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core::import_pose Namespace Reference

Namespaces

 atom_tree_diffs
 
 libraries
 
 options
 
 pose_stream
 

Classes

class  FullModelPoseBuilder
 
class  ImportPoseOptions
 This class contains all of the data which is used in the process of reading a PDB into a Pose. There is actually a substantial amount of data! More...
 
class  PDBSilentStruct
 
class  PDBSilentStructCreator
 creator for the PDBSilentStruct class More...
 
class  PoseResource
 
class  PoseResourceLoader
 
class  PoseResourceLoaderCreator
 
class  RNA_BasePairHandler
 
class  RNA_DeNovoParameters
 
class  RNA_DeNovoSetup
 
class  RNA_HelixAssembler
 The RNA de novo structure modeling protocol. More...
 
class  RNA_JumpMover
 

Typedefs

typedef std::string String
 
typedef
utility::pointer::shared_ptr
< ImportPoseOptions
ImportPoseOptionsOP
 
typedef
utility::pointer::shared_ptr
< ImportPoseOptions const > 
ImportPoseOptionsCOP
 
typedef
utility::pointer::shared_ptr
< PoseResource
PoseResourceOP
 
typedef
utility::pointer::shared_ptr
< PoseResource const > 
PoseResourceCOP
 
typedef
utility::pointer::shared_ptr
< PoseResourceLoader
PoseResourceLoaderOP
 
typedef
utility::pointer::shared_ptr
< PoseResourceLoader const > 
PoseResourceLoaderCOP
 
typedef
utility::pointer::shared_ptr
< RNA_BasePairHandler
RNA_BasePairHandlerOP
 
typedef
utility::pointer::shared_ptr
< RNA_BasePairHandler const > 
RNA_BasePairHandlerCOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoParameters
RNA_DeNovoParametersOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoParameters const > 
RNA_DeNovoParametersCOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoSetup
RNA_DeNovoSetupOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoSetup const > 
RNA_DeNovoSetupCOP
 
typedef
utility::pointer::shared_ptr
< RNA_HelixAssembler
RNA_HelixAssemblerOP
 
typedef
utility::pointer::shared_ptr
< RNA_JumpMover
RNA_JumpMoverOP
 
typedef
utility::pointer::shared_ptr
< RNA_JumpMover const > 
RNA_JumpMoverCOP
 

Enumerations

enum  FileType {
  PDB_file =1, CIF_file, MMTF_file, SRLZ_file,
  end_of_filetype_list, Unknown_file = end_of_filetype_list
}
 Enum for the file type. More...
 

Functions

static basic::Tracer TR ("core.import_pose.import_pose")
 
static basic::Tracer TR ("core.import_pose.import_pose")
 
std::ostream & operator<< (std::ostream &stream, FileType type)
 
std::string extension_from_filetype (FileType const filetype)
 Given a filetype, return the string for the extension. More...
 
void read_all_poses (utility::vector1< std::string > const &filenames, utility::vector1< core::pose::PoseOP > &poses)
 
void read_additional_pdb_data (std::string const &s, pose::Pose &pose, io::StructFileRepCOP, bool read_fold_tree)
 
void read_additional_pdb_data (std::string const &s, pose::Pose &pose, ImportPoseOptions const &options, bool read_fold_tree)
 
pose::PoseOP pose_from_file (std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Returns a PoseOP object from the Pose created from input PDB <filename> More...
 
pose::PoseOP pose_from_file (std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 Returns a PoseOP object from the Pose created from input PDB <filename>, taking a set of custom ImportPoseOptions parameters. More...
 
pose::PoseOP pose_from_file (chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Returns a PoseOP object from the Pose created by reading the input PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
 
FileType determine_file_type (std::string const &contents_of_file)
 Determine what file type is passed to function there should only be one function that calls this, pose_from_file and only calls it when the filetype is unknown. More...
 
void pose_from_file (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType file_type)
 
void pose_from_file (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads in data from input PDB <filename> and stores it in the Pose <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
 
void pose_from_file (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads in data from input PDB <filename> and stores it in the Pose <pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default. More...
 
void pose_from_file (pose::Pose &pose, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::PoseOP
poseOPs_from_files (utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::PoseOP
poseOPs_from_files (utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::Pose
poses_from_files (utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::Pose
poses_from_files (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::PoseOP
poseOPs_from_files (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
void pose_from_file (utility::vector1< pose::Pose > &poses, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using the FA_STANDARD ResidueTypeSet (fullatom) More...
 
void pose_from_file (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using ResidueTypeSet <residue_set> More...
 
void pose_from_file (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, ImportPoseOptions const &options, std::string const &filename)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, std::string const &filename)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
 
void pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options, std::string const &filename)
 
void pose_from_pdb_stream (pose::Pose &pose, std::istream &pdb_stream, std::string const &filename, ImportPoseOptions const &options)
 
void centroid_pose_from_pdb (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false)
 Reads in data from input PDB <filename> and stores it in the Pose <pose> using the CENTROID ResidueTypeSet (centroid) More...
 
void build_pose (io::StructFileRepOP fd,pose::Pose &pose, chemical::ResidueTypeSet const &residue_set)
 Create pose object, using given StructFileRep object. If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line. More...
 
void build_pose (io::StructFileRepOP fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
 Build Rosetta 3 Pose object from StructFileRep. More...
 
void build_pose_as_is (io::StructFileRepOP sfr, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
 Try to Build pose object from pdb 'as-is'. PDB file must be really clean. More...
 
void build_pose_as_is2 (io::StructFileRepCOP, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, ImportPoseOptions const &options)
 
pose::PoseOP initialize_pose_and_other_poses_from_command_line (core::chemical::ResidueTypeSetCOP rsd_set)
 
PoseOP initialize_pose_and_other_poses_from_options (core::chemical::ResidueTypeSetCOP rsd_set, utility::options::OptionCollection const &options)
 
PoseOP initialize_pose_and_other_poses_from_options_and_input_poses (core::chemical::ResidueTypeSetCOP rsd_set, utility::options::OptionCollection const &options, utility::vector1< pose::PoseOP > &input_poses)
 
void get_other_poses (utility::vector1< pose::PoseOP > &other_poses, utility::vector1< std::string > const &other_files, core::chemical::ResidueTypeSetCOP rsd_set)
 
core::pose::PoseOP get_pdb_with_full_model_info (std::string const &input_file, core::chemical::ResidueTypeSetCOP rsd_set)
 
core::pose::PoseOP get_pdb_and_cleanup (std::string const &input_file)
 
core::pose::PoseOP get_pdb_and_cleanup (std::string const &input_file, core::chemical::ResidueTypeSetCOP rsd_set)
 
void cleanup (pose::Pose &pose, bool const force_cut_at_rna_chainbreak)
 
