cm Namespace Reference

Namespaces
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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

aligner()

StringOptionKey const cm::aligner

(

"cm:aligner"

)

aln_format()

StringOptionKey const cm::aln_format

(

"cm:aln_format"

)

Referenced by input_alignments(), input_alignmentsMapped(), and main().

aln_length_filter()

IntegerOptionKey const cm::aln_length_filter

(

"cm:aln_length_filter"

)

Referenced by main().

aln_length_filter_quantile()

RealOptionKey const cm::aln_length_filter_quantile

(

"cm:aln_length_filter_quantile"

)

Referenced by main().

cm()

BooleanOptionKey const cm::cm

(

"cm"

)

ev_map()

FileVectorOptionKey const cm::ev_map

(

"cm:ev_map"

)

Referenced by generateRankedAlignments().

hh_map()

FileVectorOptionKey const cm::hh_map

(

"cm:hh_map"

)

Referenced by generateRankedAlignments().

loop_close_level()

IntegerOptionKey const cm::loop_close_level

(

"cm:loop_close_level"

)

loop_mover()

StringOptionKey const cm::loop_mover

(

"cm:loop_mover"

)

loop_rebuild_filter()

RealOptionKey const cm::loop_rebuild_filter

(

"cm:loop_rebuild_filter"

)

max_gap_extend()

RealOptionKey const cm::max_gap_extend

(

"cm:max_gap_extend"

)

max_gap_open()

RealOptionKey const cm::max_gap_open

(

"cm:max_gap_open"

)

max_loop_rebuild()

IntegerOptionKey const cm::max_loop_rebuild

(

"cm:max_loop_rebuild"

)

min_gap_extend()

RealOptionKey const cm::min_gap_extend

(

"cm:min_gap_extend"

)

Referenced by main().

min_gap_open()

RealOptionKey const cm::min_gap_open

(

"cm:min_gap_open"

)

Referenced by main().

min_loop_size()

IntegerOptionKey const cm::min_loop_size

(

"cm:min_loop_size"

)

Referenced by main().

nn()

IntegerOptionKey const cm::nn

(

"cm:nn"

)

Referenced by main().

nremain_reset()

IntegerOptionKey const cm::nremain_reset

(

"cm:nremain_reset"

)

quota_per_silent()

RealVectorOptionKey const cm::quota_per_silent

(

"cm:quota_per_silent"

)

recover_side_chains()

BooleanOptionKey const cm::recover_side_chains

(

"cm:recover_side_chains"

)

refsimilarity_cut()

RealOptionKey const cm::refsimilarity_cut

(

"cm:refsimilarity_cut"

)

seeds()

IntegerVectorOptionKey const cm::seeds

(

"cm:seeds"

)

seq_score()

StringVectorOptionKey const cm::seq_score

(

"cm:seq_score"

)

Referenced by main().

similarity_cut()

RealOptionKey const cm::similarity_cut

(

"cm:similarity_cut"

)

Referenced by calc_rmsf_and_avrg().

similarity_limit()

RealOptionKey const cm::similarity_limit

(

"cm:similarity_limit"

)

start_models_only()

BooleanOptionKey const cm::start_models_only

(

"cm:start_models_only"

)

steal_extra_residues()

FileVectorOptionKey const cm::steal_extra_residues

(

"cm:steal_extra_residues"

)