Namespaces
	carbohydrates

	copydofs

	datacache

	full_model_info

	metrics

	motif

	ncbb

	reference_pose

	rna

	signals

	symmetry

	toolbox

Classes
class	MiniPose
	lightweight version of the pose with stuff I need. More...

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	ResidueIndexDescription
	a class which can represent one of many ways in which to describe a particular residue in a pose, and can, when given a pose, find its index. The object should be constructed with all its needed parameters, but, one instance may be copied from another. More...

class	ResidueIndexDescriptionChainEnd
	a class which represents the last residue in the Pose More...

class	ResidueIndexDescriptionLastResidue
	a class which represents the last residue in the Pose More...

class	ResidueIndexDescriptionPDB
	a class which represents a residue index as a PDB information (chain, resindex, insertion code) More...

class	ResidueIndexDescriptionPoseNum
	a class which represents a residue index as a literal, Rosetta/Pose numbered integer More...

class	ResidueIndexDescriptionRefPose
	a class which represents a residue index as a reference-pose enabled information. More...

class	RID_FileSource
	Representation of a file input support A class to hold information about where a ResidueIndexDescriptor comes from, to allow for better error messages. More...

class	RID_Source
	A class to hold information about where a ResidueIndexDescriptor comes from, to allow for better error messages. More...

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

class	xyzStripeHashPose

Typedefs
typedef std::set< int >	Jumps

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

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

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

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

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

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

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

typedef std::pair< char, std::string >	ChainSegID

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

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

typedef boost::indirect_iterator < conformation::ResidueOPs::const_iterator, Residue const >	const_iterator

typedef boost::indirect_iterator < conformation::ResidueOPs::iterator, Residue const >	iterator

using	PoseOP = utility::pointer::shared_ptr< Pose >

using	PoseCOP = utility::pointer::shared_ptr< Pose const >

using	PoseAP = utility::pointer::weak_ptr< Pose >

using	PoseCAP = utility::pointer::weak_ptr< Pose const >

using	PoseUP = std::unique_ptr< Pose >

using	PoseCUP = std::unique_ptr< Pose const >

using	PoseOPs = utility::vector1< PoseOP >

using	PoseCOPs = utility::vector1< PoseCOP >

typedef utility::pointer::shared_ptr < RID_Source >	RID_SourceOP

typedef utility::pointer::shared_ptr < RID_Source const >	RID_SourceCOP

typedef utility::pointer::shared_ptr < ResidueIndexDescription >	ResidueIndexDescriptionOP

typedef utility::pointer::shared_ptr < ResidueIndexDescription const >	ResidueIndexDescriptionCOP

typedef utility::pointer::shared_ptr < xyzStripeHashPose >	xyzStripeHashPoseOP

typedef utility::pointer::shared_ptr < xyzStripeHashPose const >	xyzStripeHashPoseCOP

typedef utility::pointer::weak_ptr < xyzStripeHashPose const >	xyzStripeHashPoseCAP

Enumerations
enum	PoseCoordPickMode { PoseCoordPickMode_NBR, PoseCoordPickMode_CA, PoseCoordPickMode_CB, PoseCoordPickMode_CB_else_CA, PoseCoordPickMode_BB, PoseCoordPickMode_N_CA_C, PoseCoordPickMode_N_CA_C_CB, PoseCoordPickMode_N_C_O, PoseCoordPickMode_BNP, PoseCoordPickMode_HVY, PoseCoordPickMode_HVY_IF_NP, PoseCoordPickMode_ALL, PoseCoordPickMode_CBorCA, PoseCoordPickMode_NUL }

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

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, bool const metapatches=true)
	return a list of ResidueTypes corresponding to an annotated protein sequence More...

chemical::ResidueTypeCOPs	residue_types_from_saccharide_sequence_recursive (std::string const &sequence, chemical::ResidueTypeSet const &residue_set)
	Internal implementation detail of residue_types_from_saccharide_sequence() Returns the reorganized (but not reversed) set of residuetypes. 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, linear, IUPAC polysaccharide sequence. More...

void	append_pose_with_glycan_residues (pose::Pose &pose, chemical::ResidueTypeCOPs residue_types, core::uint resnum_to_be_appended=0)
	Append an empty or current Pose with saccharide residues, building branches as necessary. 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, bool const metapatches)

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

void	make_pose_from_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name, bool const auto_termini=true, bool const metapatches=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, bool const idealize_linkages=true)
	Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and store 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, bool const idealize_linkages=true)
	Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name> and store 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, bool const idealize_linkages=true)
	Return a Pose from an annotated, linear, IUPAC 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...

chemical::ResidueTypeCOP	get_rsd_type_from_aa (chemical::ResidueTypeSet const &residue_set, core::chemical::AA const &my_aa, bool const &is_lower_terminus, bool const &is_upper_terminus, bool const metapatches=true)
	use efficient residue type finder to find simplest residue type with this AA & requested termini. More...

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

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

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

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

utility::vector1< core::Size >	get_chains (core::pose::Pose const &pose)
	Get all the chain numbers from conformation. More...

core::Size	chain_end_res (Pose const &pose, core::Size const chain)
	compute last residue number of a chain More...

utility::vector1< core::Size >	chain_end_res (Pose const &pose)
	compute last residue numbers of all chains More...

utility::vector1< bool >	compute_unique_chains (Pose &pose)
	Compute uniq chains in a complex Returns a vector of pose length with true/false of uniq chain. 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	has_chain (std::string const &chain, core::pose::Pose const &pose)
	Does the pose have a residue with the given chain letter. More...

bool	has_chain (char const &chain, core::pose::Pose const &pose)
	Does the pose have a residue with the given chain letter. More...

bool	has_chain (core::Size chain_id, core::pose::Pose const &pose)
	Does the pose have a residue with the given chain number. More...

utility::vector1< core::Size >	get_chain_ids_from_chains (utility::vector1< std::string > const &chains, core::pose::Pose const &pose)
	Get all chain numbers for the residues with the given chain letters. More...

utility::vector1< core::Size >	get_chain_ids_from_chains (utility::vector1< char > const &chains, core::pose::Pose const &pose)
	Get all chain numbers for the residues with the given chain letters. More...

utility::vector1< core::Size >	get_chain_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
	Get all chain numbers for the residues with the given chain letter. More...

utility::vector1< core::Size >	get_chain_ids_from_chain (char const &chain, core::pose::Pose const &pose)
	Get all chain numbers for the residues with the given chain letter. More...

core::Size	get_chain_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
	Attempt to get the chain number which correspond to the given chain letter. More...

core::Size	get_chain_id_from_chain (char const &chain, core::pose::Pose const &pose)
	Attempt to get the chain number which correspond to the given chain letter. More...

char	get_chain_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)
	Get the chain letter for the first residue in a given chain number. More...

std::set< core::Size >	get_jump_ids_from_chain_ids (std::set< core::Size > const &chain_ids, core::pose::Pose const &pose)
	Attempt to get jump IDs which correspond to the given chain number. More...

core::Size	get_jump_id_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)
	Attempt to get the jump number which correspond to the given chain number. More...

utility::vector1< core::Size >	get_jump_ids_from_chain (char const &chain, core::pose::Pose const &pose)
	Get all the jump numbers for the given chain letter. More...

utility::vector1< core::Size >	get_jump_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
	Get all the jump numbers for the given chain letter. More...

core::Size	get_jump_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
	Get the jump number for the given chain letter. More...

core::Size	get_jump_id_from_chain (char const &chain, core::pose::Pose const &pose)
	Get the jump number for the given chain letter. More...

core::Size	get_chain_id_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
	Get the chain ID of the residue directly built by the given jump. More...

char	get_chain_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
	Get the chain letter of the chain built by the given jump. More...

utility::vector1< core::Size >	get_resnums_for_chain (core::pose::Pose const &pose, char chain)
	Get a vector of all residues numbers which are represented by this chain letter. More...

utility::vector1< core::Size >	get_resnums_for_chain_id (core::pose::Pose const &pose, core::Size chain_id)
	Get a vector of all residues numbers which are represented by this chain number. More...

core::conformation::ResidueCOPs	get_chain_residues (core::pose::Pose const &pose, core::Size chain_id)
	Get all residues which correspond to the given chain number. More...

core::conformation::ResidueCOPs	get_residues_from_chains (core::pose::Pose const &pose, utility::vector1< core::Size > const &chain_ids)
	Get all residues which correspond to the given chain numbers. More...

bool	res_in_chain (core::pose::Pose const &pose, core::Size resnum, std::string const &chain)
	Does this residue number have this chain letter? More...

core::Size	get_hash_from_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues with the given chain letter. More...

core::Size	get_hash_excluding_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...

std::string	get_sha1_hash_from_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues with the given chain letter. More...

std::string	get_sha1_hash_from_chains (utility::vector1< std::string > const &chains, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues with the given chain letters. More...

std::string	get_sha1_hash_excluding_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...

std::string	get_sha1_hash_excluding_chain (std::string const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...

std::string	get_sha1_hash_excluding_chains (utility::vector1< std::string > const &chains, core::pose::Pose const &pose, std::string const &extra_label="")
	Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...

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

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	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	hasPoseExtraScore (core::pose::Pose const &pose, std::string const &name)
	does this ExtraScore exist? More...

bool	hasPoseExtraScore_str (core::pose::Pose const &pose, std::string const &name)
	does this (string) ExtraScore exist? More...

bool	getPoseExtraScore (core::pose::Pose const &pose, std::string const &name, core::Real &value)
	return bool is T/F for whether the requested datum exists. "value" is the data, pass-by-ref. More...

Real	getPoseExtraScore (core::pose::Pose const &pose, std::string const &name)
	return value is ExtraScore if exist, runtime_assert if it doesn't exist More...

bool	getPoseExtraScore (core::pose::Pose const &pose, std::string const &name, std::string &value)
	return bool is T/F for whether the requested datum exists. "value" is the data, pass-by-ref. More...

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

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

void	setPoseExtraScore (core::pose::Pose &pose, std::string const &name, core::Real value)
	Set a core::Real in the pose datacache, that will be output as a score in the scorefile. More...

void	setPoseExtraScore (core::pose::Pose &pose, std::string const &name, std::string const &value)
	Set a string in the pose datacache, that will be output as a score in the scorefile. More...

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)
	Sets a PDB-style REMARK entry in the Pose. More...

void	clearPoseExtraScores (core::pose::Pose &pose)
	Clear ALL PoseExtraScores. More...

void	clearPoseExtraScore (core::pose::Pose &pose, std::string const &name)
	Clear a specific data type from the arbitrary data cache in the pose. More...

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)

utility::vector1< char >	read_psipred_ss2_file (pose::Pose const &pose, std::string const &filename)

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

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...

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

void	set_output_res_and_chain (pose::Pose &extended_pose, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_resnum_and_chain)

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

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

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

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

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

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

void	attributes_for_saved_reference_pose (utility::tag::AttributeList &attributes, std::string const &attribute_name="reference_name")
	convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable More...

void	attributes_for_saved_reference_pose_w_description (utility::tag::AttributeList &attributes, std::string const &description, std::string const &attribute_name="reference_name")
	convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable More...

core::pose::PoseOP	saved_reference_pose (utility::tag::TagCOP const in_tag, basic::datacache::DataMap &data_map, std::string const &tag_name)

core::pose::PoseCOP	saved_native_pose (basic::datacache::DataMap &data_map, std::string const &resource_str="native_pose")
	Retrieve the native pose from the DataMap which is added through the OptionsCollection during RosettaScript parsing as a resource. More...

std::ostream &	operator<< (std::ostream &out, ResidueIndexDescription const &rid)

ResidueIndexDescriptionCOP	make_rid_posenum (core::Size resnum)
	Convenience function for converting a Size (Pose numbered) into a ResidueIndexDescription. More...

bool	character_is_USA_letter (char c)

void	parse_PDBnum_icode (std::string const &token, std::string const &fname, Size const lineno, int &PDBnum, char &icode)
	Take the string "token" and try to interpret it as a PDB identifier in the form of an integer as well as an optional insertion code. For example the string "25A" would be interpretted as the residue 25 with the insertion code "A." Throws an exception if the input string is misformatted. More...

ResidueIndexDescriptionCOP	parse_resnum (std::string const &resnum, bool const check_for_refpose=false)
	Creates a ResidueIndexDescription from a string Recognizes three forms of numbering: More...

core::Size	parse_resnum (std::string const &resnum, core::pose::Pose const &pose, bool const check_for_refpose=false)
	Extracts a residue number from a string. Recognizes three 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...

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...

bool	is_referencepose_number (std::string const &str, std::string &refpose_string, core::Size &refpose_resnumber, signed long &refpose_offset)
	Is a string of the format "refpose(<refposename>,<refposenumber>)" or "refpose(<refposename>,<refposenumber>)+/-<number>"? More...

core::Size	get_resnumber_from_reference_pose (std::string const &refpose_name, core::Size const refpose_number, signed long const refpose_offset, core::pose::Pose const &pose)
	Given the name of a ReferencePose object in the pose, a residue number in that reference pose, and a residue offset, this function returns the Rosetta number of the corresponding residue in the pose. Should throw an error if the ReferencePose doesn't exist in the pose, or 0 if no corresponding residue exists in the pose. More...

std::string	get_resnum_string (utility::tag::TagCOP tag_ptr, std::string const &prefix="")
	DEPRECATED - provided for legacy usage only. Don't use for new code. Instead, just use a single option which uses the parse_resnum syntax to specify. More...

std::string	get_resnum_string (utility::tag::TagCOP tag_ptr, std::string const &prefix, std::string const &default_value)
	DEPRECATED - provided for legacy usage only. Don't use for new code. Instead, just use a single option which uses parse_resnum syntax to specify. More...

core::select::residue_selector::ResidueSelectorOP	get_resnum_selector (utility::tag::TagCOP tag_ptr, std::string const &tag)

void	attributes_for_get_resnum_string (utility::tag::AttributeList &attlist, std::string const &prefix)
	Companion function for get_resnum. More...

void	attributes_for_get_resnum_selector (utility::tag::AttributeList &attlist, utility::tag::XMLSchemaDefinition &xsd, string const &tag, string const &description)
	Companion function for get_resnum_list. More...

void	attributes_for_parse_resnum (utility::tag::AttributeList &attlist, std::string const &att_name, std::string const &description="")
	Companion function for parse_resnum. More...