FullModelParametersOP get_sequence_information (std::string const &fasta_file, vector1< Size > &cutpoint_open_in_full_model, bool const append_virtual)
 
void setup_for_density_scoring (core::pose::Pose &pose)
 
vector1< Sizeget_cutpoints_from_numbering (vector1< core::sequence::SequenceCOP > const &fasta_sequences, vector1< char > const &conventional_chains, vector1< std::string > const &conventional_segids, vector1< int > const &conventional_numbering)
 
void get_extra_cutpoints_from_names (Size const nres, vector1< Size > &cutpoints, std::map< Size, std::string > const &non_standard_residue_map)
 
vector1< Sizeget_cutpoints (vector1< core::sequence::SequenceCOP > const &fasta_sequences, std::map< Size, std::string > const &non_standard_residue_map, vector1< char > const &conventional_chains, vector1< int > const &conventional_numbering, vector1< std::string > const &conventional_segids)
 
void setup_water_bank_for_magnesiums (std::map< Size, std::string > &non_standard_residue_map, vector1< core::sequence::SequenceOP > &fasta_sequences)
 
void look_for_dna (vector1< core::sequence::SequenceOP > &fasta_sequences)
 
void setup_fold_trees (vector1< Pose * > &pose_pointers, vector1< Size > &cutpoint_open_in_full_model, vector1< Size > &fixed_domain_map, vector1< Size > const &cutpoint_closed, vector1< Size > const &extra_minimize_res, vector1< Size > const &extra_minimize_jump_res, vector1< Size > const &sample_res, vector1< Size > const &working_res, vector1< Size > const &jump_res, vector1< Size > const &preferred_root_res, vector1< Size > const &virtual_sugar_res, FullModelParameters const &full_model_parameters, vector1< vector1< Size > > const &pose_res_lists)
 
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, core::pose::full_model_info::FullModelParameters const &full_model_parameters)
 
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< pair< Size, Size > > &chain_connections, 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 (core::pose::Pose const &pose, vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< pair< Size, Size > > &chain_connections, vector1< vector1< Size > > const &all_res_in_chain, std::tuple< vector1< int >, vector1< char >, vector1< std::string > > const &resnum_and_chain_and_segid_in_pose)
 
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 update_fixed_domain_from_extra_minimize_jump_pairs (utility::vector1< Size > &fixed_domain, pose::Pose const &pose, utility::vector1< Size > const &res_list, utility::vector1< pair< Size, Size > > const &extra_minimize_jump_pairs)
 
void update_fixed_domain_from_extra_minimize_jump_res (vector1< Size > &fixed_domain, pose::Pose const &pose, vector1< Size > const &res_list, vector1< Size > const &extra_minimize_jump_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 &input_domain_map, utility::vector1< Size > const &sample_res)
 
utility::vector1< Sizefigure_out_sample_res (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &working_res)
 
void check_working_res (utility::vector1< Size > const &working_res, utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &sample_res)
 
void figure_out_motif_mode (utility::vector1< Size > &extra_min_res, utility::vector1< Size > &terminal_res, utility::vector1< Size > const &working_res, utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model)
 
void update_jump_res (utility::vector1< Size > &jump_res, utility::vector1< Size > const &extra_minimize_jump_res)
 
void add_block_stack_variants (vector1< pose::Pose * > const &pose_pointers, vector1< vector1< Size > > const &pose_res_lists, vector1< Size > const &block_stack_above_res, vector1< Size > const &block_stack_below_res)
 
void check_extra_minimize_res_are_input (utility::vector1< core::Size > const &extra_minimize_res, utility::vector1< core::Size > const &input_domain_map)
 
utility::vector1< Sizefigure_out_fixed_domain_map (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &extra_minimize_res)
 
utility::vector1< Sizefigure_out_dock_domain_map (utility::vector1< Size > &cutpoint_open_in_full_model, utility::vector1< utility::vector1< Size > > const &pose_res_lists, utility::vector1< Size > const &working_res, utility::vector1< Size > const &sample_res, Size const nres)
 
void reorder_pose (pose::Pose &pose, utility::vector1< Size > &res_list)
 
bool just_modeling_RNA (utility::vector1< std::string > const &fasta_files)
 
void initialize_native_and_align_pose (PoseOP &native_pose, PoseOP &align_pose, core::chemical::ResidueTypeSetCOP rsd_set, PoseCOP start_pose)
 
void process_input_file (std::string const &input_file, utility::vector1< pose::PoseOP > &pose_list, bool is_pdb, bool coarse_rna)
 
bool compare_RNA_char (char const char1, char const char2)
 
bool compare_RNA_secstruct (char const char1, char const char2)
 
std::string const convert_based_on_match_type (std::string const &RNA_string, Size const type)
 
Size get_anchor_rsd (pose::Pose const &pose)
 
bool involved_in_phosphate_torsion (std::string atomname)
 
void remove_cutpoint_closed (pose::Pose &pose, Size const i)
 
void remove_cutpoints_closed (pose::Pose &pose)
 
void make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)
 
void make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)
 
void get_other_poses (utility::vector1< core::pose::PoseOP > &other_poses, utility::vector1< std::string > const &other_files, core::chemical::ResidueTypeSetCOP rsd_set)
 
core::pose::full_model_info::FullModelParametersOP get_sequence_information (std::string const &fasta_file, utility::vector1< core::Size > &cutpoint_open_in_full_model, bool const add_virt=false)
 
void get_extra_cutpoints_from_names (core::Size const nres, utility::vector1< core::Size > &cutpoints, std::map< core::Size, std::string > const &non_standard_residue_map)
 
void setup_fold_trees (utility::vector1< core::pose::Pose * > &pose_pointers, utility::vector1< core::Size > &cutpoint_open_in_full_model, utility::vector1< core::Size > &fixed_domain_map, utility::vector1< core::Size > const &cutpoint_closed, utility::vector1< core::Size > const &extra_minimize_res, utility::vector1< core::Size > const &extra_minimize_jump_res, utility::vector1< core::Size > const &sample_res, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &jump_res, utility::vector1< core::Size > const &preferred_root_res, utility::vector1< core::Size > const &virtual_sugar_res, core::pose::full_model_info::FullModelParameters const &full_model_parameters, utility::vector1< utility::vector1< core::Size > > const &pose_res_lists)
 
void update_pose_fold_tree (core::pose::Pose &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &extra_min_res, utility::vector1< core::Size > const &sample_res, utility::vector1< core::Size > const &jump_res, core::pose::full_model_info::FullModelParameters const &full_model_parameters)
 
