protocols::fldsgn::MatchResidues Class Reference

#include <MatchResidues.hh>

Inheritance diagram for protocols::fldsgn::MatchResidues:

Public Types
typedef protocols::moves::Mover	Mover
typedef protocols::moves::MoverOP	MoverOP
typedef core::Real	Real
typedef core::Size	Size
typedef core::pose::Pose	Pose
typedef utility::tag::TagCOP	TagCOP
typedef basic::datacache::DataMap	DataMap
typedef utility::vector1< core::Size >	VecSize
typedef utility::vector1< VecSize >	VecVecSize

Public Member Functions
	MatchResidues ()
virtual	~MatchResidues ()
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &)
	parse xml More...
core::Real	compute (core::pose::Pose const &pose, VecSize &best_fit) const
core::Real	compute_comb (core::pose::Pose const &pose, VecSize const &comb) const
core::Real	superimpose_comb (core::pose::Pose &pose, VecSize const &comb) const
core::Real	threshold () const
void	threshold (core::Real value)

Static Public Member Functions
static void	provide_attributes_and_subelements (utility::tag::AttributeList &attlist, utility::tag::XMLSchemaSimpleSubelementList &ssl)

Private Member Functions
std::map< std::string, boost::tuple< core::Size, core::Size > >	map_ss_segments (std::string const &ss) const
void	cart_product (VecVecSize &rvvi, VecSize &rvi, VecVecSize::const_iterator me, VecVecSize::const_iterator end) const
VecVecSize	cart_product (VecVecSize const &input) const

Private Attributes
core::pose::Pose	reference_pose_
VecSize	reference_residues_indexes_
VecVecSize	mod_segment_prod_
core::Real	threshold_

Member Typedef Documentation

DataMap

typedef basic::datacache::DataMap protocols::fldsgn::MatchResidues::DataMap

Mover

typedef protocols::moves::Mover protocols::fldsgn::MatchResidues::Mover

MoverOP

typedef protocols::moves::MoverOP protocols::fldsgn::MatchResidues::MoverOP

Pose

typedef core::pose::Pose protocols::fldsgn::MatchResidues::Pose

Real

typedef core::Real protocols::fldsgn::MatchResidues::Real

Size

typedef core::Size protocols::fldsgn::MatchResidues::Size

TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::MatchResidues::TagCOP

VecSize

typedef utility::vector1< core::Size > protocols::fldsgn::MatchResidues::VecSize

VecVecSize

typedef utility::vector1< VecSize > protocols::fldsgn::MatchResidues::VecVecSize

Constructor & Destructor Documentation

MatchResidues()

protocols::fldsgn::MatchResidues::MatchResidues ( )

default

~MatchResidues()

protocols::fldsgn::MatchResidues::~MatchResidues ( )

virtualdefault

Member Function Documentation

cart_product() [1/2]

void protocols::fldsgn::MatchResidues::cart_product ( VecVecSize &  rvvi, VecSize &  rvi, VecVecSize::const_iterator  me, VecVecSize::const_iterator  end  ) const

private

References core::sequence::end.

Referenced by cart_product(), and parse_my_tag().

cart_product() [2/2]

VecVecSize protocols::fldsgn::MatchResidues::cart_product ( VecVecSize const &  input ) const

private

References cart_product().

compute()

core::Real protocols::fldsgn::MatchResidues::compute	(	core::pose::Pose const &	pose,
		VecSize &	best_fit
	)		const

References compute_comb(), mod_segment_prod_, reference_residues_indexes_, core::scoring::rms, and protocols::fldsgn::TR().

Referenced by protocols::fldsgn::MatchResiduesMover::apply().

compute_comb()

core::Real protocols::fldsgn::MatchResidues::compute_comb	(	core::pose::Pose const &	pose,
		VecSize const &	comb
	)		const

References core::chemical::ResidueType::atom_index(), reference_pose_, reference_residues_indexes_, core::pose::Pose::residue_type(), and core::scoring::rms_at_all_corresponding_atoms().

Referenced by compute().

map_ss_segments()

std::map< std::string, boost::tuple< core::Size, core::Size > > protocols::fldsgn::MatchResidues::map_ss_segments ( std::string const &  ss ) const

private

References core::sequence::end, protocols::loops::start, and core::id::to_string().

Referenced by parse_my_tag().

parse_my_tag()

void protocols::fldsgn::MatchResidues::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &
	)

parse xml

References cart_product(), map_ss_segments(), mod_segment_prod_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::sic_dock::range(), protocols::parser::BluePrint::read_blueprint(), reference_pose_, reference_residues_indexes_, protocols::parser::BluePrint::secstruct(), threshold_, and protocols::fldsgn::TR().

Referenced by protocols::fldsgn::MatchResiduesMover::parse_my_tag().

provide_attributes_and_subelements()

void protocols::fldsgn::MatchResidues::provide_attributes_and_subelements ( utility::tag::AttributeList &  attlist, utility::tag::XMLSchemaSimpleSubelementList &  ssl  )

static

References protocols::fldsgn::subtag_for_match_type().

Referenced by protocols::fldsgn::MatchResiduesMover::provide_xml_schema().

superimpose_comb()

core::Real protocols::fldsgn::MatchResidues::superimpose_comb	(	core::pose::Pose &	pose,
		VecSize const &	comb
	)		const

References core::chemical::ResidueType::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), reference_pose_, reference_residues_indexes_, core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::set(), and core::scoring::superimpose_pose().

Referenced by protocols::fldsgn::MatchResiduesMover::apply().

threshold() [1/2]

core::Real protocols::fldsgn::MatchResidues::threshold ( ) const

inline

References threshold_.

Referenced by protocols::fldsgn::MatchResiduesMover::apply().

threshold() [2/2]

void protocols::fldsgn::MatchResidues::threshold ( core::Real  value )

inline

References threshold_.

Member Data Documentation

mod_segment_prod_

VecVecSize protocols::fldsgn::MatchResidues::mod_segment_prod_

private

Referenced by compute(), and parse_my_tag().

reference_pose_

core::pose::Pose protocols::fldsgn::MatchResidues::reference_pose_

private

Referenced by compute_comb(), parse_my_tag(), and superimpose_comb().

reference_residues_indexes_

VecSize protocols::fldsgn::MatchResidues::reference_residues_indexes_

private

Referenced by compute(), compute_comb(), parse_my_tag(), and superimpose_comb().

threshold_

core::Real protocols::fldsgn::MatchResidues::threshold_

private

Referenced by parse_my_tag(), and threshold().

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

• src/protocols/fldsgn/MatchResidues.hh
• src/protocols/fldsgn/MatchResidues.cc