motifs Namespace Reference

Functions
BooleanOptionKey const	motifs ("motifs")
RealOptionKey const	close_enough ("motifs:close_enough")
IntegerOptionKey const	max_depth ("motifs:max_depth")
BooleanOptionKey const	keep_motif_xtal_location ("motifs:keep_motif_xtal_location")
RealOptionKey const	pack_score_cutoff ("motifs:pack_score_cutoff")
RealOptionKey const	hb_score_cutoff ("motifs:hb_score_cutoff")
RealOptionKey const	water_score_cutoff ("motifs:water_score_cutoff")
RealOptionKey const	pack_min_threshold ("motifs:pack_min_threshold")
RealOptionKey const	pack_max_threshold ("motifs:pack_max_threshold")
RealOptionKey const	hbond_min_threshold ("motifs:hbond_min_threshold")
RealOptionKey const	hbond_max_threshold ("motifs:hbond_max_threshold")
RealOptionKey const	elec_min_threshold ("motifs:elec_min_threshold")
RealOptionKey const	elec_max_threshold ("motifs:elec_max_threshold")
RealOptionKey const	duplicate_dist_cutoff ("motifs:duplicate_dist_cutoff")
RealOptionKey const	duplicate_angle_cutoff ("motifs:duplicate_angle_cutoff")
StringOptionKey const	motif_output_directory ("motifs:motif_output_directory")
BooleanOptionKey const	eliminate_weak_motifs ("motifs:eliminate_weak_motifs")
RealOptionKey const	duplicate_motif_cutoff ("motifs:duplicate_motif_cutoff")
BooleanOptionKey const	preminimize_motif_pdbs ("motifs:preminimize_motif_pdbs")
BooleanOptionKey const	preminimize_motif_pdbs_sconly ("motifs:preminimize_motif_pdbs_sconly")
BooleanOptionKey const	place_adduct_waters ("motifs:place_adduct_waters")
FileVectorOptionKey const	list_motifs ("motifs:list_motifs")
StringOptionKey const	motif_filename ("motifs:motif_filename")
StringOptionKey const	file_prefix ("motifs:file_prefix")
StringOptionKey const	build_residue_file ("motifs:build_residue_file")
StringOptionKey const	motif_flexible_loop_file ("motifs:motif_flexible_loop_file")
StringOptionKey const	residue_trim_file ("motifs:residue_trim_file")
StringOptionKey const	BPData ("motifs:BPData")
FileVectorOptionKey const	list_dnaconformers ("motifs:list_dnaconformers")
StringVectorOptionKey const	target_dna_defs ("motifs:target_dna_defs")
StringVectorOptionKey const	motif_build_defs ("motifs:motif_build_defs")
IntegerVectorOptionKey const	motif_build_positions ("motifs:motif_build_positions")
RealOptionKey const	r1 ("motifs:r1")
RealOptionKey const	r2 ("motifs:r2")
RealOptionKey const	z1 ("motifs:z1")
RealOptionKey const	z2 ("motifs:z2")
RealOptionKey const	dtest ("motifs:dtest")
IntegerOptionKey const	rotlevel ("motifs:rotlevel")
IntegerOptionKey const	num_repacks ("motifs:num_repacks")
BooleanOptionKey const	minimize ("motifs:minimize")
BooleanOptionKey const	minimize_dna ("motifs:minimize_dna")
BooleanOptionKey const	run_motifs ("motifs:run_motifs")
BooleanOptionKey const	expand_motifs ("motifs:expand_motifs")
BooleanOptionKey const	aromatic_motifs ("motifs:aromatic_motifs")
BooleanOptionKey const	dump_motifs ("motifs:dump_motifs")
BooleanOptionKey const	quick_and_dirty ("motifs:quick_and_dirty")
RealOptionKey const	special_rotweight ("motifs:special_rotweight")
StringOptionKey const	output_file ("motifs:output_file")
StringOptionKey const	data_file ("motifs:data_file")
StringOptionKey const	target_aa ("motifs:target_aa")
BooleanOptionKey const	flex_sugar ("motifs:flex_sugar")
BooleanOptionKey const	clear_bprots ("motifs:clear_bprots")
IntegerOptionKey const	rots2add ("motifs:rots2add")
BooleanOptionKey const	restrict_to_wt ("motifs:restrict_to_wt")
BooleanOptionKey const	rerun_motifsearch ("motifs:rerun_motifsearch")
BooleanOptionKey const	no_rotamer_bump ("motifs:no_rotamer_bump")
RealOptionKey const	ligand_motif_sphere ("motifs:ligand_motif_sphere")
BooleanOptionKey const	output_build_positions_only ("motifs:output_build_positions_only")
RealOptionKey const	specific_build_position ("motifs:specific_build_position")
BooleanOptionKey const	verbosity ("motifs:verbosity")
StringOptionKey const	params_directory_path ("motifs:params_directory_path")
StringOptionKey const	sdf_directory_path ("motifs:sdf_directory_path")
StringOptionKey const	mol2_directory_path ("motifs:mol2_directory_path")
StringOptionKey const	mol2_file ("motifs:mol2_file")
StringOptionKey const	mol2_amino_acid ("motifs:mol2_amino_acid")
StringOptionKey const	params_custom_file_name ("motifs:params_custom_file_name")
StringOptionKey const	ligand_3_letter_code ("motifs:ligand_3_letter_code")
StringOptionKey const	ligand_1_letter_code ("motifs:ligand_1_letter_code")
StringOptionKey const	ligand_full_name ("motifs:ligand_full_name")
BooleanOptionKey const	write_param_to_pdb ("motifs:write_param_to_pdb")
RealOptionKey const	protein_discovery_locus ("motifs:protein_discovery_locus")
RealOptionKey const	fa_rep_cutoff ("motifs:fa_rep_cutoff")
RealOptionKey const	fa_atr_cutoff ("motifs:fa_atr_cutoff")
BooleanOptionKey const	output_ligand_pdb ("motifs:output_ligand_pdb")
BooleanOptionKey const	check_new_param_file ("motifs:check_new_param_file")
RealOptionKey const	ddg_cutoff ("motifs:ddg_cutoff")
IntegerOptionKey const	best_pdbs_to_keep ("motifs:best_pdbs_to_keep")
IntegerOptionKey const	resolution_scale_factor ("motifs:resolution_scale_factor")
RealOptionKey const	x_min_holes ("motifs:x_min_holes")
RealOptionKey const	x_max_holes ("motifs:x_max_holes")
RealOptionKey const	y_min_holes ("motifs:y_min_holes")
RealOptionKey const	y_max_holes ("motifs:y_max_holes")
RealOptionKey const	z_min_holes ("motifs:z_min_holes")
RealOptionKey const	z_max_holes ("motifs:z_max_holes")
BooleanOptionKey const	highresdocker_allow_minimization ("motifs:highresdocker_allow_minimization")
BooleanOptionKey const	highresdocker_allow_repacking ("motifs:highresdocker_allow_repacking")
BooleanOptionKey const	highresdocker_use_all_residues ("motifs:highresdocker_use_all_residues")
StringOptionKey const	ligand_motif_output_directory_name ("motifs:ligand_motif_output_directory_name")
StringOptionKey const	ligand_motif_output_file_name ("motifs:ligand_motif_output_file_name")
BooleanOptionKey const	output_motifs_as_pdb ("motifs:output_motifs_as_pdb")
BooleanOptionKey const	output_motifs ("motifs:output_motifs")