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

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	create_subpose (Pose const &src, utility::vector1< Size > const &positions, kinematics::FoldTree const &f, Pose &pose)
	Create a subpose of the src pose. PDBInfo is set as NULL. More...

void	pdbslice (core::pose::Pose &new_pose, core::pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)
	Create a subpose of the src pose – figures out a reasonable fold tree. More...

void	pdbslice (core::pose::Pose &pose, utility::vector1< core::Size > const &slice_res)
	Create a subpose of the src pose – figures out a reasonable fold tree. More...

utility::vector1< int >	partition_pose_by_jump (pose::Pose const &src, int const jump_number, pose::Pose &partner1, pose::Pose &partner2)

void	pdbslice (pose::Pose &new_pose, pose::Pose const &pose, utility::vector1< Size > const &slice_res)
	Create a subpose of the src pose – figures out a reasonable fold tree. More...

void	pdbslice (pose::Pose &pose, utility::vector1< Size > const &slice_res)
	Create a subpose of the src pose – figures out a reasonable fold tree. More...

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

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

bool	is_position_conserved_residue (Pose const &pose, core::Size residue)
	Returns true if <residue> is positionally conserved, false otherwise Based on the POSITION_CONSERVED_RESIDUES annotation stored in the Pose DataCache. More...

bool	create_chemical_edge (core::uint start_resnum, core::uint end_resnum, core::pose::Pose const &pose, core::kinematics::FoldTree &ft)
	Create a chemical edge between two Residues. More...

void	set_reasonable_fold_tree (pose::Pose &pose)

core::chemical::ResidueTypeCOP	virtual_type_for_pose (core::pose::Pose const &pose)
	Return the appropritate ResidueType for the virtual residue for the "mode" (fullatom, centroid ...) the pose is in. 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	remove_virtual_residues (core::pose::Pose &pose)
	Removes all virtual residues from <pose> More...

numeric::xyzVector< core::Real >	get_center_of_mass (core::pose::Pose const &pose)
	Get center of mass of a pose. More...

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

void	fix_pdbinfo_damaged_by_insertion (core::pose::Pose &pose)
	Repair pdbinfo of inserted residues that may have blank chain and zero seqpos. Assumes insertions only occur after a residue. 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)
	this function compares poses for equality up to the information stored in the binary protein silent struct format. More...

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)

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)

void	replace_pose_residue_copying_existing_coordinates (pose::Pose &pose, Size const seqpos, core::chemical::ResidueType const &new_rsd_type, utility::vector1< core::Size > const &mapping)

core::chemical::ResidueTypeCOP	get_restype_for_pose (core::pose::Pose const &pose, std::string const &name)
	Return the residue type in the correct "mode" (fullatom, centroid ...) the pose is in. More...

core::chemical::ResidueTypeCOP	get_restype_for_pose (core::pose::Pose const &pose, std::string const &name, core::chemical::TypeSetMode mode)
	Return the residue type in the passed mode, respecting any modification that pose may make. More...

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...

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)

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

void	initialize_disulfide_bonds (Pose &pose, io::StructFileRep const &fd)
	detect and fix disulfide bonds 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...

Size	nres_protein (pose::Pose const &pose)
	Number of protein residues in the pose. More...

core::Real	radius_of_gyration (core::pose::Pose const &pose, numeric::xyzVector< core::Real > const &center_of_mass, utility::vector1< bool > const &residues)
	Get the radius of gyration of the selected residues. More...

numeric::xyzVector< Real >	center_of_mass (core::pose::Pose const &pose, utility::vector1< bool > const &residues)
	Get the center of the indicated residues. More...

utility::vector1< bool >	generate_vector_from_bounds (pose::Pose const &pose, int const start, int const stop)

numeric::xyzVector< core::Real >	center_of_mass (pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...

core::Vector	all_atom_center (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues)
	Get the center of the indicated residues. More...

int	residue_center_of_mass (pose::Pose const &pose, utility::vector1< bool > residues)

int	residue_center_of_mass (pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...

int	return_nearest_residue (pose::Pose const &pose, utility::vector1< bool > const &residues, Vector center)

int	return_nearest_residue (pose::Pose const &pose, int const begin, int const end, Vector center)
	finds the residue nearest some position passed in (normally a center of mass) More...

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

std::map< std::string, core::Size >	get_pdb2pose_numbering_as_stdmap (core::pose::Pose const &pose)
	Create std::map from PDBPoseMap in pose (JKLeman) More...

void	declare_cutpoint_chemical_bond (core::pose::Pose &pose, Size const cutpoint_res, Size const next_res_in)
	Create a chemical bond from lower to upper residue across CUTPOINT_LOWER/CUTPOINT_UPPER. More...

void	update_cutpoint_virtual_atoms_if_connected (core::pose::Pose &pose, core::Size const cutpoint_res, bool recurse)
	Given a pose and a position that may or may not be CUTPOINT_UPPER or CUTPOINT_LOWER, determine whether this position has either of these variant types, and if it does, determine whether it's connected to anything. If it is, update the C-OVL1-OVL2 bond lengths and bond angle (for CUTPOINT_LOWER) or OVU1-N bond length (for CUTPOINT_UPPER) to match any potentially non-ideal geometry in the residue to which it's bonded. More...

void	get_constraints_from_link_records (core::pose::Pose &pose, io::StructFileRep const &sfr)

utility::vector1< Size >	pdb_to_pose (pose::Pose const &pose, utility::vector1< int > const &pdb_res)
	Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More...

utility::vector1< Size >	pdb_to_pose (pose::Pose const &pose, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &pdb_res)
	Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More...

Size	pdb_to_pose (pose::Pose const &pose, int const res_num, char const chain)
	Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More...

utility::vector1< Size >	pose_to_pdb (pose::Pose const &pose, utility::vector1< Size > const &pose_res)
	Convert pose numbering to pdb numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More...

chemical::rings::AxEqDesignation	is_atom_axial_or_equatorial_to_ring (Pose const &pose, uint seqpos, uint query_atom, utility::vector1< uint > const &ring_atoms)
	Is the query atom in this pose residue axial or equatorial to the given ring or neither? More...

chemical::rings::AxEqDesignation	is_atom_axial_or_equatorial_to_ring (Pose const &pose, id::AtomID const &query_atom, utility::vector1< id::AtomID > const &ring_atoms)

void	set_bb_torsion (uint torsion_id, Pose &pose, core::Size sequence_position, core::Angle new_angle)

core::Angle	get_bb_torsion (uint torsion_id, Pose const &pose, core::Size sequence_position)
	Get a particular backbone torsion, phi, psi, omega (see core::types) Works with carbohydrates. Think about moving this to pose itself. More...

void	set_bfactors_from_atom_id_map (Pose &pose, id::AtomID_Map< Real > const &bfactors)
	Set bfactors in a pose PDBInfo. More...

bool	just_modeling_RNA (std::string const &sequence)

bool	stepwise_addable_pose_residue (Size const n, pose::Pose const &pose)

bool	stepwise_addable_residue (Size const n, std::map< Size, std::string > const &non_standard_residue_map)

bool	effective_lower_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model)

bool	effective_upper_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model, Size const nres_full)

bool	definite_terminal_root (utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, Size const nres, Size const i)

bool	definite_terminal_root (pose::Pose const &pose, Size const i)

Size	get_definite_terminal_root (pose::Pose const &pose, utility::vector1< Size > const &partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &fixed_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res)

Size	get_definite_terminal_root (pose::Pose const &pose, utility::vector1< Size > const &partition_res)

utility::vector1< Size >	reorder_root_partition_res (utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &fixed_domain_map)

void	reroot (pose::Pose &pose, utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &preferred_root_res, utility::vector1< Size > const &fixed_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res)

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...

int	return_nearest_residue (core::pose::Pose const &pose, int const begin, int const end, core::Vector center)

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)

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

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

conformation::ResidueOP	add_variant_type_to_residue (conformation::Residue const &old_rsd, core::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	add_variant_type_to_pose_residue (pose::Pose &pose, std::string const &variant_type, Size const seqpos)

void	add_custom_variant_type_to_pose_residue (pose::Pose &pose, std::string const &variant_type, Size const seqpos)

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)

void	correctly_add_cutpoint_variants (core::pose::Pose &pose)
	Add cutpoint variants to all residues annotated as cutpoints in the FoldTree in the Pose. More...

void	correctly_add_2prime_connection_variants (pose::Pose &pose, Size const twoprime_res, Size const next_res)

void	correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const cutpoint_res, bool const check_fold_tree, Size const next_res_in)
	Add CUTPOINT_LOWER and CUTPOINT_UPPER types to two residues, remove incompatible types, and declare a chemical bond between them. More...

void	correctly_remove_variants_incompatible_with_lower_cutpoint_variant (core::pose::Pose &pose, Size const res_index)
	Remove variant types incompatible with CUTPOINT_LOWER from a position in a pose. More...

void	correctly_remove_variants_incompatible_with_upper_cutpoint_variant (core::pose::Pose &pose, Size const res_index)
	Remove variant types incompatible with CUTPOINT_UPPER from a position in a pose. More...

bool	pose_residue_is_terminal (Pose const &pose, Size const resid)
	returns true if the given residue in the pose is a chain ending or has upper/lower terminal variants More...

bool	is_lower_terminus (pose::Pose const &pose, Size const resid)
	checks to see if this is a lower chain ending more intelligently than just checking residue variants More...

bool	is_upper_terminus (pose::Pose const &pose, Size const resid)
	checks to see if this is a lower chain ending more intelligently than just checking residue variants More...

void	fix_up_residue_type_variants_at_strand_end (pose::Pose &pose, Size const res)

void	fix_up_residue_type_variants_at_strand_beginning (pose::Pose &pose, Size const res)

void	fix_up_residue_type_variants_at_floating_base (pose::Pose &pose, Size const res)

void	update_block_stack_variants (pose::Pose &pose, Size const n)

void	fix_up_residue_type_variants (pose::Pose &pose)

core::id::AtomID_Map < platform::Real >	make_atom_map (core::pose::Pose const &p, PoseCoordPickMode m)

Typedef Documentation

typedef std::pair< char, std::string > core::pose::ChainSegID

typedef boost::indirect_iterator< conformation::ResidueOPs::const_iterator, Residue const > core::pose::const_iterator

typedef boost::indirect_iterator< conformation::ResidueOPs::iterator, Residue const > core::pose::iterator

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

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

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

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

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

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

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

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

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

using core::pose::PoseAP = typedef utility::pointer::weak_ptr< Pose >

using core::pose::PoseCAP = typedef utility::pointer::weak_ptr< Pose const >

using core::pose::PoseCOP = typedef utility::pointer::shared_ptr< Pose const >

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

using core::pose::PoseCUP = typedef std::unique_ptr< Pose const >

using core::pose::PoseOP = typedef utility::pointer::shared_ptr< Pose >

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

using core::pose::PoseUP = typedef std::unique_ptr< Pose >

typedef utility::pointer::shared_ptr< ResidueIndexDescription const > core::pose::ResidueIndexDescriptionCOP

typedef utility::pointer::shared_ptr< ResidueIndexDescription > core::pose::ResidueIndexDescriptionOP

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

typedef utility::pointer::shared_ptr< RID_Source const > core::pose::RID_SourceCOP

typedef utility::pointer::shared_ptr< RID_Source > core::pose::RID_SourceOP

typedef utility::pointer::weak_ptr< xyzStripeHashPose const > core::pose::xyzStripeHashPoseCAP

typedef utility::pointer::shared_ptr< xyzStripeHashPose const > core::pose::xyzStripeHashPoseCOP

typedef utility::pointer::shared_ptr< xyzStripeHashPose > core::pose::xyzStripeHashPoseOP

Enumeration Type Documentation

enum core::pose::PoseCoordPickMode

Enumerator
PoseCoordPickMode_NBR
PoseCoordPickMode_CA
PoseCoordPickMode_CB
PoseCoordPickMode_CB_else_CA
PoseCoordPickMode_BB
PoseCoordPickMode_N_CA_C
PoseCoordPickMode_N_CA_C_CB
PoseCoordPickMode_N_C_O
PoseCoordPickMode_BNP
PoseCoordPickMode_HVY
PoseCoordPickMode_HVY_IF_NP
PoseCoordPickMode_ALL
PoseCoordPickMode_CBorCA
PoseCoordPickMode_NUL

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(), core::pose::datacache::CacheableDataType::STRING_MAP, and protocols::hybridization::val.

Referenced by protocols::monte_carlo::GenericMonteCarloMover::accept(), protocols::antibody::clusters::add_cluster_comments_to_pose(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::add_labels_as_remark(), protocols::simple_moves::AddChainMover::add_new_chain(), protocols::evolution::NucleotideMutation::add_nt_seq_to_pose(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::Splice::add_sequence_constraints(), core::sequence::alignment_into_pose(), protocols::simple_moves::SaveSequenceToCommentsMover::apply(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::splice::RBInMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::WriteSSEMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::carbohydrates::GlycanSampler::apply(), protocols::splice::Splice::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::hbnet::HBNet::apply(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::splice::calculate_rmsd(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd(), protocols::fold_from_loops::NubInitioMover::dump_centroid(), core::io::silent::SilentStruct::energies_into_pose(), protocols::splice::SpliceManager::generate_sequence_profile(), protocols::splice::Splice::generate_sequence_profile(), protocols::hbnet::HBNet::get_additional_output(), protocols::features::PoseCommentsFeatures::load_into_pose(), protocols::hbnet::HBNet::output_networks(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::cluster::ClusterBase::print_cluster_PDBs(), read_comment_pdb(), protocols::frag_picker::nonlocal::NonlocalFrags::recover_checkpoint(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::hbnet::HBNet::set_constraints(), protocols::splice::SpliceOut::SpliceOutFilter(), protocols::simple_moves::AddChainMover::swap_chain(), protocols::denovo_design::DisulfidizeMover::tag_disulfides(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), and protocols::hbnet::HBNet::write_network_pdb().

void core::pose::add_custom_variant_type_to_pose_residue	(	pose::Pose &	pose,
		std::string const &	variant_type,
		Size const	seqpos
	)

References core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::n_possible_residue_connections(), replace_pose_residue_copying_existing_coordinates(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::conformation::Conformation::residue_type(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and core::conformation::Conformation::update_noncanonical_connection().

