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< Size >	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	get_extra_cutpoints_from_names (Size const nres, vector1< Size > &cutpoints, std::map< Size, std::string > const &non_standard_residue_map)
vector1< Size >	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)
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< Size >	figure_out_working_res (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &sample_res)
utility::vector1< Size >	figure_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< Size >	figure_out_fixed_domain_map (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &extra_minimize_res)
utility::vector1< Size >	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)
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::Size >	figure_out_working_res (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &sample_res)
utility::vector1< core::Size >	figure_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::Size >	figure_out_fixed_domain_map (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &extra_minimize_res)
utility::vector1< core::Size >	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)
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< Size >	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)
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

ImportPoseOptionsCOP

typedef utility::pointer::shared_ptr< ImportPoseOptions const > core::import_pose::ImportPoseOptionsCOP

ImportPoseOptionsOP

typedef utility::pointer::shared_ptr< ImportPoseOptions > core::import_pose::ImportPoseOptionsOP

PoseResourceCOP

typedef utility::pointer::shared_ptr< PoseResource const > core::import_pose::PoseResourceCOP

PoseResourceLoaderCOP

typedef utility::pointer::shared_ptr< PoseResourceLoader const > core::import_pose::PoseResourceLoaderCOP

PoseResourceLoaderOP

typedef utility::pointer::shared_ptr< PoseResourceLoader > core::import_pose::PoseResourceLoaderOP

PoseResourceOP

typedef utility::pointer::shared_ptr< PoseResource > core::import_pose::PoseResourceOP

RNA_BasePairHandlerCOP

typedef utility::pointer::shared_ptr< RNA_BasePairHandler const > core::import_pose::RNA_BasePairHandlerCOP

RNA_BasePairHandlerOP

typedef utility::pointer::shared_ptr< RNA_BasePairHandler > core::import_pose::RNA_BasePairHandlerOP

RNA_DeNovoParametersCOP

typedef utility::pointer::shared_ptr< RNA_DeNovoParameters const > core::import_pose::RNA_DeNovoParametersCOP

RNA_DeNovoParametersOP

typedef utility::pointer::shared_ptr< RNA_DeNovoParameters > core::import_pose::RNA_DeNovoParametersOP

RNA_DeNovoSetupCOP

typedef utility::pointer::shared_ptr< RNA_DeNovoSetup const > core::import_pose::RNA_DeNovoSetupCOP

RNA_DeNovoSetupOP

typedef utility::pointer::shared_ptr< RNA_DeNovoSetup > core::import_pose::RNA_DeNovoSetupOP

RNA_HelixAssemblerOP

typedef utility::pointer::shared_ptr< RNA_HelixAssembler > core::import_pose::RNA_HelixAssemblerOP

RNA_JumpMoverCOP

typedef utility::pointer::shared_ptr< RNA_JumpMover const > core::import_pose::RNA_JumpMoverCOP

RNA_JumpMoverOP

typedef utility::pointer::shared_ptr< RNA_JumpMover > core::import_pose::RNA_JumpMoverOP

String

typedef std::string core::import_pose::String

Enumeration Type Documentation

FileType

enum core::import_pose::FileType

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

add_block_stack_variants() [1/2]

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
	)

add_block_stack_variants() [2/2]

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
	)

References core::pose::add_variant_type_to_pose_residue(), core::chemical::BLOCK_STACK_ABOVE, core::chemical::BLOCK_STACK_BELOW, core::chemical::ResidueTypeBase::is_RNA(), and core::pose::Pose::residue_type().

add_cutpoint_closed() [1/2]

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
	)

add_cutpoint_closed() [2/2]

void core::import_pose::add_cutpoint_closed	(	pose::Pose &	pose,
		vector1< Size > const &	res_list,
		vector1< Size > const &	cutpoint_closed
	)

References core::pose::rna::apply_suite_torsion_info(), core::pose::correctly_add_cutpoint_variants(), core::pose::rna::get_suite_torsion_info(), and put_in_cutpoint().

Referenced by setup_fold_trees().

add_virtual_sugar_res() [1/2]

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
	)

add_virtual_sugar_res() [2/2]

void core::import_pose::add_virtual_sugar_res	(	pose::Pose &	pose,
		vector1< Size > const &	res_list,
		vector1< Size > const &	virtual_sugar_res
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::size(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by setup_fold_trees().

build_pose() [1/2]

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().

build_pose() [2/2]

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().

build_pose_as_is()

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(), core::chemical::ResidueTypeSet::get_self_ptr(), and core::io::pose_from_sfr::PoseFromSFRBuilder::missing_atoms().

