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Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::star::Extender Class Reference

#include <Extender.hh>

Inheritance diagram for protocols::star::Extender:
Inheritance graph
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Public Member Functions

 Extender (core::sequence::SequenceAlignmentCOP alignment, int num_residues)
 
void extend_unaligned (core::pose::Pose *pose)
 
protocols::loops::LoopsCOP unaligned () const
 Returns the unaligned regions in increasing order of start position. More...
 
protocols::loops::LoopsCOP aligned () const
 Returns the aligned regions in increasing order of start position. More...
 
const utility::vector1< int > & cutpoints () const
 Returns a set of suggested cutpoints for star fold tree construction based on information gathered during extend_unaligned(). More...
 
void set_secondary_structure (core::fragment::SecondaryStructureCOP pred_ss)
 Updates predicted secondary structure, improving cutpoint selection. More...
 

Protected Member Functions

int choose_cutpoint (int start, int stop) const
 

Private Attributes

core::sequence::SequenceAlignmentCOP alignment_
 
protocols::loops::LoopsOP unaligned_
 
protocols::loops::LoopsOP aligned_
 
core::fragment::SecondaryStructureCOP pred_ss_
 
utility::vector1< int > cutpoints_
 

Constructor & Destructor Documentation

protocols::star::Extender::Extender ( core::sequence::SequenceAlignmentCOP  alignment,
int  num_residues 
)

Member Function Documentation

protocols::loops::LoopsCOP protocols::star::Extender::aligned ( ) const
inline

Returns the aligned regions in increasing order of start position.

References aligned_.

int protocols::star::Extender::choose_cutpoint ( int  start,
int  stop 
) const
protected

Selects a cutpoint on the closed interval [start, stop] using weighted reservoir sampling. Each residue's weight is proportional to its likelihood of being a loop.

References pred_ss_, and protocols::loops::stop.

Referenced by extend_unaligned().

const utility::vector1<int>& protocols::star::Extender::cutpoints ( ) const
inline

Returns a set of suggested cutpoints for star fold tree construction based on information gathered during extend_unaligned().

References cutpoints_.

void protocols::star::Extender::extend_unaligned ( core::pose::Pose pose)

Sets unaligned residues' torsion angles to their extended values and idealizes bond lengths and angles. The placement of unaligned residues depends on the number of residues separating the adjacent aligned regions.

Given aligned regions a_1 and a_2 with (a_1.start < a_2.start):

If (a_2.start - a_1.stop) <= -abinitio:star:short_loop_len, the unaligned residues are grown off a_1.stop. Otherwise, a stochastically selected portion of the residues are grown off a_1.stop and the remainder grown off a_2.start. In both cases, the method is responsible for noting the interior cutpoints it selected.

References core::kinematics::FoldTree::add_edge(), aligned_, core::scoring::calpha_superimpose_pose(), choose_cutpoint(), core::pose::Pose::conformation(), protocols::star::copy_residues(), cutpoints_, core::pose::Pose::fold_tree(), protocols::star::generate_extended_pose(), core::conformation::idealize_position(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::sequence(), core::pose::Pose::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

void protocols::star::Extender::set_secondary_structure ( core::fragment::SecondaryStructureCOP  pred_ss)
inline

Updates predicted secondary structure, improving cutpoint selection.

References pred_ss_.

Referenced by protocols::star::StarAbinitio::apply().

protocols::loops::LoopsCOP protocols::star::Extender::unaligned ( ) const
inline

Returns the unaligned regions in increasing order of start position.

References unaligned_.

Member Data Documentation

protocols::loops::LoopsOP protocols::star::Extender::aligned_
private

Referenced by aligned(), extend_unaligned(), and Extender().

core::sequence::SequenceAlignmentCOP protocols::star::Extender::alignment_
private
utility::vector1<int> protocols::star::Extender::cutpoints_
private

Referenced by cutpoints(), and extend_unaligned().

core::fragment::SecondaryStructureCOP protocols::star::Extender::pred_ss_
private
protocols::loops::LoopsOP protocols::star::Extender::unaligned_
private

Referenced by Extender(), and unaligned().


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