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_VARIANT.

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::simple_moves::RepeatPropagationMover::add_cap_seq(), protocols::grafting::simple_movers::DeleteRegionMover::add_terminus_variants(), protocols::denovo_design::components::add_terminus_variants(), protocols::denovo_design::components::add_to_pose(), protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::hybridization::MRMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::remodel::RemodelMover::apply(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::denovo_design::construct_dummy_pose(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type(), protocols::forge::methods::grow_left_r(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_isopeptide_variants(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_variants(), protocols::fldsgn::CircularPermutation::split_chains(), and protocols::hybridization::MRMover::trim_target_pose().

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

Sets a PDB-style REMARK entry in the Pose.

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(), core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS, and protocols::hybridization::val.

Referenced by protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::cryst::CrystRMS::apply(), protocols::cryst::DockLatticeMover::apply(), protocols::moves::SwitchMover::apply(), protocols::forge::remodel::RemodelMover::apply(), core::io::silent::SilentStruct::energies_into_pose(), protocols::cryst::DockLatticeMover::initialize(), protocols::fold_from_loops::NubInitioMover::manage_constraints(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::frag_picker::FragmentCandidate::output_silent(), and protocols::fold_from_loops::NubInitioMover::template_rmsd().

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_VARIANT.

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::grafting::simple_movers::DeleteRegionMover::add_terminus_variants(), protocols::denovo_design::components::add_terminus_variants(), protocols::denovo_design::components::add_to_pose(), protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::hybridization::MRMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::fldsgn::CircularPermutation::apply(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::denovo_design::construct_dummy_pose(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type(), protocols::forge::methods::grow_right_r(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_isopeptide_variants(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_variants(), protocols::fldsgn::CircularPermutation::split_chains(), and protocols::hybridization::MRMover::trim_target_pose().

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.

E.g., make a terminus variant, and replace the original in pose.

Note: This copies any atoms in common between old and new residues, rebuilding the others.

References core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::n_possible_residue_connections(), replace_pose_residue_copying_existing_coordinates(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::conformation::Conformation::residue_type(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), update_cutpoint_virtual_atoms_if_connected(), and core::conformation::Conformation::update_noncanonical_connection().

void core::pose::add_variant_type_to_pose_residue	(	pose::Pose &	pose,
		std::string const &	variant_type,
		Size const	seqpos
	)

References core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::n_possible_residue_connections(), replace_pose_residue_copying_existing_coordinates(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::conformation::Conformation::residue_type(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), update_cutpoint_virtual_atoms_if_connected(), and core::conformation::Conformation::update_noncanonical_connection().

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.

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::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::nchi(), core::conformation::Residue::nchi(), core::pose::Pose::residue_type_set_for_pose(), TR(), and core::conformation::Residue::type().

Referenced by core::pack::rotamer_set::build_proton_chi_rotamers(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_partitioned_search_pattern(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::create_search_pattern(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), protocols::motifs::LigandMotifSearch::run(), protocols::motifs::MotifDnaPacker::run_motifs(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().

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 protocols::cluster::calibur::aa, core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_polymer(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), TR(), virtual_type_for_pose(), and protocols::kinmatch::xyz().

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), addVirtualResAsRoot(), protocols::simple_moves::VirtualRootMover::apply(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::electron_density::SetupForDensityScoringMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_ligand_score(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::electron_density::DockIntoDensityMover::density_grid_search(), protocols::electron_density::DockIntoDensityMover::do_filter(), protocols::electron_density::DockIntoDensityMover::do_refinement(), core::pose::symmetry::extract_asymmetric_unit(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::electron_density::DockIntoDensityMover::print_best_rms(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), protocols::electron_density::set_pose_and_scorefxn_for_edens_scoring(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::electron_density::DockIntoDensityMover::setNative(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::import_pose::setup_for_density_scoring(), protocols::star::StarAbinitio::setup_kinematics(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose().

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 addVirtualResAsRoot(), get_center_of_mass(), core::pose::Pose::size(), and TR().

Referenced by protocols::rbsegment_relax::restore_pose_from_rbsegs(), and protocols::rbsegment_relax::setup_pose_from_rbsegs().

core::Vector core::pose::all_atom_center	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residues
	)

Get the center of the indicated residues.

This computes an equally-weighted, all-atom (including virtuals and hydrogens) center

References center_of_mass(), protocols::splice::coords(), and core::pose::Pose::residue().

Referenced by protocols::qsar::qsarMover::apply(), protocols::qsar::RenderGridsToKinemage::apply(), protocols::ligand_docking::get_ligand_grid_scores(), protocols::ligand_docking::get_ligand_travel(), protocols::ligand_docking::get_radius_of_gyration(), and protocols::features::ResidueGridScoresFeatures::report_features().

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 protocols::mean_field::add().

Referenced by protocols::forge::build::Bridge::Bridge(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::build::GrowLeft::GrowLeft(), protocols::forge::build::GrowRight::GrowRight(), make_pose_from_sequence(), protocols::forge::build::SegmentInsert::SegmentInsert(), and protocols::forge::build::SegmentRebuild::SegmentRebuild().

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::size().

Referenced by protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::simple_moves::AddChainMover::add_new_chain(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(), protocols::splice::DesignInterfacesOperation::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::docking::membrane::MPDockingSetupMover::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::pose_length_moves::ConnectChainsMover::assemble_missing_chain(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::pose_length_moves::ConnectChainsMover::generate_best_final_pose(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::pose_creation::MakeJunctionsMover::make_pose_from_design(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses(), protocols::simple_moves::AddChainMover::swap_chain(), protocols::legacy_sewing::Assembly::to_pose(), and protocols::sewing::data_storage::SmartAssembly::to_pose().

void core::pose::append_pose_with_glycan_residues	(	pose::Pose &	pose,
		chemical::ResidueTypeCOPs	residue_types,
		core::uint	resnum_to_be_appended
	)

Append an empty or current Pose with saccharide residues, building branches as necessary.

This function was written primarily as a subroutine for code shared by make_pose_from_saccharide_sequence() and pose::carbohydrates:glycosylate_pose(). You probably do not want to call it directly.

Parameters

<pose>	The Pose must be either empty, in which case a new oligo- or polysaccharide pose will be created, or it must have a BRANCH_POINT variant residue to extend. This Residue of the Pose must have unsatisfied ResidueConnections. By default, it is assumed to be the last residue of the Pose.
<residue_types>	A list of ResidueTypes from which to build new residues for the Pose. These must be ordered such that a branch is completely finished before a new one is begun. Branches are constructed by assuming that branch connections are "satisfied" in the order in which they were created. ResidueTypes must be of the correct VariantType to be appended properly. (See pose::carbohydrates:glycosylate_pose().)
<resnum_to_be_appended>	The sequence position to which the glycan will be appended. It must be a BRANCH_POINT with an unsatisfied connection. By default, it is assumed to be the last residue of the Pose.

References core::pose::Pose::append_residue_by_atoms(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::empty(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by core::pose::carbohydrates::glycosylate_pose(), and make_pose_from_saccharide_sequence().

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::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by append_pose_to_pose(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::swap_chains().

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

void core::pose::attributes_for_get_resnum_selector	(	utility::tag::AttributeList &	attlist,
		utility::tag::XMLSchemaDefinition &	xsd,
		string const &	tag,
		string const &	description
	)

Companion function for get_resnum_list.

Companion function for get_resnum_selector.

Appends relevant XMLSchemaAttributes to the AttributeList

Appends relevant XMLSchemaAttributes to the AttributeList; needs the xsd because it adds restricted types

void core::pose::attributes_for_get_resnum_string	(	utility::tag::AttributeList &	attlist,
		std::string const &	prefix
	)

Companion function for get_resnum.

Companion function for get_resnum_string.

Appends relevant XMLSchemaAttributes to the AttributeList

void core::pose::attributes_for_parse_resnum	(	utility::tag::AttributeList &	attlist,
		std::string const &	att_name,
		std::string const &	description = `""`
	)

Companion function for parse_resnum.

Appends relevant XMLSchemaAttributes to the AttributeList

Referenced by protocols::simple_filters::AtomicDistanceFilter::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SetChiMover::provide_xml_schema(), protocols::simple_filters::StemFinder::provide_xml_schema(), protocols::rigid::RollMover::provide_xml_schema(), core::select::residue_selector::ResidueSpanSelector::provide_xml_schema(), protocols::frag_picker::FragmentScoreFilter::provide_xml_schema(), and protocols::simple_moves::Tumble::provide_xml_schema().

void core::pose::attributes_for_saved_reference_pose	(	utility::tag::AttributeList &	attributes,
		std::string const &	attribute_name
	)

convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable

References attributes_for_saved_reference_pose_w_description().

Referenced by core::simple_metrics::composite_metrics::CompositeEnergyMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema(), and core::simple_metrics::metrics::RMSDMetric::provide_xml_schema().

void core::pose::attributes_for_saved_reference_pose_w_description	(	utility::tag::AttributeList &	attributes,
		std::string const &	description,
		std::string const &	attribute_name
	)

convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable

Referenced by attributes_for_saved_reference_pose(), and protocols::rosetta_scripts::attributes_for_saved_reference_pose_w_description().

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::pose::Pose::begin(), core::pose::Pose::end(), and core::chemical::num_canonical_aas.

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

count the number of canonical residues in the pose

References core::pose::Pose::begin(), core::pose::Pose::end(), and core::chemical::num_canonical_aas.

numeric::xyzVector< core::Real > core::pose::center_of_mass	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	residues
	)

Get the center of the indicated residues.

WARNING: Despite the name, this function only calculates with a single coordinate per residue (the Calpha/neighbor atom)

References protocols::splice::coords(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::legacy_sewing::LegacyRepeatAssemblyMover::add_repeats(), protocols::legacy_sewing::Assembly::align_model(), core::conformation::UltraLightResidue::align_to_residue(), protocols::symmetry::DetectSymmetry::apply(), core::scoring::nmr::pre::PREMultiSet::calc_dr6_dS2_dXYZ(), core::scoring::nmr::pre::PREMultiSet::calc_r6_S2(), protocols::features::SmotifFeatures::calculate_angles(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), center_of_mass(), protocols::environment::com_calc(), protocols::nmr::pcs::PCSLigandTransformMover::define_ligand_frame_origin(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), core::scoring::membrane::MPSpanAngleEnergy::find_helix_vector(), protocols::sewing::movers::LigandBindingAssemblyMover::get_min_distance(), protocols::motif_grafting::movers::MotifGraftMover::get_next_nonredundant_motifmatch(), protocols::match::NumNeighborsMPM::modified_match_positions(), residue_center_of_mass(), protocols::toolbox::pose_manipulation::rigid_body_move(), core::conformation::UltraLightResidue::slide(), core::conformation::UltraLightResidue::transform(), and core::conformation::UltraLightResidue::UltraLightResidue().

numeric::xyzVector< core::Real > core::pose::center_of_mass	(	pose::Pose const &	pose,
		int const	start,
		int const	stop
	)

calculates the center of mass of a pose

Get the center of the indicated residues.

the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Author: Monica Berrondo June 14 2007

WARNING: Despite the name, this function only calculates with a single coordinate per residue (the Calpha/neighbor atom)

References center_of_mass(), and generate_vector_from_bounds().

Referenced by all_atom_center(), core::conformation::all_atom_center(), and protocols::sic_dock::get_rg().

core::Size core::pose::chain_end_res	(	Pose const &	pose,
		core::Size const	chain
	)

compute last residue number of a chain

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), has_chain(), and TR().

Referenced by protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom(), protocols::pose_creation::MergePDBMover::determine_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), and protocols::membrane::rsd_closest_to_chain_tm_com().

utility::vector1< core::Size > core::pose::chain_end_res ( Pose const & pose )

compute last residue numbers of all chains

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

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

bool core::pose::character_is_USA_letter ( char c )

Referenced by parse_PDBnum_icode().

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

Clear a specific data type from the arbitrary data cache in the pose.

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::datacache::CacheableDataType::ARBITRARY_STRING_DATA, and core::pose::Pose::data().

Referenced by protocols::simple_moves::VirtualRootMover::apply().

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

Clear ALL PoseExtraScores.

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

Referenced by protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), and protocols::jobdist::not_universal_main().

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::size(), TR(), and protocols::kinmatch::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().

utility::vector1< bool > core::pose::compute_unique_chains ( Pose & pose )

Compute uniq chains in a complex Returns a vector of pose length with true/false of uniq chain.

Compute uniq chains in a complex, based on sequence identity.

Returns a vector of pose length with true/false of uniq chain true is unique, false is not

References core::pose::Pose::chain(), core::pose::Pose::chain_sequence(), get_chains(), core::pose::Pose::size(), and TR().

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

get Conformation chain number -> PDBInfo chain mapping

Remarks: Any chains whose PDBInfo chain records are marked entirely as PDBInfo::empty_record() will be mapped to that character.

