protocols::comparative_modeling::AlignmentClustering Class Reference

#include <AlignmentClustering.hh>

Inheritance diagram for protocols::comparative_modeling::AlignmentClustering:

Collaboration diagram for protocols::comparative_modeling::AlignmentClustering:

Public Member Functions
	AlignmentClustering ()
virtual	~AlignmentClustering ()
	Deletes AlignmentClustering object More...

Private Member Functions
vector1< AlignmentClusterOP >	cluster (vector1< vector1< Real > > &gdtmms, vector1< SequenceAlignment > &rankedAlignments, Real threshold_gdt)
	Does the clustering More...
map< string, Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
	gathers the poses More...
vector1< SequenceAlignment >	generateRankedAlignments (map< string, SequenceAlignment > &alns, Real THRESHOLD_FOR_E_VAL)
	gets the aligment from file and ranks them. Some models do not have e-vals in ev_map because thy are too far down in ranking. As long as 10 models are in the hh_map or ev_map the ranking comes from there. More...

Detailed Description

Definition at line 65 of file AlignmentClustering.hh.

Constructor & Destructor Documentation

protocols::comparative_modeling::AlignmentClustering::AlignmentClustering

(

)

creates an alignment clustering object, this is in charge of clustering

Definition at line 170 of file AlignmentClustering.cc.

References core::sequence::align_poses_naive(), protocols::comparative_modeling::PartialThreadingMover::apply(), core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), protocols::abinitio::filename(), protocols::comparative_modeling::gather_coords(), core::pose::make_pose_from_sequence(), core::scoring::packstat::overlap(), protocols::comparative_modeling::poses_from_cmd_line(), core::sequence::read_aln(), core::sequence::read_fasta_file(), core::chemical::rsd_set_from_cmd_line(), core::pose::Pose::total_residue(), tr(), and core::scoring::xyz_gdtmm().

protocols::comparative_modeling::AlignmentClustering::~AlignmentClustering ( )

virtual

Deletes AlignmentClustering object

Definition at line 368 of file AlignmentClustering.cc.

Member Function Documentation

vector1< AlignmentClusterOP > protocols::comparative_modeling::AlignmentClustering::cluster ( vector1< vector1< Real > > &  gdtmms, vector1< SequenceAlignment > &  rankedAlignments, Real  threshold_gdt  )

private

Does the clustering

Definition at line 373 of file AlignmentClustering.cc.

vector1< SequenceAlignment > protocols::comparative_modeling::AlignmentClustering::generateRankedAlignments ( map< string, SequenceAlignment > &  alns, Real  THRESHOLD_FOR_E_VAL  )

private

gets the aligment from file and ranks them. Some models do not have e-vals in ev_map because thy are too far down in ranking. As long as 10 models are in the hh_map or ev_map the ranking comes from there.

Definition at line 437 of file AlignmentClustering.cc.

References protocols::swa::rna::file_exists(), protocols::abinitio::filename(), and tr().

map< string, Pose > protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line ( utility::vector1< std::string > const &  fn_list)

private

gathers the poses

Definition at line 414 of file AlignmentClustering.cc.

References core::sequence::end, protocols::swa::rna::file_exists(), core::import_pose::pose_from_pdb(), and core::chemical::rsd_set_from_cmd_line().

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

• src/protocols/comparative_modeling/AlignmentClustering.hh
• src/protocols/comparative_modeling/AlignmentClustering.cc