Referenced by build_pose().

build_pose_as_is2()

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
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::atoms_are_bonded(), core::util::auto_setup_all_metal_bonds(), core::util::auto_setup_all_metal_constraints(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_atom(), core::chemical::ResidueType::lower_connect_id(), core::import_pose::ImportPoseOptions::membrane(), core::import_pose::ImportPoseOptions::metal_bond_angle_constraint_multiplier(), core::import_pose::ImportPoseOptions::metal_bond_dist_constraint_multiplier(), core::import_pose::ImportPoseOptions::metal_bond_LJ_multiplier(), core::chemical::ResidueTypeSet::mode(), core::import_pose::ImportPoseOptions::no_optH(), core::pack::optimize_H_and_notify(), core::import_pose::ImportPoseOptions::pack_missing_sidechains(), core::pack::pack_missing_sidechains(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), core::pose::set_reasonable_fold_tree(), core::import_pose::ImportPoseOptions::set_up_metal_bonds(), core::import_pose::ImportPoseOptions::set_up_metal_constraints(), core::pose::Pose::size(), core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree(), core::chemical::ResidueType::upper_connect_atom(), and core::chemical::ResidueType::upper_connect_id().

Referenced by build_pose_as_is().

centroid_pose_from_pdb()

void core::import_pose::centroid_pose_from_pdb	(	pose::Pose &	pose,
		std::string const &	filename,
		bool	read_fold_tree
	)

Reads in data from input PDB <filename> and stores it in the Pose <pose> using the CENTROID ResidueTypeSet (centroid)

References core::chemical::CENTROID_t, protocols::abinitio::filename(), PDB_file, pose_from_file(), and core::pose::Pose::residue_type_set_for_pose().

Referenced by protocols::parser::FragmentReader::apply(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::jobdist::main_plain_mover(), protocols::jobdist::main_plain_pdb_mover(), protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::loops::read_loop_fragments(), protocols::protein_interface_design::PatchdockReader::read_poses(), and protocols::jobdist::universal_main().

check_extra_minimize_res_are_input()

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
	)

check_working_res() [1/2]

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
	)

check_working_res() [2/2]

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
	)

cleanup()

void core::import_pose::cleanup	(	pose::Pose &	pose,
		bool const	force_cut_at_rna_chainbreak
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), and core::pose::rna::virtualize_5prime_phosphates().

Referenced by core::fragment::rna::analyze_for_homology(), get_pdb_and_cleanup(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), and core::scoring::PoissonBoltzmannPotential::solve_pb().

compare_RNA_char()

bool core::import_pose::compare_RNA_char	(	char const	char1,
		char const	char2
	)

Referenced by protocols::rna::denovo::coarse::CoarseRNA_Fragments::find_source_positions(), and core::fragment::rna::FullAtomRNA_Fragments::pick_fragment_library().

compare_RNA_secstruct()

bool core::import_pose::compare_RNA_secstruct	(	char const	char1,
		char const	char2
	)

Referenced by protocols::rna::denovo::coarse::CoarseRNA_Fragments::find_source_positions(), and core::fragment::rna::FullAtomRNA_Fragments::pick_fragment_library().

convert_based_on_match_type()

std::string const core::import_pose::convert_based_on_match_type	(	std::string const &	RNA_string,
		Size const	type
	)

References core::fragment::rna::MATCH_ALL, core::fragment::rna::MATCH_YR, and TR().

Referenced by core::fragment::rna::FullAtomRNA_Fragments::get_fragment_library_pointer(), and protocols::rna::denovo::coarse::CoarseRNA_Fragments::pick_random_fragment().

ctname_for_pose_resource_loader()

std::string core::import_pose::ctname_for_pose_resource_loader

(

std::string const &

element_name

)

Referenced by core::import_pose::PoseResourceLoader::provide_xml_schema().

define_chains() [1/2]

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
	)

define_chains() [2/2]

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
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::res_in_chain(), and core::pose::Pose::size().

Referenced by update_pose_fold_tree().

determine_file_type()

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().

dump_stems()

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
	)

References core::import_pose::RNA_HelixAssembler::apply(), core::pose::Pose::dump_pdb(), core::pose::full_model_info::FullModelParameters::full_to_conventional_resnum_and_chain_and_segid(), core::pose::Pose::pdb_info(), and core::pose::rna::RNA_SecStruct::stems().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options(), core::import_pose::options::RNA_DeNovoProtocolOptions::list_options_read(), core::import_pose::RNA_DeNovoSetup::list_options_read(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::list_options_read().

extension_from_filetype()

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, protocols::cluster::calibur::filetype(), MMTF_file, PDB_file, and SRLZ_file.

