in Namespace Reference

Namespaces
	dbms
	file
	path
	rdf

Functions
BooleanOptionKey const	in ("in")
FileVectorOptionKey const	fconfig ("in:fconfig")
BooleanOptionKey const	no_fconfig ("in:no_fconfig")
BooleanOptionKey const	skip_classic_cart_setup ("in:skip_classic_cart_setup")
BooleanOptionKey const	skip_new_cart_setup ("in:skip_new_cart_setup")
StringOptionKey const	Ntermini ("in:Ntermini")
StringOptionKey const	Ctermini ("in:Ctermini")
BooleanOptionKey const	use_truncated_termini ("in:use_truncated_termini")
BooleanOptionKey const	ignore_unrecognized_res ("in:ignore_unrecognized_res")
BooleanOptionKey const	ignore_waters ("in:ignore_waters")
StringOptionKey const	water_type_if_unspecified ("in:water_type_if_unspecified")
BooleanOptionKey const	guarantee_no_DNA ("in:guarantee_no_DNA")
BooleanOptionKey const	add_orbitals ("in:add_orbitals")
BooleanOptionKey const	show_all_fixes ("in:show_all_fixes")
BooleanOptionKey const	include_sugars ("in:include_sugars")
BooleanOptionKey const	include_lipids ("in:include_lipids")
BooleanOptionKey const	include_surfaces ("in:include_surfaces")
BooleanOptionKey const	read_only_ATOM_entries ("in:read_only_ATOM_entries")
BooleanOptionKey const	auto_detect_glycan_connections ("in:auto_detect_glycan_connections")
RealOptionKey const	max_bond_length ("in:max_bond_length")
RealOptionKey const	min_bond_length ("in:min_bond_length")
RealOptionKey const	glycan_virtual_offset ("in:glycan_virtual_offset")
BooleanOptionKey const	membrane ("in:membrane")
RealOptionKey const	tuning_param ("in:tuning_param")
BooleanOptionKey const	remember_unrecognized_res ("in:remember_unrecognized_res")
BooleanOptionKey const	remember_unrecognized_water ("in:remember_unrecognized_water")
BooleanOptionKey const	preserve_crystinfo ("in:preserve_crystinfo")
BooleanOptionKey const	fast_restyping ("in:fast_restyping")
BooleanOptionKey const	detect_oops ("in:detect_oops")
BooleanOptionKey const	obey_ssbond ("in:obey_ssbond")
BooleanOptionKey const	detect_disulf ("in:detect_disulf")
RealOptionKey const	detect_disulf_tolerance ("in:detect_disulf_tolerance")
BooleanOptionKey const	constraints_from_link_records ("in:constraints_from_link_records")
BooleanOptionKey const	auto_setup_metals ("in:auto_setup_metals")
BooleanOptionKey const	prevent_auto_setup_metal_bb_variants ("in:prevent_auto_setup_metal_bb_variants")
RealOptionKey const	metals_detection_LJ_multiplier ("in:metals_detection_LJ_multiplier")
RealOptionKey const	metals_distance_constraint_multiplier ("in:metals_distance_constraint_multiplier")
RealOptionKey const	metals_angle_constraint_multiplier ("in:metals_angle_constraint_multiplier")
StringVectorOptionKey const	name3_property_codes ("in:name3_property_codes")
StringVectorOptionKey const	alternate_3_letter_codes ("in:alternate_3_letter_codes")
BooleanOptionKey const	maintain_links ("in:maintain_links")
FileOptionKey const	fix_disulf ("in:fix_disulf")
BooleanOptionKey const	missing_density_to_jump ("in:missing_density_to_jump")
IntegerVectorOptionKey const	target_residues ("in:target_residues")
IntegerVectorOptionKey const	replonly_residues ("in:replonly_residues")
BooleanOptionKey const	replonly_loops ("in:replonly_loops")
BooleanOptionKey const	use_database ("in:use_database")
StringVectorOptionKey const	select_structures_from_database ("in:select_structures_from_database")

Function Documentation

add_orbitals()

BooleanOptionKey const in::add_orbitals

(

"in:add_orbitals"

)

alternate_3_letter_codes()

StringVectorOptionKey const in::alternate_3_letter_codes

(

"in:alternate_3_letter_codes"

)

Referenced by basic::options::process().

auto_detect_glycan_connections()

BooleanOptionKey const in::auto_detect_glycan_connections

(

"in:auto_detect_glycan_connections"

)

auto_setup_metals()

BooleanOptionKey const in::auto_setup_metals

(

"in:auto_setup_metals"

)

constraints_from_link_records()

BooleanOptionKey const in::constraints_from_link_records

(

"in:constraints_from_link_records"

)

Ctermini()

StringOptionKey const in::Ctermini

(

"in:Ctermini"

)

detect_disulf()

BooleanOptionKey const in::detect_disulf

(

"in:detect_disulf"

)

Referenced by transform_pose().

detect_disulf_tolerance()