void define_chains (core::pose::Pose const &pose, utility::vector1< utility::vector1< core::Size > > &all_res_in_chain, utility::vector1< utility::vector1< core::Size > > &all_fixed_res_in_chain, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &extra_min_res)
 
void setup_user_defined_jumps (utility::vector1< core::Size > const &jump_res, utility::vector1< core::Size > &jump_partners1, utility::vector1< core::Size > &jump_partners2, utility::vector1< std::pair< core::Size, core::Size > > &chain_connections, utility::vector1< core::Size > const &res_list, utility::vector1< utility::vector1< core::Size > > const &all_res_in_chain)
 
core::Size get_chain (core::Size const i, utility::vector1< utility::vector1< core::Size > > const &all_res_in_chain)
 
void setup_jumps (core::pose::Pose const &pose, utility::vector1< core::Size > &jump_partners1, utility::vector1< core::Size > &jump_partners2, utility::vector1< std::pair< core::Size, core::Size > > &chain_connections, utility::vector1< utility::vector1< core::Size > > const &all_res_in_chain, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &resnum_and_chain_and_segid_in_pose)
 
core::kinematics::FoldTree get_tree (core::pose::Pose const &pose, utility::vector1< core::Size > const &cuts, utility::vector1< core::Size > const &jump_partners1, utility::vector1< core::Size > const &jump_partners2)
 
core::kinematics::FoldTree get_tree (core::Size const nres, utility::vector1< core::Size > const &cuts, utility::vector1< core::Size > const &jump_partners1, utility::vector1< core::Size > const &jump_partners2, utility::vector1< std::string > const &jump_atoms1, utility::vector1< std::string > const &jump_atoms2)
 
void update_fixed_domain_from_extra_minimize_jump_res (utility::vector1< core::Size > &fixed_domain, core::pose::Pose const &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &extra_minimize_jump_res)
 
void add_cutpoint_closed (core::pose::Pose &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &cutpoint_closed)
 
void add_virtual_sugar_res (core::pose::Pose &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &virtual_sugar_res)
 
utility::vector1< core::Sizefigure_out_working_res (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &sample_res)
 
utility::vector1< core::Sizefigure_out_sample_res (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &working_res)
 
void check_working_res (utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &sample_res)
 
void figure_out_motif_mode (utility::vector1< core::Size > &extra_min_res, utility::vector1< core::Size > &terminal_res, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &cutpoint_open_in_full_model)
 
void add_block_stack_variants (utility::vector1< core::pose::Pose * > const &pose_pointers, utility::vector1< utility::vector1< core::Size > > const &pose_res_lists, utility::vector1< core::Size > const &block_stack_above_res, utility::vector1< core::Size > const &block_stack_below_res)
 
void update_jump_res (utility::vector1< core::Size > &jump_res, utility::vector1< core::Size > const &extra_minimize_jump_res)
 
utility::vector1< core::Sizefigure_out_fixed_domain_map (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &extra_minimize_res)
 
utility::vector1< core::Sizefigure_out_dock_domain_map (utility::vector1< core::Size > &cutpoint_open_in_full_model, utility::vector1< utility::vector1< core::Size > > const &pose_res_lists, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &sample_res, core::Size const nres)
 
void reorder_pose (core::pose::Pose &pose, utility::vector1< core::Size > &res_list)
 
void look_for_dna (utility::vector1< core::sequence::SequenceOP > &fasta_sequences)
 
void setup_water_bank_for_magnesiums (std::map< Size, std::string > &non_standard_residue_map, utility::vector1< core::sequence::SequenceOP > &fasta_sequences)
 
utility::vector1< Sizeget_cutpoints (utility::vector1< core::sequence::SequenceCOP > const &fasta_sequences, std::map< Size, std::string > const &non_standard_residue_map, utility::vector1< char > const &conventional_chains, utility::vector1< int > const &conventional_numbering, utility::vector1< std::string > const &conventional_segids)
 
void process_input_file (std::string const &silent_file, utility::vector1< core::pose::PoseOP > &pose_list, bool is_pdb=false, bool coarse_rna=false)
 
static basic::Tracer tr ("core.import_pose.import_pose_options")
 
static basic::Tracer tr ("core.io.silent.PDBSilentStruct")
 
std::string ctname_for_pose_resource_loader (std::string const &element_name)
 
int const MAX_BULGE_LENGTH (3)
 
void dump_stems (RNA_SecStruct const &working_secstruct, std::string const &working_sequence, core::pose::full_model_info::FullModelParameters const &full_model_parameters)
 
bool is_blank_seq (char const &c)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ImportPoseOptions const > core::import_pose::ImportPoseOptionsCOP
typedef utility::pointer::shared_ptr< ImportPoseOptions > core::import_pose::ImportPoseOptionsOP
typedef utility::pointer::shared_ptr< PoseResource const > core::import_pose::PoseResourceCOP
typedef utility::pointer::shared_ptr< PoseResourceLoader const > core::import_pose::PoseResourceLoaderCOP
typedef utility::pointer::shared_ptr< PoseResourceLoader > core::import_pose::PoseResourceLoaderOP
typedef utility::pointer::shared_ptr< PoseResource > core::import_pose::PoseResourceOP
typedef utility::pointer::shared_ptr< RNA_BasePairHandler const > core::import_pose::RNA_BasePairHandlerCOP
typedef utility::pointer::shared_ptr< RNA_BasePairHandler > core::import_pose::RNA_BasePairHandlerOP
typedef utility::pointer::shared_ptr< RNA_DeNovoParameters const > core::import_pose::RNA_DeNovoParametersCOP
typedef utility::pointer::shared_ptr< RNA_DeNovoParameters > core::import_pose::RNA_DeNovoParametersOP
typedef utility::pointer::shared_ptr< RNA_DeNovoSetup const > core::import_pose::RNA_DeNovoSetupCOP
typedef utility::pointer::shared_ptr< RNA_DeNovoSetup > core::import_pose::RNA_DeNovoSetupOP
typedef utility::pointer::shared_ptr< RNA_HelixAssembler > core::import_pose::RNA_HelixAssemblerOP
typedef utility::pointer::shared_ptr< RNA_JumpMover const > core::import_pose::RNA_JumpMoverCOP
typedef utility::pointer::shared_ptr< RNA_JumpMover > core::import_pose::RNA_JumpMoverOP
typedef std::string core::import_pose::String

Enumeration Type Documentation

Enum for the file type.

If you add to this list, update the extension_from_filetype function!

