Namespaces
	carbohydrates

	copydofs

	datacache

	full_model_info

	metrics

	ncbb

	rna

	signals

	symmetry

Classes
class	CrystInfo

class	MiniPose

class	PDBInfo
	maintains pdb residue & atom information inside a Pose More...

class	PDBPoseMap
	PDBPoseMap can be queried with PDB information (chain, sequence position) and returns a pose's resid position. Useful for handing input/output in terms of PDB positions. Can be tucked into the pose for repeated access, or generated just-in-time for a single use. Basically a wrapper class for std::map. More...

class	Pose
	A molecular system including residues, kinematics, and energies. More...

class	RemarkInfo

class	Remarks

class	UnrecognizedAtomRecord
	info about an atom in a unrecognized res (not in pose, but we want to remember it) More...

Typedefs
typedef std::map< core::Size, core::Size >	ResMap

typedef utility::pointer::owning_ptr < MiniPose >	MiniPoseOP

typedef utility::pointer::owning_ptr < MiniPose const >	MiniPoseCOP

typedef utility::pointer::access_ptr < MiniPose >	MiniPoseAP

typedef utility::pointer::access_ptr < MiniPose const >	MiniPoseCAP

typedef utility::pointer::owning_ptr < PDBInfo >	PDBInfoOP

typedef utility::pointer::owning_ptr < PDBInfo const >	PDBInfoCOP

typedef utility::pointer::owning_ptr < PDBPoseMap >	PDBPoseMapOP

typedef utility::pointer::owning_ptr < PDBPoseMap const >	PDBPoseMapCOP

typedef boost::shared_ptr< Pose >	PoseSP

typedef utility::pointer::owning_ptr < Pose >	PoseOP

typedef utility::pointer::owning_ptr < Pose const >	PoseCOP

typedef utility::pointer::access_ptr < Pose >	PoseAP

typedef utility::pointer::access_ptr < Pose const >	PoseCAP

typedef utility::vector1< PoseOP >	PoseOPs

typedef utility::vector1< PoseCOP >	PoseCOPs

typedef utility::pointer::owning_ptr < Remarks >	RemarksOP

typedef std::string	String

typedef std::set< int >	Jumps

Functions
void	parse_sequence (std::string const &sequence_in, utility::vector1< std::string > &fullname_list, std::vector< Size > &oneletter_to_fullname_index, std::string &one_letter_sequence)
	parse the annotated sequence. More...

Size	get_sequence_len (std::string const &sequence_in)
	Get the length of the annotated sequence. More...

chemical::ResidueTypeCOPs	residue_types_from_sequence (std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true)
	return a list of ResidueTypes corresponding to an annotated protein sequence More...

chemical::ResidueTypeCOPs	residue_types_from_saccharide_sequence (std::string const &sequence, chemical::ResidueTypeSet const &residue_set)
	Return a list of carbohydrate ResidueTypes corresponding to an annotated polysaccharide sequence. More...

void	make_pose_from_sequence (pose::Pose &pose, chemical::ResidueTypeCOPs requested_types, bool const auto_termini=true)
	Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose> More...

void	make_pose_from_sequence (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini)

void	make_pose_from_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name, bool const auto_termini=true)
	Creates a Pose from the annotated protein sequence <sequence> with the desired <type_set_name> and stores it in <pose> More...

void	make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true)
	Create a Pose from an annotated polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>. More...

void	make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true)
	Create a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name> and stores it in <pose>. More...

pose::PoseOP	pose_from_saccharide_sequence (std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true)
	Return a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name>. More...

std::string	annotated_to_oneletter_sequence (std::string const &annotated_seq)
	Returns the oneletter_sequence that corresponds to the given annotated sequence. More...

std::ostream &	operator<< (std::ostream &os, PDBInfo const &info)

std::ostream &	operator<< (std::ostream &os, Pose const &pose)
	Test IO operator for debug and Python bindings. More...

core::Size	get_resnum (utility::tag::TagCOP const tag_ptr, core::pose::Pose const &pose, std::string const &prefix)
	a convenience function to test whether the user has specified pdb numbering rather than rosetta numbering. More...

core::Size	parse_resnum (std::string const &resnum, core::pose::Pose const &pose)
	Extracts a residue number from a string. Recognizes two forms of numbering: More...

utility::vector1< core::Size >	parse_selection_block (std::string const &sele, core::pose::Pose const &pose)
	Extracts residue numbers from a 'selection'. Recognizes two forms of numbering: More...

vector1< Size >	get_resnum_list (utility::tag::TagCOP const tag_ptr, string const &tag, pose::Pose const &pose)
	Extracts a list of residue numbers from a tag. More...

set< Size >	get_resnum_list (std::string const str, core::pose::Pose const &pose)
	returns a resnum list directly from a string More...

utility::vector1< Size >	get_resnum_list_ordered (std::string const str, core::pose::Pose const &pose)
	returns a resnum list directly from a string, preserving order More...

void	append_pose_to_pose (core::pose::Pose &pose1, core::pose::Pose const &pose2, bool new_chain=true)
	Append residues of pose2 to pose1. More...

void	append_subpose_to_pose (core::pose::Pose &pose1, core::pose::Pose const &pose2, core::Size start_res, core::Size end_res, bool new_chain=true)
	Append specified residues of pose2 to pose1. More...

void	jumps_from_pose (const core::pose::Pose &pose, Jumps *jumps)
	Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id. More...

void	remove_virtual_residues (core::pose::Pose *pose)
	Removes all virtual residues from <pose> More...

void	swap_transform (Size jump_num, const kinematics::RT &xform, Pose *pose)
	Updates the rigid-body transform of the specified jump in <pose> More...

bool	is_position_conserved_residue (const Pose &pose, core::Size residue)
	Returns true if <residue> is positionally conserved, false otherwise. More...

void	create_subpose (Pose const &src, utility::vector1< Size > const &positions, kinematics::FoldTree const &f, Pose &pose)

void	partition_pose_by_jump (pose::Pose const &src, int const jump_number, pose::Pose &partner1, pose::Pose &partner2)

void	set_ss_from_phipsi (pose::Pose &pose)
	Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that. More...

void	addVirtualResAsRoot (const numeric::xyzVector< core::Real > &xyz, core::pose::Pose &pose)
	Adds a virtual residue to the end of the pose at the specified location. Roots the structure on this residue. More...

void	addVirtualResAsRoot (core::pose::Pose &pose)
	Find residue closest to center-of-mass More...

void	read_comment_pdb (std::string const &file_name, core::pose::Pose &pose)
	Reads the comments from the pdb file and adds it into comments. More...

void	dump_comment_pdb (std::string const &file_name, core::pose::Pose const &pose)
	dumps pose+ comments to pdb file More...

bool	getPoseExtraScores (core::pose::Pose const &pose, std::string const name, core::Real &value)
	getters/setters for things in the Pose DataCache More...

void	setPoseExtraScores (core::pose::Pose &pose, std::string name, core::Real value)

void	add_comment (core::pose::Pose &pose, std::string const &key, std::string const &val)
	Adds a key-value pair to the STRING_MAP in the Pose DataCache. If there is no STRING_MAP in the DataCache, one is created. More...

void	add_score_line_string (core::pose::Pose &pose, std::string const &key, std::string const &val)
	Dumps a pdb with comments at end of file. More...

void	clearPoseExtraScores (core::pose::Pose &pose)

void	clearPoseExtraScore (core::pose::Pose &pose, std::string const &name)

bool	get_comment (core::pose::Pose const &pose, std::string const &key, std::string &val)
	Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified. More...

bool	get_score_line_string (core::pose::Pose const &pose, std::string const &key, std::string &val)

void	delete_comment (core::pose::Pose &pose, std::string const &key)
	Deletes the entry in the STRING_MAP associated with the given key. More...

std::map< std::string, std::string >	get_all_score_line_strings (core::pose::Pose const &pose)
	Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs. More...

std::map< std::string, std::string >	get_all_comments (core::pose::Pose const &pose)
	Gets a map< string, string > representing comments about the Pose in the form of key-value pairs. More...

utility::vector1< char >	read_psipred_ss2_file (pose::Pose const &pose)

void	conf2pdb_chain_default_map (core::pose::Pose const &pose, std::map< int, char > &chainmap)

std::map< int, char >	conf2pdb_chain (core::pose::Pose const &pose)
	get Conformation chain -> PDBInfo chain mapping More...

bool	renumber_pdbinfo_based_on_conf_chains (core::pose::Pose &pose, bool fix_chains, bool const start_from_existing_numbering, bool const keep_insertion_codes, bool const rotate_chain_ids)
	renumber PDBInfo based on Conformation chains; each chain starts from 1 More...

bool	is_ideal_pose (core::pose::Pose const &pose)
	checks if the pose geometry is ideal More...

bool	is_ideal_position (core::Size seqpos, core::pose::Pose const &pose)
	checks if the pose geometry is ideal in position seqpos More...

void	remove_nonprotein_residues (core::pose::Pose &pose)
	this function removes all residues from the pose which are not protein residues. More...

void	remove_ligand_canonical_residues (core::pose::Pose &pose)
	this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues. More...

