lh Namespace Reference

Namespaces
	fragpdb
	symfragrm

Functions
BooleanOptionKey const	lh ("lh")
IntegerVectorOptionKey const	loopsizes ("lh:loopsizes")
IntegerOptionKey const	num_partitions ("lh:num_partitions")
PathOptionKey const	db_path ("lh:db_path")
BooleanOptionKey const	exclude_homo ("lh:exclude_homo")
BooleanOptionKey const	bss ("lh:bss")
StringOptionKey const	refstruct ("lh:refstruct")
StringOptionKey const	homo_file ("lh:homo_file")
RealVectorOptionKey const	createdb_rms_cutoff ("lh:createdb_rms_cutoff")
RealOptionKey const	min_bbrms ("lh:min_bbrms")
RealOptionKey const	max_bbrms ("lh:max_bbrms")
RealOptionKey const	min_rms ("lh:min_rms")
RealOptionKey const	max_rms ("lh:max_rms")
BooleanOptionKey const	filter_by_phipsi ("lh:filter_by_phipsi")
IntegerOptionKey const	max_radius ("lh:max_radius")
IntegerOptionKey const	max_struct ("lh:max_struct")
IntegerOptionKey const	max_struct_per_radius ("lh:max_struct_per_radius")
RealOptionKey const	grid_space_multiplier ("lh:grid_space_multiplier")
RealOptionKey const	grid_angle_multiplier ("lh:grid_angle_multiplier")
IntegerOptionKey const	skim_size ("lh:skim_size")
IntegerOptionKey const	rounds ("lh:rounds")
StringOptionKey const	jobname ("lh:jobname")
IntegerOptionKey const	max_lib_size ("lh:max_lib_size")
IntegerOptionKey const	max_emperor_lib_size ("lh:max_emperor_lib_size")
IntegerOptionKey const	max_emperor_lib_round ("lh:max_emperor_lib_round")
IntegerOptionKey const	library_expiry_time ("lh:library_expiry_time")
StringOptionKey const	objective_function ("lh:objective_function")
IntegerOptionKey const	expire_after_rounds ("lh:expire_after_rounds")
StringOptionKey const	mpi_resume ("lh:mpi_resume")
StringOptionKey const	mpi_feedback ("lh:mpi_feedback")
IntegerOptionKey const	mpi_batch_relax_chunks ("lh:mpi_batch_relax_chunks")
IntegerOptionKey const	mpi_batch_relax_absolute_max ("lh:mpi_batch_relax_absolute_max")
IntegerOptionKey const	mpi_outbound_wu_buffer_size ("lh:mpi_outbound_wu_buffer_size")
IntegerOptionKey const	mpi_loophash_split_size ("lh:mpi_loophash_split_size ")
RealOptionKey const	mpi_metropolis_temp ("lh:mpi_metropolis_temp")
IntegerOptionKey const	mpi_save_state_interval ("lh:mpi_save_state_interval")
BooleanOptionKey const	mpi_master_save_score_only ("lh:mpi_master_save_score_only")
IntegerOptionKey const	max_loophash_per_structure ("lh:max_loophash_per_structure")
RealOptionKey const	prob_terminus_ramapert ("lh:prob_terminus_ramapert")
RealOptionKey const	rms_limit ("lh:rms_limit")
RealOptionKey const	similarity_reference ("lh:similarity_reference")
BooleanOptionKey const	centroid_only ("lh:centroid_only")
BooleanOptionKey const	write_centroid_structs ("lh:write_centroid_structs")
BooleanOptionKey const	write_all_fa_structs ("lh:write_all_fa_structs")
BooleanOptionKey const	sandbox ("lh:sandbox")
BooleanOptionKey const	create_db ("lh:create_db")
FileOptionKey const	sample_weight_file ("lh:sample_weight_file")
RealOptionKey const	radius_size ("lh:radius_size")
IntegerOptionKey const	max_ref_lib_size ("lh:max_ref_lib_size")
StringVectorOptionKey const	multi_objective_functions ("lh:multi_objective_functions")
StringVectorOptionKey const	additional_objective_functions ("lh:additional_objective_functions")
RealOptionKey const	edensity_weight_for_sampling ("lh:edensity_weight_for_sampling")
StringOptionKey const	mpi_master_schfile ("lh:mpi_master_schfile")
IntegerVectorOptionKey const	mpi_master_cpu_weight ("lh:mpi_master_cpu_weight")
StringOptionKey const	mpi_loophash_scan_type ("lh:mpi_loophash_scan_type")
BooleanOptionKey const	mpi_read_structure_for_emperor ("lh:mpi_read_structure_for_emperor")
BooleanOptionKey const	mpi_packmin_init ("lh:mpi_packmin_init")
IntegerOptionKey const	max_sample_per_structure ("lh:max_sample_per_structure")
StringOptionKey const	loop_string ("lh:loop_string")
StringOptionKey const	seg_string ("lh:seg_string")
StringVectorOptionKey const	loopresdef ("lh:loopresdef")
BooleanOptionKey const	pert_init_loop ("lh:pert_init_loop")
RealOptionKey const	NMdist ("lh:NMdist")
RealVectorOptionKey const	objective_dominate_cut ("lh:objective_dominate_cut")
RealVectorOptionKey const	objective_cut_increment ("lh:objective_cut_increment")
StringOptionKey const	similarity_method ("lh:similarity_method")
StringOptionKey const	similarity_measure ("lh:similarity_measure")
RealOptionKey const	similarity_tolerance ("lh:similarity_tolerance")
RealOptionKey const	parent_selection_kT ("lh:parent_selection_kT")
StringOptionKey const	sim_replace_obj ("lh:sim_replace_obj")
RealOptionKey const	ulr_mulfactor ("lh:ulr_mulfactor")
BooleanOptionKey const	filter_up_to_maxlib ("lh:filter_up_to_maxlib")
BooleanOptionKey const	minimize_after_nmsearch ("lh:minimize_after_nmsearch")

