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protocols::jd2::parser::BluePrint Class Reference

#include <BluePrint.hh>

Inheritance diagram for protocols::jd2::parser::BluePrint:
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Collaboration diagram for protocols::jd2::parser::BluePrint:
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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< Stringabego () 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< Sizeresnum_
 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< Stringabego_
 abego type defined in blueprint More...
 
utility::vector1< char > buildtype_
 build type at each position in blueprint More...
 
utility::vector1< Stringextra_
 extra infomation at each position in blueprint More...
 
utility::vector1< Stringinsertion_
 pdb file name for insertion More...
 
std::map< Size, Sizeresnum_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

Constructor & Destructor Documentation

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

default constructor

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

value constructor

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

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

destructor

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

copy constructor

Member Function Documentation

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

abego defined in bludprint file

abego defined in blueprint file

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

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

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

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

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

References hss_triplets_.

void protocols::jd2::parser::BluePrint::insert_ss_into_pose ( Pose pose)
BluePrint::String protocols::jd2::parser::BluePrint::insertion ( core::Size  i) const

build type at each position in blueprint

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

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

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

References resnum_map_.

Referenced by insert_ss_into_pose().

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

secondary structure at a position in blueprint file

References buildtype_, and sstype_.

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

sequence defined in blueprint file

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

References resname_.

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

set movemap based on blueprint

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

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

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

References total_residue_wolig_.

Member Data Documentation

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

abego type defined in blueprint

Referenced by abego(), and read_blueprint().

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

build type at each position in blueprint

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

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

extra infomation at each position in blueprint

Referenced by extra(), and read_blueprint().

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

helix pairings defined at the line of HHPAIR in blueprint

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

Referenced by hss_triplets(), and read_blueprint().

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

pdb file name for insertion

Referenced by insertion(), and read_blueprint().

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

amino acid type at a position in blueprint

Referenced by read_blueprint(), and sequence().

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

residue number of each position in blueprint

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

Referenced by read_blueprint(), and resnum_map().

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

amino acid sequence defined in blueprint

Referenced by read_blueprint(), and secstruct().

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

sequence defined in blueprint

Referenced by read_blueprint(), and sequence().

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

secondary structure type defined in blueprint

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

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

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

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

total residue without ligand

Referenced by read_blueprint(), and total_residue_wolig().


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