basic::options::OptionKeys::motifs Namespace Reference

Variables
BooleanOptionKey const	motifs
RealOptionKey const	close_enough
IntegerOptionKey const	max_depth
BooleanOptionKey const	keep_motif_xtal_location
RealOptionKey const	pack_score_cutoff
RealOptionKey const	hb_score_cutoff
RealOptionKey const	water_score_cutoff
RealOptionKey const	pack_min_threshold
RealOptionKey const	pack_max_threshold
RealOptionKey const	hbond_min_threshold
RealOptionKey const	hbond_max_threshold
RealOptionKey const	elec_min_threshold
RealOptionKey const	elec_max_threshold
RealOptionKey const	duplicate_dist_cutoff
RealOptionKey const	duplicate_angle_cutoff
StringOptionKey const	motif_output_directory
BooleanOptionKey const	eliminate_weak_motifs
RealOptionKey const	duplicate_motif_cutoff
BooleanOptionKey const	preminimize_motif_pdbs
BooleanOptionKey const	preminimize_motif_pdbs_sconly
BooleanOptionKey const	place_adduct_waters
FileVectorOptionKey const	list_motifs
StringOptionKey const	motif_filename
StringOptionKey const	file_prefix
StringOptionKey const	build_residue_file
StringOptionKey const	motif_flexible_loop_file
StringOptionKey const	residue_trim_file
StringOptionKey const	BPData
FileVectorOptionKey const	list_dnaconformers
StringVectorOptionKey const	target_dna_defs
StringVectorOptionKey const	motif_build_defs
IntegerVectorOptionKey const	motif_build_positions
RealOptionKey const	r1
RealOptionKey const	r2
RealOptionKey const	z1
RealOptionKey const	z2
RealOptionKey const	dtest
IntegerOptionKey const	rotlevel
IntegerOptionKey const	num_repacks
BooleanOptionKey const	minimize
BooleanOptionKey const	minimize_dna
BooleanOptionKey const	run_motifs
BooleanOptionKey const	expand_motifs
BooleanOptionKey const	aromatic_motifs
BooleanOptionKey const	dump_motifs
BooleanOptionKey const	quick_and_dirty
RealOptionKey const	special_rotweight
StringOptionKey const	output_file
StringOptionKey const	data_file
StringOptionKey const	target_aa
BooleanOptionKey const	flex_sugar
BooleanOptionKey const	clear_bprots
IntegerOptionKey const	rots2add
BooleanOptionKey const	restrict_to_wt
BooleanOptionKey const	rerun_motifsearch
BooleanOptionKey const	no_rotamer_bump
RealOptionKey const	ligand_motif_sphere
BooleanOptionKey const	output_build_positions_only
RealOptionKey const	specific_build_position
BooleanOptionKey const	verbosity
StringOptionKey const	params_directory_path
StringOptionKey const	sdf_directory_path
StringOptionKey const	mol2_directory_path
StringOptionKey const	mol2_file
StringOptionKey const	mol2_amino_acid
StringOptionKey const	params_custom_file_name
StringOptionKey const	ligand_3_letter_code
StringOptionKey const	ligand_1_letter_code
StringOptionKey const	ligand_full_name
BooleanOptionKey const	write_param_to_pdb
IntegerVectorOptionKey const	protein_discovery_locus
RealOptionKey const	fa_rep_cutoff
RealOptionKey const	fa_atr_cutoff
RealOptionKey const	fa_atr_rep_cutoff
BooleanOptionKey const	post_highresdock_fa_atr_rep_score
RealOptionKey const	ligand_wts_fxn_cutoff
BooleanOptionKey const	score_with_ligand_wts_function
BooleanOptionKey const	output_ligand_pdb
BooleanOptionKey const	check_new_param_file
RealOptionKey const	ddg_cutoff
IntegerOptionKey const	best_pdbs_to_keep
IntegerOptionKey const	resolution_scale_factor
RealOptionKey const	x_min_holes
RealOptionKey const	x_max_holes
RealOptionKey const	y_min_holes
RealOptionKey const	y_max_holes
RealOptionKey const	z_min_holes
RealOptionKey const	z_max_holes
BooleanOptionKey const	highresdocker_allow_minimization
BooleanOptionKey const	highresdocker_allow_repacking
BooleanOptionKey const	highresdocker_use_all_residues
StringOptionKey const	ligand_motif_output_directory_name
StringOptionKey const	ligand_motif_output_file_name
BooleanOptionKey const	output_motifs_as_pdb
BooleanOptionKey const	output_motifs
BooleanOptionKey const	highresdock_with_whole_score_fxn
IntegerVectorOptionKey const	target_residues_sf
IntegerVectorOptionKey const	target_residues_contact
RealOptionKey const	space_fill_cutoff_score
RealOptionKey const	space_fill_cutoff_score_sub
RealOptionKey const	space_fill_cutoff_differential_score_sub
IntegerVectorOptionKey const	binding_pocket_center_sf
IntegerVectorOptionKey const	binding_pocket_dimensions_sf
RealOptionKey const	resolution_scale_factor_float
BooleanOptionKey const	output_space_fill_matrix_pdbs
BooleanOptionKey const	use_whole_matrix_in_space_fill_pdb
BooleanOptionKey const	use_empty_space_in_space_fill_pdb
BooleanOptionKey const	collect_motifs_from_placed_ligand
IntegerVectorOptionKey const	significant_residues_for_motifs
IntegerVectorOptionKey const	mandatory_residues_for_motifs
IntegerOptionKey const	minimum_motifs_formed_cutoff
IntegerOptionKey const	minimum_significant_motifs_formed_cutoff
BooleanOptionKey const	check_if_ligand_motifs_match_real
RealOptionKey const	minimum_ratio_of_real_motifs_from_ligand
BooleanOptionKey const	clean_pdb_name