Function Documentation

additional_objective_functions()

StringVectorOptionKey const lh::additional_objective_functions

(

"lh:additional_objective_functions"

)

bss()

BooleanOptionKey const lh::bss

(

"lh:bss"

)

centroid_only()

BooleanOptionKey const lh::centroid_only

(

"lh:centroid_only"

)

create_db()

BooleanOptionKey const lh::create_db

(

"lh:create_db"

)

Referenced by main().

createdb_rms_cutoff()

RealVectorOptionKey const lh::createdb_rms_cutoff

(

"lh:createdb_rms_cutoff"

)

db_path()

PathOptionKey const lh::db_path

(

"lh:db_path"

)

Referenced by main().

edensity_weight_for_sampling()

RealOptionKey const lh::edensity_weight_for_sampling

(

"lh:edensity_weight_for_sampling"

)

exclude_homo()

BooleanOptionKey const lh::exclude_homo

(

"lh:exclude_homo"

)

expire_after_rounds()

IntegerOptionKey const lh::expire_after_rounds

(

"lh:expire_after_rounds"

)

filter_by_phipsi()

BooleanOptionKey const lh::filter_by_phipsi

(

"lh:filter_by_phipsi"

)

filter_up_to_maxlib()

BooleanOptionKey const lh::filter_up_to_maxlib

(

"lh:filter_up_to_maxlib"

)

grid_angle_multiplier()

RealOptionKey const lh::grid_angle_multiplier

(

"lh:grid_angle_multiplier"

)

grid_space_multiplier()

RealOptionKey const lh::grid_space_multiplier

(

"lh:grid_space_multiplier"

)

homo_file()

StringOptionKey const lh::homo_file

(

"lh:homo_file"

)

jobname()

StringOptionKey const lh::jobname

(

"lh:jobname"

)

lh()

BooleanOptionKey const lh::lh

(

"lh"

)

library_expiry_time()

IntegerOptionKey const lh::library_expiry_time

(

"lh:library_expiry_time"

)

loop_string()

StringOptionKey const lh::loop_string

(

"lh:loop_string"

)

loopresdef()

StringVectorOptionKey const lh::loopresdef

(

"lh:loopresdef"

)

loopsizes()

IntegerVectorOptionKey const lh::loopsizes

(

"lh:loopsizes"

)

Referenced by main().

max_bbrms()

RealOptionKey const lh::max_bbrms

(

"lh:max_bbrms"

)

Referenced by LoopHashRelax_Sampler::apply().

max_emperor_lib_round()

IntegerOptionKey const lh::max_emperor_lib_round

(

"lh:max_emperor_lib_round"

)

max_emperor_lib_size()

IntegerOptionKey const lh::max_emperor_lib_size

(

"lh:max_emperor_lib_size"

)

max_lib_size()

IntegerOptionKey const lh::max_lib_size

(

"lh:max_lib_size"

)

max_loophash_per_structure()

IntegerOptionKey const lh::max_loophash_per_structure

(

"lh:max_loophash_per_structure"

)

max_radius()

IntegerOptionKey const lh::max_radius

(

"lh:max_radius"

)

Referenced by main().

max_ref_lib_size()

IntegerOptionKey const lh::max_ref_lib_size

(

"lh:max_ref_lib_size"

)

max_rms()

RealOptionKey const lh::max_rms

(

"lh:max_rms"

)

Referenced by LoopHashRelax_Sampler::apply(), and main().

max_sample_per_structure()

IntegerOptionKey const lh::max_sample_per_structure

(

"lh:max_sample_per_structure"

)

max_struct()

IntegerOptionKey const lh::max_struct

(

"lh:max_struct"

)

max_struct_per_radius()

IntegerOptionKey const lh::max_struct_per_radius

(

"lh:max_struct_per_radius"

)

min_bbrms()

RealOptionKey const lh::min_bbrms

(

"lh:min_bbrms"

)

Referenced by LoopHashRelax_Sampler::apply().

min_rms()

RealOptionKey const lh::min_rms

(

"lh:min_rms"

)

Referenced by LoopHashRelax_Sampler::apply(), and main().

minimize_after_nmsearch()

