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Namespaces | Functions
cm Namespace Reference

Namespaces

 hybridize
 
 sanitize
 

Functions

BooleanOptionKey const cm ("cm")
 
BooleanOptionKey const start_models_only ("cm:start_models_only")
 
StringOptionKey const aln_format ("cm:aln_format")
 
BooleanOptionKey const recover_side_chains ("cm:recover_side_chains")
 
FileVectorOptionKey const steal_extra_residues ("cm:steal_extra_residues")
 
StringOptionKey const loop_mover ("cm:loop_mover")
 
IntegerOptionKey const loop_close_level ("cm:loop_close_level")
 
IntegerOptionKey const min_loop_size ("cm:min_loop_size")
 
IntegerOptionKey const max_loop_rebuild ("cm:max_loop_rebuild")
 
RealOptionKey const loop_rebuild_filter ("cm:loop_rebuild_filter")
 
RealOptionKey const aln_length_filter_quantile ("cm:aln_length_filter_quantile")
 
IntegerOptionKey const aln_length_filter ("cm:aln_length_filter")
 
StringVectorOptionKey const seq_score ("cm:seq_score")
 
StringOptionKey const aligner ("cm:aligner")
 
RealOptionKey const min_gap_open ("cm:min_gap_open")
 
RealOptionKey const max_gap_open ("cm:max_gap_open")
 
RealOptionKey const min_gap_extend ("cm:min_gap_extend")
 
RealOptionKey const max_gap_extend ("cm:max_gap_extend")
 
IntegerOptionKey const nn ("cm:nn")
 
FileVectorOptionKey const ev_map ("cm:ev_map")
 
FileVectorOptionKey const hh_map ("cm:hh_map")
 
IntegerVectorOptionKey const seeds ("cm:seeds")
 
IntegerOptionKey const nremain_reset ("cm:nremain_reset")
 
RealVectorOptionKey const quota_per_silent ("cm:quota_per_silent")
 
RealOptionKey const similarity_cut ("cm:similarity_cut")
 
RealOptionKey const similarity_limit ("cm:similarity_limit")
 
RealOptionKey const refsimilarity_cut ("cm:refsimilarity_cut")
 

Function Documentation

StringOptionKey const cm::aligner ( "cm:aligner"  )
StringOptionKey const cm::aln_format ( "cm:aln_format"  )

Referenced by main().

IntegerOptionKey const cm::aln_length_filter ( "cm:aln_length_filter"  )
RealOptionKey const cm::aln_length_filter_quantile ( "cm:aln_length_filter_quantile"  )
BooleanOptionKey const cm::cm ( "cm"  )
FileVectorOptionKey const cm::ev_map ( "cm:ev_map"  )
FileVectorOptionKey const cm::hh_map ( "cm:hh_map"  )
IntegerOptionKey const cm::loop_close_level ( "cm:loop_close_level"  )
StringOptionKey const cm::loop_mover ( "cm:loop_mover"  )
RealOptionKey const cm::loop_rebuild_filter ( "cm:loop_rebuild_filter"  )
RealOptionKey const cm::max_gap_extend ( "cm:max_gap_extend"  )
RealOptionKey const cm::max_gap_open ( "cm:max_gap_open"  )
IntegerOptionKey const cm::max_loop_rebuild ( "cm:max_loop_rebuild"  )
RealOptionKey const cm::min_gap_extend ( "cm:min_gap_extend"  )

Referenced by main().

RealOptionKey const cm::min_gap_open ( "cm:min_gap_open"  )

Referenced by main().

IntegerOptionKey const cm::min_loop_size ( "cm:min_loop_size"  )
IntegerOptionKey const cm::nn ( "cm:nn"  )
IntegerOptionKey const cm::nremain_reset ( "cm:nremain_reset"  )
RealVectorOptionKey const cm::quota_per_silent ( "cm:quota_per_silent"  )
BooleanOptionKey const cm::recover_side_chains ( "cm:recover_side_chains"  )
RealOptionKey const cm::refsimilarity_cut ( "cm:refsimilarity_cut"  )
IntegerVectorOptionKey const cm::seeds ( "cm:seeds"  )
StringVectorOptionKey const cm::seq_score ( "cm:seq_score"  )

Referenced by main().

RealOptionKey const cm::similarity_cut ( "cm:similarity_cut"  )

Referenced by calc_rmsf_and_avrg().

RealOptionKey const cm::similarity_limit ( "cm:similarity_limit"  )
BooleanOptionKey const cm::start_models_only ( "cm:start_models_only"  )
FileVectorOptionKey const cm::steal_extra_residues ( "cm:steal_extra_residues"  )