#include <BluePrint.hh>

Inheritance diagram for protocols::parser::BluePrint:

Public Types
typedef std::string	String

typedef core::Size	Size

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef core::kinematics::MoveMapOP	MoveMapOP

Public Member Functions
	BluePrint ()
	default constructor More...

	BluePrint (String const &filename)
	value constructor More...

	~BluePrint () override
	destructor More...

	BluePrint (BluePrint const &rval)
	copy constructor More...

core::Size	total_residue () const
	total residue number defined in blueprint file More...

core::Size	total_residue_wolig () const
	total residue number without ligand defined in blueprint file More...

String	sequence () const
	sequence defined in blueprint file More...

char	sequence (core::Size seqpos) const
	a~mino acid type at a position in blueprint file More...

String	secstruct () const
	secondary structures defined in blueprint file More...

char	secstruct (core::Size seqpos) const
	secondary structure at a position in blueprint file More...

utility::vector1< String >	abego () const
	abego defined in bludprint file More...

String	abego (core::Size seqpos) const
	secondary structure at a position in blueprint file More...

core::Size	resnum (core::Size seqpos) const
	residue number at each position in blueprint file More...

core::Size	resnum_map (core::Size resnum_pose) const
	translate residue number of pose to that of blueprint file More...

char	buildtype (core::Size seqpos) const
	return build type at each position More...

String	extra (core::Size seqpos) const
	return build type at each position More...

String	insertion (core::Size i) const
	build type at each position in blueprint More...

String	helix_pairings () const
	helix pairings defined at the line of HHPAIR in blueprint More...

String	strand_pairings () const
	strand pairings defined at the line of SSPAIR in blueprint More...

String	hss_triplets () const
	strand pairings defined at the line of SSPAIR in blueprint More...

bool	read_blueprint (String const &)
	secondary structure information More...

bool	read_blueprint_stream (std::istream &data, std::string const &filename)
	read blueprint file from stream More...

void	insert_ss_into_pose (Pose &pose)
	set secondary structure into pose More...

void	set_movemap (MoveMapOP &movemap)
	set movemap based on blueprint More...

Private Attributes
core::Size	total_residue_
	set strand pairings removed StrandPairings set_strand_pairings( SS_Info2_OP const & ssinfo, StrandPairings const & spairs ) const; More...

core::Size	total_residue_wolig_
	total residue without ligand More...

String	sequence_
	sequence defined in blueprint More...

String	secstruct_
	amino acid sequence defined in blueprint More...

utility::vector1< core::Size >	resnum_
	residue number of each position in blueprint More...

utility::vector1< char >	resname_
	amino acid type at a position in blueprint More...

utility::vector1< char >	sstype_
	secondary structure type defined in blueprint More...

utility::vector1< String >	abego_
	abego type defined in blueprint More...

utility::vector1< char >	buildtype_
	build type at each position in blueprint More...

utility::vector1< String >	extra_
	extra infomation at each position in blueprint More...

utility::vector1< String >	insertion_
	pdb file name for insertion More...

std::map< core::Size, core::Size >	resnum_map_
	translate pose residue number to blueprint residue number More...

String	strand_pairings_
	secondary structure information More...

String	helix_pairings_
	helix pairings defined at the line of HHPAIR in blueprint More...

String	hss_triplets_
	helix-strand-strand triple defined at the line of HSSTRIPLE in blueprint More...

Member Typedef Documentation

typedef core::kinematics::MoveMapOP protocols::parser::BluePrint::MoveMapOP

typedef core::pose::Pose protocols::parser::BluePrint::Pose

typedef core::Real protocols::parser::BluePrint::Real

typedef core::Size protocols::parser::BluePrint::Size

typedef std::string protocols::parser::BluePrint::String

Constructor & Destructor Documentation

protocols::parser::BluePrint::BluePrint ( )

default constructor

protocols::parser::BluePrint::BluePrint ( String const & filename )

value constructor

References read_blueprint(), and protocols::parser::TR().

protocols::parser::BluePrint::~BluePrint ( )

overridedefault

destructor

protocols::parser::BluePrint::BluePrint ( BluePrint const & rval )

copy constructor

Member Function Documentation

utility::vector1< BluePrint::String > protocols::parser::BluePrint::abego ( ) const

abego defined in bludprint file

abego defined in blueprint file

References abego_.

