protocols::comparative_modeling::AlignmentClustering Class Reference

#include <AlignmentClustering.hh>

Inheritance diagram for protocols::comparative_modeling::AlignmentClustering:

Public Member Functions
	AlignmentClustering ()
	~AlignmentClustering () override
	@detail Deletes AlignmentClustering object More...

Private Member Functions
utility::vector1< AlignmentClusterOP >	cluster (utility::vector1< utility::vector1< core::Real > > &gdtmms, utility::vector1< core::sequence::SequenceAlignment > &rankedAlignments, core::Real threshold_gdt)
	@detail Does the clustering More...
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
	@detail gathers the poses More...
utility::vector1< core::sequence::SequenceAlignment >	generateRankedAlignments (std::map< std::string, core::sequence::SequenceAlignment > &alns, core::Real THRESHOLD_FOR_E_VAL)
	@detail 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...

Constructor & Destructor Documentation

AlignmentClustering()

protocols::comparative_modeling::AlignmentClustering::AlignmentClustering

(

)

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

References core::sequence::align_poses_naive(), core::scoring::alignment, 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(), protocols::mean_field::max(), 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::size(), protocols::comparative_modeling::tr(), and core::scoring::xyz_gdtmm().

~AlignmentClustering()

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

overridedefault

@detail Deletes AlignmentClustering object

Member Function Documentation

cluster()

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

private

@detail Does the clustering

generateRankedAlignments()

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

private

@detail 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.

References protocols::abinitio::filename(), and protocols::comparative_modeling::tr().

poses_from_cmd_line()

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

private

@detail gathers the poses

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), 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