#include <BluePrint.hh>

Inheritance diagram for protocols::jd2::parser::BluePrint:

Collaboration diagram for protocols::jd2::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...

virtual	~BluePrint ()
	destructor More...

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

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

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 (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 (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 (Size seqpos) const
	secondary structure at a position in blueprint file More...

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

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

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

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

String	insertion (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...

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

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< 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< Size, 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...

Detailed Description

Definition at line 40 of file BluePrint.hh.

Member Typedef Documentation

typedef core::kinematics::MoveMapOP protocols::jd2::parser::BluePrint::MoveMapOP

Definition at line 48 of file BluePrint.hh.

typedef core::pose::Pose protocols::jd2::parser::BluePrint::Pose

Definition at line 47 of file BluePrint.hh.

typedef core::Real protocols::jd2::parser::BluePrint::Real

Definition at line 46 of file BluePrint.hh.

typedef core::Size protocols::jd2::parser::BluePrint::Size

Definition at line 45 of file BluePrint.hh.

typedef std::string protocols::jd2::parser::BluePrint::String

Definition at line 44 of file BluePrint.hh.

Constructor & Destructor Documentation

protocols::jd2::parser::BluePrint::BluePrint ( )

default constructor

Definition at line 43 of file BluePrint.cc.

protocols::jd2::parser::BluePrint::BluePrint ( String const & filename)

value constructor

Definition at line 55 of file BluePrint.cc.

References read_blueprint(), and protocols::jd2::parser::TR().

protocols::jd2::parser::BluePrint::~BluePrint ( )

virtual

destructor

Definition at line 72 of file BluePrint.cc.

protocols::jd2::parser::BluePrint::BluePrint ( BluePrint const & rval)

copy constructor

Definition at line 77 of file BluePrint.cc.

Member Function Documentation

utility::vector1< BluePrint::String > protocols::jd2::parser::BluePrint::abego ( ) const

abego defined in bludprint file

abego defined in blueprint file

Definition at line 137 of file BluePrint.cc.

References abego_.

Referenced by read_blueprint().

BluePrint::String protocols::jd2::parser::BluePrint::abego ( core::Size seqpos) const

secondary structure at a position in blueprint file

abego defined in blueprint file

Definition at line 144 of file BluePrint.cc.

References abego_.

char protocols::jd2::parser::BluePrint::buildtype ( core::Size seqpos) const

return build type at each position

build type at each position in blueprint

Definition at line 185 of file BluePrint.cc.

References buildtype_.

Referenced by set_movemap().

BluePrint::String protocols::jd2::parser::BluePrint::extra ( core::Size seqpos) const

return build type at each position

build type at each position in blueprint

Definition at line 193 of file BluePrint.cc.

References extra_.

Referenced by read_blueprint().

BluePrint::String protocols::jd2::parser::BluePrint::helix_pairings ( ) const

helix pairings defined at the line of HHPAIR in blueprint

Definition at line 218 of file BluePrint.cc.

References helix_pairings_.

BluePrint::String protocols::jd2::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

Definition at line 226 of file BluePrint.cc.

References hss_triplets_.

void protocols::jd2::parser::BluePrint::insert_ss_into_pose ( Pose & pose)

set secondary structure into pose

Definition at line 419 of file BluePrint.cc.

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

BluePrint::String protocols::jd2::parser::BluePrint::insertion ( core::Size i) const

build type at each position in blueprint

Definition at line 201 of file BluePrint.cc.

References insertion_.

bool protocols::jd2::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

Definition at line 242 of file BluePrint.cc.

References abego(), abego_, buildtype_, extra(), extra_, helix_pairings_, hss_triplets_, insertion_, resname_, resnum_, resnum_map_, secstruct_, sequence_, core::io::pdb::split(), sstype_, strand_pairings_, core::util::ABEGOManager::symbol2index(), total_residue(), total_residue_, total_residue_wolig_, and protocols::jd2::parser::TR().

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

BluePrint::Size protocols::jd2::parser::BluePrint::resnum ( core::Size seqpos) const

residue number at each position in blueprint file

residue number of each position in blueprint file

Definition at line 161 of file BluePrint.cc.

References buildtype_, and resnum_.

BluePrint::Size protocols::jd2::parser::BluePrint::resnum_map ( Size resnum_pose) const

translate residue number of pose to that of blueprint file

Definition at line 170 of file BluePrint.cc.

References resnum_map_.

Referenced by insert_ss_into_pose().

BluePrint::String protocols::jd2::parser::BluePrint::secstruct ( ) const

secondary structures defined in blueprint file

Definition at line 130 of file BluePrint.cc.

References secstruct_.