bool	compare_atom_coordinates (Pose const &lhs, Pose const &rhs, Size const n_dec_places=3)
	this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data. More...

bool	compare_binary_protein_silent_struct (Pose const &lhs, Pose const &rhs)

void	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, core::pose::ResMap const &res_map)
	A very useful function that copies degrees of freedom from one pose to another. More...

void	copy_dofs_match_atom_names (pose::Pose &pose, Pose const &scratch_pose)

void	copy_dofs_match_atom_names (pose::Pose &pose, MiniPose const &chunk_pose, core::pose::ResMap const &res_map)

void	copy_dofs (pose::Pose &pose, Pose const &scratch_pose)

void	copy_dofs (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map)

void	copy_dofs_match_atom_names (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map, bool const backbone_only, bool const ignore_virtual)

void	copy_dofs (pose::Pose &pose, Pose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)

void	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)

void	copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map, std::map< id::AtomID, Size > const &atom_id_domain_map)

void	setup_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose)

void	setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &reference_pose, bool const backbone_only, bool const ignore_virtual)

void	setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, MiniPose const &chunk_pose)

id::NamedAtomID	atom_id_to_named_atom_id (core::id::AtomID const &atom_id, Pose const &pose)

id::AtomID	named_atom_id_to_atom_id (core::id::NamedAtomID const &named_atom_id, Pose const &pose, bool raise_exception)

id::NamedStubID	stub_id_to_named_stub_id (id::StubID const &stub_id, core::pose::Pose const &pose)

id::StubID	named_stub_id_to_stub_id (id::NamedStubID const &named_stub_id, core::pose::Pose const &pose)

std::string	tag_from_pose (core::pose::Pose const &pose)

void	tag_into_pose (core::pose::Pose &pose, std::string const &tag)

core::Real	energy_from_pose (core::pose::Pose const &pose, core::scoring::ScoreType const &sc_type)

core::Real	energy_from_pose (core::pose::Pose const &pose, std::string const &sc_type)

core::Real	total_energy_from_pose (core::pose::Pose const &pose)

bool	sort_pose_by_score (core::pose::PoseOP const &pose1, core::pose::PoseOP const &pose2)

void	transfer_phi_psi (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose, core::Size ir, core::Size jr)

void	transfer_phi_psi (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose)

void	transfer_jumps (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose)

void	replace_pose_residue_copying_existing_coordinates (pose::Pose &pose, Size const seqpos, core::chemical::ResidueType const &new_rsd_type)

core::conformation::ResidueOP	remove_variant_type_from_residue (core::conformation::Residue const &old_rsd, core::chemical::VariantType const &variant_type, pose::Pose const &pose)
	removes variant from an existing residue More...

conformation::ResidueOP	add_variant_type_to_residue (conformation::Residue const &old_rsd, chemical::VariantType const &variant_type, pose::Pose const &pose)
	construct a variant of an existing residue More...

void	add_variant_type_to_pose_residue (pose::Pose &pose, chemical::VariantType const &variant_type, Size const seqpos)
	construct a variant of an existing pose residue More...

void	remove_variant_type_from_pose_residue (pose::Pose &pose, chemical::VariantType const &variant_type, Size const seqpos)
	construct a non-variant of an existing pose residue More...

void	add_lower_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)

void	add_upper_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)

void	remove_lower_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)

void	remove_upper_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)

core::Real	pose_max_nbr_radius (Pose const &pose)
	returns a Distance More...

void	setup_dof_to_torsion_map (pose::Pose const &pose, id::DOF_ID_Map< id::TorsionID > &dof_map)
	set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID) More...

void	setup_dof_mask_from_move_map (core::kinematics::MoveMap const &mm, pose::Pose const &pose, id::DOF_ID_Mask &dof_mask)
	convert from allow-bb/allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer More...

bool	has_chain (std::string const &chain, core::pose::Pose const &pose)

bool	has_chain (char const &chain, core::pose::Pose const &pose)

bool	has_chain (core::Size chain_id, core::pose::Pose const &pose)

std::set< core::Size >	get_jump_ids_from_chain_ids (std::set< core::Size > const chain_ids, core::pose::Pose const &pose)

core::Size	get_jump_id_from_chain_id (core::Size const &chain_id, const core::pose::Pose &pose)

core::Size	get_chain_id_from_chain (std::string const &chain, core::pose::Pose const &pose)

core::Size	get_chain_id_from_chain (char const &chain, core::pose::Pose const &pose)

utility::vector1< core::Size >	get_chain_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)

utility::vector1< core::Size >	get_chain_ids_from_chain (char const &chain, core::pose::Pose const &pose)

core::Size	get_jump_id_from_chain (std::string const &chain, core::pose::Pose const &pose)

core::Size	get_jump_id_from_chain (char const &chain, core::pose::Pose const &pose)

utility::vector1< core::Size >	get_jump_ids_from_chain (char const &chain, core::pose::Pose const &pose)

utility::vector1< core::Size >	get_jump_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)

core::Size	get_chain_id_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)

char	get_chain_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)

core::conformation::ResidueCOPs	get_chain_residues (core::pose::Pose const &pose, core::Size const chain_id)

char	get_chain_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)

core::Size	num_heavy_atoms (core::Size begin, core::Size const end, core::pose::Pose const &pose)

core::Size	num_atoms (core::Size begin, core::Size const end, core::pose::Pose const &pose)

core::Size	num_hbond_acceptors (core::Size begin, core::Size const end, core::pose::Pose const &pose)

core::Size	num_hbond_donors (core::Size begin, core::Size const end, core::pose::Pose const &pose)

core::Size	num_chi_angles (core::Size begin, core::Size const end, core::pose::Pose const &pose)

core::Real	mass (core::Size begin, core::Size const end, core::pose::Pose const &pose)

core::Size	get_hash_from_chain (char const &chain, core::pose::Pose const &pose)

core::Size	get_hash_excluding_chain (char const &chain, core::pose::Pose const &pose)

std::string	get_sha1_hash_excluding_chain (char const &chain, core::pose::Pose const &pose)

void	initialize_disulfide_bonds (Pose &pose)
	detect and fix disulfide bonds More...

std::string	extract_tag_from_pose (core::pose::Pose &pose)
	Returns a string giving the pose's tag if there is such a thing or "UnknownTag" otherwise. More...

core::id::SequenceMapping	sequence_map_from_pdbinfo (Pose const &first, Pose const &second)
	Create a sequence map of first pose onto the second, matching the PDBInfo If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching. More...

core::Size	canonical_residue_count (core::pose::Pose const &pose)
	count the number of canonical residues in the pose More...

core::Size	noncanonical_residue_count (core::pose::Pose const &pose)
	count the number of non-canonical residues in the pose More...

core::Size	canonical_atom_count (core::pose::Pose const &pose)
	count the number of canonical amino acid atoms in the pose More...

core::Size	noncanonical_atom_count (core::pose::Pose const &pose)
	count the number of non-canonical amino acids in thepose More...

core::Size	noncanonical_chi_count (core::pose::Pose const &pose)
	count the number of non-canonical chi angles in the pose More...

id::AtomID_Map< id::AtomID >	convert_from_std_map (std::map< id::AtomID, id::AtomID > const &atom_map, core::pose::Pose const &pose)

template<typename T >
void	initialize_dof_id_map (id::DOF_ID_Map< T > &dof_map, Pose const &pose)
	Initialize a DOF_ID_Map for a given Pose using the DOF_ID_Map's current default fill values. More...

template<typename T >
void	initialize_dof_id_map (id::DOF_ID_Map< T > &dof_map, Pose const &pose, T const &value)
	Initialize a DOF_ID_Map for a given Pose using a specified fill value. More...

template<typename T >
void	initialize_atomid_map (id::AtomID_Map< T > &atom_map, pose::Pose const &pose)
	Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values. More...

template<typename T >
void	initialize_atomid_map (id::AtomID_Map< T > &atom_map, pose::Pose const &pose, T const &value)
	Initialize an AtomID_Map for a given Pose using a specified fill value. More...

template<typename T >
void	initialize_atomid_map (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation)
	Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values. More...

template<typename T >
void	initialize_atomid_map (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation, T const &value)
	Initialize an AtomID_Map for a given Conformation using a specified fill value. More...

template<typename T >
void	initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, pose::Pose const &pose)
	Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values. More...

template<typename T >
void	initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, pose::Pose const &pose, T const &value)
	Initialize an AtomID_Map for a given Pose using a specified fill value. More...

template<typename T >
void	initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation)
	Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values. More...

template<typename T >
void	initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation, T const &value)
	Initialize an AtomID_Map for a given Conformation using a specified fill value. More...

void	initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, pose::Pose const &pose)

void	initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, pose::Pose const &pose, id::AtomID const &value)

void	initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, conformation::Conformation const &conformation)

void	initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, conformation::Conformation const &conformation, id::AtomID const &value)

Variables
static basic::Tracer	tr ("core.pose")

static basic::Tracer	TR ("core.pose.PDBInfo")

static basic::Tracer	TR ("core.pose.PDBPoseMap")

static basic::Tracer	TR ("core.pose.util")

