Rosetta Protocols  2014.35
Typedefs | Functions
protocols::stepwise::full_model_info Namespace Reference

Typedefs

typedef
utility::pointer::owning_ptr
< FullModelInfoSetupFromCommandLine > 
FullModelInfoSetupFromCommandLineOP
 
typedef
utility::pointer::owning_ptr
< FullModelInfoSetupFromCommandLine
const > 
FullModelInfoSetupFromCommandLineCOP
 

Functions

core::pose::PoseOP get_pdb_with_full_model_info (std::string const input_file, core::chemical::ResidueTypeSetCAP rsd_set)
 
core::pose::PoseOP get_pdb_and_cleanup (std::string const input_file, core::chemical::ResidueTypeSetCAP rsd_set)
 
void cleanup (pose::Pose &pose)
 
void initialize_native_and_align_pose (PoseOP &native_pose, PoseOP &align_pose, core::chemical::ResidueTypeSetCAP rsd_set)
 
pose::PoseOP initialize_pose_and_other_poses_from_command_line (core::chemical::ResidueTypeSetCAP rsd_set)
 
void get_other_poses (utility::vector1< pose::PoseOP > &other_poses, utility::vector1< std::string > const &other_files, core::chemical::ResidueTypeSetCAP rsd_set)
 
void fill_full_model_info_from_command_line (pose::Pose &pose)
 
void fill_full_model_info_from_command_line (vector1< PoseOP > &pose_ops)
 
void fill_full_model_info_from_command_line (pose::Pose &pose, vector1< PoseOP > &other_pose_ops)
 
std::string get_concatenated_sequence (vector1< core::sequence::SequenceCOP > const &fasta_sequences)
 
vector1< Sizeget_cutpoints (vector1< core::sequence::SequenceCOP > const &fasta_sequences)
 
void get_conventional_chains_and_numbering (vector1< core::sequence::SequenceCOP > const &fasta_sequences, vector1< char > &conventional_chains, vector1< int > &conventional_numbering)
 
void fill_full_model_info_from_command_line (vector1< Pose * > &pose_pointers)
 
void update_pose_fold_tree (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &extra_min_res, vector1< Size > const &sample_res, vector1< Size > const &jump_res, vector1< Size > const &root_res)
 
void define_chains (pose::Pose const &pose, vector1< vector1< Size > > &all_res_in_chain, vector1< vector1< Size > > &all_fixed_res_in_chain, vector1< Size > const &res_list, vector1< Size > const &moveable_res)
 
void setup_user_defined_jumps (vector1< Size > const &jump_res, vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< vector1< bool > > &chain_connected, vector1< Size > const &res_list, vector1< vector1< Size > > const &all_res_in_chain)
 
Size get_chain (Size const i, vector1< vector1< Size > > const &all_res_in_chain)
 
void setup_jumps (vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< vector1< bool > > &chain_connected, vector1< vector1< Size > > const &all_res_in_chain)
 
FoldTree get_tree (pose::Pose const &pose, vector1< Size > const &cuts, vector1< Size > const &jump_partners1, vector1< Size > const &jump_partners2)
 
FoldTree get_tree (Size const nres, vector1< Size > const &cuts, vector1< Size > const &jump_partners1, vector1< Size > const &jump_partners2, vector1< std::string > const &jump_atoms1, vector1< std::string > const &jump_atoms2)
 
void reroot (FoldTree &f, vector1< Size > const &res_list, vector1< Size > const &root_res)
 
void add_cutpoint_closed (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &cutpoint_closed)
 
void put_in_cutpoint (pose::Pose &pose, Size const i)
 
void add_virtual_sugar_res (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &virtual_sugar_res)
 
utility::vector1< Sizefigure_out_working_res (utility::vector1< Size > const &domain_map, utility::vector1< Size > const &sample_res)
 
utility::vector1< Sizefigure_out_sample_res (utility::vector1< Size > const &domain_map, utility::vector1< Size > const &working_res)
 
void check_working_res (utility::vector1< Size > const &working_res, utility::vector1< Size > const &domain_map, utility::vector1< Size > const &sample_res)
 

Typedef Documentation

Function Documentation

void protocols::stepwise::full_model_info::add_cutpoint_closed ( pose::Pose pose,
vector1< Size > const &  res_list,
vector1< Size > const &  cutpoint_closed 
)
void protocols::stepwise::full_model_info::add_virtual_sugar_res ( pose::Pose pose,
vector1< Size > const &  res_list,
vector1< Size > const &  virtual_sugar_res 
)
void protocols::stepwise::full_model_info::check_working_res ( utility::vector1< Size > const &  working_res,
utility::vector1< Size > const &  domain_map,
utility::vector1< Size > const &  sample_res 
)
void protocols::stepwise::full_model_info::cleanup ( pose::Pose pose)
void protocols::stepwise::full_model_info::define_chains ( pose::Pose const &  pose,
vector1< vector1< Size > > &  all_res_in_chain,
vector1< vector1< Size > > &  all_fixed_res_in_chain,
vector1< Size > const &  res_list,
vector1< Size > const &  moveable_res 
)
utility::vector1< core::Size > protocols::stepwise::full_model_info::figure_out_sample_res ( utility::vector1< Size > const &  domain_map,
utility::vector1< Size > const &  working_res 
)
utility::vector1< core::Size > protocols::stepwise::full_model_info::figure_out_working_res ( utility::vector1< Size > const &  domain_map,
utility::vector1< Size > const &  sample_res 
)
void protocols::stepwise::full_model_info::fill_full_model_info_from_command_line ( pose::Pose pose)
void protocols::stepwise::full_model_info::fill_full_model_info_from_command_line ( vector1< PoseOP > &  pose_ops)
void protocols::stepwise::full_model_info::fill_full_model_info_from_command_line ( pose::Pose pose,
vector1< PoseOP > &  other_pose_ops 
)
void protocols::stepwise::full_model_info::fill_full_model_info_from_command_line ( vector1< Pose * > &  pose_pointers)