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

figure_out_dock_domain_map() [1/2]

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
	)

References core::sequence::end, core::pose::full_model_info::get_connection_domains(), protocols::mean_field::max(), and TR().

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

figure_out_dock_domain_map() [2/2]

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
	)

References core::sequence::end, core::pose::full_model_info::get_connection_domains(), protocols::mean_field::max(), and TR().

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

figure_out_fixed_domain_map() [1/2]

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
	)

figure_out_fixed_domain_map() [2/2]

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
	)

figure_out_motif_mode() [1/2]

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
	)

References TR().

figure_out_motif_mode() [2/2]

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
	)

References TR().

figure_out_sample_res() [1/2]

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
	)

figure_out_sample_res() [2/2]

utility::vector1< Size > core::import_pose::figure_out_sample_res	(	utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	working_res
	)

figure_out_working_res() [1/2]

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
	)

figure_out_working_res() [2/2]

utility::vector1< Size > core::import_pose::figure_out_working_res	(	utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	sample_res
	)

get_anchor_rsd()

core::Size core::import_pose::get_anchor_rsd

(

pose::Pose const &

pose

)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::rna::get_rigid_body_jumps(), core::pose::Pose::size(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::get_alignment_domain(), protocols::cyclic_peptide::PeptideStubMover::perform_single_iteration(), and protocols::rna::denovo::translate_virtual_anchor_to_first_rigid_body().

get_chain() [1/2]

core::Size core::import_pose::get_chain	(	core::Size const	i,
		utility::vector1< utility::vector1< core::Size > > const &	all_res_in_chain
	)

get_chain() [2/2]

Size core::import_pose::get_chain	(	Size const	i,
		vector1< vector1< Size > > const &	all_res_in_chain
	)

Referenced by setup_user_defined_jumps().

get_cutpoints() [1/2]

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
	)

get_cutpoints() [2/2]

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
	)

References get_cutpoints_from_numbering(), and get_extra_cutpoints_from_names().

Referenced by get_sequence_information().

get_cutpoints_from_numbering()

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
	)

References core::chemical::rings::q, core::pose::rna::remove_bracketed(), and TR().

Referenced by get_cutpoints().

get_extra_cutpoints_from_names() [1/2]

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
	)

get_extra_cutpoints_from_names() [2/2]

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
	)

References core::pose::stepwise_addable_residue().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), get_cutpoints(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information().

get_other_poses() [1/2]

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
	)

References get_pdb_and_cleanup().

Referenced by core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(), and initialize_pose_and_other_poses_from_options_and_input_poses().

get_other_poses() [2/2]

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
	)

References get_pdb_and_cleanup().

Referenced by core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(), and initialize_pose_and_other_poses_from_options_and_input_poses().

get_pdb_and_cleanup() [1/2]

core::pose::PoseOP core::import_pose::get_pdb_and_cleanup

(

std::string const &

input_file

)

References core::chemical::FA_STANDARD, and update_ResidueType_enum_files::input_file.

Referenced by core::fragment::rna::analyze_for_homology(), protocols::jd3::full_model_inputters::PDBFullModelInputter::full_model_from_input_source(), get_other_poses(), get_pdb_with_full_model_info(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_directory(), core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(), and protocols::recces::pose_setup_from_file().

get_pdb_and_cleanup() [2/2]

core::pose::PoseOP core::import_pose::get_pdb_and_cleanup	(	std::string const &	input_file,
		core::chemical::ResidueTypeSetCOP	rsd_set
	)

References cleanup(), update_ResidueType_enum_files::input_file, core::pose::full_model_info::make_sure_full_model_info_is_setup(), PDB_file, pose_from_file(), and core::pose::tag_into_pose().

get_pdb_with_full_model_info()

core::pose::PoseOP core::import_pose::get_pdb_with_full_model_info	(	std::string const &	input_file,
		core::chemical::ResidueTypeSetCOP	rsd_set
	)

References get_pdb_and_cleanup(), and update_ResidueType_enum_files::input_file.