Typedef Documentation

typedef std::set<int> core::pose::Jumps

typedef utility::pointer::access_ptr< MiniPose > core::pose::MiniPoseAP

typedef utility::pointer::access_ptr< MiniPose const > core::pose::MiniPoseCAP

typedef utility::pointer::owning_ptr< MiniPose const > core::pose::MiniPoseCOP

typedef utility::pointer::owning_ptr< MiniPose > core::pose::MiniPoseOP

typedef utility::pointer::owning_ptr< PDBInfo const > core::pose::PDBInfoCOP

typedef utility::pointer::owning_ptr< PDBInfo > core::pose::PDBInfoOP

typedef utility::pointer::owning_ptr< PDBPoseMap const > core::pose::PDBPoseMapCOP

typedef utility::pointer::owning_ptr< PDBPoseMap > core::pose::PDBPoseMapOP

typedef utility::pointer::access_ptr< Pose > core::pose::PoseAP

typedef utility::pointer::access_ptr< Pose const > core::pose::PoseCAP

typedef utility::pointer::owning_ptr< Pose const > core::pose::PoseCOP

typedef utility::vector1< PoseCOP > core::pose::PoseCOPs

typedef utility::pointer::owning_ptr< Pose > core::pose::PoseOP

typedef utility::vector1< PoseOP > core::pose::PoseOPs

typedef boost::shared_ptr< Pose > core::pose::PoseSP

typedef utility::pointer::owning_ptr< Remarks > core::pose::RemarksOP

typedef std::map< core::Size, core::Size > core::pose::ResMap

typedef std::string core::pose::String

Function Documentation

void core::pose::add_comment	(	core::pose::Pose &	pose,
		std::string const &	key,
		std::string const &	val
	)

Adds a key-value pair to the STRING_MAP in the Pose DataCache. If there is no STRING_MAP in the DataCache, one is created.

References core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, basic::datacache::BasicDataCache::set(), and core::pose::datacache::CacheableDataType::STRING_MAP.

Referenced by core::sequence::alignment_into_pose(), core::io::pdb::build_pose_as_is1(), core::io::silent::SilentStruct::energies_into_pose(), core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(), and read_comment_pdb().

void core::pose::add_lower_terminus_type_to_pose_residue	(	pose::Pose &	pose,
		Size const	seqpos
	)

References add_variant_type_to_pose_residue(), and core::chemical::LOWER_TERMINUS.

Referenced by core::pack::rotamer_set::bb_independent_rotamers(), core::io::pdb::build_pose_as_is1(), and make_pose_from_saccharide_sequence().

void core::pose::add_score_line_string	(	core::pose::Pose &	pose,
		std::string const &	key,
		std::string const &	val
	)

Dumps a pdb with comments at end of file.

Sets a PDB-style REMARK entry in the Pose.

Detailed: This is different from a comment in its interpretation by the: silent-file output machinery. A REMARK is written on its own separate line in the output silent-file, while a comment is written as part of the Pose SCORE: lines.

References core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS, and basic::datacache::BasicDataCache::set().

Referenced by core::io::silent::SilentStruct::energies_into_pose().

void core::pose::add_upper_terminus_type_to_pose_residue	(	pose::Pose &	pose,
		Size const	seqpos
	)

References add_variant_type_to_pose_residue(), and core::chemical::UPPER_TERMINUS.

Referenced by core::pack::rotamer_set::bb_independent_rotamers(), core::io::pdb::build_pose_as_is1(), and make_pose_from_saccharide_sequence().

void core::pose::add_variant_type_to_pose_residue	(	pose::Pose &	pose,
		chemical::VariantType const &	variant_type,
		Size const	seqpos
	)

construct a variant of an existing pose residue

eg make a terminus variant, and replace the orignal in pose.

Note: this copies any atoms in common between old and new residues, rebuild the others

References core::conformation::Residue::has_variant_type(), replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue(), and runtime_assert.

Referenced by core::util::add_cutpoint_variants(), add_lower_terminus_type_to_pose_residue(), add_upper_terminus_type_to_pose_residue(), core::io::pdb::build_pose_as_is1(), core::pose::rna::correctly_add_cutpoint_variants(), and core::pose::rna::virtualize_5prime_phosphates().

conformation::ResidueOP core::pose::add_variant_type_to_residue	(	conformation::Residue const &	old_rsd,
		chemical::VariantType const &	variant_type,
		pose::Pose const &	pose
	)

construct a variant of an existing residue

Note

References core::conformation::Residue::chi(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::nchi(), core::conformation::Residue::residue_type_set(), TR, and core::conformation::Residue::type().

Referenced by core::pack::rotamer_set::RotamerSets::build_rotamers(), and core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete().

void core::pose::addVirtualResAsRoot	(	const numeric::xyzVector< core::Real > &	xyz,
		core::pose::Pose &	pose
	)

Adds a virtual residue to the end of the pose at the specified location. Roots the structure on this residue.

Adds a virtual residue to a pose as the root. Jump is to the residue closest to <xyz>. If the pose is already rooted on a VRT res, do nothing.

References core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom(), core::chemical::CENTROID, core::conformation::ResidueFactory::create_residue(), d_min, core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), fullatom, core::chemical::ChemicalManager::get_instance(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_polymer(), j, length, core::conformation::Residue::natoms(), nres, core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), residue_type_set, core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), TR, utility_exit_with_message, and core::conformation::Atom::xyz().

Referenced by addVirtualResAsRoot(), and core::pose::symmetry::extract_asymmetric_unit().

void core::pose::addVirtualResAsRoot ( core::pose::Pose & pose )

Find residue closest to center-of-mass

Adds a VRT res to the end of the pose at the center of mass. Reroots the structure on this res.

References core::chemical::aa_vrt, addVirtualResAsRoot(), j, nres, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and TR.

std::string core::pose::annotated_to_oneletter_sequence ( std::string const & annotated_seq )

Returns the oneletter_sequence that corresponds to the given annotated sequence.

References add().

Referenced by make_pose_from_sequence().

void core::pose::append_pose_to_pose	(	core::pose::Pose &	pose1,
		core::pose::Pose const &	pose2,
		bool	new_chain
	)

Append residues of pose2 to pose1.

References append_subpose_to_pose(), and core::pose::Pose::total_residue().

Referenced by core::membrane::MembraneProteinFactory::build_pose().

void core::pose::append_subpose_to_pose	(	core::pose::Pose &	pose1,
		core::pose::Pose const &	pose2,
		core::Size	start_res,
		core::Size	end_res,
		bool	new_chain
	)

Append specified residues of pose2 to pose1.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::chain(), core::conformation::Residue::is_lower_terminus(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by append_pose_to_pose().

id::NamedAtomID core::pose::atom_id_to_named_atom_id	(	core::id::AtomID const &	atom_id,
		Pose const &	pose
	)

References core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::pose::Pose::residue(), and core::id::AtomID::rsd().

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::show_def(), core::scoring::constraints::LocalCoordinateConstraint::show_def(), and stub_id_to_named_stub_id().

core::Size core::pose::canonical_atom_count ( core::pose::Pose const & pose )

count the number of canonical amino acid atoms in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::canonical_residue_count ( core::pose::Pose const & pose )

count the number of canonical residues in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void core::pose::clearPoseExtraScore	(	core::pose::Pose &	pose,
		std::string const &	name
	)

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), and basic::datacache::BasicDataCache::has().

void core::pose::clearPoseExtraScores ( core::pose::Pose & pose )

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::Pose::data(), core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS, basic::datacache::BasicDataCache::set(), and core::pose::datacache::CacheableDataType::STRING_MAP.

bool core::pose::compare_atom_coordinates	(	core::pose::Pose const &	lhs,
		core::pose::Pose const &	rhs,
		core::Size const	n_dec_places
	)

this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data.

this function compares the 3-d coordinates of two poses. Along the way it is forced to check for certain other (in)equalities to prevent vector overrruns, etc. These include: pose length, ResidueType, and # atoms in residue. Inequalities other than 3-d coordinates result in a warning message (you shouldn't have been comparing those poses!) This is NOT a complete equality operator for a pose, but I think it does a good job with the coordinates. Note that it performs floating-point coordinate comparisons by floor(X*10^n_dec_places) - this may cause failures if your pose is a billion angstroms from 0,0,0. This comparison is preferred to an epsilon comparison std::abs( a.x - b.x ) < epsilon because it can run into situations where a == b and b == c, but a != c (thanks to APL for pointing this out). The last argument, n_dec_places, is the number of decimal places of precision when comparing.

Author: Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

Parameters

[in]	lhs	one pose to compare
[in]	rhs	one pose to compare
[in]	n_dec_places	number of decimal places to compare for the coordinates (remember == doesn't work for float); defaults to 3 which is PDB accuracy

References core::conformation::Residue::atoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), TR, and xyz.

bool core::pose::compare_binary_protein_silent_struct	(	Pose const &	lhs,
		Pose const &	rhs
	)

this function compares poses for equality up to the information stored in the binary protein silent struct format.

