Rosetta Utilities  2014.35
Functions | Variables
basic::options::OptionKeys::cm::hybridize Namespace Reference

Functions

BooleanOptionKey const hybridize ("cm:hybridize")
 
FileOptionKey const template_list ("cm:hybridize:template_list")
 
IntegerVectorOptionKey const starting_template ("cm:hybridize:starting_template")
 
BooleanOptionKey const realign_domains ("cm:hybridize:realign_domains")
 
BooleanOptionKey const add_non_init_chunks ("cm:hybridize:add_non_init_chunks")
 
RealOptionKey const stage1_increase_cycles ("cm:hybridize:stage1_increase_cycles")
 
RealOptionKey const stage2_increase_cycles ("cm:hybridize:stage2_increase_cycles")
 
RealOptionKey const stage2min_increase_cycles ("cm:hybridize:stage2min_increase_cycles")
 
RealOptionKey const stage1_probability ("cm:hybridize:stage1_probability")
 
StringOptionKey const stage1_weights ("cm:hybridize:stage1_weights")
 
StringOptionKey const stage1_patch ("cm:hybridize:stage1_patch")
 
BooleanOptionKey const skip_stage2 ("cm:hybridize:skip_stage2")
 
BooleanOptionKey const no_global_frame ("cm:hybridize:no_global_frame")
 
BooleanOptionKey const linmin_only ("cm:hybridize:linmin_only")
 
StringOptionKey const stage2_weights ("cm:hybridize:stage2_weights")
 
StringOptionKey const stage2_patch ("cm:hybridize:stage2_patch")
 
IntegerOptionKey const relax ("cm:hybridize:relax")
 
RealOptionKey const frag_weight_aligned ("cm:hybridize:frag_weight_aligned")
 
IntegerOptionKey const max_registry_shift ("cm:hybridize:max_registry_shift")
 
BooleanOptionKey const alignment_from_template_seqpos ("cm:hybridize:alignment_from_template_seqpos")
 
IntegerVectorOptionKey const alignment_from_chunk_mapping ("cm:hybridize:alignment_from_chunk_mapping")
 
BooleanOptionKey const realign_domains_stage2 ("cm:hybridize:realign_domains_stage2")
 
RealOptionKey const frag_1mer_insertion_weight ("cm:hybridize:frag_1mer_insertion_weight")
 
RealOptionKey const small_frag_insertion_weight ("cm:hybridize:small_frag_insertion_weight")
 
RealOptionKey const big_frag_insertion_weight ("cm:hybridize:big_frag_insertion_weight")
 
BooleanOptionKey const auto_frag_insertion_weight ("cm:hybridize:auto_frag_insertion_weight")
 
IntegerOptionKey const stage1_1_cycles ("cm:hybridize:stage1_1_cycles")
 
IntegerOptionKey const stage1_2_cycles ("cm:hybridize:stage1_2_cycles")
 
IntegerOptionKey const stage1_3_cycles ("cm:hybridize:stage1_3_cycles")
 
IntegerOptionKey const stage1_4_cycles ("cm:hybridize:stage1_4_cycles")
 
RealOptionKey const stage2_temperature ("cm:hybridize:stage2_temperature")
 
StringOptionKey const stage1_4_cenrot_score ("cm:hybridize:stage1_4_cenrot_score")
 

