PoseWrap Struct Reference

Inheritance diagram for PoseWrap:

Public Member Functions
	PoseWrap ()
void	dump_pdb (std::string fname)
char	ss (Size i) const
string	ss (Size i, Size l) const
void	ss (Size i, char c)
Size	which_subsub (Size i)
Size	which_sub (Size i)
	PoseWrap (string tag_in, vector1< core::pose::Pose > const &poses, vector1< Size > const &rel_attach, vector1< string > const &attach_atom, vector1< string > const &ss_pref, vector1< string > const &ss_suff, vector1< string > const &res_pref, vector1< string > const &res_suff, vector1< Size > const &attach_as_sc_in, string symm_def_template, string symm_def_template_reduced, vector1< vector1< Size > > const &design_res_in, vector1< vector1< Size > > const &rep_edge_res_in, vector1< vector1< Size > > const &fixed_res_in, vector1< vector1< Size > > const &frag_res_in, vector1< vector1< Size > > const &virtual_res_in, vector1< vector1< Size > > const &scattach_res_in, vector1< vector1< xyzVector< Size > > > const &jumpcut, vector1< vector1< Size > > const &cst_sub_files, vector1< bool > const &chainbreaks_in)
void	add_floating_sc_csts ()
void	set_root_atomno (Size i)
Size	set_root_atomno ()
bool	move_chi (Size rsd)
void	validate_set_reference ()
bool	validate ()
string	tag ()
void	dump_pdb (string fname, bool fullsymm=false)
bool	is_floating_sc (Size ir)
void	align_orig_pose (Size beg, Size end)
bool	switch_to_fa ()
bool	check ()
void	switch_to_cen ()
Size	get_closest_res_for_sc_attach (Size float_rsd)
void	update_designable_packable ()
bool	is_rsd_designable (Size i) const
bool	is_rsd_repackable (Size i) const
void	add_apcs_local (bool fullatom=false)
bool	check_scattach_res ()
bool	replace_scattach_res ()
Real	rms_to_orig_subsubs ()
Real	absrms_to_orig_subsubs ()
void	center ()
	PoseWrap ()
void	set_phi (Size seqpos, Real setting)

Public Attributes
core::pose::Pose	pose
Size	nsub
Size	attach
Size	nres
bool	hascst
string	tag_
core::pose::Pose	orig_pose
core::pose::Pose	validate_reference_
Size	primary_subsub
Size	root_atomno_
string	ss_
vector1< core::pose::Pose >	poses_
vector1< string >	attach_atom_
vector1< string >	ss_pref_
vector1< string >	ss_suff_
vector1< string >	attached_scattach_res_name_
vector1< Size >	attach_rsd_
vector1< Size >	jmpu_
vector1< Size >	jmpd_
vector1< Size >	cuts_
vector1< Size >	user_cuts_
vector1< Size >	subsub_fixed_begin
vector1< Size >	subsub_fixed_end
vector1< Size >	floating_scs_
vector1< Size >	attach_as_sc_
vector1< Size >	floating_scs_subsub_
vector1< Size >	floating_scs_sub_
vector1< Size >	design_res_user
vector1< Size >	fixed_res_user
vector1< Size >	frag_res_user
vector1< Size >	virtual_res_user
vector1< Size >	subsub_ends_
vector1< Size >	subsub_starts_
vector1< Size >	attached_scattach_res_
vector1< Size >	linker_res_
vector1< Size >	rep_edge_res_
std::map< Size, Size >	attach_to_region_
vector1< bool >	is_repackable_
vector1< bool >	is_designable_
vector1< bool >	chainbreaks_
vector1< core::chemical::ResidueTypeCOP >	res_types_
bool	has_floating_sc
core::conformation::symmetry::SymmDataOP	symm_data
core::conformation::symmetry::SymmDataOP	symm_data_full
core::chemical::ResidueTypeSetCAP	fa_residue_set_
core::chemical::ResidueTypeSetCAP	cen_residue_set_
vector1< vector1< Size > >	scattach_res_user
vector1< vector1< Size > >	cst_sub_files_
bool	debug

Constructor & Destructor Documentation

PoseWrap() [1/3]

PoseWrap::PoseWrap ( )

inline

Referenced by posewrap_from_command_line().

PoseWrap() [2/3]

PoseWrap::PoseWrap ( string  tag_in, vector1< core::pose::Pose > const &  poses, vector1< Size > const &  rel_attach, vector1< string > const &  attach_atom, vector1< string > const &  ss_pref, vector1< string > const &  ss_suff, vector1< string > const &  res_pref, vector1< string > const &  res_suff, vector1< Size > const &  attach_as_sc_in, string  symm_def_template, string  symm_def_template_reduced, vector1< vector1< Size > > const &  design_res_in, vector1< vector1< Size > > const &  rep_edge_res_in, vector1< vector1< Size > > const &  fixed_res_in, vector1< vector1< Size > > const &  frag_res_in, vector1< vector1< Size > > const &  virtual_res_in, vector1< vector1< Size > > const &  scattach_res_in, vector1< vector1< xyzVector< Size > > > const &  jumpcut, vector1< vector1< Size > > const &  cst_sub_files, vector1< bool > const &  chainbreaks_in  )

inline

References docking::a1, docking::a2, add_floating_sc_csts(), attach_as_sc_, basic::options::OptionKeys::smhybrid::attach_atom, attach_atom_, attach_rsd_, docking::b1, docking::b2, begin, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, cen_residue_set_, chainbreaks_, basic::options::OptionKeys::constraints::constraints, count, basic::options::OptionKeys::smhybrid::cst_sub_files, cst_sub_files_, cuts_, debug, basic::options::OptionKeys::smhybrid::debug, design_res_user, basic::options::OptionKeys::in::file::dssp, dump_pdb(), test.T009_Exceptions::e, end, utility::options::OptionKeys::options::exit, fa_residue_set_, detail::find(), fixed_res_user, floating_scs_, floating_scs_subsub_, frag_res_user, test.T020_Pose_Bindings::ft, h, has_floating_sc, create_a3b_hbs::i, test.T008_Serialization::iss, subloop_histogram::iterator, create_a3b_hbs::j, jmpd_, jmpu_, docking::jumps, basic::options::OptionKeys::smhybrid::linker_cst, linker_res_, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::edensity::mapfile, beta_sc_scan::name3, nres, nsub, basic::options::option, option, orig_pose, pose, basic::options::OptionKeys::mp::assembly::poses, poses_, primary_subsub, basic::options::OptionKeys::smhybrid::primary_subsubunit, basic::options::OptionKeys::smhybrid::pseudosym, rep_edge_res_, replace_string(), scattach_res_user, set_root_atomno(), subloop_histogram::size, ss_, ObjexxFCL::string_of(), subsub_ends_, subsub_fixed_begin, subsub_fixed_end, subsub_starts_, basic::options::OptionKeys::smhybrid::subsubs_attract, switch_to_cen(), switch_to_fa(), symm_data, symm_data_full, basic::options::OptionKeys::smhybrid::symm_def_template, basic::options::OptionKeys::smhybrid::symm_def_template_reduced, basic::options::OptionKeys::smhybrid::symm_file_tag, TR, basic::options::OptionKeys::inout::dbms::user, user_cuts_, utility_exit_with_message, basic::options::OptionKeys::parser::view, basic::options::OptionKeys::smhybrid::virtual_nterm, virtual_res_user, basic::Tracer::Warning, x, predPRE::y, and predPRE::z.

PoseWrap() [3/3]

PoseWrap::PoseWrap ( )

inline

Member Function Documentation

absrms_to_orig_subsubs()

Real PoseWrap::absrms_to_orig_subsubs ( )

inline

References create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, orig_pose, pose, loops_kic::rms, subsub_ends_, and subsub_starts_.

Referenced by report().

add_apcs_local()

void PoseWrap::add_apcs_local ( bool  fullatom = false )

inline

References add_apc(), cst_sub_files_, end, detail::find(), frag_res_user, basic::options::OptionKeys::in::file::fullatom, create_a3b_hbs::i, basic::options::OptionKeys::smhybrid::inter_subsub_cst, create_a3b_hbs::j, nres, basic::options::option, pose, res, ss(), basic::options::OptionKeys::cutoutdomain::start, subsub_fixed_begin, subsub_fixed_end, TR, and orn_macrocycle::wt.

Referenced by switch_to_cen(), and switch_to_fa().

add_floating_sc_csts()

void PoseWrap::add_floating_sc_csts ( )

inline

References basic::options::OptionKeys::smhybrid::attach_as_sc_sub, basic::options::OptionKeys::constraints::constraints, lactamize::cs, floating_scs_, floating_scs_sub_, floating_scs_subsub_, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, mc, nres, nsub, basic::options::option, pose, docking::s, scattach_res_user, TR, and utility_exit_with_message.

Referenced by PoseWrap().

align_orig_pose()

void PoseWrap::align_orig_pose ( Size  beg, Size  end  )

inline

References end, create_a3b_hbs::i, basic::options::initialize(), orig_pose, pose, residue, and superimpose_pose().

Referenced by rms_to_orig_subsubs(), and switch_to_fa().

center()

void PoseWrap::center ( )

inline

check()

bool PoseWrap::check ( )

inline

References attached_scattach_res_, attached_scattach_res_name_, utility::io::oc::cerr, debug, create_a3b_hbs::i, and pose.

Referenced by fa_refine_and_design().

check_scattach_res()

bool PoseWrap::check_scattach_res ( )

inline

References numeric::angle_radians(), numeric::xyzVector< T >::distance(), dump_pdb(), floating_scs_, create_a3b_hbs::i, create_a3b_hbs::j, option, pose, TR, up_jump_tree(), and utility_exit_with_message.

Referenced by cen_design(), design(), doit_refine(), fa_refine_and_design(), minimize(), replace_scattach_res(), switch_to_fa(), and validate().

dump_pdb() [1/2]

void PoseWrap::dump_pdb ( std::string  fname )

inline

References basic::options::OptionKeys::smhybrid::add_cavities, basic::options::OptionKeys::smhybrid::add_metal_at_0, PREcst::fname, basic::options::option, erraser_single_res_analysis::out, output_packstat_pdb(), and pose.

Referenced by cen_fold(), check_scattach_res(), doit_refine(), fa_refine_and_design(), PoseWrap(), replace_scattach_res(), and report().

dump_pdb() [2/2]

void PoseWrap::dump_pdb ( string  fname, bool  fullsymm = false  )

inline

References basic::options::OptionKeys::smhybrid::add_atom_at_cen, basic::options::OptionKeys::smhybrid::add_cavities, basic::options::OptionKeys::smhybrid::add_metal_at_0, attach_rsd_, attached_scattach_res_, predPRE::chain, numeric::distance_squared(), ObjexxFCL::format::F(), PREcst::fname, test.T020_Pose_Bindings::ft, create_a3b_hbs::i, create_a3b_hbs::j, extract_by_sidechain_sasa_score::l, numeric::max(), N, natoms(), nres, nsub, basic::options::OptionKeys::out::file::o, basic::options::option, option, erraser_single_res_analysis::out, output_packstat_pdb(), pose, docking::s, shift, tag_, utility::UPPERCASE_LETTERS(), and which_subsub().

get_closest_res_for_sc_attach()

Size PoseWrap::get_closest_res_for_sc_attach ( Size  float_rsd )

inline

References attached_scattach_res_, basic::options::OptionKeys::constraints::constraints, lactamize::cs, create_a3b_hbs::i, nres, pose, basic::options::OptionKeys::out::sf, TR, utility_exit_with_message, and basic::Tracer::Warning.

Referenced by replace_scattach_res(), and update_designable_packable().

is_floating_sc()

bool PoseWrap::is_floating_sc ( Size  ir )

inline

References detail::find(), and floating_scs_.

is_rsd_designable()

bool PoseWrap::is_rsd_designable ( Size  i ) const

inline

References create_a3b_hbs::i, and is_designable_.

Referenced by design().

is_rsd_repackable()

bool PoseWrap::is_rsd_repackable ( Size  i ) const

inline

References create_a3b_hbs::i, and is_repackable_.

Referenced by design(), and repack().

move_chi()

bool PoseWrap::move_chi ( Size  rsd )

inline

References attach_atom_, attach_rsd_, create_a3b_hbs::i, and pose.

replace_scattach_res()

bool PoseWrap::replace_scattach_res ( )

inline

References attached_scattach_res_, attached_scattach_res_name_, check_scattach_res(), basic::options::OptionKeys::constraints::constraints, lactamize::cs, debug, dump_pdb(), fa_residue_set_, floating_scs_, floating_scs_sub_, test.T020_Pose_Bindings::ft, get_closest_res_for_sc_attach(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, nres, nsub, pose, create_a3b_hbs::r, TR, and orn_macrocycle::wt.

Referenced by switch_to_fa().

rms_to_orig_subsubs()

Real PoseWrap::rms_to_orig_subsubs ( )

inline

References align_orig_pose(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, orig_pose, pose, loops_kic::rms, subsub_ends_, and subsub_starts_.

Referenced by report().

set_phi()

void PoseWrap::set_phi ( Size  seqpos, Real  setting  )

inline

References attach, and pose.

set_root_atomno() [1/2]

Size PoseWrap::set_root_atomno ( )

inline

References root_atomno_.

Referenced by PoseWrap().

set_root_atomno() [2/2]

void PoseWrap::set_root_atomno ( Size  i )

inline

References create_a3b_hbs::i, and root_atomno_.

ss() [1/3]

char PoseWrap::ss ( Size  i ) const

inline

References create_a3b_hbs::i, and ss_.

Referenced by add_apcs_local(), make_frag_set(), make_rand_ss_h(), make_rand_ss_hs(), and update_designable_packable().

ss() [2/3]

void PoseWrap::ss ( Size  i, char  c  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, and ss_.

ss() [3/3]

string PoseWrap::ss ( Size  i, Size  l  ) const

inline

References create_a3b_hbs::i, extract_by_sidechain_sasa_score::l, and ss_.

switch_to_cen()

void PoseWrap::switch_to_cen ( )

inline

References add_apcs_local(), attach, attach_rsd_, cen_residue_set_, basic::options::OptionKeys::smhybrid::centroid_all_val, detail::find(), floating_scs_, create_a3b_hbs::i, basic::options::initialize(), create_a3b_hbs::j, natoms(), nres, nsub, basic::options::option, option, pose, rep_edge_res_, res_types_, skip(), subsub_ends_, subsub_starts_, TR, basic::options::OptionKeys::smhybrid::virtual_nterm, and basic::Tracer::Warning.

Referenced by cen_fold(), and PoseWrap().

switch_to_fa()

bool PoseWrap::switch_to_fa ( )

inline

References add_apcs_local(), align_orig_pose(), attach, attach_rsd_, basic::options::OptionKeys::smhybrid::centroid_all_val, check_scattach_res(), debug, detail::find(), floating_scs_, create_a3b_hbs::i, basic::options::initialize(), create_a3b_hbs::j, natoms(), nres, nsub, basic::options::option, orig_pose, pose, rep_edge_res_, replace_scattach_res(), res_types_, subsub_fixed_begin, subsub_fixed_end, TR, and basic::Tracer::Warning.

Referenced by doit(), doit_refine(), and PoseWrap().

tag()

string PoseWrap::tag ( )

inline

References attached_scattach_res_, create_a3b_hbs::i, create_a3b_hbs::r, ObjexxFCL::string_of(), and tag_.

Referenced by doit(), pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::parsed_protocol(), posewrap_from_command_line(), and report().

update_designable_packable()

void PoseWrap::update_designable_packable ( )

inline

References attach_atom_, attach_rsd_, attached_scattach_res_, basic::options::OptionKeys::smhybrid::design, basic::options::OptionKeys::smhybrid::design_linker, design_res_user, numeric::distance_squared(), fa_residue_set_, detail::find(), fixed_res_user, floating_scs_, get_closest_res_for_sc_attach(), create_a3b_hbs::i, is_designable_, is_repackable_, create_a3b_hbs::j, linker_res_, nres, nsub, basic::options::option, pose, create_a3b_hbs::r, basic::options::OptionKeys::smhybrid::restrict_design_to_interface, basic::options::OptionKeys::smhybrid::restrict_design_to_subsub_interface, ss(), TR, which_sub(), and which_subsub().

Referenced by design(), and repack().

validate()

bool PoseWrap::validate ( )

inline

References check_scattach_res().

Referenced by PyMOL-Rosetta-relay-client.SecretInputDialog::start_server().

validate_set_reference()

void PoseWrap::validate_set_reference ( )

inline

References pose, and validate_reference_.

which_sub()

Size PoseWrap::which_sub ( Size  i )

inline

References create_a3b_hbs::i, and nres.

Referenced by update_designable_packable().

which_subsub()

Size PoseWrap::which_subsub ( Size  i )

inline

References create_a3b_hbs::i, create_a3b_hbs::j, nres, and subsub_ends_.

Referenced by dump_pdb(), MyRotMover::MyRotMover(), and update_designable_packable().

Member Data Documentation

attach

Size PoseWrap::attach

Referenced by cen_fold(), design(), make_pose(), set_phi(), switch_to_cen(), switch_to_cen(), switch_to_fa(), and switch_to_fa().

attach_as_sc_

vector1<Size> PoseWrap::attach_as_sc_

Referenced by PoseWrap().

attach_atom_

vector1<string> PoseWrap::attach_atom_

Referenced by move_chi(), PoseWrap(), report(), and update_designable_packable().

attach_rsd_

vector1<Size> PoseWrap::attach_rsd_

Referenced by dump_pdb(), move_chi(), PoseWrap(), report(), switch_to_cen(), switch_to_fa(), and update_designable_packable().

attach_to_region_

std::map<Size,Size> PoseWrap::attach_to_region_

attached_scattach_res_

vector1<Size> PoseWrap::attached_scattach_res_

Referenced by check(), design(), dump_pdb(), get_closest_res_for_sc_attach(), repack(), replace_scattach_res(), tag(), and update_designable_packable().

attached_scattach_res_name_

vector1<string> PoseWrap::attached_scattach_res_name_

Referenced by check(), and replace_scattach_res().

cen_residue_set_

core::chemical::ResidueTypeSetCAP PoseWrap::cen_residue_set_

Referenced by PoseWrap(), and switch_to_cen().

chainbreaks_

vector1<bool> PoseWrap::chainbreaks_

Referenced by PoseWrap().

cst_sub_files_

vector1<vector1<Size> > PoseWrap::cst_sub_files_

Referenced by add_apcs_local(), and PoseWrap().

cuts_

vector1<Size> PoseWrap::cuts_

Referenced by make_frag_set(), and PoseWrap().

debug

bool PoseWrap::debug

Referenced by cen_fold(), check(), fa_refine_and_design(), erraser_option.erraser_option::finalize(), PoseWrap(), erraser_option.erraser_option::read_cmdline_erraser(), erraser_option.erraser_option::read_cmdline_erraser_single_res(), erraser_option.erraser_option::read_cmdline_full(), replace_scattach_res(), and switch_to_fa().

design_res_user

vector1<Size> PoseWrap::design_res_user

Referenced by PoseWrap(), and update_designable_packable().

fa_residue_set_

core::chemical::ResidueTypeSetCAP PoseWrap::fa_residue_set_

Referenced by PoseWrap(), replace_scattach_res(), and update_designable_packable().

fixed_res_user

vector1<Size> PoseWrap::fixed_res_user

Referenced by PoseWrap(), and update_designable_packable().

floating_scs_

vector1<Size> PoseWrap::floating_scs_

Referenced by add_floating_sc_csts(), cen_design(), cen_fold(), check_scattach_res(), doit_refine(), is_floating_sc(), minimize(), PoseWrap(), replace_scattach_res(), report(), switch_to_cen(), switch_to_fa(), and update_designable_packable().

floating_scs_sub_

vector1<Size> PoseWrap::floating_scs_sub_

Referenced by add_floating_sc_csts(), and replace_scattach_res().

floating_scs_subsub_

vector1<Size> PoseWrap::floating_scs_subsub_

Referenced by add_floating_sc_csts(), and PoseWrap().

frag_res_user

vector1<Size> PoseWrap::frag_res_user

Referenced by add_apcs_local(), and PoseWrap().

has_floating_sc

bool PoseWrap::has_floating_sc

Referenced by cen_fold(), and PoseWrap().

hascst

bool PoseWrap::hascst

is_designable_

vector1<bool> PoseWrap::is_designable_

Referenced by is_rsd_designable(), and update_designable_packable().

is_repackable_

vector1<bool> PoseWrap::is_repackable_

Referenced by is_rsd_repackable(), and update_designable_packable().

jmpd_

vector1<Size> PoseWrap::jmpd_

Referenced by PoseWrap().

jmpu_

vector1<Size> PoseWrap::jmpu_

Referenced by PoseWrap().

linker_res_

vector1<Size> PoseWrap::linker_res_

Referenced by PoseWrap(), and update_designable_packable().

nres

Size PoseWrap::nres

Referenced by add_apcs_local(), add_floating_sc_csts(), cen_design(), cen_fold(), design(), dump_pdb(), find_clashes(), get_closest_res_for_sc_attach(), make_frag_set(), make_frag_set_9mers(), make_pose(), minimize(), MyRotMover::MyRotMover(), PoseWrap(), repack(), replace_scattach_res(), report(), switch_to_cen(), switch_to_cen(), switch_to_fa(), switch_to_fa(), symm_self_rep(), update_designable_packable(), which_sub(), and which_subsub().

nsub

Size PoseWrap::nsub

Referenced by add_floating_sc_csts(), dump_pdb(), make_pose(), MyRotMover::MyRotMover(), PoseWrap(), replace_scattach_res(), switch_to_cen(), switch_to_cen(), switch_to_fa(), switch_to_fa(), and update_designable_packable().

orig_pose

core::pose::Pose PoseWrap::orig_pose

Referenced by absrms_to_orig_subsubs(), align_orig_pose(), PoseWrap(), rms_to_orig_subsubs(), and switch_to_fa().