Variable Documentation

aromatic_motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::aromatic_motifs

extern

best_pdbs_to_keep

IntegerOptionKey const basic::options::OptionKeys::motifs::best_pdbs_to_keep

extern

binding_pocket_center_sf

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::binding_pocket_center_sf

extern

binding_pocket_dimensions_sf

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::binding_pocket_dimensions_sf

extern

BPData

StringOptionKey const basic::options::OptionKeys::motifs::BPData

extern

build_residue_file

StringOptionKey const basic::options::OptionKeys::motifs::build_residue_file

extern

Referenced by find_close_motifs().

check_if_ligand_motifs_match_real

BooleanOptionKey const basic::options::OptionKeys::motifs::check_if_ligand_motifs_match_real

extern

check_new_param_file

BooleanOptionKey const basic::options::OptionKeys::motifs::check_new_param_file

extern

clean_pdb_name

BooleanOptionKey const basic::options::OptionKeys::motifs::clean_pdb_name

extern

clear_bprots

BooleanOptionKey const basic::options::OptionKeys::motifs::clear_bprots

extern

close_enough

RealOptionKey const basic::options::OptionKeys::motifs::close_enough

extern

collect_motifs_from_placed_ligand

BooleanOptionKey const basic::options::OptionKeys::motifs::collect_motifs_from_placed_ligand

extern

data_file

StringOptionKey const basic::options::OptionKeys::motifs::data_file

extern

Referenced by coarse_rna_denovo_test(), main(), rna_fullatom_score_test(), RNA_ScoreMover::RNA_ScoreMover(), and simple_opte_test().

ddg_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::ddg_cutoff

extern

dtest

RealOptionKey const basic::options::OptionKeys::motifs::dtest

extern

dump_motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::dump_motifs

extern

duplicate_angle_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_angle_cutoff

extern

Referenced by remove_duplicate_motifs().

duplicate_dist_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_dist_cutoff

extern

Referenced by remove_duplicate_motifs().

duplicate_motif_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::duplicate_motif_cutoff

extern

Referenced by process_for_motifs().

elec_max_threshold

RealOptionKey const basic::options::OptionKeys::motifs::elec_max_threshold

extern

Referenced by process_for_motifs().

elec_min_threshold

RealOptionKey const basic::options::OptionKeys::motifs::elec_min_threshold

extern

Referenced by process_for_motifs().

eliminate_weak_motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::eliminate_weak_motifs

extern

Referenced by process_for_motifs().

expand_motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::expand_motifs

extern

fa_atr_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::fa_atr_cutoff

extern

fa_atr_rep_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::fa_atr_rep_cutoff

extern

fa_rep_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::fa_rep_cutoff

extern

file_prefix

StringOptionKey const basic::options::OptionKeys::motifs::file_prefix

extern

flex_sugar

BooleanOptionKey const basic::options::OptionKeys::motifs::flex_sugar

extern

hb_score_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::hb_score_cutoff

extern

Referenced by process_for_motifs().

hbond_max_threshold

RealOptionKey const basic::options::OptionKeys::motifs::hbond_max_threshold

extern

Referenced by process_for_motifs().

hbond_min_threshold

RealOptionKey const basic::options::OptionKeys::motifs::hbond_min_threshold

extern

Referenced by process_for_motifs().