Function Documentation

aromatic_motifs()

BooleanOptionKey const motifs::aromatic_motifs

(

"motifs:aromatic_motifs"

)

best_pdbs_to_keep()

IntegerOptionKey const motifs::best_pdbs_to_keep

(

"motifs:best_pdbs_to_keep"

)

BPData()

StringOptionKey const motifs::BPData

(

"motifs:BPData"

)

build_residue_file()

StringOptionKey const motifs::build_residue_file

(

"motifs:build_residue_file"

)

check_new_param_file()

BooleanOptionKey const motifs::check_new_param_file

(

"motifs:check_new_param_file"

)

clear_bprots()

BooleanOptionKey const motifs::clear_bprots

(

"motifs:clear_bprots"

)

close_enough()

RealOptionKey const motifs::close_enough

(

"motifs:close_enough"

)

data_file()

StringOptionKey const motifs::data_file

(

"motifs:data_file"

)

ddg_cutoff()

RealOptionKey const motifs::ddg_cutoff

(

"motifs:ddg_cutoff"

)

dtest()

RealOptionKey const motifs::dtest

(

"motifs:dtest"

)

dump_motifs()

BooleanOptionKey const motifs::dump_motifs

(

"motifs:dump_motifs"

)

duplicate_angle_cutoff()

RealOptionKey const motifs::duplicate_angle_cutoff

(

"motifs:duplicate_angle_cutoff"

)

Referenced by process_for_motifs().

duplicate_dist_cutoff()

RealOptionKey const motifs::duplicate_dist_cutoff

(

"motifs:duplicate_dist_cutoff"

)

Referenced by process_for_motifs().

duplicate_motif_cutoff()

RealOptionKey const motifs::duplicate_motif_cutoff

(

"motifs:duplicate_motif_cutoff"

)

elec_max_threshold()

RealOptionKey const motifs::elec_max_threshold

(

"motifs:elec_max_threshold"

)

Referenced by process_for_motifs().

elec_min_threshold()

RealOptionKey const motifs::elec_min_threshold

(

"motifs:elec_min_threshold"