Returns: the mapping if PDBInfo available and chains appear consistent, otherwise prints a warning and returns a default mapping (1=A, 2=B_

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::pose::Pose::chain(), conf2pdb_chain_default_map(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), core::conformation::Conformation::num_chains(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), 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< core::Size, char > &	chainmap
	)

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

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

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

void core::pose::correctly_add_2prime_connection_variants	(	pose::Pose &	pose,
		Size const	twoprime_res,
		Size const	next_res
	)

References add_variant_type_to_pose_residue(), core::chemical::C2_BRANCH_POINT, core::pose::Pose::conformation(), correctly_remove_variants_incompatible_with_upper_cutpoint_variant(), core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::rna::position_cutpoint_phosphate_torsions(), remove_variant_type_from_pose_residue(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_conn_id(), core::pose::Pose::residue_type(), core::conformation::Conformation::sever_chemical_bond(), TR(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by fix_up_residue_type_variants(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants().

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

Add cutpoint variants to all residues annotated as cutpoints in the FoldTree in the Pose.

References core::pose::Pose::fold_tree(), and core::pose::Pose::size().

Referenced by core::import_pose::add_cutpoint_closed(), protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_cutpoint_variants_at_termini(), protocols::simple_moves::ChainSplitMover::apply(), protocols::medal::MedalMover::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_cutpoint_variants(), fix_up_residue_type_variants(), fix_up_residue_type_variants_at_strand_beginning(), fix_up_residue_type_variants_at_strand_end(), core::util::ChainbreakUtil::has_chainbreak(), protocols::fold_from_loops::utils::Nub::join_pieces(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::put_in_cutpoints(), protocols::stepwise::modeler::rna::setup_chain_break_variants(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), and protocols::star::StarAbinitio::setup_kinematics().

void core::pose::correctly_add_cutpoint_variants	(	core::pose::Pose &	pose,
		Size const	cutpoint_res,
		bool const	check_fold_tree,
		Size const	next_res_in
	)

Add CUTPOINT_LOWER and CUTPOINT_UPPER types to two residues, remove incompatible types, and declare a chemical bond between them.

Parameters

[in,out]	pose	The pose to modify.
[in]	cutpoint_res	The index of the CUTPOINT_LOWER residue.
[in]	check_fold_tree	If true, a check is performed to confirm that the residues in question represent a cutpoint in the foldtree in the pose.
[in]	next_res_in	The index of the CUTPOINT_UPPER residue. If not provided, or if set to 0, this defaults to the cutpoint_res + 1 residue. Must be specified for cyclic geometry.
[in]	pose	The pose to modify.
[in]	cutpoint_res	The index of the CUTPOINT_LOWER residue.
[in]	check_fold_tree	If true, a check is performed to confirm that the residues in question represent a cutpoint in the foldtree in the pose.
[in]	next_res_in	The index of the CUTPOINT_UPPER residue. If not provided, or if set to 0, this defaults to the cutpoint_res + 1 residue. Must be specified for cyclic geometry.

References add_variant_type_to_pose_residue(), correctly_remove_variants_incompatible_with_lower_cutpoint_variant(), correctly_remove_variants_incompatible_with_upper_cutpoint_variant(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, declare_cutpoint_chemical_bond(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::is_RNA(), core::pose::rna::position_cutpoint_phosphate_torsions(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and update_cutpoint_virtual_atoms_if_connected().

void core::pose::correctly_remove_variants_incompatible_with_lower_cutpoint_variant	(	core::pose::Pose &	pose,
		Size const	res_index
	)

Remove variant types incompatible with CUTPOINT_LOWER from a position in a pose.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Parameters

[in,out]	pose	The pose on which to operate.
[in]	res_index	The index of the residue on which to operate.

References core::chemical::C_METHYLAMIDATION, remove_variant_type_from_pose_residue(), core::chemical::THREE_PRIME_PHOSPHATE, and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_cutpoint_variants_at_termini(), and correctly_add_cutpoint_variants().

void core::pose::correctly_remove_variants_incompatible_with_upper_cutpoint_variant	(	core::pose::Pose &	pose,
		Size const	res_index
	)

Remove variant types incompatible with CUTPOINT_UPPER from a position in a pose.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Parameters

[in,out]	pose	The pose on which to operate.
[in]	res_index	The index of the residue on which to operate.

References core::chemical::FIVE_PRIME_PHOSPHATE, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::N_ACETYLATION, remove_variant_type_from_pose_residue(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_cutpoint_variants_at_termini(), correctly_add_2prime_connection_variants(), and correctly_add_cutpoint_variants().

bool core::pose::create_chemical_edge	(	core::uint	start_resnum,
		core::uint	end_resnum,
		core::pose::Pose const &	pose,
		core::kinematics::FoldTree &	ft
	)

Create a chemical edge between two Residues.

Parameters

<start_resnum>	the Residue index of the start of the chemical edge
<end_resnum>	the Residue index of the end of the chemical edge
<ft>	the FoldTree being modified

Returns: true if a chemical connection was found and the passed FoldTree was changed

Note: This function is used by set_reasonable_foldtree() for the primary purpose of rebuilding default FoldTrees in cases of branching or chemical conjugation.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::residue(), and TR().

Referenced by set_reasonable_fold_tree().

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

Create a subpose of the src pose. PDBInfo is set as NULL.

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(), core::kinematics::FoldTree::nres(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::simple_moves::RepeatPropagationMover::add_cap_seq_and_structure(), protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), partition_pose_by_jump(), and protocols::grafting::return_region().

void core::pose::declare_cutpoint_chemical_bond	(	core::pose::Pose &	pose,
		Size const	cutpoint_res,
		Size const	next_res_in
	)

Create a chemical bond from lower to upper residue across CUTPOINT_LOWER/CUTPOINT_UPPER.

This will prevent steric repulsion.

Parameters

[in]	pose	The pose to modify.
[in]	cutpoint_res	The index of the CUTPOINT_LOWER residue.
[in]	next_res_in	The index of the CUTPOINT_UPPER residue. If not provided, or if set to 0, this defaults to the cutpoint_res + 1 residue. Must be specified for cyclic geometry.

References core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::conformation::Conformation::declare_chemical_bond(), core::chemical::FIVEPRIME_CAP, core::conformation::Residue::has(), core::conformation::Residue::lower_connect_atom(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Conformation::sever_chemical_bond(), and core::conformation::Residue::upper_connect_atom().

Referenced by correctly_add_cutpoint_variants(), protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints(), and protocols::rna::movers::RNA_LoopCloser::rna_ccd_close().

bool core::pose::definite_terminal_root	(	utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	res_list,
		Size const	nres,
		Size const	i
	)

References effective_lower_terminus_based_on_working_res(), and effective_upper_terminus_based_on_working_res().

Referenced by definite_terminal_root(), and get_definite_terminal_root().

bool core::pose::definite_terminal_root	(	pose::Pose const &	pose,
		Size const	i
	)

References core::pose::full_model_info::const_full_model_info(), and definite_terminal_root().

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(), and core::pose::datacache::CacheableDataType::STRING_MAP.

Referenced by protocols::hbnet::HBNet::apply(), and protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs().

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 core::conformation::membrane::out.

bool core::pose::effective_lower_terminus_based_on_working_res	(	Size const	i,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	cutpoint_open_in_full_model
	)

Referenced by definite_terminal_root().

bool core::pose::effective_upper_terminus_based_on_working_res	(	Size const	i,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		Size const	nres_full
	)

Referenced by definite_terminal_root().

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(), and core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG.

Referenced by protocols::cluster::GatherPosesMover::apply(), protocols::cluster::AssignToClustersMover::apply(), protocols::cluster::ClusterBase::print_cluster_assignment(), and protocols::cluster::ClusterBase::print_summary().

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

Repair pdbinfo of inserted residues that may have blank chain and zero seqpos. Assumes insertions only occur after a residue.

That assumption is a bad simplifying assumption, but it's all I need for now.

References core::pose::PDBInfo::chain(), core::pose::PDBInfo::icode(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

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

References core::pose::full_model_info::const_full_model_info(), correctly_add_2prime_connection_variants(), correctly_add_cutpoint_variants(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::DISULFIDE, core::pose::full_model_info::FullModelInfo::disulfide_pairs(), core::chemical::FIVE_PRIME_PHOSPHATE, fix_up_residue_type_variants_at_floating_base(), fix_up_residue_type_variants_at_strand_beginning(), fix_up_residue_type_variants_at_strand_end(), core::conformation::form_disulfide(), core::chemical::LOWER_TERMINUS_VARIANT, protocols::mean_field::max(), protocols::mean_field::min(), remove_variant_type_from_pose_residue(), core::chemical::THREE_PRIME_PHOSPHATE, TR(), update_block_stack_variants(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), core::import_pose::FullModelPoseBuilder::fill_full_model_info(), protocols::stepwise::modeler::fix_up_jump_atoms_and_residue_type_variants(), protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root(), protocols::recces::pose_setup_from_file(), and protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose().

void core::pose::fix_up_residue_type_variants_at_floating_base	(	pose::Pose &	pose,
		Size const	res
	)

References add_variant_type_to_pose_residue(), core::pose::full_model_info::const_full_model_info(), core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::full_model_info::get_res_list_from_full_model_info(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::LOWER_TERMINUS_VARIANT, remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::chemical::THREE_PRIME_PHOSPHATE, core::chemical::UPPER_TERMINUS_VARIANT, and core::chemical::VIRTUAL_RIBOSE.

Referenced by fix_up_residue_type_variants().

void core::pose::fix_up_residue_type_variants_at_strand_beginning	(	pose::Pose &	pose,
		Size const	res
	)

References add_variant_type_to_pose_residue(), core::pose::full_model_info::const_full_model_info(), correctly_add_cutpoint_variants(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::FIVE_PRIME_PACKABLE_TRIPHOSPHATE, core::chemical::FIVE_PRIME_PHOSPHATE, core::chemical::FIVEPRIME_CAP, core::pose::full_model_info::get_chains_full(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_TNA(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::LOWERTERM_TRUNC_VARIANT, core::chemical::N_ACETYLATION, core::chemical::N_FORMYLATION, remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), TR(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by fix_up_residue_type_variants().

void core::pose::fix_up_residue_type_variants_at_strand_end	(	pose::Pose &	pose,
		Size const	res
	)

Referenced by fix_up_residue_type_variants().

utility::vector1< bool > core::pose::generate_vector_from_bounds	(	pose::Pose const &	pose,
		int const	start,
		int const	stop
	)

References core::pose::Pose::size(), and protocols::loops::stop.

Referenced by center_of_mass(), and return_nearest_residue().

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(), and core::pose::datacache::CacheableDataType::STRING_MAP.

Referenced by protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::hbnet::HBNet::apply(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::simple_filters::SequenceDistance::compute(), protocols::simple_filters::PoseComment::compute(), dump_comment_pdb(), core::io::silent::SilentStruct::energies_from_pose(), protocols::splice::SpliceManager::generate_sequence_profile(), protocols::splice::Splice::generate_sequence_profile(), get_comment(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pdb_comments(), protocols::splice::load_pdb_segments_from_pose_comments(), protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments(), protocols::splice::Splice::load_pdb_segments_from_pose_comments(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::features::PoseCommentsFeatures::report_features(), protocols::splice::Splice::set_fold_tree(), and protocols::simple_moves::AddChainMover::swap_chain().

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(), and core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS.

Referenced by protocols::cluster::GatherPosesMover::apply(), core::io::silent::SilentStruct::energies_from_pose(), get_score_line_string(), and protocols::cluster::ClusterBase::print_cluster_PDBs().

core::Angle core::pose::get_bb_torsion	(	uint	torsion_id,
		Pose const &	pose,
		core::Size	sequence_position
	)

Get a particular backbone torsion, phi, psi, omega (see core::types) Works with carbohydrates. Think about moving this to pose itself.

References core::pose::carbohydrates::get_glycosidic_torsion(), core::conformation::Residue::is_carbohydrate(), core::pose::Pose::omega(), core::id::omega2_dihedral, core::id::omega3_dihedral, core::id::omega_dihedral, core::pose::Pose::phi(), core::id::phi_dihedral, core::pose::Pose::psi(), core::id::psi_dihedral, and core::pose::Pose::residue().

Referenced by protocols::simple_moves::bb_sampler::SmallBBSampler::get_torsion(), protocols::simple_moves::bb_sampler::SmallBBSampler::set_torsion_to_pose(), and protocols::simple_moves::bb_sampler::SugarBBSampler::set_torsion_to_pose().

numeric::xyzVector< core::Real > core::pose::get_center_of_mass ( core::pose::Pose const & pose )

Get center of mass of a pose.

This computes an equally-weighted, all-(non-virtual)-heavy atom center.

References core::chemical::aa_vrt, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by addVirtualResAsRoot(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::membrane::chain_com(), protocols::membrane::chain_tm_com(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose().

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

Get the chain letter for the first residue in a given chain number.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Keep in mind that not all residues with the given chain number will necessarily have the returned chain letter

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

Referenced by protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::ligand_docking::Rotate_info::chain_letter(), protocols::ligand_docking::Translate_info::chain_letter(), protocols::features::InterfaceFeatures::get_all_pose_chains(), protocols::antibody::AntibodyInfo::get_CDRNameEnum_of_residue(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::antibody::AntibodyInfo::get_region_of_residue(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses(), protocols::membrane::rsd_closest_to_chain_tm_com(), protocols::antibody::select_epitope_residues(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), and protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains().

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

Get the chain letter of the chain built by the given jump.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Keep in mind that not every residue with the returned chain ID will be downstream of this jump.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), core::pose::Pose::pdb_info(), and TR().

Referenced by protocols::ligand_docking::get_ligand_grid_scores().

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

Attempt to get the chain number which correspond to the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

If the chain letter corresponds to more than one chain letter, raise an error

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

Attempt to get the chain number which correspond to the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

If the chain letter corresponds to more than one chain letter, raise an error

References get_chain_ids_from_chain(), and core::id::to_string().

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

Get the chain ID of the residue directly built by the given jump.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Keep in mind that not every residue with the returned chain ID will be downstream of this jump.

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

Referenced by protocols::features::InterfaceDdGMover::add_jump_id().