References core::io::silent::BinarySilentStruct::print_conformation().

std::map< int, char > core::pose::conf2pdb_chain ( core::pose::Pose const & pose )

get Conformation chain -> PDBInfo chain mapping

Remarks: Any chains whose PDBInfo chain records are marked entirely as PDBInfo::empty_record() will be mapped to that character. Note that Conformation -> PDBInfo is always unique, but the reverse may not be true.

Returns: the mapping if PDBInfo available and chains appear consistent, otherwise returns an empty mapping

References core::pose::Pose::chain(), conf2pdb_chain_default_map(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), utility::pointer::owning_ptr< T >::get(), core::pose::Pose::n_residue(), core::conformation::Conformation::num_chains(), pdb, core::pose::Pose::pdb_info(), and TR.

Referenced by core::pose::symmetry::make_symmetric_pose(), and renumber_pdbinfo_based_on_conf_chains().

void core::pose::conf2pdb_chain_default_map	(	core::pose::Pose const &	pose,
		std::map< int, char > &	chainmap
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), and utility_exit_with_message.

Referenced by conf2pdb_chain().

id::AtomID_Map< id::AtomID > core::pose::convert_from_std_map	(	std::map< id::AtomID, id::AtomID > const &	atom_map,
		core::pose::Pose const &	pose
	)

References core::id::BOGUS_ATOM_ID, initialize_atomid_map(), and core::id::AtomID_Map< T >::set().

Referenced by core::scoring::superimpose_pose().

void core::pose::copy_dofs	(	pose::Pose &	pose,
		MiniPose const &	scratch_pose,
		core::pose::ResMap const &	res_map
	)

A very useful function that copies degrees of freedom from one pose to another.

A very useful function that copies degrees of freedom from one pose to another. res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.

res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.

Author: rhiju, 2009.; rhiju, 2009.

References setup_atom_id_map().

Referenced by core::pose::rna::RNA_IdealCoord::apply_coords(), copy_dofs(), and copy_dofs_match_atom_names().

void core::pose::copy_dofs	(	pose::Pose &	pose,
		Pose const &	scratch_pose
	)

References copy_dofs(), runtime_assert, and core::pose::Pose::total_residue().

void core::pose::copy_dofs	(	pose::Pose &	pose,
		Pose const &	scratch_pose,
		core::pose::ResMap const &	res_map
	)

References copy_dofs(), and setup_atom_id_map().

void core::pose::copy_dofs	(	pose::Pose &	pose,
		Pose const &	scratch_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_id_map
	)

References copy_dofs().

void core::pose::copy_dofs	(	pose::Pose &	pose,
		MiniPose const &	scratch_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_id_map
	)

References core::pose::copydofs::blank_atom_id_domain_map(), and copy_dofs().

void core::pose::copy_dofs	(	pose::Pose &	pose,
		MiniPose const &	scratch_pose,
		std::map< id::AtomID, id::AtomID > const &	atom_id_map,
		std::map< id::AtomID, Size > const &	atom_id_domain_map
	)

References core::pose::copydofs::CopyDofs::apply(), and copy_dofs().

void core::pose::copy_dofs_match_atom_names	(	pose::Pose &	pose,
		Pose const &	scratch_pose
	)

References runtime_assert, and core::pose::Pose::total_residue().

Referenced by core::pose::rna::RNA_IdealCoord::apply_coords().

void core::pose::copy_dofs_match_atom_names	(	pose::Pose &	pose,
		MiniPose const &	chunk_pose,
		core::pose::ResMap const &	res_map
	)

References copy_dofs(), and setup_atom_id_map_match_atom_names().

void core::pose::copy_dofs_match_atom_names	(	pose::Pose &	pose,
		Pose const &	scratch_pose,
		core::pose::ResMap const &	res_map,
		bool const	backbone_only,
		bool const	ignore_virtual
	)

References copy_dofs(), and setup_atom_id_map_match_atom_names().

void core::pose::create_subpose	(	Pose const &	src,
		utility::vector1< Size > const &	positions,
		kinematics::FoldTree const &	f,
		Pose &	pose
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_chain_ending(), nres, core::kinematics::FoldTree::nres(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by partition_pose_by_jump().

void core::pose::delete_comment	(	core::pose::Pose &	pose,
		std::string const &	key
	)

Deletes the entry in the STRING_MAP associated with the given key.

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), and core::pose::datacache::CacheableDataType::STRING_MAP.

void core::pose::dump_comment_pdb	(	std::string const &	file_name,
		core::pose::Pose const &	pose
	)

dumps pose+ comments to pdb file

References core::pose::Pose::dump_pdb(), get_all_comments(), and out.

core::Real core::pose::energy_from_pose	(	core::pose::Pose const &	pose,
		core::scoring::ScoreType const &	sc_type
	)

References core::pose::Pose::energies(), and core::scoring::Energies::total_energies().

core::Real core::pose::energy_from_pose	(	core::pose::Pose const &	pose,
		std::string const &	sc_type
	)

References core::pose::Pose::energies(), core::scoring::score_type_from_name(), and core::scoring::Energies::total_energies().

std::string core::pose::extract_tag_from_pose ( core::pose::Pose & pose )

Returns a string giving the pose's tag if there is such a thing or "UnknownTag" otherwise.

References core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), and core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG.

std::map< std::string, std::string > core::pose::get_all_comments ( core::pose::Pose const & pose )

Gets a map< string, string > representing comments about the Pose in the form of key-value pairs.

References core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_const_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, and core::pose::datacache::CacheableDataType::STRING_MAP.

Referenced by dump_comment_pdb(), core::io::silent::SilentStruct::energies_from_pose(), get_comment(), and core::io::pdb::write_additional_pdb_data().

std::map< std::string, std::string > core::pose::get_all_score_line_strings ( core::pose::Pose const & pose )

Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs.

References core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_const_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, and core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS.

Referenced by core::io::silent::SilentStruct::energies_from_pose(), and get_score_line_string().

char core::pose::get_chain_from_chain_id	(	core::Size const &	chain_id,
		core::pose::Pose const &	pose
	)

References core::conformation::Conformation::chain_begin(), core::pose::Pose::conformation(), and core::pose::Pose::pdb_info().

Referenced by get_chain_from_jump_id(), get_chain_ids_from_chain(), and has_chain().

char core::pose::get_chain_from_jump_id	(	core::Size const &	jump_id,
		core::pose::Pose const &	pose
	)

References get_chain_from_chain_id(), and get_chain_id_from_jump_id().

core::Size core::pose::get_chain_id_from_chain	(	std::string const &	chain,
		core::pose::Pose const &	pose
	)

References utility_exit_with_message.

Referenced by get_hash_excluding_chain(), get_hash_from_chain(), get_jump_id_from_chain(), get_sha1_hash_excluding_chain(), core::scoring::constraints::SiteConstraint::setup_csts(), and core::scoring::constraints::FabConstraint::setup_csts().

core::Size core::pose::get_chain_id_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References get_chain_ids_from_chain(), and utility::to_string().

core::Size core::pose::get_chain_id_from_jump_id	(	core::Size const &	jump_id,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::chain(), core::kinematics::FoldTree::downstream_jump_residue(), and core::pose::Pose::fold_tree().

Referenced by get_chain_from_jump_id().

utility::vector1< core::Size > core::pose::get_chain_ids_from_chain	(	std::string const &	chain,
		core::pose::Pose const &	pose
	)

Referenced by get_chain_id_from_chain(), and get_jump_ids_from_chain().

utility::vector1< core::Size > core::pose::get_chain_ids_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::conformation(), get_chain_from_chain_id(), and core::conformation::Conformation::num_chains().

core::conformation::ResidueCOPs core::pose::get_chain_residues	(	core::pose::Pose const &	pose,
		core::Size const	chain_id
	)

References begin, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::end, core::pose::Pose::residue(), and residues.

bool core::pose::get_comment	(	core::pose::Pose const &	pose,
		std::string const &	key,
		std::string &	val
	)

Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified.

References get_all_comments().

Referenced by core::sequence::alignment_from_pose(), core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring(), and core::io::pdb::write_additional_pdb_data().

core::Size core::pose::get_hash_excluding_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::chain(), core::pose::Pose::conformation(), get_chain_id_from_chain(), core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::conformation::Conformation::residue(), and core::conformation::Conformation::xyz().

core::Size core::pose::get_hash_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), get_chain_id_from_chain(), core::conformation::Residue::natoms(), core::conformation::Conformation::residue(), and core::conformation::Conformation::xyz().

core::Size core::pose::get_jump_id_from_chain	(	std::string const &	chain,
		core::pose::Pose const &	pose
	)

References get_chain_id_from_chain(), and get_jump_id_from_chain_id().

core::Size core::pose::get_jump_id_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References get_chain_id_from_chain(), and get_jump_id_from_chain_id().

core::Size core::pose::get_jump_id_from_chain_id	(	core::Size const &	chain_id,
		const core::pose::Pose &	pose
	)

References core::pose::Pose::chain(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), and utility_exit.

Referenced by get_jump_id_from_chain(), get_jump_ids_from_chain(), and get_jump_ids_from_chain_ids().

utility::vector1< core::Size > core::pose::get_jump_ids_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References get_chain_ids_from_chain(), and get_jump_id_from_chain_id().