RealOptionKey const in::detect_disulf_tolerance

(

"in:detect_disulf_tolerance"

)

detect_oops()

BooleanOptionKey const in::detect_oops

(

"in:detect_oops"

)

fast_restyping()

BooleanOptionKey const in::fast_restyping

(

"in:fast_restyping"

)

fconfig()

FileVectorOptionKey const in::fconfig

(

"in:fconfig"

)

fix_disulf()

FileOptionKey const in::fix_disulf

(

"in:fix_disulf"

)

glycan_virtual_offset()

RealOptionKey const in::glycan_virtual_offset

(

"in:glycan_virtual_offset"

)

guarantee_no_DNA()

BooleanOptionKey const in::guarantee_no_DNA

(

"in:guarantee_no_DNA"

)

ignore_unrecognized_res()

BooleanOptionKey const in::ignore_unrecognized_res

(

"in:ignore_unrecognized_res"

)

Referenced by main().

ignore_waters()

BooleanOptionKey const in::ignore_waters

(

"in:ignore_waters"

)

Referenced by main().

in()

BooleanOptionKey const in::in

(

"in"

)

include_lipids()

BooleanOptionKey const in::include_lipids

(

"in:include_lipids"

)

include_sugars()

BooleanOptionKey const in::include_sugars

(

"in:include_sugars"

)

include_surfaces()

BooleanOptionKey const in::include_surfaces

(

"in:include_surfaces"

)

maintain_links()

BooleanOptionKey const in::maintain_links

(

"in:maintain_links"

)

max_bond_length()

RealOptionKey const in::max_bond_length

(

"in:max_bond_length"

)

membrane()

BooleanOptionKey const in::membrane

(

"in:membrane"

)

metals_angle_constraint_multiplier()

RealOptionKey const in::metals_angle_constraint_multiplier

(

"in:metals_angle_constraint_multiplier"

)

metals_detection_LJ_multiplier()

RealOptionKey const in::metals_detection_LJ_multiplier

(

"in:metals_detection_LJ_multiplier"

)

metals_distance_constraint_multiplier()

RealOptionKey const in::metals_distance_constraint_multiplier

(

"in:metals_distance_constraint_multiplier"

)

min_bond_length()

RealOptionKey const in::min_bond_length

(

"in:min_bond_length"

)

missing_density_to_jump()

BooleanOptionKey const in::missing_density_to_jump

(

"in:missing_density_to_jump"

)

Referenced by main().

name3_property_codes()

StringVectorOptionKey const in::name3_property_codes

(

"in:name3_property_codes"

)

no_fconfig()

BooleanOptionKey const in::no_fconfig

(

"in:no_fconfig"

)

Referenced by basic::options::pre_tracer_process().

Ntermini()

StringOptionKey const in::Ntermini

(

"in:Ntermini"

)

obey_ssbond()

BooleanOptionKey const in::obey_ssbond

(

"in:obey_ssbond"

)

preserve_crystinfo()

BooleanOptionKey const in::preserve_crystinfo

(

"in:preserve_crystinfo"

)

Referenced by basic::options::process().

prevent_auto_setup_metal_bb_variants()

BooleanOptionKey const in::prevent_auto_setup_metal_bb_variants

(

"in:prevent_auto_setup_metal_bb_variants"

)

read_only_ATOM_entries()

BooleanOptionKey const in::read_only_ATOM_entries

(

"in:read_only_ATOM_entries"

)

remember_unrecognized_res()

BooleanOptionKey const in::remember_unrecognized_res

(

"in:remember_unrecognized_res"

)

remember_unrecognized_water()

BooleanOptionKey const in::remember_unrecognized_water

(

"in:remember_unrecognized_water"

)

replonly_loops()

BooleanOptionKey const in::replonly_loops

(

"in:replonly_loops"

)

replonly_residues()

IntegerVectorOptionKey const in::replonly_residues

(

"in:replonly_residues"

)

select_structures_from_database()

StringVectorOptionKey const in::select_structures_from_database

(

"in:select_structures_from_database"

)

show_all_fixes()

BooleanOptionKey const in::show_all_fixes

(

"in:show_all_fixes"

)

skip_classic_cart_setup()

BooleanOptionKey const in::skip_classic_cart_setup

(

"in:skip_classic_cart_setup"

)

skip_new_cart_setup()

BooleanOptionKey const in::skip_new_cart_setup

(

"in:skip_new_cart_setup"

)

target_residues()

IntegerVectorOptionKey const in::target_residues

(

"in:target_residues"

)

Referenced by main(), and test().

tuning_param()

RealOptionKey const in::tuning_param

(

"in:tuning_param"

)

use_database()

BooleanOptionKey const in::use_database

(

"in:use_database"

)

use_truncated_termini()

BooleanOptionKey const in::use_truncated_termini

(

"in:use_truncated_termini"

)

water_type_if_unspecified()

StringOptionKey const in::water_type_if_unspecified

(

"in:water_type_if_unspecified"

)