highresdock_with_whole_score_fxn

BooleanOptionKey const basic::options::OptionKeys::motifs::highresdock_with_whole_score_fxn

extern

highresdocker_allow_minimization

BooleanOptionKey const basic::options::OptionKeys::motifs::highresdocker_allow_minimization

extern

highresdocker_allow_repacking

BooleanOptionKey const basic::options::OptionKeys::motifs::highresdocker_allow_repacking

extern

highresdocker_use_all_residues

BooleanOptionKey const basic::options::OptionKeys::motifs::highresdocker_use_all_residues

extern

keep_motif_xtal_location

BooleanOptionKey const basic::options::OptionKeys::motifs::keep_motif_xtal_location

extern

Referenced by output_single_motif().

ligand_1_letter_code

StringOptionKey const basic::options::OptionKeys::motifs::ligand_1_letter_code

extern

ligand_3_letter_code

StringOptionKey const basic::options::OptionKeys::motifs::ligand_3_letter_code

extern

ligand_full_name

StringOptionKey const basic::options::OptionKeys::motifs::ligand_full_name

extern

ligand_motif_output_directory_name

StringOptionKey const basic::options::OptionKeys::motifs::ligand_motif_output_directory_name

extern

ligand_motif_output_file_name

StringOptionKey const basic::options::OptionKeys::motifs::ligand_motif_output_file_name

extern

ligand_motif_sphere

RealOptionKey const basic::options::OptionKeys::motifs::ligand_motif_sphere

extern

Referenced by main().

ligand_wts_fxn_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::ligand_wts_fxn_cutoff

extern

list_dnaconformers

FileVectorOptionKey const basic::options::OptionKeys::motifs::list_dnaconformers

extern

list_motifs

FileVectorOptionKey const basic::options::OptionKeys::motifs::list_motifs

extern

Referenced by main().

mandatory_residues_for_motifs

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::mandatory_residues_for_motifs

extern

max_depth

IntegerOptionKey const basic::options::OptionKeys::motifs::max_depth

extern

minimize

BooleanOptionKey const basic::options::OptionKeys::motifs::minimize

extern

minimize_dna

BooleanOptionKey const basic::options::OptionKeys::motifs::minimize_dna

extern

minimum_motifs_formed_cutoff

IntegerOptionKey const basic::options::OptionKeys::motifs::minimum_motifs_formed_cutoff

extern

minimum_ratio_of_real_motifs_from_ligand

RealOptionKey const basic::options::OptionKeys::motifs::minimum_ratio_of_real_motifs_from_ligand

extern

minimum_significant_motifs_formed_cutoff

IntegerOptionKey const basic::options::OptionKeys::motifs::minimum_significant_motifs_formed_cutoff

extern

mol2_amino_acid

StringOptionKey const basic::options::OptionKeys::motifs::mol2_amino_acid

extern

mol2_directory_path

StringOptionKey const basic::options::OptionKeys::motifs::mol2_directory_path

extern

mol2_file

StringOptionKey const basic::options::OptionKeys::motifs::mol2_file

extern

motif_build_defs

StringVectorOptionKey const basic::options::OptionKeys::motifs::motif_build_defs

extern

motif_build_positions

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::motif_build_positions

extern

Referenced by main().

motif_filename

StringOptionKey const basic::options::OptionKeys::motifs::motif_filename

extern

Referenced by find_close_motifs(), apps::pilot::frankdt::import_motifs(), and main().

motif_flexible_loop_file

StringOptionKey const basic::options::OptionKeys::motifs::motif_flexible_loop_file

extern

Referenced by read_in_flexible_regions().

motif_output_directory

StringOptionKey const basic::options::OptionKeys::motifs::motif_output_directory

extern

Referenced by output_single_motif().

motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::motifs

extern

no_rotamer_bump

BooleanOptionKey const basic::options::OptionKeys::motifs::no_rotamer_bump

extern

num_repacks

IntegerOptionKey const basic::options::OptionKeys::motifs::num_repacks

extern

Referenced by main().

output_build_positions_only

BooleanOptionKey const basic::options::OptionKeys::motifs::output_build_positions_only

extern

output_file

StringOptionKey const basic::options::OptionKeys::motifs::output_file

extern

Referenced by convert_to_native_test(), get_options(), main(), process_file_list(), register_options(), and remove_duplicate_motifs().