Referenced by get_jump_ids_from_chain().

utility::vector1< core::Size > core::pose::get_jump_ids_from_chain	(	std::string const &	chain,
		core::pose::Pose const &	pose
	)

References get_jump_ids_from_chain().

std::set< core::Size > core::pose::get_jump_ids_from_chain_ids	(	std::set< core::Size > const	chain_ids,
		core::pose::Pose const &	pose
	)

References get_jump_id_from_chain_id().

core::Size core::pose::get_resnum	(	utility::tag::TagCOP const	tag_ptr,
		core::pose::Pose const &	pose,
		std::string const &	prefix
	)

a convenience function to test whether the user has specified pdb numbering rather than rosetta numbering.

References chain, utility::pointer::owning_ptr< T >::get(), core::pose::Pose::pdb_info(), runtime_assert, ss, TR, and utility_exit_with_message.

utility::vector1< core::Size > core::pose::get_resnum_list	(	utility::tag::TagCOP const	tag_ptr,
		string const &	tag,
		pose::Pose const &	pose
	)

Extracts a list of residue numbers from a tag.

The tag should contain a comma-separated list of numbers, in either pdb or rosetta format (

See also: parse_resnum for details)

References TR, and utility_exit.

Referenced by core::pack::task::residue_selector::ResidueIndexSelector::apply(), core::pack::task::residue_selector::NeighborhoodResidueSelector::get_focus(), and core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector::set_from_residue_list_string().

std::set< core::Size > core::pose::get_resnum_list	(	std::string const	str,
		core::pose::Pose const &	pose
	)

returns a resnum list directly from a string

References core::sequence::end, parse_resnum(), parse_selection_block(), runtime_assert, start, utility::string_split(), and utility_exit_with_message.

utility::vector1< core::Size > core::pose::get_resnum_list_ordered	(	std::string const	str,
		core::pose::Pose const &	pose
	)

returns a resnum list directly from a string, preserving order

References core::sequence::end, parse_resnum(), parse_selection_block(), runtime_assert, start, utility::string_split(), and utility_exit_with_message.

Referenced by core::pack::task::operation::PreventRepacking::apply().

bool core::pose::get_score_line_string	(	core::pose::Pose const &	pose,
		std::string const &	key,
		std::string &	val
	)

References get_all_score_line_strings().

Size core::pose::get_sequence_len ( std::string const & sequence_in )

Get the length of the annotated sequence.

Get the real length of a annotated sequence.

References parse_sequence().

std::string core::pose::get_sha1_hash_excluding_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::chain(), core::pose::Pose::conformation(), get_chain_id_from_chain(), core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::conformation::Conformation::residue(), utility::string_to_sha1(), numeric::truncate_and_serialize_xyz_vector(), and core::conformation::Conformation::xyz().

bool core::pose::getPoseExtraScores	(	core::pose::Pose const &	pose,
		std::string const	name,
		core::Real &	value
	)

getters/setters for things in the Pose DataCache

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_const_ptr(), and basic::datacache::BasicDataCache::has().

Referenced by total_energy_from_pose().

bool core::pose::has_chain	(	std::string const &	chain,
		core::pose::Pose const &	pose
	)

bool core::pose::has_chain	(	char const &	chain,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::conformation(), get_chain_from_chain_id(), and core::conformation::Conformation::num_chains().

bool core::pose::has_chain	(	core::Size	chain_id,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::conformation(), and core::conformation::Conformation::num_chains().

template<typename T >

void core::pose::initialize_atomid_map	(	id::AtomID_Map< T > &	atom_map,
		pose::Pose const &	pose
	)

Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.

References core::id::AtomID_Map< T >::clear(), core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::resize().

Referenced by core::io::pdb::build_pose_as_is1(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), core::scoring::packstat::compute_atom_packing_scores(), core::scoring::packing::compute_holes_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::packing::compute_rosettaholes_score(), convert_from_std_map(), core::scoring::sasa::SasaCalc::init(), initialize_atomid_map_AtomID(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

template<typename T >

void core::pose::initialize_atomid_map	(	id::AtomID_Map< T > &	atom_map,
		pose::Pose const &	pose,
		T const &	value
	)

Initialize an AtomID_Map for a given Pose using a specified fill value.

References core::id::AtomID_Map< T >::clear(), core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::resize().

template<typename T >

void core::pose::initialize_atomid_map	(	id::AtomID_Map< T > &	atom_map,
		conformation::Conformation const &	conformation
	)

Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values.

References core::id::AtomID_Map< T >::clear(), core::chemical::ResidueType::natoms(), core::conformation::Conformation::residue_type(), core::id::AtomID_Map< T >::resize(), and core::conformation::Conformation::size().

template<typename T >

void core::pose::initialize_atomid_map	(	id::AtomID_Map< T > &	atom_map,
		conformation::Conformation const &	conformation,
		T const &	value
	)

Initialize an AtomID_Map for a given Conformation using a specified fill value.

References core::id::AtomID_Map< T >::clear(), core::chemical::ResidueType::natoms(), core::conformation::Conformation::residue_type(), core::id::AtomID_Map< T >::resize(), and core::conformation::Conformation::size().

void core::pose::initialize_atomid_map_AtomID	(	id::AtomID_Map< id::AtomID > &	atom_map,
		pose::Pose const &	pose
	)

inline

References initialize_atomid_map().

void core::pose::initialize_atomid_map_AtomID	(	id::AtomID_Map< id::AtomID > &	atom_map,
		pose::Pose const &	pose,
		id::AtomID const &	value
	)

inline

References initialize_atomid_map().

void core::pose::initialize_atomid_map_AtomID	(	id::AtomID_Map< id::AtomID > &	atom_map,
		conformation::Conformation const &	conformation
	)

inline

References initialize_atomid_map().

void core::pose::initialize_atomid_map_AtomID	(	id::AtomID_Map< id::AtomID > &	atom_map,
		conformation::Conformation const &	conformation,
		id::AtomID const &	value
	)

inline

References initialize_atomid_map().

template<typename T >

void core::pose::initialize_atomid_map_heavy_only	(	id::AtomID_Map< T > &	atom_map,
		pose::Pose const &	pose
	)

Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.

References core::id::AtomID_Map< T >::clear(), core::pose::Pose::n_residue(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::resize().

Referenced by core::scoring::packing::get_surf_vol(), core::scoring::packing::get_surf_vol_deriv(), core::scoring::packstat::MultiProbePoseAccumulator::MultiProbePoseAccumulator(), core::scoring::packing::SurfVolEnergy::setup_for_derivatives(), core::scoring::packing::SurfEnergy::setup_for_derivatives(), core::scoring::packing::HolesEnergy::setup_for_derivatives(), and core::scoring::packing::HolesEnergyRes::setup_for_derivatives().

template<typename T >

void core::pose::initialize_atomid_map_heavy_only	(	id::AtomID_Map< T > &	atom_map,
		pose::Pose const &	pose,
		T const &	value
	)

Initialize an AtomID_Map for a given Pose using a specified fill value.

References core::id::AtomID_Map< T >::clear(), core::pose::Pose::n_residue(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::resize().

template<typename T >

void core::pose::initialize_atomid_map_heavy_only	(	id::AtomID_Map< T > &	atom_map,
		conformation::Conformation const &	conformation
	)

Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values.

References core::id::AtomID_Map< T >::clear(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Conformation::residue_type(), core::id::AtomID_Map< T >::resize(), and core::conformation::Conformation::size().

template<typename T >

void core::pose::initialize_atomid_map_heavy_only	(	id::AtomID_Map< T > &	atom_map,
		conformation::Conformation const &	conformation,
		T const &	value
	)

Initialize an AtomID_Map for a given Conformation using a specified fill value.

References core::id::AtomID_Map< T >::clear(), core::chemical::ResidueType::nheavyatoms(), core::conformation::Conformation::residue_type(), core::id::AtomID_Map< T >::resize(), and core::conformation::Conformation::size().

void core::pose::initialize_disulfide_bonds ( Pose & pose )

detect and fix disulfide bonds

References core::pose::Pose::conformation(), in::detect_disulf, core::conformation::Conformation::detect_disulfides(), core::io::raw_data::DisulfideFile::disulfides(), basic::options::OptionKeys::in::fix_disulf, core::conformation::Conformation::fix_disulfides(), core::pose::Pose::is_fullatom(), option, basic::options::option, and user.

Referenced by core::io::pdb::build_pose_as_is1(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::scoring::cryst::PhenixInterface::fitBfactors(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), and core::import_pose::pose_stream::PoseInputStream::preprocess_pose().

template<typename T >

void core::pose::initialize_dof_id_map	(	id::DOF_ID_Map< T > &	dof_map,
		Pose const &	pose
	)

Initialize a DOF_ID_Map for a given Pose using the DOF_ID_Map's current default fill values.

References core::id::DOF_ID_Map< T >::clear(), core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::id::DOF_ID_Map< T >::resize().