Referenced by protocols::rna::AlignmentEnergy::AlignmentEnergy(), initialize_native_and_align_pose(), and protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_parameters().

get_sequence_information() [1/2]

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
	)

get_sequence_information() [2/2]

FullModelParametersOP core::import_pose::get_sequence_information	(	std::string const &	fasta_file,
		vector1< Size > &	cutpoint_open_in_full_model,
		bool const	append_virtual
	)

References core::sequence::get_concatenated_sequence(), core::sequence::get_conventional_chains_and_numbering(), get_cutpoints(), look_for_dna(), core::sequence::parse_out_non_standard_residues(), core::sequence::read_fasta_file(), and setup_water_bank_for_magnesiums().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::FullModelPoseBuilder::initialize_full_model_parameters(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information().

get_tree() [1/4]

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
	)

get_tree() [2/4]

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
	)

get_tree() [3/4]

FoldTree core::import_pose::get_tree	(	pose::Pose const &	pose,
		vector1< Size > const &	cuts,
		vector1< Size > const &	jump_partners1,
		vector1< Size > const &	jump_partners2
	)

References core::chemical::rna::default_jump_atom(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::merge_two_poses(), protocols::magnesium::update_mg_hoh_fold_tree(), and update_pose_fold_tree().

get_tree() [4/4]

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
	)

References core::kinematics::FoldTree::jump_nr(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::kinematics::FoldTree::set_jump_atoms(), core::kinematics::FoldTree::size(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

initialize_native_and_align_pose()

void core::import_pose::initialize_native_and_align_pose	(	PoseOP &	native_pose,
		PoseOP &	align_pose,
		core::chemical::ResidueTypeSetCOP	rsd_set,
		PoseCOP	start_pose
	)

References get_pdb_with_full_model_info(), and core::pose::rna::virtualize_free_rna_moieties().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup().

initialize_pose_and_other_poses_from_command_line()

core::pose::PoseOP core::import_pose::initialize_pose_and_other_poses_from_command_line

(

core::chemical::ResidueTypeSetCOP

rsd_set

)

References initialize_pose_and_other_poses_from_options().

Referenced by protocols::jd2::PDBJobInputter::pose_from_job().

initialize_pose_and_other_poses_from_options()

core::pose::PoseOP core::import_pose::initialize_pose_and_other_poses_from_options	(	core::chemical::ResidueTypeSetCOP	rsd_set,
		utility::options::OptionCollection const &	options
	)

References core::import_pose::FullModelPoseBuilder::build(), core::import_pose::FullModelPoseBuilder::initialize_further_from_options(), core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(), and core::import_pose::FullModelPoseBuilder::set_options().

Referenced by initialize_pose_and_other_poses_from_command_line().

initialize_pose_and_other_poses_from_options_and_input_poses()

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
	)

References core::import_pose::FullModelPoseBuilder::build(), get_other_poses(), core::import_pose::FullModelPoseBuilder::initialize_further_from_options(), core::pose::Pose::pdb_info(), core::import_pose::FullModelPoseBuilder::set_input_poses(), core::import_pose::FullModelPoseBuilder::set_options(), and core::pose::Pose::size().

Referenced by protocols::jd3::full_model_inputters::PDBFullModelInputter::full_model_from_input_source(), and protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source().

involved_in_phosphate_torsion()

bool core::import_pose::involved_in_phosphate_torsion

(

std::string

atomname

)

References core::chemical::rna::atoms_involved_in_phosphate_torsion.

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map().

is_blank_seq()

bool core::import_pose::is_blank_seq

(

char const &

c

)

References core::init::init().

Referenced by core::import_pose::RNA_HelixAssembler::figure_out_and_remove_dangling_ends().

just_modeling_RNA()

bool core::import_pose::just_modeling_RNA

(

utility::vector1< std::string > const &

fasta_files

)

References core::pose::just_modeling_RNA(), core::sequence::parse_out_non_standard_residues(), and core::sequence::read_fasta_file_return_str().

look_for_dna() [1/2]

void core::import_pose::look_for_dna

(

utility::vector1< core::sequence::SequenceOP > &

fasta_sequences

)

look_for_dna() [2/2]

void core::import_pose::look_for_dna

(

vector1< core::sequence::SequenceOP > &

fasta_sequences

)

References core::pose::parse_sequence(), and core::chemical::rings::q.

Referenced by get_sequence_information().

make_coarse_pose()

void core::import_pose::make_coarse_pose	(	pose::Pose const &	pose,
		pose::Pose &	coarse_pose
	)

References core::chemical::COARSE_RNA, core::pose::Pose::fold_tree(), core::scoring::rna::RNA_CentroidInfo::get_base_centroid(), core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), core::pose::rna::get_sugar_centroid(), core::kinematics::Stub::M, make_extended_coarse_pose(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by protocols::rna::movers::RNA_Coarsify::apply(), and process_input_file().

make_extended_coarse_pose()

void core::import_pose::make_extended_coarse_pose	(	pose::Pose &	coarse_pose,
		std::string const &	full_sequence
	)

References core::id::BB, core::chemical::COARSE_RNA, core::pose::make_pose_from_sequence(), core::pose::Pose::set_torsion(), and core::pose::Pose::size().