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

Get all chain numbers for the residues with the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The returned chain numbers are in sorted order

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

Get all chain numbers for the residues with the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The returned chain numbers are in sorted order

References get_chain_ids_from_chains().

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

Get all chain numbers for the residues with the given chain letters.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The returned chain numbers are in sorted order

Referenced by get_chain_ids_from_chain().

utility::vector1< core::Size > core::pose::get_chain_ids_from_chains	(	utility::vector1< char > const &	chains,
		core::pose::Pose const &	pose
	)

Get all chain numbers for the residues with the given chain letters.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The returned chain numbers are in sorted order

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

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

Get all residues which correspond to the given chain number.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

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

Referenced by protocols::ligand_docking::HighResEnsemble::apply(), protocols::geometry::centroid_by_chain(), protocols::ligand_docking::Rotate::create_random_rotation(), protocols::pose_length_moves::InsertResMover::extendRegion(), get_residues_from_chains(), and protocols::ligand_docking::move_ligand_neighbor_to_desired_position().

utility::vector1< core::Size > core::pose::get_chains ( core::pose::Pose const & pose )

Get all the chain numbers from conformation.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

This is a rather silly function, as it will just return a vector with entries from 1 to pose->num_chains() (as chains numbers are sequential starting from 1

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

Referenced by protocols::pose_length_moves::InsertResMover::apply(), protocols::pose_length_moves::NearNativeLoopCloser::close_loop(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), compute_unique_chains(), protocols::membrane::create_membrane_foldtree_anchor_com(), protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::membrane::get_anchor_points_for_tmcom(), and protocols::membrane::setup_foldtree_pose_com().

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(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply_remarks(), protocols::simple_filters::PoseComment::compute(), protocols::loophash::extract_sample_weights(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pdb_parents(), protocols::jobdist::pose_matches_user_tag(), core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring(), and protocols::calc_taskop_filters::RelativePoseFilter::thread_seq().

void core::pose::get_constraints_from_link_records	(	core::pose::Pose &	pose,
		io::StructFileRep const &	sfr
	)

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::chemical::ResidueTypeBase::is_peptoid(), core::io::StructFileRep::link_map(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), TR(), and core::conformation::Residue::type().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

Size core::pose::get_definite_terminal_root	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	partition_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	fixed_domain_map,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	working_res
	)

References definite_terminal_root(), core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::possible_root().

Referenced by get_definite_terminal_root(), reroot(), and protocols::stepwise::modeler::revise_root_and_moving_res().

Size core::pose::get_definite_terminal_root	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	partition_res
	)

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), get_definite_terminal_root(), core::pose::full_model_info::FullModelInfo::res_list(), and core::pose::full_model_info::FullModelInfo::working_res().

core::Size core::pose::get_hash_excluding_chain	(	char const &	chain,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues which don't have the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::pose::Pose::conformation(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), core::pose::Pose::size(), TR(), and core::conformation::Conformation::xyz().

core::Size core::pose::get_hash_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues with the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::pose::Pose::conformation(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), core::pose::Pose::size(), TR(), and core::conformation::Conformation::xyz().

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

Get the jump number for the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The jump here is the jumps which is directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. If there's more than one jump which builds residues with the given chain letter, return the smallest numbered jump (even if it's not the jump which best partions the chain on the FoldTree). If no jump directly builds the chain, hard exit.

Referenced by protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::ligand_docking::move_ligand_neighbor_to_desired_position(), and protocols::ligand_docking::move_ligand_to_desired_centroid().

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

Get the jump number for the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The jump here is the jumps which is directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. If there's more than one jump which builds residues with the given chain letter, return the smallest numbered jump (even if it's not the jump which best partions the chain on the FoldTree). If no jump directly builds the chain, hard exit.

References get_jump_ids_from_chain(), and TR().

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

Attempt to get the jump number which correspond to the given chain number.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The jump here is the jump which is directly upstream of a residue in the given chain, (i.e. a residue on the given chain number is built directly from the jump) rather than logically upstream. If there's more than one jump which builds the given chain, return the smallest numbered jump (even if it's not the jump which best partions the chain on the FoldTree). If no jump directly builds the chain (unlikely), hard exit.

References get_jump_ids_from_chain_ids(), has_chain(), core::id::to_string(), and TR().

Referenced by protocols::ligand_docking::SlideTogether::apply(), protocols::ligand_docking::Transform::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::simple_ddg::ddG::calculate(), protocols::simple_ddg::DdgFilter::compute(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::simple_ddg::ddG::do_minimize(), protocols::ligand_docking::Rotate_info::jump_id(), protocols::ligand_docking::Translate_info::jump_id(), protocols::ligand_docking::TransformEnsemble_info::jump_ids(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::simple_ddg::ddG::setup_task(), protocols::ligand_docking::Rotate_info::tag_along_jumps(), protocols::features::InterfaceDdGMover::unbind(), protocols::simple_ddg::ddG::unbind(), and protocols::ligand_docking::Translate::uniform_translate_ligand().

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

Get all the jump numbers for the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The jumps here are the jumps which are directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. Return all jumps which build residues with the given chain letter. If no jumps directly builds residues with the given chain letters, return an empty vector.

The returned jump numbers are in sorted order

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::Pose::num_jump(), core::pose::Pose::pdb_info(), and TR().

Referenced by protocols::ligand_docking::HighResDocker::create_rigid_body_movers(), protocols::ligand_docking::MinimizeBackbone::find_attach_pts(), get_jump_id_from_chain(), get_jump_ids_from_chain(), and protocols::ligand_docking::set_jumps().

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

Get all the jump numbers for the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The jumps here are the jumps which are directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. Return all jumps which build residues with the given chain letter. If no jumps directly builds residues with the given chain letters, return an empty vector.

The returned jump numbers are in sorted order

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
	)

Attempt to get jump IDs which correspond to the given chain number.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The jumps here are the jumps which are directly upstream of a residue in the given chains, (i.e. a residue on the given chain number is built directly from the jump) rather than logically upstream. Return all jumps which build a given chain. If no jumps directly builds the given chains (unlikely), return an empty set.

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

Referenced by get_jump_id_from_chain_id().

std::map< std::string, core::Size > core::pose::get_pdb2pose_numbering_as_stdmap ( core::pose::Pose const & pose )

Create std::map from PDBPoseMap in pose (JKLeman)

Create std::map from PDBPoseMap.

References nres_protein(), core::pose::Pose::pdb_info(), and core::id::to_string().

Referenced by protocols::membrane::AddMembraneMover::apply().

core::conformation::ResidueCOPs core::pose::get_residues_from_chains	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	chain_ids
	)

Get all residues which correspond to the given chain numbers.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References get_chain_residues().

Referenced by protocols::geometry::centroid_by_chains(), and protocols::ligand_docking::HighResEnsemble::prepare_single_ligand_pose().

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(), and protocols::loops::start.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::simple_moves::FavorSequenceProfile::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::task_operations::DesignAroundOperation::apply(), core::select::residue_selector::ResidueIndexSelector::apply(), protocols::simple_filters::DomainInterfaceFilter::apply(), core::pack::task::residue_selector::ClashBasedShellSelector::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::residue_selectors::LigandMetalContactSelector::calculate_ligand_resnums(), protocols::residue_selectors::HBondSelector::compute_input_set(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), protocols::simple_moves::SetupMetalsMover::find_contact_resnums(), protocols::simple_moves::SetupMetalsMover::find_metal_resnums(), protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_resnums(), core::select::residue_selector::NeighborhoodResidueSelector::get_focus(), core::select::residue_selector::BondedResidueSelector::get_input_set(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset(), and core::select::residue_selector::InterGroupInterfaceByVectorSelector::set_from_residue_list_string().

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(), and protocols::loops::start.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::sewing::hashing::AlignmentFileGeneratorMover::alignment_settings_from_tag(), protocols::task_operations::LinkResidues::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), core::pack::task::operation::PreventRepacking::apply(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::simple_filters::NMerPSSMEnergyFilter::compute(), protocols::simple_filters::NMerSVMEnergyFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::constraint_generator::parse_custom_torsion(), protocols::membrane::AddMembraneMover::parse_my_tag(), protocols::task_operations::LinkResidues::remap_allowed_residues_to_template(), and protocols::hybridization::HybridizeProtocol::setup_templates_and_sampling_options().

core::select::residue_selector::ResidueSelectorOP core::pose::get_resnum_selector	(	utility::tag::TagCOP	tag_ptr,
		std::string const &	tag
	)

References TR().

std::string core::pose::get_resnum_string	(	utility::tag::TagCOP	tag_ptr,
		std::string const &	prefix = `""`
	)

DEPRECATED - provided for legacy usage only. Don't use for new code. Instead, just use a single option which uses the parse_resnum syntax to specify.

Checks for either/both of pdb_num/res_num in the tag, and pulls out the appropriate string

std::string core::pose::get_resnum_string	(	utility::tag::TagCOP	tag_ptr,
		std::string const &	prefix,
		std::string const &	default_value
	)

DEPRECATED - provided for legacy usage only. Don't use for new code. Instead, just use a single option which uses parse_resnum syntax to specify.

Checks for either/both of pdb_num/res_num in the tag, and pulls out the appropriate string

core::Size core::pose::get_resnumber_from_reference_pose	(	std::string const &	refpose_name,
		core::Size const	refpose_number,
		signed long const	refpose_offset,
		core::pose::Pose const &	pose
	)

Given the name of a ReferencePose object in the pose, a residue number in that reference pose, and a residue offset, this function returns the Rosetta number of the corresponding residue in the pose. Should throw an error if the ReferencePose doesn't exist in the pose, or 0 if no corresponding residue exists in the pose.

Author: Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::pose::Pose::corresponding_residue_in_current(), and core::pose::Pose::size().

Referenced by core::pose::ResidueIndexDescriptionRefPose::resolve_index().

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

Get a vector of all residues numbers which are represented by this chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The returned residue numbers are in sorted order

References core::pose::Pose::pdb_info(), core::pose::Pose::size(), and TR().

Referenced by protocols::qsar::qsarMover::apply(), protocols::qsar::RenderGridsToKinemage::apply(), protocols::nmr::pcs::PCSLigandTransformMover::apply(), protocols::ligand_docking::get_ligand_grid_scores(), protocols::ligand_docking::get_ligand_RMSDs(), protocols::ligand_docking::get_ligand_travel(), protocols::ligand_docking::get_radius_of_gyration(), core::select::residue_selector::SSElementSelector::parse_ss(), and protocols::features::ResidueGridScoresFeatures::report_features().

utility::vector1< core::Size > core::pose::get_resnums_for_chain_id	(	core::pose::Pose const &	pose,
		core::Size	chain_id
	)

Get a vector of all residues numbers which are represented by this chain number.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

The returned residue numbers are in sorted order

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

Referenced by protocols::pose_creation::MergePDBMover::determine_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), and protocols::qsar::scoring_grid::GridSet::total_score().

core::chemical::ResidueTypeCOP core::pose::get_restype_for_pose	(	core::pose::Pose const &	pose,
		std::string const &	name
	)

Return the residue type in the correct "mode" (fullatom, centroid ...) the pose is in.

References core::pose::Pose::conformation(), core::chemical::FULL_ATOM_t, core::chemical::MIXED_t, and core::conformation::Conformation::residue_typeset_mode().

Referenced by core::util::add_covalent_linkage_helper(), protocols::kinmatch::alapose(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::magnesium::MgMonteCarlo::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::scoring::motif::Xfrag::insert(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::simple_moves::MutateResidue::make_mutation(), core::scoring::motif::Xfres::place_sidechain_in_pose(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::denovo_design::components::rsd_op(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), and virtual_type_for_pose().

core::chemical::ResidueTypeCOP core::pose::get_restype_for_pose	(	core::pose::Pose const &	pose,
		std::string const &	name,
		core::chemical::TypeSetMode	mode
	)

Return the residue type in the passed mode, respecting any modification that pose may make.

References core::pose::Pose::residue_type_set_for_pose(), and TR().

core::chemical::ResidueTypeCOP core::pose::get_rsd_type_from_aa	(	chemical::ResidueTypeSet const &	residue_set,
		chemical::AA const &	my_aa,
		bool const &	is_lower_terminus,
		bool const &	is_upper_terminus,
		bool const	metapatches
	)

use efficient residue type finder to find simplest residue type with this AA & requested termini.

ResidueTypeFinder finds simplest residue type with this AA & requested termini.

References core::chemical::ResidueTypeFinder::aa(), core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::ResidueTypeFinder::variants(), and update_ResidueType_enum_files::variants.

Referenced by residue_types_from_sequence().

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().

Referenced by protocols::loophash::BackboneDB::add_pose(), and protocols::cryst::DockLatticeMover::apply().

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().

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

std::string core::pose::get_sha1_hash_excluding_chain	(	char const &	chain,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues which don't have the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References get_sha1_hash_excluding_chains(), and core::id::to_string().

Referenced by protocols::ligand_docking::StartFrom::apply().

std::string core::pose::get_sha1_hash_excluding_chain	(	std::string const &	chain,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues which don't have the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References get_sha1_hash_excluding_chains().

std::string core::pose::get_sha1_hash_excluding_chains	(	utility::vector1< std::string > const &	chains,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues which don't have the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::pose::Pose::conformation(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), core::pose::Pose::size(), core::id::to_string(), TR(), and core::conformation::Conformation::xyz().

Referenced by protocols::qsar::scoring_grid::GridManager::get_grids(), and get_sha1_hash_excluding_chain().

std::string core::pose::get_sha1_hash_from_chain	(	char const &	chain,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues with the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References get_sha1_hash_from_chains(), and core::id::to_string().

std::string core::pose::get_sha1_hash_from_chains	(	utility::vector1< std::string > const &	chains,
		core::pose::Pose const &	pose,
		std::string const &	extra_label = `""`
	)

Get a value representing the position of all the atoms for residues with the given chain letters.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::pose::Pose::conformation(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::conformation::Conformation::residue(), core::pose::Pose::size(), core::id::to_string(), TR(), and core::conformation::Conformation::xyz().

