basic::options::OptionKeys::frags Namespace Reference

Namespaces
	ABEGO
	contacts
	nonlocal
	picking
	scoring

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

Variable Documentation

allowed_pdb

FileOptionKey const basic::options::OptionKeys::frags::allowed_pdb

extern

annotate

BooleanOptionKey const basic::options::OptionKeys::frags::annotate

extern

Referenced by main(), and protocols::abinitio::JumpSpecificAbrelax::setup_fragments().

bounded_protocol

BooleanOptionKey const basic::options::OptionKeys::frags::bounded_protocol

extern

denied_pdb

FileOptionKey const basic::options::OptionKeys::frags::denied_pdb

extern

depth

FileOptionKey const basic::options::OptionKeys::frags::depth

extern

Referenced by add_vrts(), numeric::kdtree::construct_kd_tree(), numeric::geometry::hashing::SixDOffsetTree::insert(), numeric::geometry::hashing::SixDOffsetTree::lookup(), and main().

describe_fragments

StringOptionKey const basic::options::OptionKeys::frags::describe_fragments

extern

filter_JC

BooleanOptionKey const basic::options::OptionKeys::frags::filter_JC

extern

frag_sizes

IntegerVectorOptionKey const basic::options::OptionKeys::frags::frag_sizes

extern

Referenced by CartRefineWrapperMover::apply(), dna_dr_loop_test(), loop_modeling_test(), loop_rebuilding_test(), main(), and Prepare().

fragment_contacts

BooleanOptionKey const basic::options::OptionKeys::frags::fragment_contacts

extern

frags

BooleanOptionKey const basic::options::OptionKeys::frags::frags

extern

Referenced by cen_fold(), dna_deriv_test(), dna_deriv_test_old(), dna_dr_loop_test(), dna_io_test(), dna_nbr_radii_test(), protocols::jumping::SpecificJumpSetup::generate_jump_frags(), loop_modeling_test(), loop_rebuilding_test(), main(), make_frag_set(), make_frag_set_9mers(), ThisApplication::pick_frags(), DockFragmentsMover::run(), run_pep_prep(), set_fullatom_flag_test(), setup_frags_from_vall(), simple_frag_test(), and simple_loop_modeling_test().

j

IntegerOptionKey const basic::options::OptionKeys::frags::j

extern

keep_all_protocol

BooleanOptionKey const basic::options::OptionKeys::frags::keep_all_protocol

extern

n_candidates

IntegerOptionKey const basic::options::OptionKeys::frags::n_candidates

extern

n_frags

IntegerOptionKey const basic::options::OptionKeys::frags::n_frags

extern

Referenced by main(), SwapElementsMover1::pick_fragments(), SwapElementsMover2::pick_fragments(), pick_fragments(), VarLengthBuildKristin::public_pick_fragments(), and run().

nonlocal_pairs

BooleanOptionKey const basic::options::OptionKeys::frags::nonlocal_pairs

extern

nr_large_copies

IntegerOptionKey const basic::options::OptionKeys::frags::nr_large_copies

extern

Referenced by main(), and protocols::abinitio::JumpSpecificAbrelax::setup_fragments().

output_index

BooleanOptionKey const basic::options::OptionKeys::frags::output_index

extern

output_silent

BooleanOptionKey const basic::options::OptionKeys::frags::output_silent

extern

p_value_selection

BooleanOptionKey const basic::options::OptionKeys::frags::p_value_selection

extern

picking_old_max_score

RealOptionKey const basic::options::OptionKeys::frags::picking_old_max_score

extern

quota_protocol

BooleanOptionKey const basic::options::OptionKeys::frags::quota_protocol

extern

rama_B

RealOptionKey const basic::options::OptionKeys::frags::rama_B

extern

rama_C

RealOptionKey const basic::options::OptionKeys::frags::rama_C

extern

rama_norm

RealOptionKey const basic::options::OptionKeys::frags::rama_norm

extern

score_output_silent

BooleanOptionKey const basic::options::OptionKeys::frags::score_output_silent

extern

seqsim_E

RealOptionKey const basic::options::OptionKeys::frags::seqsim_E

extern

seqsim_H

RealOptionKey const basic::options::OptionKeys::frags::seqsim_H

extern

seqsim_L

RealOptionKey const basic::options::OptionKeys::frags::seqsim_L

extern

sigmoid_cs_A

RealOptionKey const basic::options::OptionKeys::frags::sigmoid_cs_A

extern

sigmoid_cs_B

RealOptionKey const basic::options::OptionKeys::frags::sigmoid_cs_B

extern

spine_x

FileOptionKey const basic::options::OptionKeys::frags::spine_x

extern

ss_pred

StringVectorOptionKey const basic::options::OptionKeys::frags::ss_pred

extern

Referenced by main(), and predict_ss().

write_ca_coordinates

BooleanOptionKey const basic::options::OptionKeys::frags::write_ca_coordinates

extern

write_rama_tables

BooleanOptionKey const basic::options::OptionKeys::frags::write_rama_tables

extern

write_scores

BooleanOptionKey const basic::options::OptionKeys::frags::write_scores

extern

write_sequence_only

BooleanOptionKey const basic::options::OptionKeys::frags::write_sequence_only

extern