Referenced by make_coarse_pose().

MAX_BULGE_LENGTH()

int const core::import_pose::MAX_BULGE_LENGTH

(

3

)

Referenced by core::import_pose::RNA_BasePairHandler::get_base_pair_steps(), core::import_pose::libraries::BasePairStepLibrary::initialize(), and core::import_pose::libraries::BasePairStepSequence::subdir().

operator<<()

std::ostream & core::import_pose::operator<<	(	std::ostream &	stream,
		FileType	type
	)

References CIF_file, MMTF_file, PDB_file, and SRLZ_file.

pose_from_file() [1/10]

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 protocols::abinitio::filename(), and pose_from_file().

pose_from_file() [2/10]

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 protocols::abinitio::filename(), and pose_from_file().

pose_from_file() [3/10]

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
	)

References build_pose(), core::chemical::CENTROID_t, CIF_file, core::pose::Pose::conformation(), core::io::mmcif::create_sfr_from_cif_file_op(), core::io::mmtf::create_sfr_from_mmtf_filename(), core::io::pdb::create_sfr_from_pdb_file_contents(), determine_file_type(), protocols::abinitio::filename(), MMTF_file, core::chemical::ResidueTypeSet::mode(), PDB_file, read_additional_pdb_data(), core::conformation::Conformation::same_type_as_me(), core::pose::Pose::set_new_conformation(), core::pose::set_ss_from_phipsi(), protocols::sparta::split(), SRLZ_file, TR(), and Unknown_file.

pose_from_file() [4/10]

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 protocols::abinitio::filename(), and pose_from_file().

pose_from_file() [5/10]

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

References core::import_pose::ImportPoseOptions::centroid(), core::chemical::CENTROID_t, protocols::abinitio::filename(), core::chemical::FULL_ATOM_t, pose_from_file(), core::pose::Pose::residue_type_set_for_pose(), core::import_pose::ImportPoseOptions::residue_type_set_mode(), and TR().

pose_from_file() [6/10]

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

References protocols::abinitio::filename().

