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Public Types | Public Member Functions | Private Attributes | List of all members
protocols::parser::BluePrint Class Reference

#include <BluePrint.hh>

Inheritance diagram for protocols::parser::BluePrint:
Inheritance graph
[legend]

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< Stringabego () 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::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< core::Size, core::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

◆ MoveMapOP

◆ Pose

◆ Real

◆ Size

◆ String

Constructor & Destructor Documentation

◆ BluePrint() [1/3]

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

default constructor

◆ BluePrint() [2/3]

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

◆ ~BluePrint()

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

destructor

◆ BluePrint() [3/3]

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

copy constructor

Member Function Documentation

◆ abego() [1/2]

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().

◆ abego() [2/2]

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_.

◆ buildtype()

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().

◆ extra()

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().

◆ helix_pairings()

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().

◆ hss_triplets()

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().

◆ insert_ss_into_pose()

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().

◆ insertion()

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

build type at each position in blueprint

References insertion_.

◆ read_blueprint()

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 protocols::abinitio::filename(), read_blueprint_stream(), and protocols::parser::TR().

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

◆ read_blueprint_stream()

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

◆ resnum()

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_.

◆ resnum_map()

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().

◆ secstruct() [1/2]

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

◆ secstruct() [2/2]

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

secondary structure at a position in blueprint file

References buildtype_, and sstype_.

◆ sequence() [1/2]

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

sequence defined in blueprint file

References sequence_.

◆ sequence() [2/2]

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_.

◆ set_movemap()

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

set movemap based on blueprint

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

◆ strand_pairings()

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

◆ total_residue()

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

total residue number defined in blueprint file

References total_residue_.

Referenced by read_blueprint_stream().

◆ total_residue_wolig()

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

◆ abego_

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

abego type defined in blueprint

Referenced by abego(), and read_blueprint_stream().

◆ buildtype_

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

build type at each position in blueprint

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

◆ extra_

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

extra infomation at each position in blueprint

Referenced by extra(), and read_blueprint_stream().

◆ helix_pairings_

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().

◆ hss_triplets_

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().

◆ insertion_

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

pdb file name for insertion

Referenced by insertion(), and read_blueprint_stream().

◆ resname_

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

amino acid type at a position in blueprint

Referenced by read_blueprint_stream(), and sequence().

◆ resnum_

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

residue number of each position in blueprint

Referenced by read_blueprint_stream(), and resnum().

◆ resnum_map_

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().

◆ secstruct_

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

amino acid sequence defined in blueprint

Referenced by read_blueprint_stream(), and secstruct().

◆ sequence_

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

sequence defined in blueprint

Referenced by read_blueprint_stream(), and sequence().

◆ sstype_

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

secondary structure type defined in blueprint

Referenced by read_blueprint_stream(), and secstruct().

◆ strand_pairings_

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().

◆ total_residue_

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().

◆ total_residue_wolig_

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: