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core::pose::full_model_info::FullModelInfo Class Reference

Keep track of all information related to how a subpose 'fits in' to global modeling scheme. More...

#include <FullModelInfo.hh>

Inheritance diagram for core::pose::full_model_info::FullModelInfo:
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Public Member Functions

 FullModelInfo (std::string const &full_sequence, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &res_numbers_in_pose)
 
 FullModelInfo (FullModelParametersCOP full_model_parameters)
 
 FullModelInfo (pose::Pose &pose)
 
 FullModelInfo (FullModelInfo const &src)
 
 ~FullModelInfo () override
 
basic::datacache::CacheableDataOP clone () const override
 
FullModelInfoOP clone_info () const
 
FullModelParametersCOP full_model_parameters () const
 
void set_full_model_parameters (FullModelParametersCOP setting)
 
std::string const & full_sequence () const
 
std::string const & global_sequence () const
 
utility::vector1< Size > const & global_mapping () const
 
utility::vector1< int > const & conventional_numbering () const
 
utility::vector1< char > const & conventional_chains () const
 
utility::vector1< std::string >
const & 
conventional_segids () const
 
utility::vector1< Size > const & cutpoint_open_in_full_model () const
 
utility::vector1< Size > const & dock_domain_map () const
 
utility::vector1< Size > const & fixed_domain_map () const
 
utility::vector1< Size > const & input_domain_map () const
 
utility::vector1< Size > const & extra_minimize_res () const
 
utility::vector1< Size > const & preferred_root_res () const
 
utility::vector1< Size > const & sample_res () const
 
utility::vector1< Size > const & working_res () const
 
utility::vector1< Size > const & calc_rms_res () const
 
utility::vector1< Size > const & rna_syn_chi_res () const
 
utility::vector1< Size > const & rna_anti_chi_res () const
 
utility::vector1< Size > const & rna_terminal_res () const
 
utility::vector1< Size > const & rna_block_stack_above_res () const
 
utility::vector1< Size > const & rna_block_stack_below_res () const
 
utility::vector1< Size > const & rna_bulge_res () const
 
utility::vector1< Size > const & alignment_anchor_res () const
 
utility::vector1< Size > const & rna_sample_sugar_res () const
 
utility::vector1< std::pair
< Size, Size > > 
fiveprime_cap () const
 
utility::vector1< std::pair
< Size, Size > > 
jump_pairs () const
 
utility::vector1< std::pair
< Size, Size > > 
disulfide_pairs () const
 
utility::vector1< std::pair
< Size, Size > > 
cyclize_res () const
 
utility::vector1< std::pair
< Size, Size > > 
twoprime_res () const
 
utility::vector1< Size > const & jump_res_map () const
 
void clear_res_list ()
 
void clear_other_pose_list ()
 
utility::vector1
< core::pose::PoseOP > const & 
other_pose_list () const
 
utility::vector1< Size > const & res_list () const
 
utility::vector1< Sizefull_to_sub (utility::vector1< Size > const &res_in_full_model_numbering) const
 
Size full_to_sub (Size const res_in_full_model_numbering) const
 
utility::vector1< Sizesub_to_full (utility::vector1< Size > const &res) const
 
std::map< Size, Sizefull_to_sub () const
 
Size sub_to_full (Size const &res) const
 
void add_other_pose (core::pose::PoseOP pose)
 
void set_other_pose_list (utility::vector1< pose::PoseOP > const &setting)
 
void set_res_list (utility::vector1< Size > const &res_list)
 
void remove_other_pose_at_idx (Size const idx)
 
Size find_index_in_other_pose_list (pose::Pose const &pose) const
 
Size get_idx_for_other_pose_with_residues (utility::vector1< Size > const &input_res) const
 return index of pose in other_pose_list More...
 
Size get_idx_for_other_pose_with_residue (Size const input_res) const
 
Size get_idx_for_other_pose (pose::Pose const &pose) const
 
utility::vector1< Sizechains_in_full_model () const
 
Size size () const
 
utility::vector1
< SubMotifInfoOP > & 
submotif_info_list () const
 
bool is_a_submotif () const
 Return true if res_list_ matches a submotif exactly. More...
 
bool is_a_submotif_seed () const
 Return true if res_list_ matches a submotif_seed exactly. More...
 
bool is_a_submotif (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
 Return true if residues match a submotif exactly. More...
 
bool is_a_submotif_seed (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
 Return true if residues match a submotif_seed exactly. More...
 
SubMotifInfoOP submotif_info (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
 Return a submotif_info_op with matching residues (in full model numbering). More...
 
bool in_a_submotif (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
 Return true if residues are found in a submotif. More...
 
bool in_a_submotif_seed (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
 Return true if residues are found in a submotif_seed. More...
 
SubMotifInfoOP submotif_info_containing_residues (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
 Return the submotif_info_op that contains (but not limited to) input residues. More...
 
void update_submotif_info_list ()
 Delete submotif_infos with residues that are not found in res_list_. More...
 
void add_submotif_info (utility::vector1< Size > const &res_list, std::string const &tag, bool const &seed=false)
 Create new SubMotifInfoOP and add it to the submotif_info_list_. More...
 
void add_submotif_info (utility::vector1< SubMotifInfoOP > submotif_info_list)
 Add a list of SubMotifInfoOPs to the submotif_info_list_. More...
 
void add_submotif_info (SubMotifInfoOP submotif_info_op)
 Add a SubMotifInfoOP to the submotif_info_list_. More...
 
void delete_submotif_info (utility::vector1< Size > const &res_list, std::string const &tag, bool const &seed=false)
 Delete SubMotifInfoOP (with equal values) from submotif_info_list_. More...
 
void delete_submotif_info (utility::vector1< SubMotifInfoOP > submotif_info_list)
 Delete a list of SubMotifInfoOPs from submotif_info_list_. More...
 
void delete_submotif_info (SubMotifInfoOP submotif_info_op)
 Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true? More...
 
void show_submotif_info_list (bool const &for_all_poses=false) const
 Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true? More...
 

Private Member Functions

utility::vector1< Sizeget_cutpoint_open_from_pdb_info (pose::Pose const &pose) const
 
void get_sequence_with_gaps_filled_with_n (pose::Pose const &pose, std::string &sequence, utility::vector1< Size > &full_numbering) const
 

Private Attributes

utility::vector1< Sizeres_list_
 
utility::vector1
< core::pose::PoseOP
other_pose_list_
 
FullModelParametersCOP full_model_parameters_
 
utility::vector1< SubMotifInfoOPsubmotif_info_list_
 

Detailed Description

Keep track of all information related to how a subpose 'fits in' to global modeling scheme.

See FullModelParameters for more information on the global modeling scheme, including full_sequence, etc.

Constructor & Destructor Documentation

core::pose::full_model_info::FullModelInfo::FullModelInfo ( std::string const &  full_sequence,
utility::vector1< Size > const &  cutpoint_open_in_full_model,
utility::vector1< Size > const &  res_numbers_in_pose 
)
core::pose::full_model_info::FullModelInfo::FullModelInfo ( FullModelParametersCOP  full_model_parameters)
core::pose::full_model_info::FullModelInfo::FullModelInfo ( pose::Pose pose)
core::pose::full_model_info::FullModelInfo::FullModelInfo ( FullModelInfo const &  src)

Copy constructors must copy all data, not just some...

References other_pose_list_.

core::pose::full_model_info::FullModelInfo::~FullModelInfo ( )
overridedefault

Member Function Documentation

void core::pose::full_model_info::FullModelInfo::add_other_pose ( core::pose::PoseOP  pose)
void core::pose::full_model_info::FullModelInfo::add_submotif_info ( utility::vector1< Size > const &  res_list,
std::string const &  tag,
bool const &  seed = false 
)

Create new SubMotifInfoOP and add it to the submotif_info_list_.

Referenced by add_submotif_info().

void core::pose::full_model_info::FullModelInfo::add_submotif_info ( utility::vector1< SubMotifInfoOP submotif_info_list)

Add a list of SubMotifInfoOPs to the submotif_info_list_.

References add_submotif_info().

void core::pose::full_model_info::FullModelInfo::add_submotif_info ( SubMotifInfoOP  submotif_info_op)

Add a SubMotifInfoOP to the submotif_info_list_.

References submotif_info_list_.

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::alignment_anchor_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::calc_rms_res ( ) const
utility::vector1< Size > core::pose::full_model_info::FullModelInfo::chains_in_full_model ( ) const
void core::pose::full_model_info::FullModelInfo::clear_other_pose_list ( )

References other_pose_list_.

void core::pose::full_model_info::FullModelInfo::clear_res_list ( )

References res_list_.

basic::datacache::CacheableDataOP core::pose::full_model_info::FullModelInfo::clone ( ) const
inlineoverride
FullModelInfoOP core::pose::full_model_info::FullModelInfo::clone_info ( ) const
inline
utility::vector1< char > const & core::pose::full_model_info::FullModelInfo::conventional_chains ( ) const
utility::vector1< int > const & core::pose::full_model_info::FullModelInfo::conventional_numbering ( ) const
utility::vector1< std::string > const & core::pose::full_model_info::FullModelInfo::conventional_segids ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model ( ) const
utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::cyclize_res ( ) const
void core::pose::full_model_info::FullModelInfo::delete_submotif_info ( utility::vector1< Size > const &  res_list,
std::string const &  tag,
bool const &  seed = false 
)

Delete SubMotifInfoOP (with equal values) from submotif_info_list_.

Referenced by delete_submotif_info(), and update_submotif_info_list().

void core::pose::full_model_info::FullModelInfo::delete_submotif_info ( utility::vector1< SubMotifInfoOP submotif_info_list)

Delete a list of SubMotifInfoOPs from submotif_info_list_.

References delete_submotif_info().

void core::pose::full_model_info::FullModelInfo::delete_submotif_info ( SubMotifInfoOP  submotif_info_op)

Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true?

References submotif_info_list_.

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::disulfide_pairs ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::dock_domain_map ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::extra_minimize_res ( ) const
Size core::pose::full_model_info::FullModelInfo::find_index_in_other_pose_list ( pose::Pose const &  pose) const

References other_pose_list_.

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::fiveprime_cap ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::fixed_domain_map ( ) const
FullModelParametersCOP core::pose::full_model_info::FullModelInfo::full_model_parameters ( ) const
std::string const & core::pose::full_model_info::FullModelInfo::full_sequence ( ) const
utility::vector1< Size > core::pose::full_model_info::FullModelInfo::full_to_sub ( utility::vector1< Size > const &  res_in_full_model_numbering) const
Size core::pose::full_model_info::FullModelInfo::full_to_sub ( Size const  res_in_full_model_numbering) const

References res_list_.

std::map< Size, Size > core::pose::full_model_info::FullModelInfo::full_to_sub ( ) const

References res_list_, and size().

utility::vector1< Size > core::pose::full_model_info::FullModelInfo::get_cutpoint_open_from_pdb_info ( pose::Pose const &  pose) const
private
Size core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose ( pose::Pose const &  pose) const
Size core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue ( Size const  input_res) const
Size core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residues ( utility::vector1< Size > const &  input_res) const

return index of pose in other_pose_list

References get_idx_for_other_pose_with_residue().

void core::pose::full_model_info::FullModelInfo::get_sequence_with_gaps_filled_with_n ( pose::Pose const &  pose,
std::string &  sequence,
utility::vector1< Size > &  full_numbering 
) const
private
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::global_mapping ( ) const
std::string const & core::pose::full_model_info::FullModelInfo::global_sequence ( ) const
bool core::pose::full_model_info::FullModelInfo::in_a_submotif ( utility::vector1< Size > const &  res_list,
bool const &  check_other_poses = false 
) const
bool core::pose::full_model_info::FullModelInfo::in_a_submotif_seed ( utility::vector1< Size > const &  res_list,
bool const &  check_other_poses = false 
) const

Return true if residues are found in a submotif_seed.

References in_a_submotif(), and submotif_info_containing_residues().

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::input_domain_map ( ) const
bool core::pose::full_model_info::FullModelInfo::is_a_submotif ( ) const

Return true if res_list_ matches a submotif exactly.

References res_list_, and submotif_info_list_.

Referenced by is_a_submotif_seed(), and protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles().

bool core::pose::full_model_info::FullModelInfo::is_a_submotif ( utility::vector1< Size > const &  res_list,
bool const &  check_other_poses = false 
) const

Return true if residues match a submotif exactly.

References submotif_info().

bool core::pose::full_model_info::FullModelInfo::is_a_submotif_seed ( ) const
bool core::pose::full_model_info::FullModelInfo::is_a_submotif_seed ( utility::vector1< Size > const &  res_list,
bool const &  check_other_poses = false 
) const

Return true if residues match a submotif_seed exactly.

References is_a_submotif(), and submotif_info().

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::jump_pairs ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::jump_res_map ( ) const
utility::vector1< core::pose::PoseOP > const& core::pose::full_model_info::FullModelInfo::other_pose_list ( ) const
inline

References other_pose_list_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::already_instantiated_in_pose(), protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_already_docked(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_from_scratch_delete_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_other_poses(), core::io::silent::SilentStruct::fill_other_struct_list(), protocols::stepwise::monte_carlo::get_all_res_list(), core::pose::full_model_info::get_current_global_sequence(), core::pose::full_model_info::get_residue(), core::io::rna::get_rna_data_info(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::share_chains(), protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_recursively(), protocols::stepwise::modeler::switch_focus_among_poses_randomly(), protocols::stepwise::modeler::switch_focus_to_other_pose(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters(), and core::pose::full_model_info::update_pose_domain_map_const().

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::preferred_root_res ( ) const
void core::pose::full_model_info::FullModelInfo::remove_other_pose_at_idx ( Size const  idx)
utility::vector1< Size > const& core::pose::full_model_info::FullModelInfo::res_list ( ) const
inline

References res_list_.

Referenced by core::pose::rna::add_chi_constraints(), core::pose::full_model_info::add_new_sequence_into_global_sequence(), core::pose::full_model_info::append_virtual_residue_to_full_model_info(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), core::pose::full_model_info::check_all_residues_sampled(), protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), core::pose::full_model_info::check_sample_sugar_in_full_model_info(), core::pose::full_model_info::full_to_sub(), protocols::stepwise::monte_carlo::mover::AddMover::get_add_res(), core::pose::get_definite_terminal_root(), protocols::stepwise::modeler::get_domain_boundary_suites(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), get_idx_for_other_pose_with_residue(), core::pose::full_model_info::get_input_domain_from_full_model_info_const(), core::pose::full_model_info::get_move_elements_from_full_model_info_const(), core::pose::full_model_info::get_moving_res_from_full_model_info(), core::pose::full_model_info::get_moving_res_from_full_model_info_const(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), core::pose::full_model_info::get_residue(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), protocols::magnesium::remove_mg_bound_waters(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::modeler::reroot_based_on_full_model_info(), core::scoring::methods::FreeDOF_Energy::residue_energy(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), set_res_list(), core::scoring::rna::RNA_PartitionEnergy::set_up_residuearrayannealableenergy_for_packing(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::pose::stepwise_addable_pose_residue(), core::pose::full_model_info::sub_to_full(), submotif_info(), protocols::stepwise::modeler::test_merge_and_slice_with_two_helix_test_case(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_calc_rms_atom_id_map(), core::pose::full_model_info::update_constraint_set_from_full_model_info(), core::pose::full_model_info::update_disulfides_from_full_model_info(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters(), and core::pose::full_model_info::update_pose_domain_map_const().

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_anti_chi_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_block_stack_above_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_block_stack_below_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_bulge_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_sample_sugar_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_syn_chi_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_terminal_res ( ) const
utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::sample_res ( ) const
void core::pose::full_model_info::FullModelInfo::set_full_model_parameters ( FullModelParametersCOP  setting)
void core::pose::full_model_info::FullModelInfo::set_other_pose_list ( utility::vector1< pose::PoseOP > const &  setting)
void core::pose::full_model_info::FullModelInfo::set_res_list ( utility::vector1< Size > const &  res_list)
inline

References res_list(), and res_list_.

void core::pose::full_model_info::FullModelInfo::show_submotif_info_list ( bool const &  for_all_poses = false) const

Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true?

References core::pose::full_model_info::const_full_model_info(), other_pose_list_, show_submotif_info_list(), and submotif_info_list_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), and show_submotif_info_list().

Size core::pose::full_model_info::FullModelInfo::size ( ) const
utility::vector1< Size > core::pose::full_model_info::FullModelInfo::sub_to_full ( utility::vector1< Size > const &  res) const
Size core::pose::full_model_info::FullModelInfo::sub_to_full ( Size const &  res) const

References res_list_.

SubMotifInfoOP core::pose::full_model_info::FullModelInfo::submotif_info ( utility::vector1< Size > const &  res_list,
bool const &  check_other_poses = false 
) const
SubMotifInfoOP core::pose::full_model_info::FullModelInfo::submotif_info_containing_residues ( utility::vector1< Size > const &  res_list,
bool const &  check_other_poses = false 
) const
utility::vector1< SubMotifInfoOP >& core::pose::full_model_info::FullModelInfo::submotif_info_list ( ) const
inline
utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::twoprime_res ( ) const
void core::pose::full_model_info::FullModelInfo::update_submotif_info_list ( )

Delete submotif_infos with residues that are not found in res_list_.

References delete_submotif_info(), res_list_, and submotif_info_list_.

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::working_res ( ) const

Member Data Documentation

FullModelParametersCOP core::pose::full_model_info::FullModelInfo::full_model_parameters_
private
utility::vector1< core::pose::PoseOP > core::pose::full_model_info::FullModelInfo::other_pose_list_
private
utility::vector1< Size > core::pose::full_model_info::FullModelInfo::res_list_
private
utility::vector1< SubMotifInfoOP > core::pose::full_model_info::FullModelInfo::submotif_info_list_
mutableprivate

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