Referenced by core::optimization::MinimizerMap::reset(), setup_dof_mask_from_move_map(), setup_dof_to_torsion_map(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

template<typename T >

void core::pose::initialize_dof_id_map	(	id::DOF_ID_Map< T > &	dof_map,
		Pose const &	pose,
		T const &	value
	)

Initialize a DOF_ID_Map for a given Pose using a specified fill value.

References core::id::DOF_ID_Map< T >::clear(), core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::id::DOF_ID_Map< T >::resize().

bool core::pose::is_ideal_pose ( core::pose::Pose const & pose )

checks if the pose geometry is ideal

Returns true if the <pose> geometry is ideal.

Parameters

[in] pose The Pose to check.

Returns: true if all pose positions have ideal bond lengths and angles up to some very small epsilon

References is_ideal_position(), and core::pose::Pose::total_residue().

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), and core::io::pdb::write_additional_pdb_data().

bool core::pose::is_ideal_position	(	core::Size	seqpos,
		core::pose::Pose const &	pose
	)

checks if the pose geometry is ideal in position seqpos

Returns true if the <pose> geometry is ideal in position <seqpos>

Parameters

[in] pose The Pose to check.

Returns: true if position seqpos has ideal bond lengths and angles up to some very small epsilon

References core::pose::Pose::conformation(), and core::conformation::is_ideal_position().

Referenced by is_ideal_pose().

bool core::pose::is_position_conserved_residue	(	const Pose &	pose,
		core::Size	residue
	)

Returns true if <residue> is positionally conserved, false otherwise.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::POSITION_CONSERVED_RESIDUES, and core::pose::Pose::total_residue().

void core::pose::jumps_from_pose	(	const core::pose::Pose &	pose,
		Jumps *	jumps
	)

Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id.

References core::pose::Pose::num_jump().

void core::pose::make_pose_from_saccharide_sequence	(	pose::Pose &	pose,
		std::string const &	sequence,
		chemical::ResidueTypeSet const &	residue_set,
		bool const	auto_termini
	)

Create a Pose from an annotated polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>.

Parameters

[in]	<pose>	the Pose to fill
[in]	<sequence>	an annotated polysaccharide sequence, e.g., "alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-D-Glcp"
[in]	<residue_set>	the desired residue set
[in]	<auto_termini>	if true (default) creates termini variants of terminal residues

Format for <sequence>:
Prefixes apply to the residue to which they are attached, below indicated by residue n.
Residues are listed from N to 1, where N is the total number of residues in the saccharide.
The sequence is parsed by reading to the next hyphen, so hyphens are crucial.
Linkage indication: "(a->x)-" specifies the linkage of residue n, where a is the anomeric carbon number of residue (n+1) and x is the oxygen number of residue n. The first residue listed in the annotated sequence (residue N) need not have the linkage prefix. A ->4) ResidueType will automatically be assigned by default if not specified.
Anomer indication: The strings "alpha-" or "beta-" are supplied next, which determines the stereochemistry of the anomeric carbon of the residue to which it is prefixed. An alpha ResidueType will automatically be assigned by default.
Stereochemical indication: "L-" or "D-" specifies whether residue n is an L- or D-sugar. The default is "D-".
3-Letter code: A three letter code (in sentence case) MUST be supplied next. This specifies the "base sugar name", e.g., Glc is for glucose. (A list of all recognized 3-letter codes for sugars can be found in src/core/chemical/carbohydrates/CarbohydrateInfo.cc.)
1-Letter suffix: If no suffix follows, residue n will be linear. If a letter is present, it indicates the ring size, where "f" is furanose, "p" is puranose, and "s" is septanose.

Remarks: The order of residues in the created pose is in the opposite direction as the annotated sequence of saccharide residues, as sugars are named with the 1st residue as the "main chain", with all other residues named as substituents and written as prefixes. In other words, sugars are usually drawn and named with residue 1 to the right.
At present time, param files only exist for a limited number of sugars! ~ Labonte

References add_lower_terminus_type_to_pose_residue(), add_upper_terminus_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::chain_sequence(), chemical, core::pose::Pose::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::conformation::ResidueFactory::create_residue(), residue_types_from_saccharide_sequence(), core::pose::Pose::set_phi(), and core::pose::Pose::total_residue().

Referenced by make_pose_from_saccharide_sequence(), and pose_from_saccharide_sequence().

void core::pose::make_pose_from_saccharide_sequence	(	pose::Pose &	pose,
		std::string const &	sequence,
		std::string const &	type_set_name,
		bool const	auto_termini
	)

Create a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name> and stores it in <pose>.

Overloaded version of make_pose_from_saccharide_sequence() that takes the string name for a residue type set instead of a ResidueTypeSet object. A convenience method for PyRosetta.

References chemical, make_pose_from_saccharide_sequence(), and residue_type_set.

void core::pose::make_pose_from_sequence	(	pose::Pose &	pose,
		chemical::ResidueTypeCOPs	requested_types,
		bool const	auto_termini = `true`
	)

Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>

Note: : any existing data in <pose> is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

example(s): make_pose_from_sequence(pose,"THANKSEVAN","fa_standard") See also: Pose PDBInfo pose_from_pdb pose_from_rcsb pose_from_sequence

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_vrt, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::N_ACETYLATION, and core::pose::Pose::sequence().

Referenced by core::import_pose::pose_stream::ExtendedPoseInputStream::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::fragment::make_pose_from_frags(), make_pose_from_sequence(), and core::fragment::FragmentRmsd::rmsd().

void core::pose::make_pose_from_sequence	(	pose::Pose &	pose,
		std::string const &	sequence_in,
		chemical::ResidueTypeSet const &	residue_set,
		bool const	auto_termini
	)

Given a Pose, a protein sequence where each character represents an amino acid, and a ResidueTypeSet, give the Pose a conformation of covalently linked residues that match the sequence. NOTE: support making pose from a fully annotated sequence now, that is, for each residue variant or ligand which cannot be deduced from one letter code directly, a [] is added directly following the one letter code containing the residue's fullname, e.g. K[lys_p:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu_p:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distinguished HIS tautomers, various chain termini and cutpoint variants etc. Currently not working with disulfide variant CYD, but this is on to-do list.

References annotated_to_oneletter_sequence(), length, make_pose_from_sequence(), and residue_types_from_sequence().

void core::pose::make_pose_from_sequence	(	pose::Pose &	pose,
		std::string const &	sequence_in,
		std::string const &	type_set_name,
		bool const	auto_termini
	)

Creates a Pose from the annotated protein sequence <sequence> with the desired <type_set_name> and stores it in <pose>

overloaded version of make_pose_from_sequence, does the same function, but reads in a string of the residue type set instead of a ResidueTypeSet object.

Note: : any existing data in <pose> is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

References core::chemical::ChemicalManager::get_instance(), make_pose_from_sequence(), and residue_type_set.

core::Real core::pose::mass	(	core::Size	begin,
		core::Size const	end,
		core::pose::Pose const &	pose
	)

References core::sequence::end, core::chemical::ResidueType::mass(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by core::scoring::TenANeighborNode::neighbor_mass(), and core::util::switch_to_residue_type_set().

id::AtomID core::pose::named_atom_id_to_atom_id	(	core::id::NamedAtomID const &	named_atom_id,
		Pose const &	pose,
		bool	raise_exception
	)

returns an AtomID corresponding to your NamedAtomID check for a valid AtomID after this. following conditions return invalid ID : rsd > total_residue atom not present in residue ( e.g., no CB in GLY )

References core::id::NamedAtomID::atom(), core::chemical::ResidueType::atom_index(), core::id::BOGUS_ATOM_ID, core::chemical::ResidueType::has(), core::pose::Pose::residue_type(), core::id::NamedAtomID::rsd(), core::pose::Pose::total_residue(), and core::id::NamedAtomID::valid().

id::StubID core::pose::named_stub_id_to_stub_id	(	id::NamedStubID const &	named_stub_id,
		core::pose::Pose const &	pose
	)

References core::id::NamedStubID::atom(), core::id::NamedStubID::center(), named_atom_id_to_atom_id(), and core::id::NamedAtomID::valid().

Referenced by core::fragment::DownJumpSRFD::apply(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::fragment::DownJumpSRFD::steal(), and core::pose::Pose::stub_from_id().

core::Size core::pose::noncanonical_atom_count ( core::pose::Pose const & pose )

count the number of non-canonical amino acids in thepose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::noncanonical_chi_count ( core::pose::Pose const & pose )

count the number of non-canonical chi angles in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::noncanonical_residue_count ( core::pose::Pose const & pose )

count the number of non-canonical residues in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::num_atoms	(	core::Size	begin,
		core::Size const	end,
		core::pose::Pose const &	pose
	)

References core::sequence::end, core::conformation::Residue::natoms(), core::pose::Pose::residue(), and TR.