Variables

BooleanOptionKey const hybridize
 
FileOptionKey const template_list
 
IntegerVectorOptionKey const starting_template
 
BooleanOptionKey const realign_domains
 
BooleanOptionKey const add_non_init_chunks
 
RealOptionKey const stage1_increase_cycles
 
RealOptionKey const stage2_increase_cycles
 
RealOptionKey const stage2min_increase_cycles
 
RealOptionKey const stage1_probability
 
StringOptionKey const stage1_weights
 
StringOptionKey const stage1_patch
 
BooleanOptionKey const skip_stage2
 
BooleanOptionKey const no_global_frame
 
BooleanOptionKey const linmin_only
 
StringOptionKey const stage2_weights
 
StringOptionKey const stage2_patch
 
IntegerOptionKey const relax
 
RealOptionKey const frag_weight_aligned
 
IntegerOptionKey const max_registry_shift
 
BooleanOptionKey const alignment_from_template_seqpos
 
IntegerVectorOptionKey const alignment_from_chunk_mapping
 
BooleanOptionKey const realign_domains_stage2
 
RealOptionKey const frag_1mer_insertion_weight
 
RealOptionKey const small_frag_insertion_weight
 
RealOptionKey const big_frag_insertion_weight
 
BooleanOptionKey const auto_frag_insertion_weight
 
IntegerOptionKey const stage1_1_cycles
 
IntegerOptionKey const stage1_2_cycles
 
IntegerOptionKey const stage1_3_cycles
 
IntegerOptionKey const stage1_4_cycles
 
RealOptionKey const stage2_temperature
 
StringOptionKey const stage1_4_cenrot_score
 

Function Documentation

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::add_non_init_chunks ( "cm:hybridize:add_non_init_chunks"  )
IntegerVectorOptionKey const basic::options::OptionKeys::cm::hybridize::alignment_from_chunk_mapping ( "cm:hybridize:alignment_from_chunk_mapping"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::alignment_from_template_seqpos ( "cm:hybridize:alignment_from_template_seqpos"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::auto_frag_insertion_weight ( "cm:hybridize:auto_frag_insertion_weight"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::big_frag_insertion_weight ( "cm:hybridize:big_frag_insertion_weight"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::frag_1mer_insertion_weight ( "cm:hybridize:frag_1mer_insertion_weight"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::frag_weight_aligned ( "cm:hybridize:frag_weight_aligned"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::hybridize ( "cm:hybridize"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::linmin_only ( "cm:hybridize:linmin_only"  )
IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::max_registry_shift ( "cm:hybridize:max_registry_shift"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::no_global_frame ( "cm:hybridize:no_global_frame"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::realign_domains ( "cm:hybridize:realign_domains"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::realign_domains_stage2 ( "cm:hybridize:realign_domains_stage2"  )
IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::relax ( "cm:hybridize:relax"  )
BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::skip_stage2 ( "cm:hybridize:skip_stage2"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::small_frag_insertion_weight ( "cm:hybridize:small_frag_insertion_weight"  )
IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_1_cycles ( "cm:hybridize:stage1_1_cycles"  )
IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_2_cycles ( "cm:hybridize:stage1_2_cycles"  )
IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_3_cycles ( "cm:hybridize:stage1_3_cycles"  )
StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_4_cenrot_score ( "cm:hybridize:stage1_4_cenrot_score"  )
IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_4_cycles ( "cm:hybridize:stage1_4_cycles"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_increase_cycles ( "cm:hybridize:stage1_increase_cycles"  )
StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_patch ( "cm:hybridize:stage1_patch"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_probability ( "cm:hybridize:stage1_probability"  )
StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_weights ( "cm:hybridize:stage1_weights"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_increase_cycles ( "cm:hybridize:stage2_increase_cycles"  )
StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_patch ( "cm:hybridize:stage2_patch"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_temperature ( "cm:hybridize:stage2_temperature"  )
StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_weights ( "cm:hybridize:stage2_weights"  )
RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage2min_increase_cycles ( "cm:hybridize:stage2min_increase_cycles"  )
IntegerVectorOptionKey const basic::options::OptionKeys::cm::hybridize::starting_template ( "cm:hybridize:starting_template"  )
FileOptionKey const basic::options::OptionKeys::cm::hybridize::template_list ( "cm:hybridize:template_list"  )

Variable Documentation

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::add_non_init_chunks("cm:hybridize:add_non_init_chunks")

Referenced by add_rosetta_options_1().

IntegerVectorOptionKey const basic::options::OptionKeys::cm::hybridize::alignment_from_chunk_mapping("cm:hybridize:alignment_from_chunk_mapping")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::alignment_from_template_seqpos("cm:hybridize:alignment_from_template_seqpos")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::auto_frag_insertion_weight("cm:hybridize:auto_frag_insertion_weight")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::big_frag_insertion_weight("cm:hybridize:big_frag_insertion_weight")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::frag_1mer_insertion_weight("cm:hybridize:frag_1mer_insertion_weight")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::frag_weight_aligned("cm:hybridize:frag_weight_aligned")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::hybridize("cm:hybridize")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::linmin_only("cm:hybridize:linmin_only")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::max_registry_shift("cm:hybridize:max_registry_shift")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::no_global_frame("cm:hybridize:no_global_frame")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::realign_domains("cm:hybridize:realign_domains")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::realign_domains_stage2("cm:hybridize:realign_domains_stage2")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::relax("cm:hybridize:relax")

Referenced by add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::cm::hybridize::skip_stage2("cm:hybridize:skip_stage2")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::small_frag_insertion_weight("cm:hybridize:small_frag_insertion_weight")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_1_cycles("cm:hybridize:stage1_1_cycles")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_2_cycles("cm:hybridize:stage1_2_cycles")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_3_cycles("cm:hybridize:stage1_3_cycles")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_4_cenrot_score("cm:hybridize:stage1_4_cenrot_score")

Referenced by add_rosetta_options_1().

IntegerOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_4_cycles("cm:hybridize:stage1_4_cycles")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_increase_cycles("cm:hybridize:stage1_increase_cycles")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_patch("cm:hybridize:stage1_patch")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_probability("cm:hybridize:stage1_probability")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage1_weights("cm:hybridize:stage1_weights")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_increase_cycles("cm:hybridize:stage2_increase_cycles")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_patch("cm:hybridize:stage2_patch")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_temperature("cm:hybridize:stage2_temperature")

Referenced by add_rosetta_options_1().

StringOptionKey const basic::options::OptionKeys::cm::hybridize::stage2_weights("cm:hybridize:stage2_weights")

Referenced by add_rosetta_options_1().

RealOptionKey const basic::options::OptionKeys::cm::hybridize::stage2min_increase_cycles("cm:hybridize:stage2min_increase_cycles")

Referenced by add_rosetta_options_1().

IntegerVectorOptionKey const basic::options::OptionKeys::cm::hybridize::starting_template("cm:hybridize:starting_template")

Referenced by add_rosetta_options_1().

FileOptionKey const basic::options::OptionKeys::cm::hybridize::template_list("cm:hybridize:template_list")

Referenced by add_rosetta_options_1().