Referenced by read_blueprint_stream().

BluePrint::String protocols::parser::BluePrint::abego ( core::Size seqpos ) const

secondary structure at a position in blueprint file

abego defined in blueprint file

References abego_.

char protocols::parser::BluePrint::buildtype ( core::Size seqpos ) const

return build type at each position

build type at each position in blueprint

References buildtype_.

Referenced by set_movemap().

BluePrint::String protocols::parser::BluePrint::extra ( core::Size seqpos ) const

return build type at each position

build type at each position in blueprint

References extra_.

Referenced by read_blueprint_stream().

BluePrint::String protocols::parser::BluePrint::helix_pairings ( ) const

helix pairings defined at the line of HHPAIR in blueprint

References helix_pairings_.

Referenced by protocols::fldsgn::potentials::SetSecStructEnergies::init_from_blueprint().

BluePrint::String protocols::parser::BluePrint::hss_triplets ( ) const

strand pairings defined at the line of SSPAIR in blueprint

helix-strand-strand set at the line of HSSTRIPLET in blueprint

References hss_triplets_.

Referenced by protocols::fldsgn::potentials::SetSecStructEnergies::init_from_blueprint().

void protocols::parser::BluePrint::insert_ss_into_pose ( Pose & pose )

set secondary structure into pose

References resnum_map(), secstruct(), core::pose::Pose::set_secstruct(), and core::pose::Pose::size().

BluePrint::String protocols::parser::BluePrint::insertion ( core::Size i ) const

build type at each position in blueprint

References insertion_.

bool protocols::parser::BluePrint::read_blueprint ( String const & filename )

secondary structure information

secondary structure information BluePrint::SS_Info2_OP BluePrint::ssinfo() const { return ss_info_; }

reading blueprint files

read blueprint file

References read_blueprint_stream(), and protocols::parser::TR().

Referenced by BluePrint(), and protocols::fldsgn::MatchResidues::parse_my_tag().

bool protocols::parser::BluePrint::read_blueprint_stream	(	std::istream &	data,
		std::string const &	filename = `""`
	)

read blueprint file from stream

References protocols::cluster::calibur::aa, abego(), abego_, buildtype_, extra(), extra_, protocols::abinitio::filename(), helix_pairings_, hss_triplets_, insertion_, resname_, resnum_, resnum_map_, secstruct_, sequence_, protocols::sparta::split(), sstype_, strand_pairings_, core::sequence::ABEGOManager::symbol2index(), total_residue(), total_residue_, total_residue_wolig_, and protocols::parser::TR().

Referenced by read_blueprint().

BluePrint::Size protocols::parser::BluePrint::resnum ( core::Size seqpos ) const

residue number at each position in blueprint file

residue number of each position in blueprint file

References buildtype_, and resnum_.

BluePrint::Size protocols::parser::BluePrint::resnum_map ( core::Size resnum_pose ) const

translate residue number of pose to that of blueprint file

References resnum_map_.

Referenced by insert_ss_into_pose().

BluePrint::String protocols::parser::BluePrint::secstruct ( ) const

secondary structures defined in blueprint file

References secstruct_.

Referenced by protocols::fldsgn::potentials::SetSecStructEnergies::init_from_blueprint(), insert_ss_into_pose(), protocols::denovo_design::filters::SSShapeComplementarityFilter::parse_my_tag(), protocols::fldsgn::MatchResidues::parse_my_tag(), protocols::fldsgn::filters::HelixKinkFilter::parse_my_tag(), protocols::fldsgn::filters::StrandCurvatureByLevels::parse_my_tag(), protocols::fldsgn::filters::StrandHelixGeometryFilter::parse_my_tag(), protocols::fldsgn::filters::InterlockingAromaFilter::parse_my_tag(), protocols::fldsgn::filters::SheetTopologyFilter::parse_my_tag(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct_from_blueprint(), and protocols::fldsgn::filters::HelixBendFilter::set_secstruct_from_bp().

char protocols::parser::BluePrint::secstruct ( core::Size seqpos ) const

secondary structure at a position in blueprint file

References buildtype_, and sstype_.

