protocols::jd2::parser::FragmentReader Class Reference

#include <FragmentReader.hh>

Inheritance diagram for protocols::jd2::parser::FragmentReader:

Collaboration diagram for protocols::jd2::parser::FragmentReader:

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::TagPtr	TagPtr

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

Private Member Functions
void	parse_tag (TagPtr 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

typedef core::fragment::FragSetOP protocols::jd2::parser::FragmentReader::FragSetOP

typedef utility::pointer::ReferenceCount protocols::jd2::parser::FragmentReader::Parent

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

typedef core::Size protocols::jd2::parser::FragmentReader::Size

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

typedef utility::tag::Tag protocols::jd2::parser::FragmentReader::Tag

typedef utility::tag::TagPtr protocols::jd2::parser::FragmentReader::TagPtr

Constructor & Destructor Documentation

protocols::jd2::parser::FragmentReader::FragmentReader

(

)

default constructor

protocols::jd2::parser::FragmentReader::FragmentReader

(

TagPtr 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)

main opeartion

References aa_, begin_, blueprint_, core::pack::dunbrack::c, core::chemical::CENTROID, core::import_pose::centroid_pose_from_pdb(), core::sequence::end, end_, protocols::abinitio::filename(), filename_, frag_size_, core::chemical::ChemicalManager::get_instance(), nfrags_, core::fragment::picking_old::vall::pick_fragments(), core::fragment::picking_old::vall::pick_fragments_by_ss(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), read_type_, core::chemical::ChemicalManager::residue_type_set(), set_fragments(), ss_, steal_times_, core::pose::Pose::total_residue(), protocols::jd2::parser::TR(), and use_abego_.

void protocols::jd2::parser::FragmentReader::parse_tag ( TagPtr const &  tag)

private

parse tag

References aa_, begin_, blueprint_, end_, filename_, frag_size_, nfrags_, read_type_, ss_, steal_times_, protocols::jd2::parser::TR(), and use_abego_.

Referenced by FragmentReader().

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().

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

• src/protocols/jd2/parser/FragmentReader.hh
• src/protocols/jd2/parser/FragmentReader.cc