Enumerator
PDB_file 
CIF_file 
MMTF_file 
SRLZ_file 
end_of_filetype_list 
Unknown_file 

Function Documentation

void core::import_pose::add_block_stack_variants ( utility::vector1< core::pose::Pose * > const &  pose_pointers,
utility::vector1< utility::vector1< core::Size > > const &  pose_res_lists,
utility::vector1< core::Size > const &  block_stack_above_res,
utility::vector1< core::Size > const &  block_stack_below_res 
)
void core::import_pose::add_block_stack_variants ( vector1< pose::Pose * > const &  pose_pointers,
vector1< vector1< Size > > const &  pose_res_lists,
vector1< Size > const &  block_stack_above_res,
vector1< Size > const &  block_stack_below_res 
)
void core::import_pose::add_cutpoint_closed ( core::pose::Pose pose,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  cutpoint_closed 
)
void core::import_pose::add_cutpoint_closed ( pose::Pose pose,
vector1< Size > const &  res_list,
vector1< Size > const &  cutpoint_closed 
)
void core::import_pose::add_virtual_sugar_res ( core::pose::Pose pose,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  virtual_sugar_res 
)
void core::import_pose::add_virtual_sugar_res ( pose::Pose pose,
vector1< Size > const &  res_list,
vector1< Size > const &  virtual_sugar_res 
)
void core::import_pose::build_pose ( io::StructFileRepOP  fd,
pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set 
)

Create pose object, using given StructFileRep object. If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line.

Referenced by core::import_pose::PDBSilentStruct::fill_pose(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), pose_from_file(), and pose_from_pdbstring().

void core::import_pose::build_pose ( io::StructFileRepOP  fd,
pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
ImportPoseOptions const &  options 
)

Build Rosetta 3 Pose object from StructFileRep.

Create pose object, using given StructFileRep object. If PDB cleanin specified - it will be applied first.

References build_pose_as_is(), and TR().

void core::import_pose::build_pose_as_is ( io::StructFileRepOP  sfr,
pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
ImportPoseOptions const &  options 
)

Try to Build pose object from pdb 'as-is'. PDB file must be really clean.

Create pose object, using given StructFileRep object. No PDB cleanin will be appliend.

References core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(), build_pose_as_is2(), and core::chemical::ResidueTypeSet::get_self_ptr().

Referenced by build_pose().

void core::import_pose::build_pose_as_is2 ( io::StructFileRepCOP  ,
pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
id::AtomID_Mask &  missing,
ImportPoseOptions const &  options 
)
void core::import_pose::centroid_pose_from_pdb ( pose::Pose pose,
std::string const &  filename,
bool  read_fold_tree 
)
void core::import_pose::check_extra_minimize_res_are_input ( utility::vector1< core::Size > const &  extra_minimize_res,
utility::vector1< core::Size > const &  input_domain_map 
)
void core::import_pose::check_working_res ( utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  input_domain_map,
utility::vector1< core::Size > const &  sample_res 
)
void core::import_pose::check_working_res ( utility::vector1< Size > const &  working_res,
utility::vector1< Size > const &  input_domain_map,
utility::vector1< Size > const &  sample_res 
)
void core::import_pose::cleanup ( pose::Pose pose,
bool const  force_cut_at_rna_chainbreak 
)
bool core::import_pose::compare_RNA_char ( char const  char1,
char const  char2 
)
bool core::import_pose::compare_RNA_secstruct ( char const  char1,
char const  char2 
)
std::string const core::import_pose::convert_based_on_match_type ( std::string const &  RNA_string,
Size const  type 
)
std::string core::import_pose::ctname_for_pose_resource_loader ( std::string const &  element_name)
void core::import_pose::define_chains ( core::pose::Pose const &  pose,
utility::vector1< utility::vector1< core::Size > > &  all_res_in_chain,
utility::vector1< utility::vector1< core::Size > > &  all_fixed_res_in_chain,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  extra_min_res 
)
void core::import_pose::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 
)
FileType core::import_pose::determine_file_type ( std::string const &  contents_of_file)

Determine what file type is passed to function there should only be one function that calls this, pose_from_file and only calls it when the filetype is unknown.

References CIF_file, core::io::pdb::create_records_from_pdb_lines(), PDB_file, and Unknown_file.

Referenced by pose_from_file().

void core::import_pose::dump_stems ( RNA_SecStruct const &  working_secstruct,
std::string const &  working_sequence,
core::pose::full_model_info::FullModelParameters const &  full_model_parameters 
)
std::string core::import_pose::extension_from_filetype ( FileType const  filetype)

Given a filetype, return the string for the extension.

Extensions are in lowercase (e.g. "pdb", "cif", "mmtf"), etc.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References CIF_file, MMTF_file, PDB_file, and SRLZ_file.

Referenced by protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_output_format().

utility::vector1< core::Size > core::import_pose::figure_out_dock_domain_map ( utility::vector1< core::Size > &  cutpoint_open_in_full_model,
utility::vector1< utility::vector1< core::Size > > const &  pose_res_lists,
utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  sample_res,
core::Size const  nres 
)
utility::vector1< Size > core::import_pose::figure_out_dock_domain_map ( utility::vector1< Size > &  cutpoint_open_in_full_model,
utility::vector1< utility::vector1< Size > > const &  pose_res_lists,
utility::vector1< Size > const &  working_res,
utility::vector1< Size > const &  sample_res,
Size const  nres 
)
utility::vector1< core::Size > core::import_pose::figure_out_fixed_domain_map ( utility::vector1< core::Size > const &  input_domain_map,
utility::vector1< core::Size > const &  extra_minimize_res 
)
utility::vector1< Size > core::import_pose::figure_out_fixed_domain_map ( utility::vector1< Size > const &  input_domain_map,
utility::vector1< Size > const &  extra_minimize_res 
)
void core::import_pose::figure_out_motif_mode ( utility::vector1< core::Size > &  extra_min_res,
utility::vector1< core::Size > &  terminal_res,
utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  input_domain_map,
utility::vector1< core::Size > const &  cutpoint_open_in_full_model 
)
void core::import_pose::figure_out_motif_mode ( utility::vector1< Size > &  extra_min_res,
utility::vector1< Size > &  terminal_res,
utility::vector1< Size > const &  working_res,
utility::vector1< Size > const &  input_domain_map,
utility::vector1< Size > const &  cutpoint_open_in_full_model 
)
utility::vector1< core::Size > core::import_pose::figure_out_sample_res ( utility::vector1< core::Size > const &  input_domain_map,
utility::vector1< core::Size > const &  working_res 
)
utility::vector1< Size > core::import_pose::figure_out_sample_res ( utility::vector1< Size > const &  input_domain_map,
utility::vector1< Size > const &  working_res 
)
utility::vector1< core::Size > core::import_pose::figure_out_working_res ( utility::vector1< core::Size > const &  input_domain_map,
utility::vector1< core::Size > const &  sample_res 
)
utility::vector1< Size > core::import_pose::figure_out_working_res ( utility::vector1< Size > const &  input_domain_map,
utility::vector1< Size > const &  sample_res 
)
core::Size core::import_pose::get_anchor_rsd ( pose::Pose const &  pose)
core::Size core::import_pose::get_chain ( core::Size const  i,
utility::vector1< utility::vector1< core::Size > > const &  all_res_in_chain 
)
Size core::import_pose::get_chain ( Size const  i,
vector1< vector1< Size > > const &  all_res_in_chain 
)
utility::vector1< Size > core::import_pose::get_cutpoints ( utility::vector1< core::sequence::SequenceCOP > const &  fasta_sequences,
std::map< Size, std::string > const &  non_standard_residue_map,
utility::vector1< char > const &  conventional_chains,
utility::vector1< int > const &  conventional_numbering,
utility::vector1< std::string > const &  conventional_segids 
)
vector1< Size > core::import_pose::get_cutpoints ( vector1< core::sequence::SequenceCOP > const &  fasta_sequences,
std::map< Size, std::string > const &  non_standard_residue_map,
vector1< char > const &  conventional_chains,
vector1< int > const &  conventional_numbering,
vector1< std::string > const &  conventional_segids 
)
vector1< Size > core::import_pose::get_cutpoints_from_numbering ( vector1< core::sequence::SequenceCOP > const &  fasta_sequences,
vector1< char > const &  conventional_chains,
vector1< std::string > const &  conventional_segids,
vector1< int > const &  conventional_numbering 
)
void core::import_pose::get_extra_cutpoints_from_names ( core::Size const  nres,
utility::vector1< core::Size > &  cutpoints,
std::map< core::Size, std::string > const &  non_standard_residue_map 
)
void core::import_pose::get_extra_cutpoints_from_names ( Size const  nres,
vector1< Size > &  cutpoints,
std::map< Size, std::string > const &  non_standard_residue_map 
)
void core::import_pose::get_other_poses ( utility::vector1< core::pose::PoseOP > &  other_poses,
utility::vector1< std::string > const &  other_files,
core::chemical::ResidueTypeSetCOP  rsd_set 
)
void core::import_pose::get_other_poses ( utility::vector1< pose::PoseOP > &  other_poses,
utility::vector1< std::string > const &  other_files,
core::chemical::ResidueTypeSetCOP  rsd_set 
)
core::pose::PoseOP core::import_pose::get_pdb_and_cleanup ( std::string const &  input_file)
core::pose::PoseOP core::import_pose::get_pdb_and_cleanup ( std::string const &  input_file,
core::chemical::ResidueTypeSetCOP  rsd_set 
)
core::pose::PoseOP core::import_pose::get_pdb_with_full_model_info ( std::string const &  input_file,
core::chemical::ResidueTypeSetCOP  rsd_set 
)
core::pose::full_model_info::FullModelParametersOP core::import_pose::get_sequence_information ( std::string const &  fasta_file,
utility::vector1< core::Size > &  cutpoint_open_in_full_model,
bool const  add_virt = false 
)
FullModelParametersOP core::import_pose::get_sequence_information ( std::string const &  fasta_file,
vector1< Size > &  cutpoint_open_in_full_model,
bool const  append_virtual 
)
core::kinematics::FoldTree core::import_pose::get_tree ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  cuts,
utility::vector1< core::Size > const &  jump_partners1,
utility::vector1< core::Size > const &  jump_partners2 
)
core::kinematics::FoldTree core::import_pose::get_tree ( core::Size const  nres,
utility::vector1< core::Size > const &  cuts,
utility::vector1< core::Size > const &  jump_partners1,
utility::vector1< core::Size > const &  jump_partners2,
utility::vector1< std::string > const &  jump_atoms1,
utility::vector1< std::string > const &  jump_atoms2 
)
FoldTree core::import_pose::get_tree ( pose::Pose const &  pose,
vector1< Size > const &  cuts,
vector1< Size > const &  jump_partners1,
vector1< Size > const &  jump_partners2 
)
FoldTree core::import_pose::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 core::import_pose::initialize_native_and_align_pose ( PoseOP native_pose,
PoseOP align_pose,
core::chemical::ResidueTypeSetCOP  rsd_set,
PoseCOP  start_pose 
)
core::pose::PoseOP core::import_pose::initialize_pose_and_other_poses_from_command_line ( core::chemical::ResidueTypeSetCOP  rsd_set)
core::pose::PoseOP core::import_pose::initialize_pose_and_other_poses_from_options ( core::chemical::ResidueTypeSetCOP  rsd_set,
utility::options::OptionCollection const &  options 
)
core::pose::PoseOP core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses ( core::chemical::ResidueTypeSetCOP  rsd_set,
utility::options::OptionCollection const &  options,
utility::vector1< pose::PoseOP > &  input_poses 
)
bool core::import_pose::involved_in_phosphate_torsion ( std::string  atomname)
bool core::import_pose::is_blank_seq ( char const &  c)
bool core::import_pose::just_modeling_RNA ( utility::vector1< std::string > const &  fasta_files)
void core::import_pose::look_for_dna ( utility::vector1< core::sequence::SequenceOP > &  fasta_sequences)
void core::import_pose::look_for_dna ( vector1< core::sequence::SequenceOP > &  fasta_sequences)
void core::import_pose::make_coarse_pose ( pose::Pose const &  pose,
pose::Pose coarse_pose 
)
void core::import_pose::make_extended_coarse_pose ( pose::Pose coarse_pose,
std::string const &  full_sequence 
)
int const core::import_pose::MAX_BULGE_LENGTH ( )
std::ostream & core::import_pose::operator<< ( std::ostream &  stream,
FileType  type 
)

References CIF_file, MMTF_file, PDB_file, and SRLZ_file.

pose::PoseOP core::import_pose::pose_from_file ( std::string const &  filename,
bool  read_fold_tree = false,
FileType  type = Unknown_file 
)

Returns a PoseOP object from the Pose created from input PDB <filename>

Note
: in PyRosetta, this will return a Pose object

example(s): pose = pose_from_file("YFP.pdb") See also: Pose PDBInfo make_pose_from_sequence pose_from_rcsb pose_from_sequence

Referenced by protocols::abinitio::StructureStore::add(), protocols::topology_broker::add_cmdline_claims(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::simple_filters::ChiWellRmsdEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::ContactMapEvaluatorCreator::add_evaluators(), protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::simple_filters::RdcTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdEvaluatorCreator::add_evaluators(), protocols::simple_filters::RmsdTargetEvaluatorCreator::add_evaluators(), protocols::task_operations::JointSequenceOperation::add_native_pdb(), protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::task_operations::JointSequenceOperation::add_pdb(), protocols::hybridization::HybridizeProtocol::add_template(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_poses(), protocols::loop_build::LoopBuildMover::apply(), protocols::cutoutdomain::CutOutDomain::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::splice::RBOutMover::apply(), protocols::simple_moves::SuperimposeMover::apply(), protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::medal::MedalMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::residue_selectors::NativeSelector::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::boinc::boincOutputFilter(), protocols::antibody_legacy::CDRH3Modeler::build_centroid_loop(), protocols::simple_ddg::ddG::calculate(), centroid_pose_from_pdb(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ligand_discrimination_data(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::enzdes::DesignVsNativeComparison::compare_to_native(), protocols::protein_interface_design::filters::ClashWithTargetFilter::compute(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::cryst::CrystRMS::CrystRMS(), protocols::ddG_main(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), core::import_pose::pose_stream::PDBPoseInputStream::fill_pose(), core::fragment::fill_template_frames_from_pdb(), protocols::docking::DockingProtocol::finalize_setup(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::pose_creation::MakeJunctionsMover::get_and_cache_pdb(), protocols::md::CartesianMD::get_native_info(), get_pdb_and_cleanup(), core::import_pose::RNA_DeNovoSetup::get_seq_and_resnum(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_seq_and_resnum(), protocols::motifs::get_targetconformers_user(), protocols::tcr::graft_cdr(), protocols::tcr::graft_framework(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::import_and_set_up_native(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose(), protocols::mpi_refinement::Serial_Refine::init(), protocols::hybridization::HybridizeProtocol::init(), protocols::hybridization::FoldTreeHybridize::init(), protocols::simple_moves::ExplicitWaterMover::init(), protocols::docking::membrane::QuickRelaxPartnersSeparately::init_from_cmd(), protocols::docking::membrane::MPFindInterfaceMover::init_from_cmd(), protocols::membrane::MPQuickRelaxMover::init_from_cmd(), protocols::relax::membrane::MPRangeRelaxMover::init_from_cmd(), protocols::relax::RangeRelaxMover::init_from_cmd(), protocols::docking::membrane::MPDockingMover::init_from_cmd(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), protocols::docking::DockingProtocol::init_from_options(), protocols::anchored_design::AnchoredDesignMover::init_on_new_input(), protocols::antibody_legacy::AntibodyModeler::init_on_new_input(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::rna::denovo::coarse::CoarseRNA_Fragments::initialize_frag_source_pose(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::initialize_from_command_line(), protocols::scoring::methods::TargetClashEnergy::initiate_voxel(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::dna::load_checkpoint(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::rosetta_scripts::RosettaScriptsParser::load_native(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::load_native_pose_from_disk(), protocols::simple_moves::AddChainMover::load_pose(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::simple_filters::load_poses(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::indexed_structure_store::DirStructureStoreBackend::load_store(), protocols::antibody::Ab_TemplateInfo::load_templates_from_pdbs(), protocols::jobdist::main_atom_tree_diff_mover(), protocols::jobdist::main_plain_mover(), protocols::jobdist::main_plain_pdb_mover(), protocols::frag_picker::scores::MakePhiPsiRmsd::make(), protocols::frag_picker::scores::MakeGunnCostScore::make(), protocols::frag_picker::scores::MakePhiPsiSquareWell::make(), protocols::frag_picker::scores::MakeFragmentDME::make(), protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(), protocols::frag_picker::scores::MakeFragmentChunkCrms::make(), protocols::protein_interface_design::movers::VLB::make_manager(), protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb(), protocols::fibril::make_symmetric_fibril(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::jobdist::not_universal_main(), protocols::rotamer_recovery::RRProtocolReferenceStructure::parse_attributes_from_tag(), protocols::motif_grafting::movers::MotifGraftMover::parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables(), protocols::splice::AlignEndsMover::parse_my_tag(), protocols::simple_moves::AlignChainMover::parse_my_tag(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CAcstGenerator::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::simple_filters::SSMotifFinder::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::simple_moves::SuperimposeMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::pose_creation::MergePDBatOverlapMover::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::rbsegment_relax::OptimizeThreadingMover::parse_my_tag(), protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), protocols::ligand_docking::Transform::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::fldsgn::MatchResidues::parse_my_tag(), protocols::abinitio::abscript::RigidChunkCM::parse_my_tag(), protocols::ligand_docking::TransformEnsemble::parse_my_tag(), protocols::hybridization::CartesianSampler::parse_my_tag(), protocols::relax::membrane::MPRangeRelaxMover::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::docking::membrane::MPDockingSetupMover::parse_my_tag(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::pose_creation::MergePDBMover::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::simple_moves::ExplicitWaterMover::parse_my_tag(), protocols::splice::SpliceOut::parse_SpliceOut_tags(), protocols::task_operations::SelectByDeltaScoreOperation::parse_tag(), protocols::task_operations::DatabaseThread::parse_tag(), protocols::task_operations::RestrictToAlignedSegmentsOperation::parse_tag(), protocols::matdes::BuildingBlockInterfaceOperation::parse_tag(), protocols::task_operations::PreventResiduesFromRepackingOperation::parse_tag(), protocols::task_operations::RestrictNativeResiduesOperation::parse_tag(), protocols::task_operations::RestrictResiduesToRepackingOperation::parse_tag(), protocols::fold_from_loops::utils::Nub::parse_tag(), protocols::splice::SpliceManager::parse_tags(), protocols::calc_taskop_filters::RelativePoseFilter::pdb_name(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::pockets::PocketExemplarMultifunc::PocketExemplarMultifunc(), pose_from_file(), protocols::jd3::pose_inputters::PDBPoseInputter::pose_from_input_source(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), poseOPs_from_files(), protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line(), protocols::comparative_modeling::poses_from_cmd_line(), poses_from_files(), process_input_file(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), read_all_poses(), protocols::sic_dock::read_biounit(), protocols::topology_broker::CoordConstraintClaimer::read_cst_pose(), protocols::hotspot_hashing::HotspotStubSet::read_data(), protocols::pmut_scan::PointMutScanDriver::read_in_structures(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose(), protocols::ddG::ddGData::read_mut_data(), protocols::enzdes::enzutil::read_pose_from_file(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::docking::membrane::MPDockingSetupMover::read_poses(), core::fragment::read_std_frags_from_cmd(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox(), protocols::ddG::ddGData::read_wt_data(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::symmetric_docking::SymDockProtocol::register_options(), protocols::relax::Relax_main(), protocols::rotamer_recovery::RRProtocolReferenceStructure::run(), protocols::legacy_sewing::see_whether_model_is_H_bonded_by_terminal_strands(), protocols::antibody_legacy::GraftOneMover::set_default(), protocols::mpi_refinement::MPI_Refinement::set_defaults(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::cryst::DockLatticeMover::set_defaults(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), protocols::jd2::set_native_in_mover(), protocols::forge::remodel::RemodelLoopMover::set_starting_pdb(), protocols::abinitio::AbrelaxApplication::setup(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), protocols::tcr::setup_template_from_pdbfile(), protocols::motifs::single_motif_from_filename(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::source_pose(), protocols::loop_modeling::utilities::TrajectoryLogger::TrajectoryLogger(), and protocols::jobdist::universal_main().