BluePrint::String protocols::parser::BluePrint::sequence ( ) const

sequence defined in blueprint file

References sequence_.

char protocols::parser::BluePrint::sequence ( core::Size seqpos ) const

a~mino acid type at a position in blueprint file

amino acid type at a position in blueprint file

References resname_.

void protocols::parser::BluePrint::set_movemap ( MoveMapOP & movemap )

set movemap based on blueprint

References buildtype(), total_residue_, and protocols::parser::TR().

BluePrint::String protocols::parser::BluePrint::strand_pairings ( ) const

strand pairings defined at the line of SSPAIR in blueprint

References strand_pairings_.

Referenced by protocols::fldsgn::potentials::SetSecStructEnergies::init_from_blueprint(), and protocols::fldsgn::filters::SheetTopologyFilter::parse_my_tag().

BluePrint::Size protocols::parser::BluePrint::total_residue ( ) const

total residue number defined in blueprint file

References total_residue_.

Referenced by read_blueprint_stream().

BluePrint::Size protocols::parser::BluePrint::total_residue_wolig ( ) const

total residue number without ligand defined in blueprint file

total residue number defined in blueprint file

References total_residue_wolig_.

Member Data Documentation

utility::vector1< String > protocols::parser::BluePrint::abego_

private

abego type defined in blueprint

Referenced by abego(), and read_blueprint_stream().

utility::vector1< char > protocols::parser::BluePrint::buildtype_

private

build type at each position in blueprint

Referenced by buildtype(), read_blueprint_stream(), resnum(), and secstruct().

utility::vector1< String > protocols::parser::BluePrint::extra_

private

extra infomation at each position in blueprint

Referenced by extra(), and read_blueprint_stream().

String protocols::parser::BluePrint::helix_pairings_

private

helix pairings defined at the line of HHPAIR in blueprint

Referenced by helix_pairings(), and read_blueprint_stream().

String protocols::parser::BluePrint::hss_triplets_

private

helix-strand-strand triple defined at the line of HSSTRIPLE in blueprint

Referenced by hss_triplets(), and read_blueprint_stream().

utility::vector1< String > protocols::parser::BluePrint::insertion_

private

pdb file name for insertion

Referenced by insertion(), and read_blueprint_stream().

utility::vector1< char > protocols::parser::BluePrint::resname_

private

amino acid type at a position in blueprint

Referenced by read_blueprint_stream(), and sequence().

utility::vector1< core::Size > protocols::parser::BluePrint::resnum_

private

residue number of each position in blueprint

Referenced by read_blueprint_stream(), and resnum().

std::map< core::Size, core::Size > protocols::parser::BluePrint::resnum_map_

private

translate pose residue number to blueprint residue number

Referenced by read_blueprint_stream(), and resnum_map().

String protocols::parser::BluePrint::secstruct_

private

amino acid sequence defined in blueprint

Referenced by read_blueprint_stream(), and secstruct().

String protocols::parser::BluePrint::sequence_

private

sequence defined in blueprint

Referenced by read_blueprint_stream(), and sequence().

utility::vector1< char > protocols::parser::BluePrint::sstype_

private

secondary structure type defined in blueprint

Referenced by read_blueprint_stream(), and secstruct().

String protocols::parser::BluePrint::strand_pairings_

private

secondary structure information

strand pairings defined at the line of SSPAIR in blueprint

Referenced by read_blueprint_stream(), and strand_pairings().

core::Size protocols::parser::BluePrint::total_residue_

private

set strand pairings removed StrandPairings set_strand_pairings( SS_Info2_OP const & ssinfo, StrandPairings const & spairs ) const;

total residue number defined in blueprint

Referenced by read_blueprint_stream(), set_movemap(), and total_residue().

core::Size protocols::parser::BluePrint::total_residue_wolig_

private

total residue without ligand

Referenced by read_blueprint_stream(), and total_residue_wolig().

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

src/protocols/parser/BluePrint.hh
src/protocols/parser/BluePrint.cc

Public Types

Public Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation