protocols::fldsgn::MatchResidues Class Reference

#include <MatchResidues.hh>

Inheritance diagram for protocols::fldsgn::MatchResidues:

Collaboration 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::TagPtr	TagPtr
typedef protocols::moves::DataMap	DataMap
typedef protocols::moves::Movers_map	Movers_map
typedef protocols::filters::Filters_map	Filters_map
typedef utility::vector1< Size >	VecSize
typedef utility::vector1< VecSize >	VecVecSize

Public Member Functions
	MatchResidues ()
virtual	~MatchResidues ()
void	parse_my_tag (TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, Pose const &)
	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)

Private Member Functions
std::map< std::string, boost::tuple< Size, 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_

Detailed Description

Definition at line 41 of file MatchResidues.hh.

Member Typedef Documentation

typedef protocols::moves::DataMap protocols::fldsgn::MatchResidues::DataMap

Definition at line 51 of file MatchResidues.hh.

typedef protocols::filters::Filters_map protocols::fldsgn::MatchResidues::Filters_map

Definition at line 53 of file MatchResidues.hh.

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

Definition at line 44 of file MatchResidues.hh.

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

Definition at line 45 of file MatchResidues.hh.

typedef protocols::moves::Movers_map protocols::fldsgn::MatchResidues::Movers_map

Definition at line 52 of file MatchResidues.hh.

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

Definition at line 48 of file MatchResidues.hh.

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

Definition at line 46 of file MatchResidues.hh.

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

Definition at line 47 of file MatchResidues.hh.

typedef utility::tag::TagPtr protocols::fldsgn::MatchResidues::TagPtr

Definition at line 50 of file MatchResidues.hh.

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

Definition at line 54 of file MatchResidues.hh.

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

Definition at line 55 of file MatchResidues.hh.

Constructor & Destructor Documentation

protocols::fldsgn::MatchResidues::MatchResidues

(

)

Definition at line 61 of file MatchResidues.cc.

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

virtual

Definition at line 66 of file MatchResidues.cc.

Member Function Documentation

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

private

Definition at line 118 of file MatchResidues.cc.

References core::sequence::end.

Referenced by cart_product(), and parse_my_tag().

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

private

Definition at line 142 of file MatchResidues.cc.

References cart_product().

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

Definition at line 97 of file MatchResidues.cc.

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

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

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

Definition at line 71 of file MatchResidues.cc.

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().

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

private

Definition at line 220 of file MatchResidues.cc.

References core::sequence::end, and protocols::loops::start.

Referenced by parse_my_tag().

void protocols::fldsgn::MatchResidues::parse_my_tag	(	TagPtr const	tag,
		DataMap &	,
		Filters_map const &	,
		Movers_map const &	,
		Pose const &
	)

parse xml

Definition at line 159 of file MatchResidues.cc.

References cart_product(), map_ss_segments(), mod_segment_prod_, core::import_pose::pose_from_pdb(), protocols::sic_dock::range(), protocols::jd2::parser::BluePrint::read_blueprint(), reference_pose_, reference_residues_indexes_, protocols::jd2::parser::BluePrint::secstruct(), threshold_, and protocols::fldsgn::TR().

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

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

Definition at line 83 of file MatchResidues.cc.

References core::chemical::ResidueType::atom_index(), core::id::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().

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

inline

Definition at line 80 of file MatchResidues.hh.

References threshold_.

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

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

inline

Definition at line 81 of file MatchResidues.hh.

References threshold_.

Member Data Documentation

VecVecSize protocols::fldsgn::MatchResidues::mod_segment_prod_

private

Definition at line 93 of file MatchResidues.hh.

Referenced by compute(), and parse_my_tag().

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

private

Definition at line 91 of file MatchResidues.hh.

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

VecSize protocols::fldsgn::MatchResidues::reference_residues_indexes_

private

Definition at line 92 of file MatchResidues.hh.

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

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

private

Definition at line 95 of file MatchResidues.hh.

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