BooleanOptionKey const lh::minimize_after_nmsearch

(

"lh:minimize_after_nmsearch"

)

mpi_batch_relax_absolute_max()

IntegerOptionKey const lh::mpi_batch_relax_absolute_max

(

"lh:mpi_batch_relax_absolute_max"

)

mpi_batch_relax_chunks()

IntegerOptionKey const lh::mpi_batch_relax_chunks

(

"lh:mpi_batch_relax_chunks"

)

mpi_feedback()

StringOptionKey const lh::mpi_feedback

(

"lh:mpi_feedback"

)

mpi_loophash_scan_type()

StringOptionKey const lh::mpi_loophash_scan_type

(

"lh:mpi_loophash_scan_type"

)

mpi_loophash_split_size()

IntegerOptionKey const lh::mpi_loophash_split_size

(

"lh:mpi_loophash_split_size "

)

mpi_master_cpu_weight()

IntegerVectorOptionKey const lh::mpi_master_cpu_weight

(

"lh:mpi_master_cpu_weight"

)

mpi_master_save_score_only()

BooleanOptionKey const lh::mpi_master_save_score_only

(

"lh:mpi_master_save_score_only"

)

mpi_master_schfile()

StringOptionKey const lh::mpi_master_schfile

(

"lh:mpi_master_schfile"

)

mpi_metropolis_temp()

RealOptionKey const lh::mpi_metropolis_temp

(

"lh:mpi_metropolis_temp"

)

Referenced by LoopHashRelax_Sampler::apply().

mpi_outbound_wu_buffer_size()

IntegerOptionKey const lh::mpi_outbound_wu_buffer_size

(

"lh:mpi_outbound_wu_buffer_size"

)

mpi_packmin_init()

BooleanOptionKey const lh::mpi_packmin_init

(

"lh:mpi_packmin_init"

)

mpi_read_structure_for_emperor()

BooleanOptionKey const lh::mpi_read_structure_for_emperor

(

"lh:mpi_read_structure_for_emperor"

)

mpi_resume()

StringOptionKey const lh::mpi_resume

(

"lh:mpi_resume"

)

mpi_save_state_interval()

IntegerOptionKey const lh::mpi_save_state_interval

(

"lh:mpi_save_state_interval"

)

multi_objective_functions()

StringVectorOptionKey const lh::multi_objective_functions

(

"lh:multi_objective_functions"

)

NMdist()

RealOptionKey const lh::NMdist

(

"lh:NMdist"

)

num_partitions()

IntegerOptionKey const lh::num_partitions

(

"lh:num_partitions"

)

objective_cut_increment()

RealVectorOptionKey const lh::objective_cut_increment

(

"lh:objective_cut_increment"

)

objective_dominate_cut()

RealVectorOptionKey const lh::objective_dominate_cut

(

"lh:objective_dominate_cut"

)

objective_function()

StringOptionKey const lh::objective_function

(

"lh:objective_function"

)

parent_selection_kT()

RealOptionKey const lh::parent_selection_kT

(

"lh:parent_selection_kT"

)

pert_init_loop()

BooleanOptionKey const lh::pert_init_loop

(

"lh:pert_init_loop"

)

prob_terminus_ramapert()

RealOptionKey const lh::prob_terminus_ramapert

(

"lh:prob_terminus_ramapert"

)

radius_size()

RealOptionKey const lh::radius_size

(

"lh:radius_size"

)

refstruct()

StringOptionKey const lh::refstruct

(

"lh:refstruct"

)

Referenced by LoopHashRelax_Sampler::apply().

rms_limit()

RealOptionKey const lh::rms_limit

(

"lh:rms_limit"

)

rounds()

IntegerOptionKey const lh::rounds

(

"lh:rounds"

)

sample_weight_file()

FileOptionKey const lh::sample_weight_file

(

"lh:sample_weight_file"

)

sandbox()

BooleanOptionKey const lh::sandbox

(

"lh:sandbox"

)

Referenced by main().

seg_string()

StringOptionKey const lh::seg_string

(

"lh:seg_string"

)

sim_replace_obj()

StringOptionKey const lh::sim_replace_obj

(

"lh:sim_replace_obj"

)

similarity_measure()

StringOptionKey const lh::similarity_measure

(

"lh:similarity_measure"

)

similarity_method()

StringOptionKey const lh::similarity_method

(

"lh:similarity_method"

)

similarity_reference()

RealOptionKey const lh::similarity_reference

(

"lh:similarity_reference"

)

similarity_tolerance()

RealOptionKey const lh::similarity_tolerance

(

"lh:similarity_tolerance"

)

skim_size()

IntegerOptionKey const lh::skim_size

(

"lh:skim_size"

)

Referenced by LoopHashRelax_Sampler::apply().

ulr_mulfactor()

RealOptionKey const lh::ulr_mulfactor

(

"lh:ulr_mulfactor"

)

write_all_fa_structs()

BooleanOptionKey const lh::write_all_fa_structs

(

"lh:write_all_fa_structs"

)

write_centroid_structs()

BooleanOptionKey const lh::write_centroid_structs

(

"lh:write_centroid_structs"

)