output_ligand_pdb

BooleanOptionKey const basic::options::OptionKeys::motifs::output_ligand_pdb

extern

output_motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::output_motifs

extern

output_motifs_as_pdb

BooleanOptionKey const basic::options::OptionKeys::motifs::output_motifs_as_pdb

extern

output_space_fill_matrix_pdbs

BooleanOptionKey const basic::options::OptionKeys::motifs::output_space_fill_matrix_pdbs

extern

pack_max_threshold

RealOptionKey const basic::options::OptionKeys::motifs::pack_max_threshold

extern

Referenced by process_for_motifs().

pack_min_threshold

RealOptionKey const basic::options::OptionKeys::motifs::pack_min_threshold

extern

Referenced by process_for_motifs().

pack_score_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::pack_score_cutoff

extern

Referenced by process_for_motifs().

params_custom_file_name

StringOptionKey const basic::options::OptionKeys::motifs::params_custom_file_name

extern

params_directory_path

StringOptionKey const basic::options::OptionKeys::motifs::params_directory_path

extern

Referenced by main().

place_adduct_waters

BooleanOptionKey const basic::options::OptionKeys::motifs::place_adduct_waters

extern

Referenced by place_waters_and_minimize().

post_highresdock_fa_atr_rep_score

BooleanOptionKey const basic::options::OptionKeys::motifs::post_highresdock_fa_atr_rep_score

extern

preminimize_motif_pdbs

BooleanOptionKey const basic::options::OptionKeys::motifs::preminimize_motif_pdbs

extern

Referenced by place_waters_and_minimize().

preminimize_motif_pdbs_sconly

BooleanOptionKey const basic::options::OptionKeys::motifs::preminimize_motif_pdbs_sconly

extern

Referenced by place_waters_and_minimize().

protein_discovery_locus

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::protein_discovery_locus

extern

Referenced by main().

quick_and_dirty

BooleanOptionKey const basic::options::OptionKeys::motifs::quick_and_dirty

extern

r1

RealOptionKey const basic::options::OptionKeys::motifs::r1

extern

Referenced by add_lig_cst(), add_triazole_constraints(), PickBAB::apply(), calc_scores(), Solver_NU::calculate_rho(), correct_dunbrack(), MatchSet::cross(), MatchSet::cross_homodimer(), design_dyad(), double_linked_fold_tree(), double_unlinked_fold_tree(), numeric::crick_equations::dx_ddelta_omega1(), numeric::crick_equations::dx_domega1(), numeric::crick_equations::dy_ddelta_omega1(), numeric::crick_equations::dy_domega1(), get_aln(), get_rsrpl(), getRotID(), getxform(), Hit::Hit(), ConstraintConfig::hub_seq_sep(), interface_between_chains(), main(), makerots(), MatchLig::MatchLig(), multimodel_gdt(), ConstraintConfig::parse_config_file(), print_cst_file(), refine(), register_options(), residues_too_distant(), rna_design_test(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), same_coordinates(), ScoreFragInfo::ScoreFragInfo(), write_hbgeoms_to_database(), numeric::crick_equations::x(), numeric::crick_equations::X_BUNDLE(), Arch::xform1(), numeric::crick_equations::xyz(), numeric::crick_equations::XYZ_BUNDLE(), numeric::crick_equations::y(), numeric::crick_equations::Y_BUNDLE(), and numeric::crick_equations::Z_BUNDLE().

r2

RealOptionKey const basic::options::OptionKeys::motifs::r2

extern

Referenced by add_lig_cst(), add_triazole_constraints(), PickBAB::apply(), calc_scores(), Solver_NU::calculate_rho(), correct_dunbrack(), MatchSet::cross(), MatchSet::cross_homodimer(), design_dyad(), double_linked_fold_tree(), double_unlinked_fold_tree(), evaluate_score(), get_aln(), get_rsrpl(), getRotID(), getxform(), Hit::Hit(), ConstraintConfig::hub_seq_sep(), interface_between_chains(), main(), makerots(), MatchLig::MatchLig(), multimodel_gdt(), ConstraintConfig::parse_config_file(), print_cst_file(), refine(), residues_too_distant(), rna_design_test(), run_diiron_glu(), run_m8(), run_tyr_his(), run_zn2his(), same_coordinates(), ScoreFragInfo::ScoreFragInfo(), write_hbgeoms_to_database(), and Arch::xform2().

rerun_motifsearch

BooleanOptionKey const basic::options::OptionKeys::motifs::rerun_motifsearch

extern

residue_trim_file

StringOptionKey const basic::options::OptionKeys::motifs::residue_trim_file

extern

Referenced by find_close_motifs().

resolution_scale_factor

IntegerOptionKey const basic::options::OptionKeys::motifs::resolution_scale_factor

extern

Referenced by main().

