frags Namespace Reference

Namespaces
	ABEGO
	contacts
	nonlocal
	picking
	scoring

Functions
BooleanOptionKey const	frags ("frags")
IntegerOptionKey const	j ("frags:j")
BooleanOptionKey const	filter_JC ("frags:filter_JC")
BooleanOptionKey const	bounded_protocol ("frags:bounded_protocol")
BooleanOptionKey const	keep_all_protocol ("frags:keep_all_protocol")
BooleanOptionKey const	quota_protocol ("frags:quota_protocol")
BooleanOptionKey const	nonlocal_pairs ("frags:nonlocal_pairs")
BooleanOptionKey const	fragment_contacts ("frags:fragment_contacts")
BooleanOptionKey const	p_value_selection ("frags:p_value_selection")
IntegerOptionKey const	n_frags ("frags:n_frags")
FileOptionKey const	allowed_pdb ("frags:allowed_pdb")
StringVectorOptionKey const	ss_pred ("frags:ss_pred")
FileOptionKey const	spine_x ("frags:spine_x")
FileOptionKey const	depth ("frags:depth")
FileOptionKey const	denied_pdb ("frags:denied_pdb")
IntegerVectorOptionKey const	frag_sizes ("frags:frag_sizes")
BooleanOptionKey const	write_ca_coordinates ("frags:write_ca_coordinates")
BooleanOptionKey const	write_scores ("frags:write_scores")
BooleanOptionKey const	annotate ("frags:annotate")
IntegerOptionKey const	nr_large_copies ("frags:nr_large_copies")
IntegerOptionKey const	n_candidates ("frags:n_candidates")
BooleanOptionKey const	write_rama_tables ("frags:write_rama_tables")
RealOptionKey const	rama_C ("frags:rama_C")
RealOptionKey const	rama_B ("frags:rama_B")
RealOptionKey const	sigmoid_cs_A ("frags:sigmoid_cs_A")
RealOptionKey const	sigmoid_cs_B ("frags:sigmoid_cs_B")
RealOptionKey const	seqsim_H ("frags:seqsim_H")
RealOptionKey const	seqsim_E ("frags:seqsim_E")
RealOptionKey const	seqsim_L ("frags:seqsim_L")
RealOptionKey const	rama_norm ("frags:rama_norm")
StringOptionKey const	describe_fragments ("frags:describe_fragments")
RealOptionKey const	picking_old_max_score ("frags:picking_old_max_score")
BooleanOptionKey const	write_sequence_only ("frags:write_sequence_only")
BooleanOptionKey const	output_silent ("frags:output_silent")
BooleanOptionKey const	output_index ("frags:output_index")
BooleanOptionKey const	score_output_silent ("frags:score_output_silent")

Function Documentation

allowed_pdb()

FileOptionKey const frags::allowed_pdb

(

"frags:allowed_pdb"

)

Referenced by main(), and register_options().

annotate()

BooleanOptionKey const frags::annotate

(

"frags:annotate"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and register_options_broker().

bounded_protocol()

BooleanOptionKey const frags::bounded_protocol

(

"frags:bounded_protocol"

)

Referenced by main(), and register_options().

denied_pdb()

FileOptionKey const frags::denied_pdb

(

"frags:denied_pdb"

)

Referenced by main(), and register_options().

depth()

FileOptionKey const frags::depth

(

"frags:depth"

)

describe_fragments()

StringOptionKey const frags::describe_fragments

(

"frags:describe_fragments"

)

Referenced by main(), and register_options().

filter_JC()

BooleanOptionKey const frags::filter_JC

(

"frags:filter_JC"

)

frag_sizes()

IntegerVectorOptionKey const frags::frag_sizes

(

"frags:frag_sizes"

)

Referenced by main(), and register_options().

fragment_contacts()

BooleanOptionKey const frags::fragment_contacts

(

"frags:fragment_contacts"

)

frags()

BooleanOptionKey const frags::frags

(

"frags"

)

j()

IntegerOptionKey const frags::j

(

"frags:j"

)

Referenced by register_options().

keep_all_protocol()

BooleanOptionKey const frags::keep_all_protocol

(

"frags:keep_all_protocol"

)

Referenced by main(), and register_options().

n_candidates()

IntegerOptionKey const frags::n_candidates

(

"frags:n_candidates"

)

Referenced by main(), PickSSE::PickSSE(), and register_options().

n_frags()

IntegerOptionKey const frags::n_frags

(

"frags:n_frags"

)

Referenced by main(), PickSSE::PickSSE(), and register_options().

nonlocal_pairs()

BooleanOptionKey const frags::nonlocal_pairs

(

"frags:nonlocal_pairs"

)

Referenced by register_options().

nr_large_copies()

IntegerOptionKey const frags::nr_large_copies

(

"frags:nr_large_copies"

)

Referenced by protocols::abinitio::JumpSpecificAbrelax::register_options(), and register_options_broker().

output_index()

BooleanOptionKey const frags::output_index

(

"frags:output_index"

)

output_silent()

BooleanOptionKey const frags::output_silent

(

"frags:output_silent"

)

p_value_selection()

BooleanOptionKey const frags::p_value_selection

(

"frags:p_value_selection"

)

Referenced by main().

picking_old_max_score()

RealOptionKey const frags::picking_old_max_score

(

"frags:picking_old_max_score"

)

quota_protocol()

BooleanOptionKey const frags::quota_protocol

(

"frags:quota_protocol"

)

Referenced by main(), and register_options().

rama_B()

RealOptionKey const frags::rama_B

(

"frags:rama_B"

)

rama_C()

RealOptionKey const frags::rama_C

(

"frags:rama_C"

)

rama_norm()

RealOptionKey const frags::rama_norm

(

"frags:rama_norm"

)

score_output_silent()

BooleanOptionKey const frags::score_output_silent

(

"frags:score_output_silent"

)

seqsim_E()

RealOptionKey const frags::seqsim_E

(

"frags:seqsim_E"

)

seqsim_H()

RealOptionKey const frags::seqsim_H

(

"frags:seqsim_H"

)

seqsim_L()

RealOptionKey const frags::seqsim_L

(

"frags:seqsim_L"

)

sigmoid_cs_A()

RealOptionKey const frags::sigmoid_cs_A

(

"frags:sigmoid_cs_A"

)

sigmoid_cs_B()

RealOptionKey const frags::sigmoid_cs_B

(

"frags:sigmoid_cs_B"

)

spine_x()

FileOptionKey const frags::spine_x

(

"frags:spine_x"

)

ss_pred()

StringVectorOptionKey const frags::ss_pred

(

"frags:ss_pred"

)

Referenced by main(), and register_options().

write_ca_coordinates()

BooleanOptionKey const frags::write_ca_coordinates

(

"frags:write_ca_coordinates"

)

Referenced by main(), and register_options().

write_rama_tables()

BooleanOptionKey const frags::write_rama_tables

(

"frags:write_rama_tables"

)

write_scores()

BooleanOptionKey const frags::write_scores

(

"frags:write_scores"

)

write_sequence_only()

BooleanOptionKey const frags::write_sequence_only

(

"frags:write_sequence_only"

)