Rosetta 3.4
Public Member Functions | Protected Member Functions
protocols::star::Extender Class Reference

#include <Extender.hh>

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List of all members.

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

Protected Member Functions

int choose_cutpoint (int start, int stop) const

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.

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.

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().

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(), core::scoring::calpha_superimpose_pose(), choose_cutpoint(), core::pose::Pose::conformation(), protocols::star::copy_residues(), core::pose::Pose::fold_tree(), protocols::star::generate_extended_pose(), core::conformation::idealize_position(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::sequence(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::total_residue().

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

Updates predicted secondary structure, improving cutpoint selection.

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.


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