Referenced by core::conformation::annotated_atom_graph_from_conformation(), core::conformation::atom_graph_from_conformation(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), core::scoring::residue_sc_rmsd_no_super(), core::scoring::rmsd_no_super(), core::scoring::rmsd_no_super_subset(), core::scoring::rmsd_with_super(), core::scoring::rmsd_with_super_subset(), and core::scoring::sym_rmsd_with_super_subset().

core::Size core::pose::num_chi_angles	(	core::Size	begin,
		core::Size const	end,
		core::pose::Pose const &	pose
	)

References core::sequence::end, core::conformation::Residue::nchi(), and core::pose::Pose::residue().

core::Size core::pose::num_hbond_acceptors	(	core::Size	begin,
		core::Size const	end,
		core::pose::Pose const &	pose
	)

References core::sequence::end, core::conformation::Residue::n_hbond_acceptors(), core::pose::Pose::residue(), and TR.

core::Size core::pose::num_hbond_donors	(	core::Size	begin,
		core::Size const	end,
		core::pose::Pose const &	pose
	)

References core::sequence::end, core::conformation::Residue::n_hbond_donors(), core::pose::Pose::residue(), and TR.

core::Size core::pose::num_heavy_atoms	(	core::Size	begin,
		core::Size const	end,
		core::pose::Pose const &	pose
	)

References core::sequence::end, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and TR.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor().

std::ostream & core::pose::operator<<	(	std::ostream &	os,
		PDBInfo const &	info
	)

References core::pose::PDBInfo::show().

std::ostream & core::pose::operator<<	(	std::ostream &	os,
		Pose const &	pose
	)

Test IO operator for debug and Python bindings.

References core::pose::Pose::fold_tree(), core::pose::Pose::pdb_info(), core::pose::Pose::sequence(), and core::pose::Pose::total_residue().

core::Size core::pose::parse_resnum	(	std::string const &	resnum,
		core::pose::Pose const &	pose
	)

Extracts a residue number from a string. Recognizes two forms of numbering:

Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID.
Returns
the rosetta residue number for the string, or 0 upon an error

References chain, core::pose::Pose::pdb_info(), runtime_assert, ss, and TR.

Referenced by get_resnum_list(), get_resnum_list_ordered(), and parse_selection_block().

utility::vector1<core::Size> core::pose::parse_selection_block	(	std::string const &	sele,
		core::pose::Pose const &	pose
	)

Extracts residue numbers from a 'selection'. Recognizes two forms of numbering:

Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID.
name3=ALA selects all alanines
Returns
the rosetta residue numbers for the string, or 0 upon an error

References core::pose::Pose::n_residue(), core::conformation::Residue::name3(), parse_resnum(), and core::pose::Pose::residue().

Referenced by get_resnum_list(), and get_resnum_list_ordered().

void core::pose::parse_sequence	(	std::string const &	sequence_in,
		utility::vector1< std::string > &	fullname_list,
		std::vector< Size > &	oneletter_to_fullname_index,
		std::string &	one_letter_sequence
	)

parse the annotated sequence.

Parse the input annotated sequence.

Referenced by get_sequence_len(), and residue_types_from_sequence().

void core::pose::partition_pose_by_jump	(	pose::Pose const &	src,
		int const	jump_number,
		pose::Pose &	partner1,
		pose::Pose &	partner2
	)

References create_subpose(), core::pose::Pose::fold_tree(), nres, core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::total_residue(), and TR.

pose::PoseOP core::pose::pose_from_saccharide_sequence	(	std::string const &	sequence,
		std::string const &	type_set_name,
		bool const	auto_termini
	)

Return a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name>.

A convenience method for PyRosetta.

References make_pose_from_saccharide_sequence().

core::Real core::pose::pose_max_nbr_radius ( Pose const & pose )

returns a Distance

References core::conformation::Residue::nbr_radius(), core::chemical::ResidueType::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), core::scoring::solid_surface::SurfaceEnergies::fill_point_graph(), core::scoring::Energies::fill_point_graph(), and core::scoring::NeighborList::setup().

void core::pose::read_comment_pdb	(	std::string const &	file_name,
		core::pose::Pose &	pose
	)

Reads the comments from the pdb file and adds it into comments.

References add_comment(), getline(), key, utility::string_split(), TR, and utility_exit.

utility::vector1< char > core::pose::read_psipred_ss2_file ( pose::Pose const & pose )

References filename(), getline(), core::conformation::Residue::is_protein(), nres, option, core::pose::Pose::residue(), sec(), core::pose::Pose::total_residue(), and TR.

void core::pose::remove_ligand_canonical_residues ( core::pose::Pose & pose )

this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues.

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void core::pose::remove_lower_terminus_type_from_pose_residue	(	pose::Pose &	pose,
		Size const	seqpos
	)

References core::chemical::LOWER_TERMINUS, and remove_variant_type_from_pose_residue().

void core::pose::remove_nonprotein_residues ( core::pose::Pose & pose )

this function removes all residues from the pose which are not protein residues.

this function removes all residues from the pose which are not protein residues. This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).

This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void core::pose::remove_upper_terminus_type_from_pose_residue	(	pose::Pose &	pose,
		Size const	seqpos
	)

References remove_variant_type_from_pose_residue(), and core::chemical::UPPER_TERMINUS.

void core::pose::remove_variant_type_from_pose_residue	(	pose::Pose &	pose,
		chemical::VariantType const &	variant_type,
		Size const	seqpos
	)

construct a non-variant of an existing pose residue

eg remove a terminus variant, and replace the orignal in pose.

Note: this copies any atoms in common between old and new residues, rebuild the others

References core::conformation::Residue::has_variant_type(), replace_pose_residue_copying_existing_coordinates(), and core::pose::Pose::residue().

Referenced by core::pose::rna::correctly_add_cutpoint_variants(), core::util::remove_cutpoint_variants(), remove_lower_terminus_type_from_pose_residue(), and remove_upper_terminus_type_from_pose_residue().

conformation::ResidueOP core::pose::remove_variant_type_from_residue	(	core::conformation::Residue const &	old_rsd,
		core::chemical::VariantType const &	variant_type,
		pose::Pose const &	pose
	)

removes variant from an existing residue

Note

References core::conformation::Residue::chi(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::nchi(), core::conformation::Residue::residue_type_set(), core::conformation::Residue::set_chi(), TR, and core::conformation::Residue::type().

Referenced by core::pack::rotamer_set::build_five_prime_phosphate_rotamers(), core::pack::rotamer_set::RotamerSets::build_rotamers(), and core::pack::rotamer_set::build_three_prime_phosphate_rotamers().

void core::pose::remove_virtual_residues ( core::pose::Pose * pose )

Removes all virtual residues from <pose>

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::chemical::ResidueType::name(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

bool core::pose::renumber_pdbinfo_based_on_conf_chains	(	core::pose::Pose &	pose,
		bool	fix_chains,
		bool const	start_from_existing_numbering,
		bool const	keep_insertion_codes,
		bool const	rotate_chain_ids
	)

renumber PDBInfo based on Conformation chains; each chain starts from 1

Parameters

[in,out]	pose	The Pose to modify.
[in]	fix_chains	If true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)
[in]	start_from_existing_numbering	If true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)
[in]	keep_insertion_codes	If true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)
[in]	rotate_chain_ids	If true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)

Remarks: If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.

Returns: true if renumbering successful, false otherwise

References chain, core::pose::Pose::chain(), core::pose::PDBInfo::chain(), core::conformation::Conformation::chain_endings(), conf2pdb_chain(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), utility::pointer::owning_ptr< T >::get(), core::pose::PDBInfo::icode(), j, core::pose::Pose::n_residue(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), runtime_assert, core::pose::PDBInfo::set_resinfo(), and TR.

void core::pose::replace_pose_residue_copying_existing_coordinates	(	pose::Pose &	pose,
		Size const	seqpos,
		core::chemical::ResidueType const &	new_rsd_type
	)

helper function for residue replacement/residuetype switching these functions should probably move to pose/util.cc

Note: Will call new_rsd->fill_missing_atoms if the new residue has atoms that the old one doesn't

References core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::replace_residue(), and core::pose::Pose::residue().

Referenced by add_variant_type_to_pose_residue(), and remove_variant_type_from_pose_residue().

chemical::ResidueTypeCOPs core::pose::residue_types_from_saccharide_sequence	(	std::string const &	sequence,
		chemical::ResidueTypeSet const &	residue_set
	)

Return a list of carbohydrate ResidueTypes corresponding to an annotated polysaccharide sequence.

Parameters

[in]	<sequence>	an annotated polysaccharide sequence, e.g., "alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-D-Glcp"
[in]	<residue_set>	the desired residue set

Returns: a 1-indexed vector of ResidueType owning pointers, from left-to-right, as indicated by the sequence

Format for <sequence>:
Prefixes apply to the residue to which they are attached, below indicated by residue n.
Residues are listed from N to 1, where N is the total number of residues in the saccharide.
The sequence is parsed by reading to the next hyphen, so hyphens are crucial.
Linkage indication: "(a->x)-" specifies the linkage of residue n, where a is the anomeric carbon number of residue (n+1) and x is the oxygen number of residue n. The first residue listed in the annotated sequence (residue N) need not have the linkage prefix. A ->4) ResidueType will automatically be assigned by default if not specified.
Anomer indication: The strings "alpha-" or "beta-" are supplied next, which determines the stereochemistry of the anomeric carbon of the residue to which it is prefixed. An alpha ResidueType will automatically be assigned by default.
Stereochemical indication: "L-" or "D-" specifies whether residue n is an L- or D-sugar. The default is "D-".
3-Letter code: A three letter code (in sentence case) MUST be supplied next. This specifies the "base sugar name", e.g., Glc is for glucose. (A list of all recognized 3-letter codes for sugars can be found in the database.)
1-Letter suffix: If no suffix follows, residue n will be linear. If a letter is present, it indicates the ring size, where "f" is furanose, "p" is pyranose, and "s" is septanose.

