateJumpSetup::is_helix_jump

(

core::scoring::dssp::Pairing const &

p

)

const

References helix_pairings_, and core::scoring::dssp::Pairing::reverse().

Referenced by generate_jump_frags().

type_name()

std::string protocols::abinitio::TemplateJumpSetup::type_name ( ) const

inlineoverridevirtual

Implements protocols::jumping::BaseJumpSetup.

Member Data Documentation

helix_pairings_

core::scoring::dssp::PairingList protocols::abinitio::TemplateJumpSetup::helix_pairings_

private

Referenced by create_jump_sample(), and is_helix_jump().

secstruct_

core::fragment::SecondaryStructureCOP protocols::abinitio::TemplateJumpSetup::secstruct_

private

Referenced by clean_jumps(), and create_jump_sample().

strand_stats_

PairingStatisticsCOP protocols::abinitio::TemplateJumpSetup::strand_stats_

private

Referenced by clean_jumps(), create_jump_sample(), and generate_jump_frags().

templates_

TemplatesCOP protocols::abinitio::TemplateJumpSetup::templates_

private

Referenced by create_jump_sample(), and generate_jump_frags().

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

• src/protocols/abinitio/TemplateJumpSetup.hh
• src/protocols/abinitio/TemplateJumpSetup.cc