pose::PoseOP core::import_pose::pose_from_file ( std::string const &  filename,
ImportPoseOptions const &  options,
bool  read_fold_tree,
FileType  type 
)

Returns a PoseOP object from the Pose created from input PDB <filename>, taking a set of custom ImportPoseOptions parameters.

Note
: in PyRosetta, this will return a Pose object

example(s): pose = pose_from_file("YFP.pdb") See also: Pose PDBInfo make_pose_from_sequence pose_from_rcsb pose_from_sequence

References pose_from_file().

pose::PoseOP core::import_pose::pose_from_file ( chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
bool  read_fold_tree,
FileType  type 
)

Returns a PoseOP object from the Pose created by reading the input PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set>

References pose_from_file().

void core::import_pose::pose_from_file ( pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
ImportPoseOptions const &  options,
bool  read_fold_tree,
FileType  file_type 
)
void core::import_pose::pose_from_file ( pose::Pose pose,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
bool  read_fold_tree,
FileType  type 
)

Reads in data from input PDB <filename> and stores it in the Pose <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set>

References pose_from_file().

void core::import_pose::pose_from_file ( pose::Pose pose,
std::string const &  filename,
bool  read_fold_tree = false,
FileType  type = Unknown_file 
)

Reads in data from input PDB <filename> and stores it in the Pose <pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default.

Note
: will use centroid if in::file::centroid_input is true

example(s): pose_from_file(pose,"YFP.pdb") See also: Pose PDBInfo

References pose_from_file().

void core::import_pose::pose_from_file ( pose::Pose pose,
std::string const &  filename,
ImportPoseOptions const &  options,
bool  read_fold_tree,
FileType  type 
)
void core::import_pose::pose_from_file ( utility::vector1< pose::Pose > &  poses,
std::string const &  filename,
bool  read_fold_tree,
FileType  type 
)

Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using the FA_STANDARD ResidueTypeSet (fullatom)

References core::chemical::FA_STANDARD, and pose_from_file().

void core::import_pose::pose_from_file ( utility::vector1< pose::Pose > &  poses,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
bool  read_fold_tree,
FileType  type 
)

Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using ResidueTypeSet <residue_set>

References pose_from_file().

void core::import_pose::pose_from_file ( utility::vector1< pose::Pose > &  poses,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename,
ImportPoseOptions const &  options,
bool  read_fold_tree,
FileType  type 
)
void core::import_pose::pose_from_pdb_stream ( pose::Pose pose,
std::istream &  pdb_stream,
std::string const &  filename,
ImportPoseOptions const &  options 
)
void core::import_pose::pose_from_pdbstring ( pose::Pose pose,
std::string const &  pdbcontents,
ImportPoseOptions const &  options,
std::string const &  filename 
)
void core::import_pose::pose_from_pdbstring ( pose::Pose pose,
std::string const &  pdbcontents,
std::string const &  filename 
)

References pose_from_pdbstring().

void core::import_pose::pose_from_pdbstring ( pose::Pose pose,
std::string const &  pdbcontents,
chemical::ResidueTypeSet const &  residue_set,
std::string const &  filename 
)

References pose_from_pdbstring().