Remarks: At present time, param files only exist for a few saccharide residues! ~ Labonte

References carbohydrates, chemical, core::chemical::ResidueTypeSet::name_map(), suffix, and utility_exit_with_message.

Referenced by make_pose_from_saccharide_sequence().

chemical::ResidueTypeCOPs core::pose::residue_types_from_sequence	(	std::string const &	sequence_in,
		chemical::ResidueTypeSet const &	residue_set,
		bool const	auto_termini
	)

return a list of ResidueTypes corresponding to an annotated protein sequence

Given a protein sequence where each character represents an amino acid, and a ResidueTypeSet, return the residue types that match the sequence. NOTE: support making residue types from a fully annotated sequence now, that is, for each residue variant or ligand which cannot be deduced from one letter code directly, a [] is added directly following the one letter code containing the residue's fullname, for example K[lys_p:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu_p:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distinguished HIS tautomers, various chain termini and cutpoint variants etc. Currently not working with disulfide variant CYD, but this is on to-do list.

Parameters

[in]	sequence_in	an annotated sequence
[in]	residue_set	the desired residue set
[in]	auto_termini	mark position 1, last_residue with lower, upper termini; default true

References core::chemical::aa_from_oneletter_code(), core::chemical::ResidueTypeSet::aa_map(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_polymer(), j, core::chemical::LOWER_TERMINUS, core::chemical::ResidueTypeSet::name_map(), parse_sequence(), core::chemical::UPPER_TERMINUS, utility_exit_with_message, and core::chemical::ResidueType::variant_types().

Referenced by make_pose_from_sequence().

core::id::SequenceMapping core::pose::sequence_map_from_pdbinfo	(	Pose const &	first,
		Pose const &	second
	)

Create a sequence map of first pose onto the second, matching the PDBInfo If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching.

References core::sequence::map_seq1_seq2(), core::pose::Pose::pdb_info(), core::pose::Pose::total_residue(), and TR.

void core::pose::set_ss_from_phipsi ( pose::Pose & pose )

Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that.

Crude way to guess secondary structure given a pose. This function sets the sec_struct array of pose.conformation_ to the result of the guesswork. This has been ported directly from rosetta++.

References core::chemical::ResidueType::is_protein(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::pose::Pose::set_secstruct(), ss, and core::pose::Pose::total_residue().

Referenced by core::import_pose::pose_from_pdb(), core::fragment::read_std_frags_from_cmd(), core::io::sequence_comparation::DesignContrast::setSecStruct(), core::fragment::steal_constant_length_frag_set_from_pose(), and core::fragment::steal_frag_set_from_pose().

void core::pose::setPoseExtraScores	(	core::pose::Pose &	pose,
		std::string	name,
		core::Real	value
	)

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::Pose::data(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, and basic::datacache::BasicDataCache::set().

Referenced by core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(), core::scoring::DockingScoreFunction::operator()(), and core::scoring::MinScoreScoreFunction::operator()().

void core::pose::setup_atom_id_map	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		ResMap const &	res_map,
		core::pose::Pose const &	pose
	)

References j, and core::pose::Pose::residue_type().

Referenced by copy_dofs().

void core::pose::setup_atom_id_map_match_atom_names	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		ResMap const &	res_map,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	reference_pose,
		bool const	backbone_only,
		bool const	ignore_virtual
	)

References core::pose::Pose::residue_type().

Referenced by copy_dofs_match_atom_names().

void core::pose::setup_atom_id_map_match_atom_names	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		ResMap const &	res_map,
		core::pose::Pose const &	pose,
		MiniPose const &	chunk_pose
	)

References core::pose::MiniPose::atom_names_list(), and core::pose::Pose::residue_type().

void core::pose::setup_dof_mask_from_move_map	(	kinematics::MoveMap const &	mm,
		pose::Pose const &	pose,
		id::DOF_ID_Mask &	dof_mask
	)

convert from allow-bb/allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer

References core::id::BB, core::chemical::rna::CHI, core::pose::Pose::conformation(), core::id::D, core::kinematics::MoveMap::dof_id_begin(), core::kinematics::MoveMap::dof_id_end(), core::conformation::Conformation::dof_id_from_torsion_id(), core::kinematics::MoveMap::get(), core::kinematics::MoveMap::get_jump(), initialize_dof_id_map(), j, core::id::JUMP, core::pose::Pose::n_residue(), core::id::NU, core::pose::Pose::num_jump(), core::chemical::PHI, core::pose::Pose::residue(), core::id::DOF_ID_Map< T >::set(), core::chemical::THETA, and TR.

Referenced by core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

void core::pose::setup_dof_to_torsion_map	(	pose::Pose const &	pose,
		id::DOF_ID_Map< id::TorsionID > &	dof_map
	)

set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID)

References core::id::BB, core::id::BOGUS_TORSION_ID, core::id::CHI, core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), initialize_dof_id_map(), j, core::id::JUMP, core::pose::Pose::n_residue(), core::pose::Pose::num_jump(), and core::pose::Pose::residue().

Referenced by core::optimization::MinimizerMap::assign_rosetta_torsions(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

bool core::pose::sort_pose_by_score	(	core::pose::PoseOP const &	pose1,
		core::pose::PoseOP const &	pose2
	)

References total_energy_from_pose().

id::NamedStubID core::pose::stub_id_to_named_stub_id	(	id::StubID const &	stub_id,
		core::pose::Pose const &	pose
	)

References core::id::StubID::atom(), atom_id_to_named_atom_id(), core::id::StubID::center(), and core::id::AtomID::valid().

Referenced by core::scoring::constraints::LocalCoordinateConstraint::show_def().

void core::pose::swap_transform	(	Size	jump_num,
		const kinematics::RT &	xform,
		Pose *	pose
	)

Updates the rigid-body transform of the specified jump in <pose>

References core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::conformation::Conformation::set_stub_transform(), TR, core::kinematics::FoldTree::upstream_jump_residue(), and core::id::StubID::valid().

std::string core::pose::tag_from_pose ( core::pose::Pose const & pose )

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, and tag.

Referenced by core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

void core::pose::tag_into_pose	(	core::pose::Pose &	pose,
		std::string const &	tag
	)

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, and basic::datacache::BasicDataCache::set().

core::Real core::pose::total_energy_from_pose ( core::pose::Pose const & pose )

References core::pose::Pose::energies(), getPoseExtraScores(), and core::scoring::Energies::total_energy().

Referenced by sort_pose_by_score().

void core::pose::transfer_jumps	(	const core::pose::Pose &	srcpose,
		core::pose::Pose &	tgtpose
	)

References core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::jump_nr(), core::pose::Pose::num_jump(), core::pose::Pose::set_jump(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and TR.

void core::pose::transfer_phi_psi	(	const core::pose::Pose &	srcpose,
		core::pose::Pose &	tgtpose,
		core::Size	ir,
		core::Size	jr
	)

References core::chemical::ResidueType::is_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

Referenced by transfer_phi_psi().

void core::pose::transfer_phi_psi	(	const core::pose::Pose &	srcpose,
		core::pose::Pose &	tgtpose
	)

References core::pose::Pose::total_residue(), and transfer_phi_psi().

Variable Documentation

basic::Tracer core::pose::TR("core.pose.PDBPoseMap")

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basic::Tracer core::pose::tr("core.pose")

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basic::Tracer core::pose::TR("core.pose.PDBInfo")

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Referenced by core::pose::ncbb::add_hbs_constraint(), core::pose::ncbb::add_oop_constraint(), add_variant_type_to_residue(), addVirtualResAsRoot(), core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), core::pose::full_model_info::check_full_model_info_OK(), compare_atom_coordinates(), conf2pdb_chain(), core::pose::carbohydrates::find_seqpos_of_parent_residue(), core::pose::carbohydrates::get_glycosidic_bond_residues(), core::pose::carbohydrates::get_glycosidic_torsion(), core::pose::carbohydrates::get_reference_atoms_for_1st_omega(), core::pose::carbohydrates::get_reference_atoms_for_phi(), core::pose::carbohydrates::get_reference_atoms_for_psi(), get_resnum(), get_resnum_list(), num_atoms(), num_hbond_acceptors(), num_hbond_donors(), num_heavy_atoms(), parse_resnum(), partition_pose_by_jump(), read_comment_pdb(), read_psipred_ss2_file(), remove_variant_type_from_residue(), renumber_pdbinfo_based_on_conf_chains(), sequence_map_from_pdbinfo(), setup_dof_mask_from_move_map(), swap_transform(), and transfer_jumps().

basic::Tracer core::pose::TR("core.pose.util")

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