Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::jd2::parser::FragmentReader Class Reference

#include <FragmentReader.hh>

Public Types

typedef
utility::pointer::ReferenceCount 
Parent
 
typedef core::Size Size
 
typedef std::string String
 
typedef core::pose::Pose Pose
 
typedef core::fragment::FragSetOP FragSetOP
 
typedef utility::tag::Tag Tag
 
typedef utility::tag::TagCOP TagCOP
 

Public Member Functions

 FragmentReader ()
 default constructor More...
 
 FragmentReader (TagCOP const &tag)
 value constructor More...
 
virtual ~FragmentReader ()
 destructor More...
 
void apply (FragSetOP &fragset)
 main opeartion More...
 

Private Member Functions

void parse_tag (TagCOP const &tag)
 parse tag More...
 
void set_fragments (Pose const &pose, FragSetOP const &fragset)
 set fragments just for helper function More...
 

Private Attributes

String read_type_
 way of reading fragments from pdbs, silent, fragfiles, or vall More...
 
String filename_
 input file name, pdbs, silent, fragfiles of vall More...
 
Size frag_size_
 length of fragments More...
 
Size begin_
 the begin of sequence positions where fragments are stealed More...
 
Size end_
 the end of sequence positions where fragments are stealed More...
 
Size steal_times_
 number of stealing fragments if read_type_ is pdbs or silent More...
 
Size nfrags_
 maximum number of fragments when a silent file is used More...
 
String ss_
 secondary structure assignment to pick fragment from vall More...
 
String aa_
 amino acids to pick fragment from vall More...
 
bool use_abego_
 abego assignment to pick fragment from vall More...
 
protocols::jd2::parser::BluePrintOP blueprint_
 blueprint More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jd2::parser::FragmentReader::FragmentReader ( )

default constructor

protocols::jd2::parser::FragmentReader::FragmentReader ( TagCOP const &  tag)

value constructor

References parse_tag().

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

destructor

Member Function Documentation

void protocols::jd2::parser::FragmentReader::apply ( FragSetOP fragset)
void protocols::jd2::parser::FragmentReader::parse_tag ( TagCOP const &  tag)
private
void protocols::jd2::parser::FragmentReader::set_fragments ( Pose const &  pose,
FragSetOP const &  fragset 
)
private

set fragments just for helper function

References begin_, end_, frag_size_, and core::fragment::steal_frag_set_from_pose().

Referenced by apply().

Member Data Documentation

String protocols::jd2::parser::FragmentReader::aa_
private

amino acids to pick fragment from vall

Referenced by apply(), and parse_tag().

Size protocols::jd2::parser::FragmentReader::begin_
private

the begin of sequence positions where fragments are stealed

Referenced by apply(), parse_tag(), and set_fragments().

protocols::jd2::parser::BluePrintOP protocols::jd2::parser::FragmentReader::blueprint_
private

blueprint

Referenced by apply(), and parse_tag().

Size protocols::jd2::parser::FragmentReader::end_
private

the end of sequence positions where fragments are stealed

Referenced by apply(), parse_tag(), and set_fragments().

String protocols::jd2::parser::FragmentReader::filename_
private

input file name, pdbs, silent, fragfiles of vall

Referenced by apply(), and parse_tag().

Size protocols::jd2::parser::FragmentReader::frag_size_
private

length of fragments

Referenced by apply(), parse_tag(), and set_fragments().

Size protocols::jd2::parser::FragmentReader::nfrags_
private

maximum number of fragments when a silent file is used

Referenced by apply(), and parse_tag().

String protocols::jd2::parser::FragmentReader::read_type_
private

way of reading fragments from pdbs, silent, fragfiles, or vall

Referenced by apply(), and parse_tag().

String protocols::jd2::parser::FragmentReader::ss_
private

secondary structure assignment to pick fragment from vall

Referenced by apply(), and parse_tag().

Size protocols::jd2::parser::FragmentReader::steal_times_
private

number of stealing fragments if read_type_ is pdbs or silent

Referenced by apply(), and parse_tag().

bool protocols::jd2::parser::FragmentReader::use_abego_
private

abego assignment to pick fragment from vall

Referenced by apply(), and parse_tag().


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