Referenced by protocols::qsar::scoring_grid::GridManager::get_grids(), and get_sha1_hash_from_chain().

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

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

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

return bool is T/F for whether the requested datum exists. "value" is the data, pass-by-ref.

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

Real core::pose::getPoseExtraScore	(	core::pose::Pose const &	pose,
		std::string const &	name
	)

return value is ExtraScore if exist, runtime_assert if it doesn't exist

References getPoseExtraScore().

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

return bool is T/F for whether the requested datum exists. "value" is the data, pass-by-ref.

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

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

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

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

Does the pose have a residue with the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Referenced by protocols::features::InterfaceDdGMover::add_chain_id(), protocols::features::InterfaceDdGMover::add_chain_name(), protocols::pose_length_moves::InsertResMover::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::pose_creation::MergePDBMover::apply(), protocols::pose_creation::MergePDBatOverlapMover::apply_helper(), chain_end_res(), protocols::features::InterfaceFeatures::chains_exist_in_pose(), protocols::antibody::clusters::check_if_pose_renumbered_for_clusters(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), protocols::antibody::design::disable_conserved_framework_positions(), protocols::pose_creation::MakeJunctionsMover::generate_start_pose(), get_jump_id_from_chain_id(), protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_scores(), protocols::antibody::AntibodyInfo::identify_antibody(), and core::select::residue_selector::SSElementSelector::parse_ss().

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

Does the pose have a residue with the given chain letter.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References core::pose::Pose::pdb_info(), core::pose::Pose::size(), and TR().

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

Does the pose have a residue with the given chain number.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

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

bool core::pose::hasPoseExtraScore	(	core::pose::Pose const &	pose,
		std::string const &	name
	)

does this ExtraScore exist?

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

Referenced by protocols::stepwise::modeler::align::StepWiseClusterer::check_screen_and_kick_out_displaced_model(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), and protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop().

bool core::pose::hasPoseExtraScore_str	(	core::pose::Pose const &	pose,
		std::string const &	name
	)

does this (string) ExtraScore exist?

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

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

Referenced by protocols::loops::addScoresForLoopParts(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::helical_bundle::align_mainchain_atoms(), protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), core::scoring::motif::align_motif_pose_NCAC_super(), core::scoring::motif::align_motif_pose_super(), core::import_pose::libraries::RNA_ChunkLibrary::align_to_chunk(), protocols::antibody_legacy::Antibody::align_to_native(), protocols::antibody::align_to_native(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::align_with_offset(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::minimization_packing::RepackSidechainsMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), core::scoring::atomic_depth::atomic_depth(), core::scoring::atomic_depth::atoms_deeper_than(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), protocols::fldsgn::topology::calc_delta_sasa(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::calc_per_res_hydrophobic_sasa(), core::select::util::SelectResiduesByLayer::calc_rsd_sasa(), protocols::forge::methods::calc_rsd_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), core::scoring::sasa::LeGrandSasa::calculate(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::antibody::cdr_backbone_rmsds(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::scoring::packstat::compute_atom_packing_scores(), core::scoring::packing::compute_holes_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::sasa_scores::compute_residue_sasas_for_sasa_scores(), core::scoring::packing::compute_rosettaholes_score(), convert_from_std_map(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights(), core::io::pose_to_sfr::PoseToStructFileRepConverter::determine_atom_indices(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_atoms_within_radius(), protocols::simple_filters::BuriedUnsatHbondFilter::get_deep_apo_atoms(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::motif::get_motif_atom_mask(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_present_atoms(), protocols::sic_dock::SICFast::init(), core::scoring::sc::ElectrostaticComplementarityCalculator::Init(), core::scoring::sasa::SasaCalc::init(), initialize_atomid_map_AtomID(), protocols::loops::loop_rmsd_with_superimpose_core(), make_atom_map(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::tcr::orient_tcr_chain(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::features::HBondFeatures::report_features(), protocols::hybridization::DomainAssembly::run(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), core::scoring::PoissonBoltzmannPotential::solve_pb(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::grafting::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), protocols::simple_moves::SuperimposeMover::superimposebb(), protocols::docking::ConformerSwitchMover::switch_conformer(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::hybridization::TMalign_poses(), and protocols::hybridization::update_atom_map().

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

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().

Referenced by protocols::protein_interface_design::movers::TopologyBrokerMover::apply().

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

Referenced by core::scoring::packing::get_surf_vol(), core::scoring::packing::get_surf_vol_deriv(), core::scoring::packstat::MultiProbePoseAccumulator::MultiProbePoseAccumulator(), core::scoring::packing::SurfEnergy::setup_for_derivatives(), core::scoring::packing::SurfVolEnergy::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::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), and core::pose::Pose::size().

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(), core::conformation::Conformation::detect_disulfides(), core::io::raw_data::DisulfideFile::disulfides(), core::conformation::Conformation::fix_disulfides(), and core::pose::Pose::is_fullatom().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::scoring::cryst::PhenixInterface::fitBfactors(), protocols::motif_grafting::movers::MotifGraftMover::generate_match_pose(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), core::pose::symmetry::make_symmetric_pose(), protocols::features::DatabaseJobInputter::pose_from_job(), core::import_pose::pose_stream::PoseInputStream::preprocess_pose(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

void core::pose::initialize_disulfide_bonds	(	Pose &	pose,
		io::StructFileRep const &	sfr
	)

detect and fix disulfide bonds

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::io::raw_data::DisulfideFile::disulfides(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::is_fullatom(), core::pose::Pose::pdb_info(), core::io::StructFileRep::ssbond_map(), and TR().

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

Referenced by core::optimization::symmetry::atom_tree_dfunc(), 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::conformation::Residue::natoms(), core::pose::Pose::residue(), core::id::DOF_ID_Map< T >::resize(), and core::pose::Pose::size().

chemical::rings::AxEqDesignation core::pose::is_atom_axial_or_equatorial_to_ring	(	Pose const &	pose,
		uint	seqpos,
		uint	query_atom,
		utility::vector1< uint > const &	ring_atoms
	)

Is the query atom in this pose residue axial or equatorial to the given ring or neither?

This function calculates an average plane and determines whether the coordinates of a given atom are axial or equatorial to it (or neither).

Parameters

<pose>	The Pose containing the Residue in question.
<seqpos>	The sequence position in the Pose of the Residue containing the atoms in question.
<query_atom>	The index of the atom in question.
<ring_atoms>	A list of indices for the atoms of a monocyclic ring system in sequence.

Returns: An AxEqDesignation enum type value: AXIAL, EQUATORIAL, or NEITHER

Author: Labonte JwLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References core::conformation::is_atom_axial_or_equatorial_to_ring(), and core::pose::Pose::residue().

chemical::rings::AxEqDesignation core::pose::is_atom_axial_or_equatorial_to_ring	(	Pose const &	pose,
		id::AtomID const &	query_atom,
		utility::vector1< id::AtomID > const &	ring_atoms
	)

This function calculates an average plane and determines whether the coordinates of a given atom are axial or equatorial to it (or neither).

Parameters

<pose>	The Pose containing the atoms in question.
<query_atom>	The AtomID of the atom in question.
<ring_atoms>	A list of AtomIDs for the atoms of a monocyclic ring system in sequence.

Returns: An AxEqDesignation enum type value: AXIAL, EQUATORIAL, or NEITHER

Author: Labonte JwLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References core::id::AtomID::atomno(), core::conformation::is_atom_axial_or_equatorial_to_ring(), core::chemical::rings::NEITHER, core::pose::Pose::residue(), core::id::AtomID::rsd(), and TR().

Referenced by core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_psi_for_residue_in_pose(), and core::scoring::carbohydrates::get_omega_preference_for_residue_in_pose().

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::size().

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), and protocols::frag_picker::FragmentPicker::nonlocal_pairs().

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 protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), and is_ideal_pose().

bool core::pose::is_lower_terminus	(	pose::Pose const &	pose,
		Size const	resid
	)

checks to see if this is a lower chain ending more intelligently than just checking residue variants

References core::pose::Pose::chain(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by protocols::denovo_design::movers::add_overlap_to_loops(), protocols::hybridization::MRMover::apply(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::loops::fold_tree_from_loops(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_4_redo_termini(), pose_residue_is_terminal(), core::io::serialization::read_binary(), residue_types_from_sequence(), and protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops().

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

Returns true if <residue> is positionally conserved, false otherwise Based on the POSITION_CONSERVED_RESIDUES annotation stored in the Pose DataCache.

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

bool core::pose::is_referencepose_number	(	std::string const &	str,
		std::string &	refpose_string,
		core::Size &	refpose_resnumber,
		signed long &	refpose_offset
	)

Is a string of the format "refpose(<refposename>,<refposenumber>)" or "refpose(<refposename>,<refposenumber>)+/-<number>"?

If this successfully determines that this is a string of this format, it populates the refpose_string, refpose_resnumber, and refpose_offset variables with the name of the ReferencePose, the number of the residue in the reference pose, and the +/- offset number parsed from this string.

Author: Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by parse_resnum().

bool core::pose::is_upper_terminus	(	pose::Pose const &	pose,
		Size const	resid
	)

checks to see if this is a lower chain ending more intelligently than just checking residue variants

References core::pose::Pose::chain(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::denovo_design::movers::add_overlap_to_loops(), protocols::denovo_design::components::add_to_pose(), protocols::hybridization::MRMover::apply(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::denovo_design::filters::PreProlineFilter::compute_simple(), protocols::denovo_design::filters::PreProlineFilter::compute_spline(), protocols::loops::fold_tree_from_loops(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_4_redo_termini(), pose_residue_is_terminal(), residue_types_from_sequence(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), and protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops().

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

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

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

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

bool core::pose::just_modeling_RNA ( std::string const & sequence )

Referenced by core::import_pose::just_modeling_RNA().

core::id::AtomID_Map< platform::Real > core::pose::make_atom_map	(	core::pose::Pose const &	p,
		PoseCoordPickMode	m
	)

References core::conformation::Residue::atom_index(), initialize_atomid_map(), PoseCoordPickMode_BB, PoseCoordPickMode_CA, PoseCoordPickMode_CB, PoseCoordPickMode_CB_else_CA, PoseCoordPickMode_HVY, PoseCoordPickMode_HVY_IF_NP, PoseCoordPickMode_N_C_O, PoseCoordPickMode_N_CA_C, PoseCoordPickMode_N_CA_C_CB, PoseCoordPickMode_NBR, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::pose::xyzStripeHashPose::extract_pose_balls(), protocols::motif_grafting::movers::MotifGraftMover::get_matching_fragments(), protocols::motif_grafting::movers::MotifGraftMover::test_epigraft_and_contextStructure_clashes(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().

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

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and store it in <pose>.

Parameters

[in]	<pose>	the Pose to fill
[in]	<sequence>	an annotated IUPAC 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 for the main chain

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 database/chemical/carbohydrates/codes_to_roots.map.)
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.
Branches are indicated using nested brackets and are best explained by example:
beta-D-Galp-(1->4)-[alpha-L-Fucp-(1->3)]-D-GlcpNAc is:
beta-D-Galp-(1->4)-D-GlcpNAc
|
alpha-L-Fucp-(1->3)

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 append_pose_with_glycan_residues(), core::pose::Pose::chain_sequence(), core::pose::Pose::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::pose::Pose::glycan_tree_set(), core::pose::carbohydrates::idealize_last_n_glycans_in_pose(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::pdb_info(), residue_types_from_saccharide_sequence(), core::conformation::Conformation::setup_glycan_trees(), and core::chemical::UPPER_TERMINUS_VARIANT.

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,
		bool const	idealize_linkages
	)

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name> and store 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 make_pose_from_saccharide_sequence().

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",core::chemical::FA_STANDARD) See also: Pose PDBInfo pose_from_pdb pose_from_rcsb pose_from_sequence

References core::chemical::aa_h2o, 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::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::N_ACETYLATION, and core::pose::Pose::sequence().

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), core::fragment::rna::analyze_for_homology(), protocols::domain_assembly::CombineChainsMover::apply(), protocols::pose_creation::ExtendedPoseMover::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::membrane::HelixFromSequence::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::pose_creation::PoseFromSequenceMover::apply(), protocols::loop_grower::LoopGrower::apply(), core::pose::rna::assert_phosphate_nomenclature_matches_mini(), core::import_pose::RNA_HelixAssembler::build_init_pose(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::pack_daemon::create_entity_resfile_contents(), protocols::simple_moves::ConstrainToIdealMover::create_pose_reference(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::forge::build::BuildManager::dummy_modify(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), core::import_pose::pose_stream::ExtendedPoseInputStream::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::FragmentAllAtomCrmsd(), protocols::frag_picker::scores::FragmentChunkCrms::FragmentChunkCrms(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::star::generate_extended_pose(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), protocols::mainchain_potential::GenerateMainchainPotential::generate_pose(), protocols::indexed_structure_store::initial_pose_for_residues(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::initialize_ghost_pose(), protocols::topology_broker::TopologyBroker::initialize_sequence(), protocols::features::PoseConformationFeatures::load_sequence(), core::import_pose::make_extended_coarse_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::make_extended_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_fasta_contents(), core::fragment::make_pose_from_frags(), make_pose_from_sequence(), protocols::topology_broker::SequenceClaimer::make_sequence_claim(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), protocols::abinitio::IterativeBase::reassign_noesy_data(), core::fragment::FragmentRmsd::rmsd(), protocols::abinitio::run_boinc_debug(), protocols::frag_picker::scores::RDCScore::score(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), core::pose::full_model_info::FullModelParameters::update_pose_and_cst_set_from_cst_string(), and protocols::frag_picker::VallProvider::vallChunksFromLibrary().

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

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:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu: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(), make_pose_from_sequence(), and residue_types_from_sequence().

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

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:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu: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(), 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,
		bool const	metapatches
	)

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 make_pose_from_sequence().