)

Referenced by process_for_motifs().

eliminate_weak_motifs()

BooleanOptionKey const motifs::eliminate_weak_motifs

(

"motifs:eliminate_weak_motifs"

)

expand_motifs()

BooleanOptionKey const motifs::expand_motifs

(

"motifs:expand_motifs"

)

fa_atr_cutoff()

RealOptionKey const motifs::fa_atr_cutoff

(

"motifs:fa_atr_cutoff"

)

fa_rep_cutoff()

RealOptionKey const motifs::fa_rep_cutoff

(

"motifs:fa_rep_cutoff"

)

file_prefix()

StringOptionKey const motifs::file_prefix

(

"motifs:file_prefix"

)

flex_sugar()

BooleanOptionKey const motifs::flex_sugar

(

"motifs:flex_sugar"

)

hb_score_cutoff()

RealOptionKey const motifs::hb_score_cutoff

(

"motifs:hb_score_cutoff"

)

hbond_max_threshold()

RealOptionKey const motifs::hbond_max_threshold

(

"motifs:hbond_max_threshold"

)

Referenced by process_for_motifs().

hbond_min_threshold()

RealOptionKey const motifs::hbond_min_threshold

(

"motifs:hbond_min_threshold"

)

Referenced by process_for_motifs().

highresdocker_allow_minimization()

BooleanOptionKey const motifs::highresdocker_allow_minimization

(

"motifs:highresdocker_allow_minimization"

)

highresdocker_allow_repacking()

BooleanOptionKey const motifs::highresdocker_allow_repacking

(

"motifs:highresdocker_allow_repacking"

)

highresdocker_use_all_residues()

BooleanOptionKey const motifs::highresdocker_use_all_residues

(

"motifs:highresdocker_use_all_residues"

)

keep_motif_xtal_location()

BooleanOptionKey const motifs::keep_motif_xtal_location

(

"motifs:keep_motif_xtal_location"

)

ligand_1_letter_code()

StringOptionKey const motifs::ligand_1_letter_code

(

"motifs:ligand_1_letter_code"

)

ligand_3_letter_code()

StringOptionKey const motifs::ligand_3_letter_code

(

"motifs:ligand_3_letter_code"

)

ligand_full_name()

StringOptionKey const motifs::ligand_full_name

(

"motifs:ligand_full_name"

)

ligand_motif_output_directory_name()

StringOptionKey const motifs::ligand_motif_output_directory_name

(

"motifs:ligand_motif_output_directory_name"

)

ligand_motif_output_file_name()

StringOptionKey const motifs::ligand_motif_output_file_name

(

"motifs:ligand_motif_output_file_name"

)

ligand_motif_sphere()

RealOptionKey const motifs::ligand_motif_sphere

(

"motifs:ligand_motif_sphere"

)

list_dnaconformers()

FileVectorOptionKey const motifs::list_dnaconformers

(

"motifs:list_dnaconformers"

)

list_motifs()

FileVectorOptionKey const motifs::list_motifs

(

"motifs:list_motifs"

)

max_depth()

IntegerOptionKey const motifs::max_depth

(

"motifs:max_depth"

)

minimize()

BooleanOptionKey const motifs::minimize

(

"motifs:minimize"

)

minimize_dna()

BooleanOptionKey const motifs::minimize_dna

(

"motifs:minimize_dna"

)

mol2_amino_acid()

StringOptionKey const motifs::mol2_amino_acid

(

"motifs:mol2_amino_acid"

)

mol2_directory_path()

StringOptionKey const motifs::mol2_directory_path

(

"motifs:mol2_directory_path"

)

mol2_file()

StringOptionKey const motifs::mol2_file

(

"motifs:mol2_file"

)

motif_build_defs()

StringVectorOptionKey const motifs::motif_build_defs

(

"motifs:motif_build_defs"

)

motif_build_positions()

IntegerVectorOptionKey const motifs::motif_build_positions

(

"motifs:motif_build_positions"

)

motif_filename()

StringOptionKey const motifs::motif_filename

(

"motifs:motif_filename"

)

Referenced by find_close_motifs().

motif_flexible_loop_file()

StringOptionKey const motifs::motif_flexible_loop_file

(

"motifs:motif_flexible_loop_file"

)

motif_output_directory()

StringOptionKey const motifs::motif_output_directory

(

"motifs:motif_output_directory"

)

motifs()

BooleanOptionKey const motifs::motifs

(

"motifs"

)

no_rotamer_bump()

BooleanOptionKey const motifs::no_rotamer_bump

(

"motifs:no_rotamer_bump"

)

num_repacks()

IntegerOptionKey const motifs::num_repacks

(

"motifs:num_repacks"

)

output_build_positions_only()