pose

core::pose::Pose PoseWrap::pose

Referenced by pyrosetta.bindings.pose.PoseScoreAccessor::__delitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iadd__(), pyrosetta.bindings.pose.PoseResidueAccessor::__imul__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iter__(), pyrosetta.bindings.pose.PoseResidueAccessor::__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__repr__(), pyrosetta.bindings.pose.PoseResidueAccessor::__reversed__(), pyrosetta.bindings.pose.PoseScoreAccessor::__setitem__(), absrms_to_orig_subsubs(), add_apcs_local(), add_floating_sc_csts(), align_orig_pose(), pyrosetta.bindings.pose.PoseScoreAccessor::all(), ChiMover::apply(), MySlideMover::apply(), MyTransMover::apply(), MyRotMover::apply(), FloatScRotMover::apply(), ScMinMover::apply(), BBMover::apply(), FloatScRandomChi::apply(), FloatScMonteCarlo::apply(), cen_design(), cen_fold(), check(), check_scattach_res(), ChiMover::ChiMover(), pyrosetta.bindings.pose.PoseScoreAccessor::clear(), design(), doit(), doit_refine(), dump_pdb(), pyrosetta.bindings.pose.PoseScoreAccessor::energies(), pyrosetta.bindings.pose.PoseScoreAccessor::extra(), fa_refine_and_design(), find_clashes(), flxbb_nobu(), get_closest_res_for_sc_attach(), interface_energy_ratio(), jumps_to_root(), main(), make_float_sc_min_mover(), make_pose(), minimize(), move_chi(), MyRotMover::MyRotMover(), MySlideMover::MySlideMover(), MyTransMover::MyTransMover(), PoseWrap(), repack(), replace_scattach_res(), report(), rms_to_orig_subsubs(), ScMinMover::ScMinMover(), set_phi(), switch_to_cen(), switch_to_cen(), switch_to_fa(), switch_to_fa(), symm_self_rep(), update_designable_packable(), pyrosetta.distributed.packed_pose.core.PackedPose::update_scores(), and validate_set_reference().

poses_

vector1<core::pose::Pose> PoseWrap::poses_

Referenced by PoseWrap().

primary_subsub

Size PoseWrap::primary_subsub

Referenced by PoseWrap().

rep_edge_res_

vector1<Size> PoseWrap::rep_edge_res_

Referenced by PoseWrap(), switch_to_cen(), and switch_to_fa().

res_types_

vector1<core::chemical::ResidueTypeCOP> PoseWrap::res_types_

Referenced by switch_to_cen(), and switch_to_fa().

root_atomno_

Size PoseWrap::root_atomno_

Referenced by set_root_atomno().

scattach_res_user

vector1<vector1<Size> > PoseWrap::scattach_res_user

Referenced by add_floating_sc_csts(), and PoseWrap().

ss_

string PoseWrap::ss_

Referenced by PoseWrap(), and ss().

ss_pref_

vector1<string> PoseWrap::ss_pref_

ss_suff_

vector1<string> PoseWrap::ss_suff_

subsub_ends_

vector1<Size> PoseWrap::subsub_ends_

Referenced by absrms_to_orig_subsubs(), MyRotMover::MyRotMover(), PoseWrap(), rms_to_orig_subsubs(), switch_to_cen(), and which_subsub().

subsub_fixed_begin

vector1<Size> PoseWrap::subsub_fixed_begin

Referenced by add_apcs_local(), PoseWrap(), and switch_to_fa().

subsub_fixed_end

vector1<Size> PoseWrap::subsub_fixed_end

Referenced by add_apcs_local(), PoseWrap(), and switch_to_fa().

subsub_starts_

vector1<Size> PoseWrap::subsub_starts_

Referenced by absrms_to_orig_subsubs(), MyRotMover::MyRotMover(), PoseWrap(), rms_to_orig_subsubs(), and switch_to_cen().

symm_data

core::conformation::symmetry::SymmDataOP PoseWrap::symm_data

Referenced by PoseWrap().

symm_data_full

core::conformation::symmetry::SymmDataOP PoseWrap::symm_data_full

Referenced by PoseWrap().

tag_

string PoseWrap::tag_

Referenced by dump_pdb(), and tag().

user_cuts_

vector1<Size> PoseWrap::user_cuts_

Referenced by PoseWrap().

validate_reference_

core::pose::Pose PoseWrap::validate_reference_

Referenced by validate_set_reference().

virtual_res_user

vector1<Size> PoseWrap::virtual_res_user

Referenced by PoseWrap().

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The documentation for this struct was generated from the following files:

• src/apps/pilot/will/old/bpy.cc
• src/apps/pilot/will/old/smhybrid.cc
• src/apps/pilot/will/old/spiro.cc