ResidueIndexDescriptionCOP core::pose::make_rid_posenum ( core::Size resnum )

Convenience function for converting a Size (Pose numbered) into a ResidueIndexDescription.

Referenced by protocols::pose_metric_calculators::FragQualCalculator::begin(), protocols::calc_taskop_movers::ForceDisulfidesMover::disulfides(), protocols::pose_metric_calculators::FragQualCalculator::end(), protocols::simple_filters::StemFinder::from_res(), protocols::splice::Splice::from_res(), protocols::protein_interface_design::movers::LoopLengthChange::loop_cut(), protocols::protein_interface_design::movers::LoopLengthChange::loop_end(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), protocols::rigid::RollMover::parse_my_tag(), protocols::simple_moves::Tumble::parse_my_tag(), parse_resnum(), protocols::protein_interface_design::filters::Torsion::resnum(), protocols::simple_moves::sidechain_moves::SetChiMover::resnum(), protocols::pose_metric_calculators::FragQualCalculator::set_region(), protocols::moves::ResId::set_resid(), protocols::rigid::RigidBodyTiltMover::tilt1_center(), protocols::rigid::RigidBodyTiltMover::tilt2_center(), protocols::simple_filters::StemFinder::to_res(), and protocols::splice::Splice::to_res().

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 protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), core::scoring::TenANeighborNode::neighbor_mass(), protocols::toolbox::reset_x(), core::scoring::nmr::pre::PREMultiSet::set_protein_mass(), protocols::cartesian::MolecularDynamics::setInitialSpeeds(), and core::util::switch_to_centroid_rot_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 > size atom not present in residue ( e.g., no CB in GLY )

References core::id::NamedAtomID::atom(), core::chemical::ResidueType::atom_index(), core::id::GLOBAL_BOGUS_ATOM_ID, core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), core::id::NamedAtomID::rsd(), core::chemical::ResidueType::show_all_atom_names(), core::pose::Pose::size(), TR(), 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(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::forge::build::ConnectRight::extract_rt(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::forge::build::ConnectRight::modify_impl(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), protocols::jumping::MembraneJump::rt_templates(), protocols::topology_broker::CoordConstraintClaimer::set_cst_root(), protocols::jumping::PairingLibrary::set_tmh_jump(), 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::pose::Pose::begin(), core::pose::Pose::end(), and core::chemical::num_canonical_aas.

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::pose::Pose::begin(), core::pose::Pose::end(), and core::chemical::num_canonical_aas.

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

count the number of non-canonical residues in the pose

References core::pose::Pose::begin(), core::pose::Pose::end(), and core::chemical::num_canonical_aas.

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

Number of protein residues in the pose.

No virtuals, membrane residues or embedding residues counted

References core::pose::Pose::begin(), and core::pose::Pose::end().

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(), protocols::ligand_docking::AtomCountFilter::apply(), core::conformation::atom_graph_from_conformation(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::fiber_diffraction::centroid_scatter(), protocols::pockets::PocketGrid::GetExemplarNumAtoms(), protocols::stepwise::modeler::rna::print_heavy_atoms(), core::scoring::residue_sc_rmsd_no_super(), core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), 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().

Referenced by protocols::ligand_docking::Rotate::create_random_rotations(), and protocols::ligand_docking::passes_filters().

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().

Referenced by protocols::ligand_docking::HBondAcceptorFilter::apply().

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().

Referenced by protocols::ligand_docking::HBondDonorFilter::apply().

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(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::ligand_docking::passes_filters(), and protocols::ligand_docking::HeavyAtomFilter::report_sm().

std::ostream & core::pose::operator<<	(	std::ostream &	out,
		ResidueIndexDescription const &	rid
	)

References core::conformation::membrane::out, and core::pose::ResidueIndexDescription::show().

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

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

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

References core::pose::UnrecognizedAtomRecord::atom_name(), core::pose::UnrecognizedAtomRecord::coords(), core::pose::UnrecognizedAtomRecord::res_num(), and core::pose::UnrecognizedAtomRecord::temp().

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

Test IO operator for debug and Python bindings.

References core::pose::Pose::conformation(), core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::conformation::Conformation::is_membrane(), core::conformation::Conformation::membrane_info(), core::pose::Pose::pdb_info(), core::pose::Pose::sequence(), and core::pose::Pose::size().

void core::pose::parse_PDBnum_icode	(	std::string const &	token,
		std::string const &	fname,
		Size const	lineno,
		int &	PDBnum,
		char &	icode
	)

Take the string "token" and try to interpret it as a PDB identifier in the form of an integer as well as an optional insertion code. For example the string "25A" would be interpretted as the residue 25 with the insertion code "A." Throws an exception if the input string is misformatted.

References character_is_USA_letter().

Referenced by core::pack::task::ResfileContents::parse_resid().

ResidueIndexDescriptionCOP core::pose::parse_resnum	(	std::string const &	resnum,
		bool const	check_for_refpose = `false`
	)

Creates a ResidueIndexDescription from a string Recognizes three 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. IMPORTANT: This does not currently handle insertion codes.

Reference pose numbers. These have the form refpose([refpose name], [refpose number]). In addition, relative numbers are permitted (of the form +[number] or -[number]) in conjunction with reference pose numbering. For example, one might say "refpose(state1,17)+3", which means three residues past the residue correpsonding to residue 17 in the reference pose called "state1".

Returns: a ResidueIndexDescription that will yield a residue number when applied to pose. Returns a nullptr if there's an error with parsing the string

References is_referencepose_number(), make_rid_posenum(), and TR().

core::Size core::pose::parse_resnum	(	std::string const &	resnum,
		core::pose::Pose const &	pose,
		bool const	check_for_refpose = `false`
	)

Extracts a residue number from a string. Recognizes three 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. IMPORTANT: This does not currently handle insertion codes.

Reference pose numbers. These have the form refpose([refpose name], [refpose number]). In addition, relative numbers are permitted (of the form +[number] or -[number]) in conjunction with reference pose numbering. For example, one might say "refpose(state1,17)+3", which means three residues past the residue correpsonding to residue 17 in the reference pose called "state1".

Returns: the rosetta residue number for the string, or 0 upon an error

References parse_resnum().

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

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.

References protocols::cluster::calibur::aa.

Referenced by core::import_pose::libraries::ChunkSet::filter_poses_have_same_sequence_and_variants(), get_sequence_len(), core::import_pose::look_for_dna(), core::sequence::parse_out_non_standard_residues(), and residue_types_from_sequence().

utility::vector1< int > 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(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::size(), and TR().

Referenced by protocols::splice::DesignInterfacesOperation::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::simple_filters::BuriedUnsatHbondFilter::get_deep_apo_atoms(), protocols::docking::move_together(), and protocols::membrane::split_topology_by_jump().

utility::vector1< Size > core::pose::pdb_to_pose	(	pose::Pose const &	pose,
		utility::vector1< int > const &	pdb_res
	)

Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju.

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by pdb_to_pose().

utility::vector1< Size > core::pose::pdb_to_pose	(	pose::Pose const &	pose,
		std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &	pdb_res
	)

Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju.

Convert PDB numbering/chain to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju.

References pdb_to_pose().

Size core::pose::pdb_to_pose	(	pose::Pose const &	pose,
		int const	res_num,
		char const	chain
	)

Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju.

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by protocols::magnesium::get_hoh_xyz(), and protocols::magnesium::get_hydration_stats().

void core::pose::pdbslice	(	pose::Pose &	new_pose,
		pose::Pose const &	pose,
		utility::vector1< Size > const &	slice_res
	)

Create a subpose of the src pose – figures out a reasonable fold tree.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::clear(), core::conformation::Residue::clone(), core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::full_model_info_defined(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::N_ACETYLATION, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::full_model_info::set_full_model_info(), core::pose::Pose::size(), tag_from_pose(), and tag_into_pose().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::simple_moves::RepeatPropagationMover::determine_overlap(), protocols::pose_creation::MergePDBMover::determine_overlap(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::pose_creation::SliceToMiniProteinMover::parse_chunks(), pdbslice(), core::import_pose::reorder_pose(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), protocols::magnesium::strip_out_magnesiums(), and protocols::pose_creation::SliceToMiniProteinMover::trim_chunks().

void core::pose::pdbslice	(	pose::Pose &	pose,
		utility::vector1< Size > const &	slice_res
	)

Create a subpose of the src pose – figures out a reasonable fold tree.

References pdbslice(), and core::pose::Pose::size().

void core::pose::pdbslice	(	core::pose::Pose &	new_pose,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	slice_res
	)

Create a subpose of the src pose – figures out a reasonable fold tree.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::clear(), core::conformation::Residue::clone(), core::pose::full_model_info::FullModelInfo::clone_info(), core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::full_model_info_defined(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::N_ACETYLATION, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::full_model_info::set_full_model_info(), core::pose::Pose::size(), tag_from_pose(), and tag_into_pose().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::simple_moves::RepeatPropagationMover::determine_overlap(), protocols::pose_creation::MergePDBMover::determine_overlap(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::pose_creation::SliceToMiniProteinMover::parse_chunks(), pdbslice(), core::import_pose::reorder_pose(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), protocols::magnesium::strip_out_magnesiums(), and protocols::pose_creation::SliceToMiniProteinMover::trim_chunks().

void core::pose::pdbslice	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	slice_res
	)

Create a subpose of the src pose – figures out a reasonable fold tree.

References pdbslice(), and core::pose::Pose::size().

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

Return a Pose from an annotated, linear, IUPAC 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::chemical::ResidueType::nbr_radius(), core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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().

bool core::pose::pose_residue_is_terminal	(	Pose const &	pose,
		Size const	resid
	)

returns true if the given residue in the pose is a chain ending or has upper/lower terminal variants

References is_lower_terminus(), and is_upper_terminus().

Referenced by core::select::residue_selector::SecondaryStructureSelector::add_overlap().

utility::vector1< Size > core::pose::pose_to_pdb	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	pose_res
	)

Convert pose numbering to pdb numbering. Must exist somewhere else, but I couldn't find it. – rhiju.

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by protocols::magnesium::get_hydration_stats().

core::Real core::pose::radius_of_gyration	(	core::pose::Pose const &	pose,
		numeric::xyzVector< core::Real > const &	center_of_mass,
		utility::vector1< bool > const &	residues
	)

Get the radius of gyration of the selected residues.

WARNING: Despite the name, this function only calculates with a single coordinate per residue (the Calpha/neighbor atom)

Requires the center_of_mass as an input because often people will want both com and rg and this ensures that we only calculate com once.

References core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::motif_grafting::movers::MotifGraftMover::get_next_nonredundant_motifmatch(), and protocols::features::RadiusOfGyrationFeatures::write_radius_of_gyration_table_schema().

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(), and TR().

Referenced by protocols::simple_moves::LoadPDBMover::apply().

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

References protocols::abinitio::filename().

Referenced by protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::simple_filters::AbinitioBaseFilter::get_protein_sstype(), and protocols::loops::set_secstruct_from_psipred_ss2().

utility::vector1< char > core::pose::read_psipred_ss2_file	(	pose::Pose const &	pose,
		std::string const &	filename
	)

References protocols::cluster::calibur::aa, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), 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::size().

Referenced by protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose().

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

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

Referenced by protocols::simple_moves::RepeatPropagationMover::add_cap_seq(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::denovo_design::components::add_to_pose(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), protocols::relax::cyclize_pose(), protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::mainchain_potential::GenerateMainchainPotential::generate_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses(), protocols::forge::build::Bridge::modify_impl(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::perform_reaction(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::hotspot_hashing::HotspotStub::scaffold_match(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_isopeptide_variants(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_native(), protocols::grafting::superimpose_overhangs_heavy(), and protocols::seeded_abinitio::SwapSegment::swap_segment().

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::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose().

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_VARIANT.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::denovo_design::components::add_to_pose(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::pose_length_moves::NearNativeLoopCloser::combine_chains(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), protocols::relax::cyclize_pose(), protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::mainchain_potential::GenerateMainchainPotential::generate_pose(), core::pose::carbohydrates::glycosylate_pose(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses(), protocols::forge::build::Bridge::modify_impl(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::hotspot_hashing::HotspotStub::scaffold_match(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_isopeptide_variants(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_native(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::grafting::superimpose_overhangs_heavy(), and protocols::seeded_abinitio::SwapSegment::swap_segment().

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.

E.g., remove a terminus variant, and replace the original in pose.

Note: This copies any atoms in common between old and new residues, rebuilding the others.

References core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::n_possible_residue_connections(), replace_pose_residue_copying_existing_coordinates(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::conformation::Conformation::residue_type(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and core::conformation::Conformation::update_noncanonical_connection().

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
	)

Remove variant from an existing residue.

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::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::nchi(), core::conformation::Residue::nchi(), core::pose::Pose::residue_type_set_for_pose(), TR(), and core::conformation::Residue::type().

Referenced by protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO::alter_rotamer_set(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), core::pack::rotamer_set::build_five_prime_phosphate_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pack::rotamer_set::build_three_prime_phosphate_rotamers(), core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(), protocols::stepwise::modeler::merge_two_poses(), protocols::environment::Environment::remove_chainbreak_variants(), and protocols::stepwise::modeler::slice().

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::ResidueTypeBase::name(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by protocols::simple_moves::ResetFoldTree::apply().

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

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

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 core::pose::PDBInfo::chain(), core::pose::Pose::chain(), core::conformation::Conformation::chain_endings(), conf2pdb_chain(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), core::pose::PDBInfo::icode(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), core::pose::PDBInfo::set_resinfo(), core::pose::Pose::size(), and TR().

utility::vector1< Size > core::pose::reorder_root_partition_res	(	utility::vector1< Size > const &	root_partition_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	fixed_domain_map
	)

References protocols::mean_field::max().

Referenced by reroot().

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 Will match up old and new atoms based on their atom names.