resolution_scale_factor_float

RealOptionKey const basic::options::OptionKeys::motifs::resolution_scale_factor_float

extern

restrict_to_wt

BooleanOptionKey const basic::options::OptionKeys::motifs::restrict_to_wt

extern

rotlevel

IntegerOptionKey const basic::options::OptionKeys::motifs::rotlevel

extern

rots2add

IntegerOptionKey const basic::options::OptionKeys::motifs::rots2add

extern

run_motifs

BooleanOptionKey const basic::options::OptionKeys::motifs::run_motifs

extern

score_with_ligand_wts_function

BooleanOptionKey const basic::options::OptionKeys::motifs::score_with_ligand_wts_function

extern

sdf_directory_path

StringOptionKey const basic::options::OptionKeys::motifs::sdf_directory_path

extern

significant_residues_for_motifs

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::significant_residues_for_motifs

extern

space_fill_cutoff_differential_score_sub

RealOptionKey const basic::options::OptionKeys::motifs::space_fill_cutoff_differential_score_sub

extern

space_fill_cutoff_score

RealOptionKey const basic::options::OptionKeys::motifs::space_fill_cutoff_score

extern

space_fill_cutoff_score_sub

RealOptionKey const basic::options::OptionKeys::motifs::space_fill_cutoff_score_sub

extern

special_rotweight

RealOptionKey const basic::options::OptionKeys::motifs::special_rotweight

extern

specific_build_position

RealOptionKey const basic::options::OptionKeys::motifs::specific_build_position

extern

target_aa

StringOptionKey const basic::options::OptionKeys::motifs::target_aa

extern

Referenced by main(), output_single_motif(), process_for_motifs(), and zero_occ_for_deleted_atoms().

target_dna_defs

StringVectorOptionKey const basic::options::OptionKeys::motifs::target_dna_defs

extern

target_residues_contact

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::target_residues_contact

extern

target_residues_sf

IntegerVectorOptionKey const basic::options::OptionKeys::motifs::target_residues_sf

extern

use_empty_space_in_space_fill_pdb

BooleanOptionKey const basic::options::OptionKeys::motifs::use_empty_space_in_space_fill_pdb

extern

use_whole_matrix_in_space_fill_pdb

BooleanOptionKey const basic::options::OptionKeys::motifs::use_whole_matrix_in_space_fill_pdb

extern

verbosity

BooleanOptionKey const basic::options::OptionKeys::motifs::verbosity

extern

Referenced by main().

water_score_cutoff

RealOptionKey const basic::options::OptionKeys::motifs::water_score_cutoff

extern

Referenced by process_for_motifs().

write_param_to_pdb

BooleanOptionKey const basic::options::OptionKeys::motifs::write_param_to_pdb

extern

x_max_holes

RealOptionKey const basic::options::OptionKeys::motifs::x_max_holes

extern

Referenced by main().

x_min_holes

RealOptionKey const basic::options::OptionKeys::motifs::x_min_holes

extern

Referenced by main().

y_max_holes

RealOptionKey const basic::options::OptionKeys::motifs::y_max_holes

extern

Referenced by main().

y_min_holes

RealOptionKey const basic::options::OptionKeys::motifs::y_min_holes

extern

Referenced by main().

z1

RealOptionKey const basic::options::OptionKeys::motifs::z1

extern

Referenced by base_doublet_rmsd_test(), coarse_to_full_test(), numeric::kinematic_closure::dixon_sturm(), get_backbone_rotamers(), CrystFFTDock::get_transform_distance(), numeric::alignment::QCPKernel< Real >::inner_product(), main(), numeric::crick_equations::P_omega0(), numeric::crick_equations::PP(), numeric::linear_algebra::qzvec(), register_options(), numeric::crick_equations::X_BUNDLE(), numeric::crick_equations::XYZ_BUNDLE(), numeric::crick_equations::Y_BUNDLE(), and numeric::crick_equations::Z_BUNDLE().

z2

RealOptionKey const basic::options::OptionKeys::motifs::z2

extern

Referenced by base_doublet_rmsd_test(), numeric::alignment::QCPKernel< Real >::calc_rmsd_Theobald_method(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), coarse_to_full_test(), numeric::kinematic_closure::dixon_sturm(), CrystFFTDock::get_transform_distance(), and numeric::alignment::QCPKernel< Real >::inner_product().

z_max_holes

RealOptionKey const basic::options::OptionKeys::motifs::z_max_holes

extern

Referenced by main().

z_min_holes

RealOptionKey const basic::options::OptionKeys::motifs::z_min_holes

extern

Referenced by main().