void core::import_pose::pose_from_pdbstring ( pose::Pose pose,
std::string const &  pdbcontents,
chemical::ResidueTypeSet const &  residue_set,
ImportPoseOptions const &  options,
std::string const &  filename 
)
utility::vector1< core::pose::PoseOP > core::import_pose::poseOPs_from_files ( utility::vector1< std::string > const &  filenames,
bool  read_fold_tree,
FileType  type 
)
utility::vector1< core::pose::PoseOP > core::import_pose::poseOPs_from_files ( utility::vector1< std::string > const &  filenames,
ImportPoseOptions const &  options,
bool  read_fold_tree,
FileType  type 
)
utility::vector1< core::pose::PoseOP > core::import_pose::poseOPs_from_files ( chemical::ResidueTypeSet const &  residue_set,
utility::vector1< std::string > const &  filenames,
ImportPoseOptions const &  options,
bool  read_fold_tree,
FileType  type 
)
utility::vector1< core::pose::Pose > core::import_pose::poses_from_files ( utility::vector1< std::string > const &  filenames,
bool  read_fold_tree,
FileType  type 
)
utility::vector1< core::pose::Pose > core::import_pose::poses_from_files ( chemical::ResidueTypeSet const &  residue_set,
utility::vector1< std::string > const &  filenames,
bool  read_fold_tree,
FileType  type 
)
void core::import_pose::process_input_file ( std::string const &  silent_file,
utility::vector1< core::pose::PoseOP > &  pose_list,
bool  is_pdb = false,
bool  coarse_rna = false 
)
void core::import_pose::process_input_file ( std::string const &  input_file,
utility::vector1< pose::PoseOP > &  pose_list,
bool  is_pdb,
bool  coarse_rna 
)
void core::import_pose::put_in_cutpoint ( pose::Pose pose,
Size const  i 
)
void core::import_pose::read_additional_pdb_data ( std::string const &  s,
pose::Pose pose,
io::StructFileRepCOP  ,
bool  read_fold_tree 
)
void core::import_pose::read_additional_pdb_data ( std::string const &  s,
pose::Pose pose,
ImportPoseOptions const &  options,
bool  read_fold_tree 
)
void core::import_pose::read_all_poses ( utility::vector1< std::string > const &  filenames,
utility::vector1< core::pose::PoseOP > &  poses 
)
void core::import_pose::remove_cutpoint_closed ( pose::Pose pose,
Size const  i 
)
void core::import_pose::remove_cutpoints_closed ( pose::Pose pose)
void core::import_pose::reorder_pose ( core::pose::Pose pose,
utility::vector1< core::Size > &  res_list 
)
void core::import_pose::reorder_pose ( pose::Pose pose,
utility::vector1< Size > &  res_list 
)
void core::import_pose::setup_fold_trees ( utility::vector1< core::pose::Pose * > &  pose_pointers,
utility::vector1< core::Size > &  cutpoint_open_in_full_model,
utility::vector1< core::Size > &  fixed_domain_map,
utility::vector1< core::Size > const &  cutpoint_closed,
utility::vector1< core::Size > const &  extra_minimize_res,
utility::vector1< core::Size > const &  extra_minimize_jump_res,
utility::vector1< core::Size > const &  sample_res,
utility::vector1< core::Size > const &  working_res,
utility::vector1< core::Size > const &  jump_res,
utility::vector1< core::Size > const &  preferred_root_res,
utility::vector1< core::Size > const &  virtual_sugar_res,
core::pose::full_model_info::FullModelParameters const &  full_model_parameters,
utility::vector1< utility::vector1< core::Size > > const &  pose_res_lists 
)
void core::import_pose::setup_fold_trees ( vector1< Pose * > &  pose_pointers,
vector1< Size > &  cutpoint_open_in_full_model,
vector1< Size > &  fixed_domain_map,
vector1< Size > const &  cutpoint_closed,
vector1< Size > const &  extra_minimize_res,
vector1< Size > const &  extra_minimize_jump_res,
vector1< Size > const &  sample_res,
vector1< Size > const &  working_res,
vector1< Size > const &  jump_res,
vector1< Size > const &  preferred_root_res,
vector1< Size > const &  virtual_sugar_res,
FullModelParameters const &  full_model_parameters,
vector1< vector1< Size > > const &  pose_res_lists 
)
void core::import_pose::setup_for_density_scoring ( core::pose::Pose pose)
void core::import_pose::setup_jumps ( core::pose::Pose const &  pose,
utility::vector1< core::Size > &  jump_partners1,
utility::vector1< core::Size > &  jump_partners2,
utility::vector1< std::pair< core::Size, core::Size > > &  chain_connections,
utility::vector1< utility::vector1< core::Size > > const &  all_res_in_chain,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  resnum_and_chain_and_segid_in_pose 
)
void core::import_pose::setup_jumps ( core::pose::Pose const &  pose,
vector1< Size > &  jump_partners1,
vector1< Size > &  jump_partners2,
vector1< pair< Size, Size > > &  chain_connections,
vector1< vector1< Size > > const &  all_res_in_chain,
std::tuple< vector1< int >, vector1< char >, vector1< std::string > > const &  resnum_and_chain_and_segid_in_pose 
)
void core::import_pose::setup_user_defined_jumps ( utility::vector1< core::Size > const &  jump_res,
utility::vector1< core::Size > &  jump_partners1,
utility::vector1< core::Size > &  jump_partners2,
utility::vector1< std::pair< core::Size, core::Size > > &  chain_connections,
utility::vector1< core::Size > const &  res_list,
utility::vector1< utility::vector1< core::Size > > const &  all_res_in_chain 
)
void core::import_pose::setup_user_defined_jumps ( vector1< Size > const &  jump_res,
vector1< Size > &  jump_partners1,
vector1< Size > &  jump_partners2,
vector1< pair< Size, Size > > &  chain_connections,
vector1< Size > const &  res_list,
vector1< vector1< Size > > const &  all_res_in_chain 
)
void core::import_pose::setup_water_bank_for_magnesiums ( std::map< Size, std::string > &  non_standard_residue_map,
utility::vector1< core::sequence::SequenceOP > &  fasta_sequences 
)
void core::import_pose::setup_water_bank_for_magnesiums ( std::map< Size, std::string > &  non_standard_residue_map,
vector1< core::sequence::SequenceOP > &  fasta_sequences 
)
static basic::Tracer core::import_pose::tr ( "core.import_pose.import_pose_options"  )
static
static basic::Tracer core::import_pose::tr ( "core.io.silent.PDBSilentStruct"  )
static
static basic::Tracer core::import_pose::TR ( "core.import_pose.import_pose"  )
static

Referenced by core::import_pose::RNA_HelixAssembler::add_capping_base_pairs_to_full_sequence(), core::import_pose::RNA_HelixAssembler::apply(), core::import_pose::RNA_HelixAssembler::build_helix(), build_pose(), protocols::rna::denovo::check_base_pair(), core::import_pose::libraries::check_base_pair_step_availability(), core::import_pose::libraries::RNA_ChunkLibrary::check_fold_tree_OK(), protocols::rna::denovo::classify_base_pairs_lores(), convert_based_on_match_type(), protocols::rna::denovo::create_rna_vall_torsions(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), figure_out_dock_domain_map(), figure_out_motif_mode(), core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants(), core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), get_cutpoints_from_numbering(), protocols::rna::denovo::get_default_allowed_bulge_res(), core::import_pose::libraries::BasePairStepLibrary::initialize_data(), core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options(), core::import_pose::RNA_HelixAssembler::minimize_base_step(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), pose_from_file(), protocols::rna::denovo::print_hbonds(), protocols::rna::denovo::print_internal_coords(), read_additional_pdb_data(), core::import_pose::RNA_DeNovoParameters::read_parameters_from_file(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), setup_fold_trees(), setup_for_density_scoring(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), and protocols::rna::denovo::virtualize_bulges().

static basic::Tracer core::import_pose::TR ( "core.import_pose.import_pose"  )
static
void core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs ( utility::vector1< Size > &  fixed_domain,
pose::Pose const &  pose,
utility::vector1< Size > const &  res_list,
utility::vector1< pair< Size, Size > > const &  extra_minimize_jump_pairs 
)
void core::import_pose::update_fixed_domain_from_extra_minimize_jump_res ( utility::vector1< core::Size > &  fixed_domain,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  extra_minimize_jump_res 
)
void core::import_pose::update_fixed_domain_from_extra_minimize_jump_res ( vector1< Size > &  fixed_domain,
pose::Pose const &  pose,
vector1< Size > const &  res_list,
vector1< Size > const &  extra_minimize_jump_res 
)
void core::import_pose::update_jump_res ( utility::vector1< core::Size > &  jump_res,
utility::vector1< core::Size > const &  extra_minimize_jump_res 
)
void core::import_pose::update_jump_res ( utility::vector1< Size > &  jump_res,
utility::vector1< Size > const &  extra_minimize_jump_res 
)
void core::import_pose::update_pose_fold_tree ( core::pose::Pose pose,
utility::vector1< core::Size > const &  res_list,
utility::vector1< core::Size > const &  extra_min_res,
utility::vector1< core::Size > const &  sample_res,
utility::vector1< core::Size > const &  jump_res,
core::pose::full_model_info::FullModelParameters const &  full_model_parameters 
)
void core::import_pose::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,
core::pose::full_model_info::FullModelParameters const &  full_model_parameters 
)