BooleanOptionKey const motifs::output_build_positions_only

(

"motifs:output_build_positions_only"

)

output_file()

StringOptionKey const motifs::output_file

(

"motifs:output_file"

)

output_ligand_pdb()

BooleanOptionKey const motifs::output_ligand_pdb

(

"motifs:output_ligand_pdb"

)

output_motifs()

BooleanOptionKey const motifs::output_motifs

(

"motifs:output_motifs"

)

output_motifs_as_pdb()

BooleanOptionKey const motifs::output_motifs_as_pdb

(

"motifs:output_motifs_as_pdb"

)

pack_max_threshold()

RealOptionKey const motifs::pack_max_threshold

(

"motifs:pack_max_threshold"

)

Referenced by process_for_motifs().

pack_min_threshold()

RealOptionKey const motifs::pack_min_threshold

(

"motifs:pack_min_threshold"

)

Referenced by process_for_motifs().

pack_score_cutoff()

RealOptionKey const motifs::pack_score_cutoff

(

"motifs:pack_score_cutoff"

)

params_custom_file_name()

StringOptionKey const motifs::params_custom_file_name

(

"motifs:params_custom_file_name"

)

params_directory_path()

StringOptionKey const motifs::params_directory_path

(

"motifs:params_directory_path"

)

place_adduct_waters()

BooleanOptionKey const motifs::place_adduct_waters

(

"motifs:place_adduct_waters"

)

preminimize_motif_pdbs()

BooleanOptionKey const motifs::preminimize_motif_pdbs

(

"motifs:preminimize_motif_pdbs"

)

preminimize_motif_pdbs_sconly()

BooleanOptionKey const motifs::preminimize_motif_pdbs_sconly

(

"motifs:preminimize_motif_pdbs_sconly"

)

protein_discovery_locus()

RealOptionKey const motifs::protein_discovery_locus

(

"motifs:protein_discovery_locus"

)

quick_and_dirty()

BooleanOptionKey const motifs::quick_and_dirty

(

"motifs:quick_and_dirty"

)

r1()

RealOptionKey const motifs::r1

(

"motifs:r1"

)

r2()

RealOptionKey const motifs::r2

(

"motifs:r2"

)

rerun_motifsearch()

BooleanOptionKey const motifs::rerun_motifsearch

(

"motifs:rerun_motifsearch"

)

residue_trim_file()

StringOptionKey const motifs::residue_trim_file

(

"motifs:residue_trim_file"

)

resolution_scale_factor()

IntegerOptionKey const motifs::resolution_scale_factor

(

"motifs:resolution_scale_factor"

)

restrict_to_wt()

BooleanOptionKey const motifs::restrict_to_wt

(

"motifs:restrict_to_wt"

)

rotlevel()

IntegerOptionKey const motifs::rotlevel

(

"motifs:rotlevel"

)

rots2add()

IntegerOptionKey const motifs::rots2add

(

"motifs:rots2add"

)

run_motifs()

BooleanOptionKey const motifs::run_motifs

(

"motifs:run_motifs"

)

sdf_directory_path()

StringOptionKey const motifs::sdf_directory_path

(

"motifs:sdf_directory_path"

)

special_rotweight()

RealOptionKey const motifs::special_rotweight

(

"motifs:special_rotweight"

)

specific_build_position()

RealOptionKey const motifs::specific_build_position

(

"motifs:specific_build_position"

)

target_aa()

StringOptionKey const motifs::target_aa

(

"motifs:target_aa"

)

Referenced by main().

target_dna_defs()

StringVectorOptionKey const motifs::target_dna_defs

(

"motifs:target_dna_defs"

)

verbosity()

BooleanOptionKey const motifs::verbosity

(

"motifs:verbosity"

)

water_score_cutoff()

RealOptionKey const motifs::water_score_cutoff

(

"motifs:water_score_cutoff"

)

write_param_to_pdb()

BooleanOptionKey const motifs::write_param_to_pdb

(

"motifs:write_param_to_pdb"

)

x_max_holes()

RealOptionKey const motifs::x_max_holes

(

"motifs:x_max_holes"

)

x_min_holes()

RealOptionKey const motifs::x_min_holes

(

"motifs:x_min_holes"

)

y_max_holes()

RealOptionKey const motifs::y_max_holes

(

"motifs:y_max_holes"

)

y_min_holes()

RealOptionKey const motifs::y_min_holes

(

"motifs:y_min_holes"

)

z1()

RealOptionKey const motifs::z1

(

"motifs:z1"

)

z2()

RealOptionKey const motifs::z2

(

"motifs:z2"

)

z_max_holes()

RealOptionKey const motifs::z_max_holes

(

"motifs:z_max_holes"

)

z_min_holes()

RealOptionKey const motifs::z_min_holes

(

"motifs:z_min_holes"

)