Referenced by protocols::abinitio::StructureStore::add(), protocols::topology_broker::add_cmdline_claims(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(), protocols::simple_filters::ChiWellRmsdEvaluatorCreator::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::docking::DockingEnsemblePrepackProtocol::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::cryst::CrystRMS::apply(), protocols::cutoutdomain::CutOutDomain::apply(), protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::glycan_docking::GlycanDockProtocol::apply(), protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::loop_build::LoopBuildMover::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::medal::MedalMover::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::SuperimposeMover::apply(), protocols::splice::RBOutMover::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::residue_selectors::NativeSelector::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::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::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::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose(), 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(), protocols::electron_density::DockPDBIntoDensityMover::get_points_to_search(), core::import_pose::RNA_DeNovoSetup::get_seq_and_resnum(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_seq_and_resnum(), protocols::pose_sewing::data_storage::PoseWithTerminalSegmentsOfKnownDSSP::get_source_pose_op(), 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::hybridization::FoldTreeHybridize::init(), protocols::mpi_refinement::Serial_Refine::init(), protocols::simple_moves::ExplicitWaterMover::init(), protocols::docking::membrane::MPDockingMover::init_from_cmd(), protocols::docking::membrane::MPFindInterfaceMover::init_from_cmd(), protocols::docking::membrane::QuickRelaxPartnersSeparately::init_from_cmd(), protocols::membrane::MPQuickRelaxMover::init_from_cmd(), protocols::relax::membrane::MPRangeRelaxMover::init_from_cmd(), protocols::relax::RangeRelaxMover::init_from_cmd(), protocols::antibody::AntibodyModelerProtocol::init_from_options(), protocols::antibody::GraftCDRLoopsProtocol::init_from_options(), protocols::docking::DockingProtocol::init_from_options(), protocols::antibody_legacy::AntibodyModeler::init_on_new_input(), protocols::anchored_design::AnchoredDesignMover::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::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), 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::MakeFragmentAllAtomCrmsd::make(), protocols::frag_picker::scores::MakeFragmentChunkCrms::make(), protocols::frag_picker::scores::MakeFragmentCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(), protocols::frag_picker::scores::MakeFragmentDME::make(), protocols::frag_picker::scores::MakeGunnCostScore::make(), protocols::frag_picker::scores::MakePhiPsiRmsd::make(), protocols::frag_picker::scores::MakePhiPsiSquareWell::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::fldsgn::MatchResidues::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::docking::membrane::MPDockingSetupMover::parse_my_tag(), protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::relax::membrane::MPRangeRelaxMover::parse_my_tag(), protocols::seeded_abinitio::CAcstGenerator::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::SSMotifFinder::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::abinitio::abscript::RigidChunkCM::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::hybridization::CartesianSampler::parse_my_tag(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag(), protocols::pose_creation::MergePDBMover::parse_my_tag(), protocols::rbsegment_relax::ConfChangeMover::parse_my_tag(), protocols::rbsegment_relax::OptimizeThreadingMover::parse_my_tag(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), protocols::simple_moves::AlignChainMover::parse_my_tag(), protocols::simple_moves::ExplicitWaterMover::parse_my_tag(), protocols::splice::AlignEndsMover::parse_my_tag(), protocols::ligand_docking::Transform::parse_my_tag(), protocols::ligand_docking::TransformEnsemble::parse_my_tag(), protocols::simple_filters::SymmetricMotifFilter::parse_my_tag(), protocols::simple_moves::SuperimposeMover::parse_my_tag(), protocols::pose_creation::MergePDBatOverlapMover::parse_my_tag(), protocols::splice::SpliceOut::parse_SpliceOut_tags(), protocols::matdes::BuildingBlockInterfaceOperation::parse_tag(), protocols::task_operations::RestrictNativeResiduesOperation::parse_tag(), protocols::task_operations::SelectByDeltaScoreOperation::parse_tag(), protocols::task_operations::DatabaseThread::parse_tag(), protocols::task_operations::PreventResiduesFromRepackingOperation::parse_tag(), protocols::task_operations::RestrictResiduesToRepackingOperation::parse_tag(), protocols::task_operations::RestrictToAlignedSegmentsOperation::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(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::populate_from_pdb_list(), pose_from_file(), protocols::jd3::pose_inputters::PDBPoseInputter::pose_from_input_source(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::PDBJobInputter::pose_from_job(), protocols::jd2::ScreeningJobInputter::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::docking::membrane::MPDockingSetupMover::read_poses(), protocols::protein_interface_design::PatchdockReader::read_poses(), core::fragment::read_std_frags_from_cmd(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::topology_broker::FibrilModelingClaimer::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::cryst::DockLatticeMover::set_defaults(), protocols::mpi_refinement::MPI_Refinement::set_defaults(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), protocols::jd2::set_native_in_mover(), protocols::glycopeptide_docking::GlycopeptideDockingProtocol::set_ref_pose_from_filename(), 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::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file(), protocols::motifs::single_motif_from_filename(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::source_pose(), protocols::loop_modeling::utilities::TrajectoryLogger::TrajectoryLogger(), and protocols::jobdist::universal_main().

pose_from_file() [7/10]

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 protocols::abinitio::filename(), and pose_from_file().

pose_from_file() [8/10]

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 protocols::abinitio::filename(), and pose_from_file().

pose_from_file() [9/10]

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
	)

References build_pose(), core::io::pdb::create_sfr_from_pdb_file_contents(), protocols::abinitio::filename(), PDB_file, read_additional_pdb_data(), TR(), and Unknown_file.

pose_from_file() [10/10]

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, protocols::abinitio::filename(), and pose_from_file().

pose_from_pdb_stream()

void core::import_pose::pose_from_pdb_stream	(	pose::Pose &	pose,
		std::istream &	pdb_stream,
		std::string const &	filename,
		ImportPoseOptions const &	options
	)

References protocols::abinitio::filename(), pose_from_pdbstring(), core::pose::Pose::residue_type_set_for_pose(), and core::import_pose::ImportPoseOptions::residue_type_set_mode().

Referenced by core::import_pose::PoseResourceLoader::create_resource().

pose_from_pdbstring() [1/4]

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
	)

References build_pose(), core::io::pdb::create_sfr_from_pdb_file_contents(), protocols::abinitio::filename(), read_additional_pdb_data(), and core::import_pose::ImportPoseOptions::read_fold_tree().

pose_from_pdbstring() [2/4]

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

References protocols::abinitio::filename(), and pose_from_pdbstring().

pose_from_pdbstring() [3/4]

void core::import_pose::pose_from_pdbstring	(	pose::Pose &	pose,
		std::string const &	pdbcontents,
		ImportPoseOptions const &	options,
		std::string const &	filename
	)

References protocols::abinitio::filename(), core::chemical::FULL_ATOM_t, and core::pose::Pose::residue_type_set_for_pose().

Referenced by protocols::simple_moves::PDBReloadMover::apply(), protocols::pack_daemon::DynamicAggregateFunctionDriver::assign_jobs_to_local_daemon_set(), pose_from_pdb_stream(), pose_from_pdbstring(), protocols::pack_daemon::DaemonSet::process_add_daemon_message(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), protocols::pack_daemon::MPIMultistateFitnessFunction::recover_poses_from_states(), and protocols::rpc::JSON_RPC::run().

pose_from_pdbstring() [4/4]

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

References protocols::abinitio::filename(), and pose_from_pdbstring().

poseOPs_from_files() [1/3]

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
	)

References protocols::abinitio::filename(), and pose_from_file().

poseOPs_from_files() [2/3]

utility::vector1< core::pose::PoseOP > core::import_pose::poseOPs_from_files	(	utility::vector1< std::string > const &	filenames,
		bool	read_fold_tree,
		FileType	type
	)

Referenced by poseOPs_from_files(), protocols::mean_field::GenMeanFieldMover::prepare_task_poses(), and protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

poseOPs_from_files() [3/3]

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
	)

References core::chemical::CENTROID, core::import_pose::ImportPoseOptions::centroid(), core::chemical::FA_STANDARD, core::chemical::FULL_ATOM_t, poseOPs_from_files(), core::import_pose::ImportPoseOptions::residue_type_set_mode(), core::chemical::string_from_type_set_mode(), and TR().

poses_from_files() [1/2]

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
	)

References protocols::abinitio::filename(), and pose_from_file().

poses_from_files() [2/2]

utility::vector1< core::pose::Pose > core::import_pose::poses_from_files	(	utility::vector1< std::string > const &	filenames,
		bool	read_fold_tree,
		FileType	type
	)

Only returns full-atom poses

References core::chemical::FA_STANDARD.

Referenced by protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::docking::DockingEnsemble::load_ensemble(), and protocols::comparative_modeling::templates_from_cmd_line().

process_input_file() [1/2]

void core::import_pose::process_input_file	(	std::string const &	input_file,
		utility::vector1< pose::PoseOP > &	pose_list,
		bool	is_pdb,
		bool	coarse_rna
	)

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), core::sequence::end, core::chemical::FA_STANDARD, core::pose::rna::figure_out_reasonable_rna_fold_tree(), update_ResidueType_enum_files::input_file, make_coarse_pose(), PDB_file, pose_from_file(), core::io::silent::SilentFileData::read_file(), remove_cutpoints_closed(), and core::pose::rna::virtualize_5prime_phosphates().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::add_chunk_set(), core::import_pose::libraries::BasePairStepLibrary::initialize_data(), and core::import_pose::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library().

process_input_file() [2/2]

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
	)

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), core::sequence::end, core::chemical::FA_STANDARD, core::pose::rna::figure_out_reasonable_rna_fold_tree(), update_ResidueType_enum_files::input_file, make_coarse_pose(), PDB_file, pose_from_file(), core::io::silent::SilentFileData::read_file(), remove_cutpoints_closed(), and core::pose::rna::virtualize_5prime_phosphates().

Referenced by core::import_pose::libraries::RNA_ChunkLibrary::add_chunk_set(), core::import_pose::libraries::BasePairStepLibrary::initialize_data(), and core::import_pose::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library().

put_in_cutpoint()

void core::import_pose::put_in_cutpoint	(	pose::Pose &	pose,
		Size const	i
	)

References core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by add_cutpoint_closed(), and setup_fold_trees().

read_additional_pdb_data() [1/2]

void core::import_pose::read_additional_pdb_data	(	std::string const &	s,
		pose::Pose &	pose,
		ImportPoseOptions const &	options,
		bool	read_fold_tree
	)

References core::pose::Pose::fold_tree(), core::import_pose::ImportPoseOptions::fold_tree_io(), core::kinematics::FoldTree::nres(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), protocols::loops::start, and TR().

read_additional_pdb_data() [2/2]

void core::import_pose::read_additional_pdb_data	(	std::string const &	s,
		pose::Pose &	pose,
		io::StructFileRepCOP	,
		bool	read_fold_tree
	)

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

read_all_poses()

void core::import_pose::read_all_poses	(	utility::vector1< std::string > const &	filenames,
		utility::vector1< core::pose::PoseOP > &	poses
	)

References protocols::abinitio::filename(), PDB_file, and pose_from_file().