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_custom_variant_type_to_pose_residue(), add_variant_type_to_pose_residue(), protocols::kinmatch::alapose(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::metal_interface::MatchGrafter::graft(), protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose(), core::pose::Pose::real_to_virtual(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), remove_variant_type_from_pose_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::forge::components::VarLengthBuild::set_starting_non_canonical(), protocols::forge::remodel::RemodelLoopMover::set_starting_sequence(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::simple_moves::ResTypeFragmentMover::swap_residue_types(), and core::pose::Pose::virtual_to_real().

void core::pose::replace_pose_residue_copying_existing_coordinates	(	pose::Pose &	pose,
		Size const	seqpos,
		core::chemical::ResidueType const &	new_rsd_type,
		utility::vector1< core::Size > const &	mapping
	)

Helper function for residue replacement/residuetype switching Matches up old an new atoms based on the provided map. (Indexed by new_rsd_type atom number, giving corresponding atom number in the current pose residue.)

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().

void core::pose::reroot	(	pose::Pose &	pose,
		utility::vector1< Size > const &	root_partition_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	preferred_root_res,
		utility::vector1< Size > const &	fixed_domain_map,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	working_res
	)

References core::pose::Pose::fold_tree(), get_definite_terminal_root(), core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), reorder_root_partition_res(), and TR().

Referenced by protocols::stepwise::modeler::reroot_based_on_full_model_info(), and core::import_pose::setup_fold_trees().

bool core::pose::res_in_chain	(	core::pose::Pose const &	pose,
		core::Size	resnum,
		std::string const &	chain
	)

Does this residue number have this chain letter?

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

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

Referenced by core::import_pose::define_chains(), protocols::pose_creation::MergePDBMover::determine_overlap(), and protocols::pose_creation::MergePDBMover::generate_overlaps().

int core::pose::residue_center_of_mass	(	pose::Pose const &	pose,
		utility::vector1< bool >	residues
	)

References core::conformation::membrane::center, center_of_mass(), return_nearest_residue(), and core::pose::Pose::size().

Referenced by protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_key_residues(), protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), protocols::docking::setup_foldtree(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(), protocols::ncbb::setup_pert_foldtree(), and protocols::hotspot_hashing::stub_tgt_angle().

int core::pose::residue_center_of_mass	(	pose::Pose const &	pose,
		int const	start,
		int const	stop
	)

calculates the center of mass of a pose

the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Author: Monica Berrondo June 14 2007

References core::conformation::membrane::center, center_of_mass(), and return_nearest_residue().

Referenced by protocols::membrane::rsd_closest_to_chain_com(), protocols::docking::setup_foldtree(), and protocols::membrane::setup_foldtree_pose_com().

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, linear, IUPAC polysaccharide sequence.

Parameters

[in]	<sequence>	an annotated IUPAC 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, in Rosetta order. That is, the first residue will be the reducing end (the last residue in the sequence), and all branches will be consecutive, with earlier branches earlier in set of residue types.

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.
Branches are indicated using nested brackets and are best explained by example:
beta-D-Galp-(1->4)-[alpha-L-Fucp-(1->3)]-D-GlcpNAc is:
beta-D-Galp-(1->4)-D-GlcpNAc
|
alpha-L-Fucp-(1->3)

Note: make_pose_from_saccharide_sequence() will generate a pose with a proper lower terminus. glycosylate_pose() will append the fragment by bond.

References residue_types_from_saccharide_sequence_recursive().

Referenced by core::pose::carbohydrates::glycosylate_pose(), and make_pose_from_saccharide_sequence().

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

Internal implementation detail of residue_types_from_saccharide_sequence() Returns the reorganized (but not reversed) set of residuetypes.

References core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueType::get_self_ptr(), core::chemical::ResidueTypeSet::name_mapOP(), core::conformation::membrane::out, core::io::carbohydrates::sugar_modifications_from_suffix(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by residue_types_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,
		bool const	metapatches
	)

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:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu: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.

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 protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), get_rsd_type_from_aa(), is_lower_terminus(), is_upper_terminus(), core::chemical::ResidueTypeSet::name_mapOP(), and parse_sequence().

Referenced by protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::LoopComparator::fill_pose(), core::import_pose::RNA_HelixAssembler::get_residue(), make_pose_from_sequence(), protocols::forge::build::GrowRight::modify_impl(), protocols::forge::build::GrowLeft::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::rna::movers::RNAThreadAndMinimizeMover::obtain_rtypes_for_target_sequence(), protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

int core::pose::return_nearest_residue	(	core::pose::Pose const &	pose,
		int const	begin,
		int const	end,
		core::Vector	center
	)

int core::pose::return_nearest_residue	(	pose::Pose const &	pose,
		utility::vector1< bool > const &	residues,
		Vector	center
	)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), residue_center_of_mass(), return_nearest_residue(), and protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors().

int core::pose::return_nearest_residue	(	pose::Pose const &	pose,
		int const	begin,
		int const	end,
		Vector	center
	)

finds the residue nearest some position passed in (normally a center of mass)

the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Author: Monica Berrondo June 14 2007

References generate_vector_from_bounds(), and return_nearest_residue().

Referenced by protocols::membrane::rsd_closest_to_pose_tm_com().

core::pose::PoseCOP core::pose::saved_native_pose	(	basic::datacache::DataMap &	data_map,
		std::string const &	resource_str = `"native_pose"`
	)

Retrieve the native pose from the DataMap which is added through the OptionsCollection during RosettaScript parsing as a resource.

If the resource is not present, will return a nullptr.

References TR().

Referenced by protocols::residue_selectors::NativeSelector::parse_my_tag(), core::simple_metrics::metrics::SequenceSimilarityMetric::parse_my_tag(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), core::simple_metrics::metrics::DihedralDistanceMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::parse_my_tag(), and core::simple_metrics::metrics::RMSDMetric::parse_my_tag().

core::pose::PoseOP core::pose::saved_reference_pose	(	utility::tag::TagCOP const	in_tag,
		basic::datacache::DataMap &	data_map,
		std::string const &	tag_name
	)

References TR().

Referenced by protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), core::simple_metrics::metrics::DihedralDistanceMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::parse_my_tag(), core::simple_metrics::metrics::RMSDMetric::parse_my_tag(), and protocols::rosetta_scripts::saved_reference_pose().

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::size(), and TR().

Referenced by protocols::constraint_generator::AtomPairConstraintGenerator::create_sequence_mapping(), and protocols::constraint_generator::generate_seqmap_from_poses().

void core::pose::set_bb_torsion	(	uint	torsion_id,
		Pose &	pose,
		core::Size	sequence_position,
		core::Angle	new_angle
	)

This function calculates an average plane and determines whether the coordinates of a given atom are axial or equatorial to it (or neither). The ring is requested from the Residue.

Parameters

<pose>	The Pose containing the Residue in question.
<seqpos>	The sequence position in the Pose of the Residue containing the atoms in question.
<query_atom>	The index of the atom in question.

Returns: An AxEqDesignation enum type value: AXIAL, EQUATORIAL, or NEITHER

Author: Labonte JwLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

This function calculates an average plane and determines whether the coordinates of a given atom are axial or equatorial to it (or neither). The ring is requested from the corresponding Residue.

Parameters

<pose>	The Pose containing the atoms in question.
<query_atom>	The AtomID of the atom in question.

Returns: An AxEqDesignation enum type value: AXIAL, EQUATORIAL, or NEITHER

Author: Labonte JwLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Set the BB torsion, phi, psi, omega (see core::types). Works with carbohydrates. Think about moving this to pose itself.

References core::conformation::Residue::is_carbohydrate(), core::id::omega2_dihedral, core::id::omega3_dihedral, core::id::omega_dihedral, core::id::phi_dihedral, core::id::psi_dihedral, core::pose::Pose::residue(), core::pose::carbohydrates::set_glycosidic_torsion(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by protocols::simple_moves::bb_sampler::SmallBBSampler::set_torsion_to_pose().

void core::pose::set_bfactors_from_atom_id_map	(	Pose &	pose,
		id::AtomID_Map< Real > const &	bfactors
	)

Set bfactors in a pose PDBInfo.

Is the query atom in this pose axial or equatorial to the given ring or neither?

Is the query atom in this pose residue axial or equatorial or neither? Is the query atom in this pose axial or equatorial or neither? Set bfactors in a pose PDBInfo

References core::id::AtomID_Map< T >::has(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::size().

void core::pose::set_output_res_and_chain	(	pose::Pose &	extended_pose,
		std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &	output_resnum_and_chain
	)

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::RNA_DeNovoSetup::get_refine_pose_list(), core::import_pose::RNA_DeNovoSetup::initialize_from_command_line(), and core::import_pose::RNA_DeNovoSetup::initialize_from_options().

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

If all ligand residues and polymer branches have been appended by a jump, this method creates a new FoldTree without jumps through ligands, using CHEMICAL EDGEs instead.

References core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), create_chemical_edge(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_bonded(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::is_polymer(), core::conformation::Residue::is_polymer(), core::kinematics::Edge::label(), protocols::make_rot_lib::PEPTIDE, core::pose::Pose::residue(), core::pose::Pose::size(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and TR().

Referenced by protocols::simple_moves::DeleteChainsMover::apply(), core::import_pose::build_pose_as_is2(), protocols::grafting::insert_pose_into_pose(), protocols::rna::movers::RNAThreadAndMinimizeMover::long_mutate_strategy(), protocols::rna::movers::RNAThreadAndMinimizeMover::mutate_all_at_once(), and protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains().

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::ResidueTypeBase::is_protein(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::pose::Pose::set_secstruct(), and core::pose::Pose::size().

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

Set a core::Real in the pose datacache, that will be output as a score in the scorefile.

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

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

Set a string in the pose datacache, that will be output as a score in the scorefile.

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

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::chemical::aa_his, core::id::BB, core::id::BRANCH, 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(), core::chemical::is_mainchain_torsion_also_ring_torsion(), core::id::JUMP, core::id::NU, core::pose::Pose::num_jump(), core::chemical::rings::PHI, core::pose::Pose::residue(), core::pose::Pose::size(), core::chemical::rings::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::TorsionID::BOGUS_TORSION_ID(), core::id::BRANCH, core::chemical::rna::CHI, core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), initialize_dof_id_map(), core::id::JUMP, core::id::NU, core::pose::Pose::num_jump(), core::pose::Pose::residue(), and core::pose::Pose::size().

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().

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::finalize(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_sugar_modeling_set(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_parameters_and_input(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::pose_selection_by_full_score(), and protocols::stepwise::modeler::align::StepWiseClusterer::sort_pose_list().

bool core::pose::stepwise_addable_pose_residue	(	Size const	n,
		pose::Pose const &	pose
	)

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::res_list(), and stepwise_addable_residue().

Referenced by protocols::stepwise::modeler::packer::figure_out_working_interface_res(), and protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements().

bool core::pose::stepwise_addable_residue	(	Size const	n,
		std::map< Size, std::string > const &	non_standard_residue_map
	)

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), core::import_pose::get_extra_cutpoints_from_names(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::is_addable_res(), and stepwise_addable_pose_residue().

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,
		kinematics::RT const &	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::pose::Pose::fold_tree(), core::conformation::Residue::natoms(), core::pose::Pose::num_jump(), 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(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, and protocols::kinmatch::str().

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

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

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

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

Referenced by protocols::stepwise::modeler::align::StepWiseClusterer::check_screen_and_kick_out_displaced_model(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::cluster_pose_list(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::do_some_filtering(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::initialize_parameters_and_input(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::pass_all_filters(), and sort_pose_by_score().

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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

static

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().

Referenced by protocols::loophash::LoopHashSampler::build_structures().

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

References core::chemical::ResidueTypeBase::is_protein(), protocols::mean_field::min(), 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::size().

Referenced by protocols::loophash::LoopHashSampler::build_structures(), protocols::loophash::LoopHashLibrary::get_all(), protocols::loophash::LoopHashLibrary::graft_loop(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), and transfer_phi_psi().

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

References protocols::mean_field::min(), core::pose::Pose::size(), and transfer_phi_psi().

void core::pose::update_block_stack_variants	(	pose::Pose &	pose,
		Size const	n
	)

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

Referenced by fix_up_residue_type_variants().

void core::pose::update_cutpoint_virtual_atoms_if_connected	(	core::pose::Pose &	pose,
		core::Size const	cutpoint_res,
		bool	recurse
	)

Given a pose and a position that may or may not be CUTPOINT_UPPER or CUTPOINT_LOWER, determine whether this position has either of these variant types, and if it does, determine whether it's connected to anything. If it is, update the C-OVL1-OVL2 bond lengths and bond angle (for CUTPOINT_LOWER) or OVU1-N bond length (for CUTPOINT_UPPER) to match any potentially non-ideal geometry in the residue to which it's bonded.

Requires a little bit of special-casing for gamma-amino acids. Throws an exception if the residue to which a CUTPOINT_LOWER is bonded does not have an "N" and a "CA" or "C4". Safe to call repeatedly, or if cutpoint variant types are absent; in these cases, the function does nothing.

Note: By default, this function calls itself again once on residues to which this residue is connected, to update their geometry. Set recurse=false to disable this.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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

Referenced by add_variant_type_to_pose_residue(), and correctly_add_cutpoint_variants().

core::chemical::ResidueTypeCOP core::pose::virtual_type_for_pose ( core::pose::Pose const & pose )

Return the appropritate ResidueType for the virtual residue for the "mode" (fullatom, centroid ...) the pose is in.

Return the appropritate ResidueType for the virtual residue for the i "mode" (fullatom, centroid ...) the pose is in.

References get_restype_for_pose().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::toolbox::sample_around::add_another_virtual_res(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::toolbox::sample_around::add_virtual_res(), protocols::relax::add_virtual_residue_to_cterm(), addVirtualResAsRoot(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::relax::coordinate_constrain_selection(), protocols::forge::build::BuildManager::modify(), protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), and protocols::topology_broker::SymmetryClaimer::symmetry_duplicate().

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