References add_cutpoint_closed(), add_virtual_sugar_res(), core::pose::full_model_info::CALC_RMS, full_model::calc_rms_res, check_working_res(), full_model::cutpoint_closed, core::chemical::CUTPOINT_LOWER, core::pose::full_model_info::CUTPOINT_OPEN, full_model::cutpoint_open, core::chemical::CUTPOINT_UPPER, core::pose::Pose::data(), full_model::extra_min_res, core::pose::full_model_info::EXTRA_MINIMIZE, in::file::fasta, figure_out_sample_res(), figure_out_working_res(), core::pose::full_model_info::FIXED_DOMAIN, core::pose::Pose::fold_tree(), full_model::rna::force_syn_chi_res_list, core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, core::pose::full_model_info::get_chains_from_pdb_info(), get_concatenated_sequence(), get_conventional_chains_and_numbering(), get_cutpoints(), core::pose::full_model_info::get_res_num_from_pdb_info(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), full_model::jump_res, core::pose::full_model_info::make_sure_full_model_info_is_setup(), option, put_in_cutpoint(), core::sequence::read_fasta_file(), core::pose::Pose::residue_type(), core::pose::full_model_info::RNA_SYN_CHI, core::pose::full_model_info::RNA_TERMINAL, full_model::root_res, runtime_assert, core::pose::full_model_info::SAMPLE, sample_res, full_model::sample_res, basic::datacache::BasicDataCache::set(), full_model::rna::terminal_res, core::pose::Pose::total_residue(), core::pose::TR, core::pose::full_model_info::update_pdb_info_from_full_model_info(), update_pose_fold_tree(), user, utility_exit_with_message, full_model::virtual_sugar_res, core::pose::full_model_info::WORKING, working_res, and full_model::working_res.

Referenced by fill_full_model_info_from_command_line(), get_pdb_with_full_model_info(), and initialize_pose_and_other_poses_from_command_line().

core::Size protocols::stepwise::full_model_info::get_chain ( Size const  i,
vector1< vector1< Size > > const &  all_res_in_chain 
)

References has_value().

Referenced by setup_user_defined_jumps().

std::string protocols::stepwise::full_model_info::get_concatenated_sequence ( vector1< core::sequence::SequenceCOP > const &  fasta_sequences)
void protocols::stepwise::full_model_info::get_conventional_chains_and_numbering ( vector1< core::sequence::SequenceCOP > const &  fasta_sequences,
vector1< char > &  conventional_chains,
vector1< int > &  conventional_numbering 
)
vector1< Size > protocols::stepwise::full_model_info::get_cutpoints ( vector1< core::sequence::SequenceCOP > const &  fasta_sequences)
void protocols::stepwise::full_model_info::get_other_poses ( utility::vector1< pose::PoseOP > &  other_poses,
utility::vector1< std::string > const &  other_files,
core::chemical::ResidueTypeSetCAP  rsd_set 
)
core::pose::PoseOP protocols::stepwise::full_model_info::get_pdb_and_cleanup ( std::string const  input_file,
core::chemical::ResidueTypeSetCAP  rsd_set 
)
core::pose::PoseOP protocols::stepwise::full_model_info::get_pdb_with_full_model_info ( std::string const  input_file,
core::chemical::ResidueTypeSetCAP  rsd_set 
)
FoldTree protocols::stepwise::full_model_info::get_tree ( pose::Pose const &  pose,
vector1< Size > const &  cuts,
vector1< Size > const &  jump_partners1,
vector1< Size > const &  jump_partners2 
)
FoldTree protocols::stepwise::full_model_info::get_tree ( Size const  nres,
vector1< Size > const &  cuts,
vector1< Size > const &  jump_partners1,
vector1< Size > const &  jump_partners2,
vector1< std::string > const &  jump_atoms1,
vector1< std::string > const &  jump_atoms2 
)
void protocols::stepwise::full_model_info::initialize_native_and_align_pose ( PoseOP native_pose,
PoseOP align_pose,
core::chemical::ResidueTypeSetCAP  rsd_set 
)
core::pose::PoseOP protocols::stepwise::full_model_info::initialize_pose_and_other_poses_from_command_line ( core::chemical::ResidueTypeSetCAP  rsd_set)
void protocols::stepwise::full_model_info::put_in_cutpoint ( pose::Pose pose,
Size const  i 
)
void protocols::stepwise::full_model_info::reroot ( FoldTree f,
vector1< Size > const &  res_list,
vector1< Size > const &  root_res 
)
void protocols::stepwise::full_model_info::setup_jumps ( vector1< Size > &  jump_partners1,
vector1< Size > &  jump_partners2,
vector1< vector1< bool > > &  chain_connected,
vector1< vector1< Size > > const &  all_res_in_chain 
)

Referenced by update_pose_fold_tree().

void protocols::stepwise::full_model_info::setup_user_defined_jumps ( vector1< Size > const &  jump_res,
vector1< Size > &  jump_partners1,
vector1< Size > &  jump_partners2,
vector1< vector1< bool > > &  chain_connected,
vector1< Size > const &  res_list,
vector1< vector1< Size > > const &  all_res_in_chain 
)
void protocols::stepwise::full_model_info::update_pose_fold_tree ( pose::Pose pose,
vector1< Size > const &  res_list,
vector1< Size > const &  extra_min_res,
vector1< Size > const &  sample_res,
vector1< Size > const &  jump_res,
vector1< Size > const &  root_res 
)