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligand_conformers().

remove_cutpoint_closed()

void core::import_pose::remove_cutpoint_closed	(	pose::Pose &	pose,
		Size const	i
	)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by remove_cutpoints_closed().

remove_cutpoints_closed()

void core::import_pose::remove_cutpoints_closed

(

pose::Pose &

pose

)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), remove_cutpoint_closed(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by process_input_file().

reorder_pose() [1/2]

void core::import_pose::reorder_pose	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > &	res_list
	)

References core::pose::pdbslice().

reorder_pose() [2/2]

void core::import_pose::reorder_pose	(	pose::Pose &	pose,
		utility::vector1< Size > &	res_list
	)

References core::pose::pdbslice().

setup_fold_trees() [1/2]

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
	)

setup_fold_trees() [2/2]

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
	)

References add_cutpoint_closed(), add_virtual_sugar_res(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_virtual_residue(), put_in_cutpoint(), core::pose::reroot(), core::pose::Pose::residue_type(), core::pose::Pose::size(), TR(), update_fixed_domain_from_extra_minimize_jump_res(), and update_pose_fold_tree().

setup_for_density_scoring()

void core::import_pose::setup_for_density_scoring

(

core::pose::Pose &

pose

)

References core::pose::addVirtualResAsRoot(), and TR().

setup_jumps() [1/2]

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
	)

setup_jumps() [2/2]

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
	)

References core::pose::full_model_info::get_connection_domains(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::nheavyatoms(), core::chemical::rings::q, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by update_pose_fold_tree().

setup_user_defined_jumps() [1/2]

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
	)

setup_user_defined_jumps() [2/2]

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
	)

References get_chain(), and core::pose::full_model_info::get_connection_domains().

Referenced by update_pose_fold_tree().

setup_water_bank_for_magnesiums() [1/2]

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
	)

setup_water_bank_for_magnesiums() [2/2]

void core::import_pose::setup_water_bank_for_magnesiums	(	std::map< Size, std::string > &	non_standard_residue_map,
		vector1< core::sequence::SequenceOP > &	fasta_sequences
	)

References protocols::kinmatch::str().

Referenced by get_sequence_information().

TR() [1/2]

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(), 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(), poseOPs_from_files(), 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().

TR() [2/2]

static basic::Tracer core::import_pose::TR ( "core.import_pose.import_pose"  )

static

tr() [1/2]

static basic::Tracer core::import_pose::tr ( "core.import_pose.import_pose_options"  )

static

Referenced by core::import_pose::PDBSilentStruct::get_CA_xyz(), core::import_pose::PDBSilentStruct::get_debug_rmsd(), core::import_pose::PDBSilentStruct::init_from_lines(), and core::import_pose::ImportPoseOptions::init_from_options().

tr() [2/2]

static basic::Tracer core::import_pose::tr ( "core.io.silent.PDBSilentStruct"  )

static

update_fixed_domain_from_extra_minimize_jump_pairs()

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
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::jump_exists(), core::kinematics::FoldTree::jump_nr(), protocols::mean_field::max(), core::kinematics::FoldTree::partition_by_jump(), and core::pose::Pose::size().

Referenced by update_fixed_domain_from_extra_minimize_jump_res().

update_fixed_domain_from_extra_minimize_jump_res() [1/2]

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
	)

update_fixed_domain_from_extra_minimize_jump_res() [2/2]

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
	)

References update_fixed_domain_from_extra_minimize_jump_pairs().

Referenced by setup_fold_trees().

update_jump_res() [1/2]

void core::import_pose::update_jump_res	(	utility::vector1< core::Size > &	jump_res,
		utility::vector1< core::Size > const &	extra_minimize_jump_res
	)

References core::chemical::rings::q.

update_jump_res() [2/2]

void core::import_pose::update_jump_res	(	utility::vector1< Size > &	jump_res,
		utility::vector1< Size > const &	extra_minimize_jump_res
	)

References core::chemical::rings::q.

update_pose_fold_tree() [1/2]

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
	)

update_pose_fold_tree() [2/2]

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
	)

References define_chains(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelParameters::full_to_conventional_resnum_and_chain_and_segid(), get_tree(), setup_jumps(), setup_user_defined_jumps(), and core::pose::Pose::size().

Referenced by setup_fold_trees().