Referenced by insert_ss_into_pose(), protocols::fldsgn::MatchResidues::parse_my_tag(), protocols::fldsgn::filters::HelixKinkFilter::parse_my_tag(), protocols::fldsgn::filters::InterlockingAromaFilter::parse_my_tag(), and protocols::fldsgn::filters::SheetTopologyFilter::parse_my_tag().

char protocols::jd2::parser::BluePrint::secstruct ( core::Size seqpos) const

secondary structure at a position in blueprint file

Definition at line 152 of file BluePrint.cc.

References buildtype_, and sstype_.

BluePrint::String protocols::jd2::parser::BluePrint::sequence ( ) const

sequence defined in blueprint file

Definition at line 113 of file BluePrint.cc.

References sequence_.

char protocols::jd2::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

Definition at line 121 of file BluePrint.cc.

References resname_.

void protocols::jd2::parser::BluePrint::set_movemap ( MoveMapOP & movemap)

set movemap based on blueprint

Definition at line 392 of file BluePrint.cc.

References buildtype(), total_residue_, and protocols::jd2::parser::TR().

BluePrint::String protocols::jd2::parser::BluePrint::strand_pairings ( ) const

strand pairings defined at the line of SSPAIR in blueprint

Definition at line 210 of file BluePrint.cc.

References strand_pairings_.

Referenced by protocols::fldsgn::filters::SheetTopologyFilter::parse_my_tag().

BluePrint::Size protocols::jd2::parser::BluePrint::total_residue ( ) const

total residue number defined in blueprint file

Definition at line 97 of file BluePrint.cc.

References total_residue_.

Referenced by read_blueprint().

BluePrint::Size protocols::jd2::parser::BluePrint::total_residue_wolig ( ) const

total residue number without ligand defined in blueprint file

total residue number defined in blueprint file

Definition at line 105 of file BluePrint.cc.

References total_residue_wolig_.

Member Data Documentation

utility::vector1< String > protocols::jd2::parser::BluePrint::abego_

private

abego type defined in blueprint

Definition at line 164 of file BluePrint.hh.

Referenced by abego(), and read_blueprint().

utility::vector1< char > protocols::jd2::parser::BluePrint::buildtype_

private

build type at each position in blueprint

Definition at line 167 of file BluePrint.hh.

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

utility::vector1< String > protocols::jd2::parser::BluePrint::extra_

private

extra infomation at each position in blueprint

Definition at line 170 of file BluePrint.hh.

Referenced by extra(), and read_blueprint().

String protocols::jd2::parser::BluePrint::helix_pairings_

private

helix pairings defined at the line of HHPAIR in blueprint

Definition at line 185 of file BluePrint.hh.

Referenced by helix_pairings(), and read_blueprint().

String protocols::jd2::parser::BluePrint::hss_triplets_

private

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

Definition at line 188 of file BluePrint.hh.

Referenced by hss_triplets(), and read_blueprint().

utility::vector1< String > protocols::jd2::parser::BluePrint::insertion_

private

pdb file name for insertion

Definition at line 173 of file BluePrint.hh.

Referenced by insertion(), and read_blueprint().

utility::vector1< char > protocols::jd2::parser::BluePrint::resname_

private

amino acid type at a position in blueprint

Definition at line 158 of file BluePrint.hh.

Referenced by read_blueprint(), and sequence().

utility::vector1< Size > protocols::jd2::parser::BluePrint::resnum_

private

residue number of each position in blueprint

Definition at line 155 of file BluePrint.hh.

Referenced by read_blueprint(), and resnum().

std::map< Size, Size > protocols::jd2::parser::BluePrint::resnum_map_

private

translate pose residue number to blueprint residue number

Definition at line 176 of file BluePrint.hh.

Referenced by read_blueprint(), and resnum_map().

String protocols::jd2::parser::BluePrint::secstruct_

private

amino acid sequence defined in blueprint

Definition at line 152 of file BluePrint.hh.

Referenced by read_blueprint(), and secstruct().

String protocols::jd2::parser::BluePrint::sequence_

private

sequence defined in blueprint

Definition at line 149 of file BluePrint.hh.

Referenced by read_blueprint(), and sequence().

utility::vector1< char > protocols::jd2::parser::BluePrint::sstype_

private

secondary structure type defined in blueprint

Definition at line 161 of file BluePrint.hh.

Referenced by read_blueprint(), and secstruct().

String protocols::jd2::parser::BluePrint::strand_pairings_

private

secondary structure information

strand pairings defined at the line of SSPAIR in blueprint

Definition at line 182 of file BluePrint.hh.

Referenced by read_blueprint(), and strand_pairings().

Size protocols::jd2::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

Definition at line 143 of file BluePrint.hh.

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

Size protocols::jd2::parser::BluePrint::total_residue_wolig_

private

total residue without ligand

Definition at line 146 of file BluePrint.hh.

Referenced by read_blueprint(), and total_residue_wolig().

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

src/protocols/jd2/parser/BluePrint.hh
src/protocols/jd2/parser/BluePrint.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation