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

#include <PDBInfo.hh>

Classes
struct	AtomRecord
	internal struct for storing PDB atom related information More...

struct	ResidueRecord
	internal struct for storing PDB residue related information More...

Public Types
typedef utility::pointer::ReferenceCount	Super

typedef core::Size	Size

typedef core::Real	Real

typedef std::string	String

typedef core::pose::Remarks	Remarks

Public Member Functions
	PDBInfo ()
	default constructor, obsolete is true More...

	PDBInfo (Size const n)
	size constructor (ensure space for 'n' residue records), obsolete is true More...

	PDBInfo (Pose const &pose, bool init=true)
	Pose constructor (ensures space for residue and atom records relative to Pose) More...

	PDBInfo (PDBInfo const &info)
	copy constructor More...

virtual	~PDBInfo ()
	default destructor More...

PDBInfo &	operator= (PDBInfo const &info)
	copy assignment More...

core::conformation::Conformation const *	is_observing ()
	Returns the Conformation if this PDBInfo is currently observing a conformation, otherwise return NULL. More...

void	attach_to (core::conformation::Conformation &conf)
	Attaches the Conformation <conf> and begins observation. More...

void	detach_from ()
	Detaches the Conformation and stops observation. More...

void	on_connection_change (core::conformation::signals::ConnectionEvent const &event)
	Updates when connection to Conformation is changed. More...

void	on_identity_change (core::conformation::signals::IdentityEvent const &event)
	Updates atom records when residue identity changes in Conformation. More...

void	on_length_change (core::conformation::signals::LengthEvent const &event)
	Updates residue and atom records when length changes in Conformation, obsoletes PDBInfo. More...

bool	obsolete () const
	Returns true if PDBInfo is obsolete and needs updating. More...

void	obsolete (bool flag)
	Sets the obsolete state to <flag> More...

Size	nres () const
	Returns the number of residues represented in PDBInfo. More...

Size	natoms (Size const res) const
	Returns the number of atoms represented for the residue <res> More...

void	resize_residue_records (Size const n)
	Resizes for <n> residue records. More...

void	resize_atom_records (Size const res, Size const n, bool const zero=true)
	Ensures <n> atom records for residue <res> are available. More...

void	resize_atom_records (Size const n, bool const zero=true)
	Ensures <n> atom records for residue <res> are available. More...

void	resize_atom_records (Pose const &pose)
	Updates the number of atom records with respect to atoms in <pose> More...

void	tighten_memory ()
	Tightens memory usage. More...

String const &	name () const
	Returns the pdb name. More...

void	name (String const &s)
	Sets the pdb name. More...

String const &	modeltag () const
	Returns the model tag for a multi-model pdb. More...

void	modeltag (String const &tag)
	Sets the model tag for a multi-model pdb to <tag> More...

Remarks const &	remarks () const
	Returns the pdb remarks (const) More...

Remarks &	remarks ()
	Returns the pdb remarks (mutable) More...

void	remarks (Remarks const &in)
	Sets the pdb remarks to <in> More...

CrystInfo	crystinfo () const
	Returns the pdb crystinfo. More...

void	set_crystinfo (CrystInfo crystinfoin)
	Sets the pdb crystinfo. More...

void	header_information (io::pdb::HeaderInformation *header_information)
	For structures deposited into the protein databank, the header information record stores the classfication, deposition date and the 4 character identification code. More...

io::pdb::HeaderInformationCOP	header_information () const

io::pdb::HeaderInformationOP	header_information ()

char const &	chain (Size const res) const
	Returns the chain id for pose residue <res> More...

int const &	number (Size const res) const
	Returns the pdb sequence number of pose residue <res> More...

char const &	icode (Size const res) const
	Returns the pdb insertion code of residue <res> More...

Size	pdb2pose (char const chain, int const res, char const icode= ' ') const
	Returns the pose numbering of the pdb residue with chain <chain>, pdb residue <res>, and insertion code <icode> More...

String	pose2pdb (Size const res) const
	Returns the pdb numbering string of pose residue <res> More...

utility::vector1< std::string >	get_reslabels (Size const res) const
	returns the pose(number) labels associated to the residue More...

void	chain (Size const res, char const chain_id)
	Sets the chain id of pose residue <res> to <chain_id> More...

void	number (Size const res, int const pdb_res)
	Sets the pdb sequence residue number of pose residue <res> to <pdb_res> More...

void	icode (Size const res, char const ins_code)
	Sets the insertion code of pose residue <res> to <ins_code> More...

void	set_resinfo (Size const res, char const chain_id, int const pdb_res, char const ins_code= ' ')
	Sets the chain id, pdb sequence residue numbering, and insertion code for pose residue <res> to <chain_id> , <pdb_res> , and <ins_code> respectfully. More...

void	add_reslabel (Size const res, std::string const label)
	adds a label associated to a pose resid. More...

void	clear_reslabel (Size const res)
	clean all the label(s) associated to a pose resid. More...

bool	res_haslabel (Size const res, std::string const target_label) const
	uses std iterators to check if a residue has a label associated to it More...

bool const &	is_het (Size const res, Size const atom_index) const
	Returns true if the <atom_index> atom of pose residue <res> is a heteratom. More...

char const &	alt_loc (Size const res, Size const atom_index) const
	Returns the alternate location for the <atom_index> atom of pose residue <res> More...

Real const &	occupancy (Size const res, Size const atom_index) const
	Returns the occupancy for the <atom_index> atom of pose residue <res> More...

Real const &	temperature (Size const res, Size const atom_index) const
	Returns the temperature for the <atom_index> atom of pose residue <res> More...

void	is_het (Size const res, Size const atom_index, bool const flag)
	Sets the heteroatom flag of the <atom_index> atom of pose residue <res> to <flag> More...

void	alt_loc (Size const res, Size const atom_index, char const loc)
	Sets the alternate location of the <atom_index> atom of pose residue <res> to <loc> More...

void	occupancy (Size const res, Size const atom_index, Real const occ)
	Sets the occupancy of the <atom_index> atom of pose residue <res> to <occ> More...

void	temperature (Size const res, Size const atom_index, Real const t)
	Sets the temperature of the <atom_index> atom of pose residue <res> to <t> More...

PDBPoseMap const &	pdb2pose () const
	Returns the internally maintained PDBPoseMap. More...

void	show (std::ostream &out) const
	Displays segments of PDB information, segments may or may not be entire chains. More...

void	set_chains (char const id)
	Sets all residue chain ids to the character <id> More...

template<typename CharIterator >
void	set_chains (CharIterator const &begin, CharIterator const &end)
	Sets the residue chain ids from some char container, iterator version. More...

template<typename CharContainer >
void	set_chains (CharContainer const &c)
	Sets the residue chain ids from some char container, e.g. utility::vector1. More...

template<typename IntIterator >
void	set_numbering (IntIterator const &begin, IntIterator const &end)
	Sets the pdb sequence residue numbering from some int container, iterator version. More...

template<typename IntContainer >
void	set_numbering (IntContainer const &c)
	Sets the pdb sequence residue numbering from some int container, e.g. utility::vector1. More...

template<typename CharIterator >
void	set_icodes (CharIterator const &begin, CharIterator const &end)
	Sets the insertion codes from some char container, iterator version. More...

template<typename CharContainer >
void	set_icodes (CharContainer const &c)
	Sets the insertion codes from some char container, e.g. utility::vector1. More...

void	copy (PDBInfo const &input_info, Size const copy_from, Size const copy_to, Size const start_from)
	Copyies a section from PDBInfo <input_info> More...

void	append_res (Size const res, Size const natoms, Size const n=1)
	Appends residue records given a pose residue number <res> More...

void	prepend_res (Size const res, Size const natoms, Size const n=1)
	Prepends residue records before given pose residue number <res> More...

void	replace_res (Size const res, Size const natoms)
	"Replaces" residue record for pose residue <res> More...

void	replace_res_remap_bfactors (Size const res, conformation::Residue const &tgt)
	same as replace_res BUT remaps B factors from src to tgt More...

void	delete_res (Size const res, Size const n=1)
	Deletes <n> residue records starting from pose residue <res> More...

utility::vector1 < UnrecognizedAtomRecord > const &	get_unrecognized_atoms () const
	remembers info about atoms not read into the pose More...

core::Size const &	get_num_unrecognized_atoms () const

core::Size const &	get_num_unrecognized_res () const

std::string const &	get_unrecognized_res_name (core::Size const &i) const

core::Size const &	get_unrecognized_res_size (core::Size const &i) const

void	add_unrecognized_atom (Size resnum, std::string resname, std::string atomname, numeric::xyzVector< Real > coords, Real temp)
	remembers info about atoms not read into the pose More...

void	rebuild_pdb2pose ()
	rebuilds PDBPoseMap from scratch More...

Static Public Member Functions
static char	empty_record ()
	Returns the chain id character specifying "empty record", currently '^'. More...

Private Types
typedef utility::vector1 < AtomRecord >	AtomRecords

typedef utility::vector1 < ResidueRecord >	ResidueRecords

Private Member Functions
void	check_residue_records_size (Size const size) const
	if size of residue records != passed value, fail fast More...

Private Attributes
bool	obsolete_
	indicates object is out of sync with reference (e.g. parent Pose) More...

String	name_
	name of pdb/structure More...

String	modeltag_
	model tag for multi-model pdbs More...

io::pdb::HeaderInformationOP	header_information_
	header information More...

Remarks	remarks_
	pdb remarks More...

ResidueRecords	residue_rec_
	residue records in internal rosetta numbering from 1 .. n More...

PDBPoseMap	pdb2pose_
	maps PDB chain,residue -> internal residue numbering More...

core::conformation::Conformation const *	conf_
	Conformation being observed, NULL if not attached. More...

utility::vector1 < UnrecognizedAtomRecord >	unrecognized_atoms_
	information about unrecognized residues More...

std::map< core::Size, std::string >	unrecognized_res_num2name_

std::map< core::Size, core::Size >	unrecognized_res_size_

core::Size	num_unrecognized_res_

core::Size	num_unrecognized_atoms_

CrystInfo	crystinfo_

Detailed Description

maintains pdb residue & atom information inside a Pose

Upon creation of new residue records, e.g. when calling the constructors without 'init' or appending/prepending residues, the chain id for the new records will be set to a character, currently '^', denoting "empty record". This character may be looked up by calling the static method PDBInfo::empty_record().

Remarks: Class implementation is biased towards simplicity and fast lookup. Residue/atom information are kept in vectors. An internally maintained PDBPoseMap provides mapping from pdb -> pose residue numbering. This causes residue mutators to be a bit more expensive due to map updates, but this is ok because they are typically called sparingly. Accessors and mutators have overloaded method convention, while special mutators use .set_* convention.

Member Typedef Documentation

typedef utility::vector1< AtomRecord > core::pose::PDBInfo::AtomRecords

private

typedef core::Real core::pose::PDBInfo::Real

typedef core::pose::Remarks core::pose::PDBInfo::Remarks

typedef utility::vector1< ResidueRecord > core::pose::PDBInfo::ResidueRecords

private

typedef core::Size core::pose::PDBInfo::Size

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

typedef utility::pointer::ReferenceCount core::pose::PDBInfo::Super

Constructor & Destructor Documentation

core::pose::PDBInfo::PDBInfo ( )

default constructor, obsolete is true

core::pose::PDBInfo::PDBInfo ( Size const n )

size constructor (ensure space for 'n' residue records), obsolete is true

core::pose::PDBInfo::PDBInfo	(	Pose const &	pose,
		bool	init = `true`
	)

Pose constructor (ensures space for residue and atom records relative to Pose)

Parameters

[in]	pose	Pose
[in]	init	if true (default), then residue records are initialized and obsolete set to false, otherwise obsolete is true using Pose residue numbering and chains of the Residues in the Conformation

References core::conformation::Residue::chain(), core::pose::PDBInfo::ResidueRecord::chainID, chr_chains(), rebuild_pdb2pose(), core::pose::Pose::residue(), residue_rec_, resize_atom_records(), core::pose::PDBInfo::ResidueRecord::resSeq, and core::pose::Pose::total_residue().

core::pose::PDBInfo::PDBInfo ( PDBInfo const & info )

copy constructor

core::pose::PDBInfo::~PDBInfo ( )

virtual

default destructor

References detach_from().

Member Function Documentation

void core::pose::PDBInfo::add_reslabel	(	Size const	res,
		std::string const	label
	)

adds a label associated to a pose resid.

Parameters

[in]	res	residue in pose numbering
[in]	label	string that is the "label"

References core::pose::PDBInfo::ResidueRecord::label, PyAssert, and residue_rec_.

void core::pose::PDBInfo::add_unrecognized_atom	(	Size	resnum,
		std::string	resname,
		std::string	atomname,
		numeric::xyzVector< Real >	coords,
		Real	temp
	)

remembers info about atoms not read into the pose

References num_unrecognized_atoms_, num_unrecognized_res_, unrecognized_atoms_, unrecognized_res_num2name_, and unrecognized_res_size_.

Referenced by core::io::pdb::build_pose_as_is1().

char const& core::pose::PDBInfo::alt_loc	(	Size const	res,
		Size const	atom_index
	)		const

inline

Returns the alternate location for the <atom_index> atom of pose residue <res>

example(s): pose.pdb_info().alt_loc(1,1) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References residue_rec_.

void core::pose::PDBInfo::alt_loc	(	Size const	res,
		Size const	atom_index,
		char const	loc
	)

inline

Sets the alternate location of the <atom_index> atom of pose residue <res> to <loc>

Note: : <loc> is an alternate location character

References residue_rec_.

void core::pose::PDBInfo::append_res	(	Size const	res,
		Size const	natoms,
		Size const	n = `1`
	)

Appends residue records given a pose residue number <res>

append residue records after given residue number

Parameters

[in]	res	residue to append after (in internal/pose numbering)
[in]	natoms	number of atoms in type of appended residue
[in]	n	number of residue records to append

References core::pose::PDBInfo::ResidueRecord::atomRec, core::pose::PDBPoseMap::insert(), pdb2pose_, and residue_rec_.

Referenced by on_length_change().

void core::pose::PDBInfo::attach_to ( core::conformation::Conformation & conf )

Attaches the Conformation <conf> and begins observation.

attach to Conformation and begin observation

example(s):

See also: Pose PDBInfo

References core::conformation::Conformation::attach_connection_obs(), core::conformation::Conformation::attach_identity_obs(), core::conformation::Conformation::attach_length_obs(), conf_, detach_from(), on_connection_change(), on_identity_change(), and on_length_change().

Referenced by core::pose::Pose::pdb_info().

char const& core::pose::PDBInfo::chain ( Size const res ) const

inline

Returns the chain id for pose residue <res>

example(s): pose.pdb_info().chain(3) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), core::pose::renumber_pdbinfo_based_on_conf_chains(), show(), and core::pose::Pose::update_pose_chains_from_pdb_chains().

void core::pose::PDBInfo::chain	(	Size const	res,
		char const	chain_id
	)

Sets the chain id of pose residue <res> to <chain_id>

set chain id for residue

Remarks: chain id should not be the empty record character, currently '^' Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().chain(3,"R") See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

Remarks: chain id should not be the empty record character, currently '^'

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, PyAssert, residue_rec_, and core::pose::PDBInfo::ResidueRecord::resSeq.

void core::pose::PDBInfo::check_residue_records_size ( Size const size ) const

private

if size of residue records != passed value, fail fast

Note: This is meant to be used only for en masse methods, not individual residue/atom methods

References basic::Error(), residue_rec_, core::io::serialization::size(), and utility_exit.

Referenced by set_chains(), set_icodes(), and set_numbering().

void core::pose::PDBInfo::clear_reslabel ( Size const res )

clean all the label(s) associated to a pose resid.

Parameters

[in] res residue in pose numbering

References core::pose::PDBInfo::ResidueRecord::label, PyAssert, and residue_rec_.

void core::pose::PDBInfo::copy	(	PDBInfo const &	input_info,
		Size const	copy_from,
		Size const	copy_to,
		Size const	start_from
	)

Copyies a section from PDBInfo <input_info>

copy a section from another PDBInfo

Parameters

[in]	input_info	the PDBInfo to copy from
[in]	copy_from	the first residue position in input_info to copy
[in]	copy_to	the final residue position in input_info to copy
[in]	start_from	the first residue position in this PDBInfo to copy into

References begin, core::sequence::end, core::pose::PDBPoseMap::erase(), core::pose::PDBPoseMap::insert(), pdb2pose_, and residue_rec_.

CrystInfo core::pose::PDBInfo::crystinfo ( ) const

inline

Returns the pdb crystinfo.

References crystinfo_.

void core::pose::PDBInfo::delete_res	(	Size const	res,
		Size const	n = `1`
	)

Deletes <n> residue records starting from pose residue <res>

delete 'n' residue records starting from given residue

Parameters

[in]	res	residue to start deleting from (in internal/pose numbering)
[in]	n	number of residue records to delete

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, residue_rec_, core::pose::PDBInfo::ResidueRecord::resSeq, and start.

Referenced by on_length_change().

void core::pose::PDBInfo::detach_from ( )

Detaches the Conformation and stops observation.

detach from Conformation and stop observation

Remarks: takes no arguments because PDBInfo can only observe one Conformation at a time

example(s): pose.pdb_info().detach_from() See also: Pose PDBInfo

Remarks: takes no arguments because PDBInfo can only observe one Conformation at a time

References conf_, core::conformation::Conformation::detach_connection_obs(), core::conformation::Conformation::detach_identity_obs(), core::conformation::Conformation::detach_length_obs(), on_connection_change(), on_identity_change(), and on_length_change().

Referenced by attach_to(), on_connection_change(), on_identity_change(), on_length_change(), core::pose::Pose::pdb_info(), and ~PDBInfo().

static char core::pose::PDBInfo::empty_record ( )

inlinestatic

Returns the chain id character specifying "empty record", currently '^'.

Referenced by core::pose::conf2pdb_chain(), core::pose::PDBPoseMap::insert(), and core::pose::renumber_pdbinfo_based_on_conf_chains().

core::Size const& core::pose::PDBInfo::get_num_unrecognized_atoms ( ) const

inline

References num_unrecognized_atoms_.

core::Size const& core::pose::PDBInfo::get_num_unrecognized_res ( ) const

inline

References num_unrecognized_res_.

utility::vector1< std::string > core::pose::PDBInfo::get_reslabels ( Size const res ) const

returns the pose(number) labels associated to the residue

returns for pose( resnumber) the label associated to the residue

Parameters

[in] res residue in pose numbering

Note: the retrun string is a concatenation of all the strings inside of the vector label<>

Parameters

[in] res residue in pose numbering

References PyAssert, and residue_rec_.

utility::vector1< UnrecognizedAtomRecord > const& core::pose::PDBInfo::get_unrecognized_atoms ( ) const

inline

remembers info about atoms not read into the pose

References unrecognized_atoms_.

std::string const& core::pose::PDBInfo::get_unrecognized_res_name ( core::Size const & i ) const

inline

References unrecognized_res_num2name_.

core::Size const& core::pose::PDBInfo::get_unrecognized_res_size ( core::Size const & i ) const

inline

References unrecognized_res_size_.

void core::pose::PDBInfo::header_information ( io::pdb::HeaderInformation * header_information )

inline

For structures deposited into the protein databank, the header information record stores the classfication, deposition date and the 4 character identification code.

For now only allow initalizing it with copy and accessing it with a constant owning pointer. Note: The header information is only initialized if it is needed. Generally this requires using the -run:preserve_header options flag.

References header_information(), and header_information_.

Referenced by core::io::pdb::build_pose_as_is1().

io::pdb::HeaderInformationCOP core::pose::PDBInfo::header_information ( ) const

inline

References header_information_.

Referenced by header_information().

io::pdb::HeaderInformationOP core::pose::PDBInfo::header_information ( )

inline

References header_information_.

char const& core::pose::PDBInfo::icode ( Size const res ) const

inline

Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().icode(3) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), pdb2pose(), core::pose::renumber_pdbinfo_based_on_conf_chains(), and show().

void core::pose::PDBInfo::icode	(	Size const	res,
		char const	ins_code
	)

Sets the insertion code of pose residue <res> to <ins_code>

set insertion code for residue

Returns the pdb insertion code of residue <res>

example(s):

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, PyAssert, residue_rec_, and core::pose::PDBInfo::ResidueRecord::resSeq.

bool const& core::pose::PDBInfo::is_het	(	Size const	res,
		Size const	atom_index
	)		const

inline

Returns true if the <atom_index> atom of pose residue <res> is a heteratom.

Note: : atom index within instance of core::conformation::Residue, currently Rosetta's pdb file output treats the value of .is_het() as an override – if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)

References residue_rec_.

void core::pose::PDBInfo::is_het	(	Size const	res,
		Size const	atom_index,
		bool const	flag
	)

inline

Sets the heteroatom flag of the <atom_index> atom of pose residue <res> to <flag>

Note: currently Rosetta's pdb file output treats the value of .is_het() as an override – if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)

References residue_rec_.

core::conformation::Conformation const * core::pose::PDBInfo::is_observing ( )

Returns the Conformation if this PDBInfo is currently observing a conformation, otherwise return NULL.

is this PDBInfo currently observing a conformation?

example(s): pose.pdb_info().is_observing() See also: Pose PDBInfo

Returns: the Conformation being observed, otherwise NULL

References conf_.

String const& core::pose::PDBInfo::modeltag ( ) const

inline

Returns the model tag for a multi-model pdb.

example(s): pose.pdb_info().modeltag() See also: Pose PDBInfo

References modeltag_.

Referenced by core::io::pdb::build_pose_as_is1().

void core::pose::PDBInfo::modeltag ( String const & tag )

inline

Sets the model tag for a multi-model pdb to <tag>

example(s): pose.pdb_info().modeltag('Number1') See also: Pose PDBInfo

References modeltag_.

String const& core::pose::PDBInfo::name ( ) const

inline

Returns the pdb name.

example(s): pose.pdb_info().name() See also: Pose PDBInfo

References name_.

Referenced by core::io::pdb::build_pose_as_is1(), and show().

void core::pose::PDBInfo::name ( String const & s )

inline

Sets the pdb name.

example(s): pose.pdb_info().name('MyPDB') See also: Pose PDBInfo

References name_.

Size core::pose::PDBInfo::natoms ( Size const res ) const

inline

Returns the number of atoms represented for the residue <res>

Note: : residue <res> must be in pose numbering

example(s): pose.pdb_info().natoms(3) See also: Pose PDBInfo

References residue_rec_.

Referenced by show().

Size core::pose::PDBInfo::nres ( ) const

inline

Returns the number of residues represented in PDBInfo.

example(s): pose.pdb_info().nres() See also: Pose PDBInfo

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), core::pose::Pose::pdb_info(), and show().

int const& core::pose::PDBInfo::number ( Size const res ) const

inline

Returns the pdb sequence number of pose residue <res>

example(s): pose.pdb_info().number(3) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), core::pose::renumber_pdbinfo_based_on_conf_chains(), and show().

void core::pose::PDBInfo::number	(	Size const	res,
		int const	pdb_res
	)

Sets the pdb sequence residue number of pose residue <res> to <pdb_res>

set pdb residue sequence number

Returns the pdb insertion code of residue <res>

example(s): pose.pdb_info().number(3,81) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, PyAssert, residue_rec_, and core::pose::PDBInfo::ResidueRecord::resSeq.

bool core::pose::PDBInfo::obsolete ( ) const

inline

Returns true if PDBInfo is obsolete and needs updating.

This flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.

example(s): pose.pdb_info().obsolete() See also: Pose PDBInfo

References obsolete_.

Referenced by core::io::pdb::build_pose_as_is1(), on_connection_change(), on_identity_change(), and on_length_change().

void core::pose::PDBInfo::obsolete ( bool flag )

inline

Sets the obsolete state to <flag>

this flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.

References obsolete_.

Real const& core::pose::PDBInfo::occupancy	(	Size const	res,
		Size const	atom_index
	)		const

inline

Returns the occupancy for the <atom_index> atom of pose residue <res>

example(s): pose.pdb_info().occupancy(1,1) See also: Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

References residue_rec_.

void core::pose::PDBInfo::occupancy	(	Size const	res,
		Size const	atom_index,
		Real const	occ
	)

inline

Sets the occupancy of the <atom_index> atom of pose residue <res> to <occ>

References residue_rec_.

void core::pose::PDBInfo::on_connection_change ( core::conformation::signals::ConnectionEvent const & event )

Updates when connection to Conformation is changed.

update when connection to Conformation is changed

References detach_from(), obsolete(), and core::conformation::signals::ConnectionEvent::tag.

Referenced by attach_to(), and detach_from().

void core::pose::PDBInfo::on_identity_change ( core::conformation::signals::IdentityEvent const & event )

Updates atom records when residue identity changes in Conformation.

update atom records when residue identity changes in Conformation

References detach_from(), obsolete(), option, core::conformation::signals::IdentityEvent::position, in::preserve_crystinfo, replace_res(), replace_res_remap_bfactors(), core::conformation::signals::IdentityEvent::residue, and core::conformation::signals::IdentityEvent::tag.

Referenced by attach_to(), and detach_from().

void core::pose::PDBInfo::on_length_change ( core::conformation::signals::LengthEvent const & event )

Updates residue and atom records when length changes in Conformation, obsoletes PDBInfo.

update residue and atom records when length changes in Conformation, obsoletes PDBInfo

Residue and atoms records in PDBInfo will be automatically resized and the obsolete flag will be set to true, causing PDBInfo to not be used on pdb output. Existing data inside the PDBInfo is not touched. After filling in the data for the newly updated residues, setting PDBInfo::obsolete( false ) will re-enable usage of PDBInfo on pdb output. If PDBInfo receives a LengthEvent::INVALIDATE, it will obsolete and then detach itself for safety.

References append_res(), delete_res(), detach_from(), core::conformation::signals::LengthEvent::length_change, obsolete(), core::conformation::signals::LengthEvent::position, prepend_res(), core::conformation::signals::LengthEvent::residue, and core::conformation::signals::LengthEvent::tag.

Referenced by attach_to(), and detach_from().

PDBInfo & core::pose::PDBInfo::operator= ( PDBInfo const & info )

copy assignment

any Conformation already being observed stays constant, there is no re-assignment

References crystinfo_, header_information_, modeltag_, name_, num_unrecognized_atoms_, num_unrecognized_res_, obsolete_, pdb2pose_, remarks_, residue_rec_, unrecognized_atoms_, unrecognized_res_num2name_, and unrecognized_res_size_.

Size core::pose::PDBInfo::pdb2pose	(	char const	chain,
		int const	res,
		char const	icode = `' '`
	)		const

inline

Returns the pose numbering of the pdb residue with chain <chain>, pdb residue <res>, and insertion code <icode>

Note: : <icode> is not required, returns 0 if not found, pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s): pose.pdb_info().pdb2pose("B",5) See also: Pose PDBInfo PDBInfo.pose2pdb

References core::pose::PDBPoseMap::find(), icode(), and pdb2pose_.

PDBPoseMap const& core::pose::PDBInfo::pdb2pose ( ) const

inline

Returns the internally maintained PDBPoseMap.

example(s):

References pdb2pose_.

PDBInfo::String core::pose::PDBInfo::pose2pdb ( Size const res ) const

Returns the pdb numbering string of pose residue <res>

translates the pose number to pdb numbering string for use in PyRosetta.

Note: : pdb string contains the chainID and number pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s): pose.pdb_info().pose2pdb(25) See also: Pose PDBInfo PDBInfo.pdb2pose

Parameters

[in] res pose residue number

Returns: pdb string containing chainID and number

References PyAssert, and residue_rec_.

void core::pose::PDBInfo::prepend_res	(	Size const	res,
		Size const	natoms,
		Size const	n = `1`
	)

Prepends residue records before given pose residue number <res>

prepend residue records before given residue number

Parameters

[in]	res	residue to prepend before (in internal/pose numbering)
[in]	natoms	number of atoms in type of appended residue
[in]	n	number of residue records to prepend

References core::pose::PDBInfo::ResidueRecord::atomRec, core::pose::PDBPoseMap::insert(), pdb2pose_, and residue_rec_.

Referenced by on_length_change().

void core::pose::PDBInfo::rebuild_pdb2pose ( )

rebuilds PDBPoseMap from scratch

References core::pose::PDBPoseMap::clear(), core::pose::PDBPoseMap::fill(), and pdb2pose_.

Referenced by PDBInfo(), resize_residue_records(), set_chains(), set_icodes(), and set_numbering().

Remarks const& core::pose::PDBInfo::remarks ( ) const

inline

Returns the pdb remarks (const)

example(s): pose.pdb_info().remarks() See also: Pose PDBInfo

References remarks_.

Referenced by core::io::pdb::build_pose_as_is1().

Remarks& core::pose::PDBInfo::remarks ( )

inline

Returns the pdb remarks (mutable)

Note: we allow direct access to the remarks vector because its state is independent of the rest of PDBInfo and it's much more convenient for the user

example(s): pose.pdb_info().remarks() See also: Pose PDBInfo

References remarks_.

void core::pose::PDBInfo::remarks ( Remarks const & in )

inline

Sets the pdb remarks to <in>

example(s):

See also: Pose PDBInfo

References remarks_.

void core::pose::PDBInfo::replace_res	(	Size const	res,
		Size const	natoms
	)

"Replaces" residue record for pose residue <res>

"replace" residue record for given residue number

Leaves information in residue record untouched, but resizes and zeroes atom records for the residue.

Parameters

[in]	res	residue to replace
[in]	natoms	number of atoms in type of residue

References residue_rec_.

Referenced by on_identity_change().

void core::pose::PDBInfo::replace_res_remap_bfactors	(	Size const	res,
		conformation::Residue const &	tgt
	)

same as replace_res BUT remaps B factors from src to tgt

References core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), residue_rec_, and temperature().

Referenced by on_identity_change().

bool core::pose::PDBInfo::res_haslabel	(	Size const	res,
		std::string const	target_label
	)		const

inline

uses std iterators to check if a residue has a label associated to it

Parameters

[in]	res	residue in pose numbering
[in]	target_label	string to look for inside the labes associated to the residue

References residue_rec_.

void core::pose::PDBInfo::resize_atom_records	(	Size const	res,
		Size const	n,
		bool const	zero = `true`
	)

Ensures <n> atom records for residue <res> are available.

ensure 'n' available atom records for particular residue

Note: : if <zero> is true, zero the atom records for this residue

Parameters

[in]	res	residue
[in]	n	number of atoms
[in]	zero	if true, zero the atom records for this residue

References residue_rec_.

Referenced by core::io::pdb::build_pose_as_is1(), and PDBInfo().

void core::pose::PDBInfo::resize_atom_records	(	Size const	n,
		bool const	zero = `true`
	)

Ensures <n> atom records for residue <res> are available.

ensure 'n' available atom records for every residue

Note: : if <zero> is true, zero the atom records for this residue

Parameters

[in]	res	residue
[in]	n	number of atoms
[in]	zero	if true, zero the atom records

References residue_rec_.

void core::pose::PDBInfo::resize_atom_records ( Pose const & pose )

Updates the number of atom records with respect to atoms in <pose>

update number of atom records with respect to atoms in Pose

Number of internally available atom records will be adjusted to match number of atoms within each residue in Pose. Only newly created records will be zeroed, any existing records are untouched.

References core::pose::Pose::n_residue(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and residue_rec_.

void core::pose::PDBInfo::resize_residue_records ( Size const n )

Resizes for <n> residue records.

resize for 'n' residue records

Leaves atom record state inconsistent. Atom records for remaining residues are untouched while new residues have no atom records, so make sure and call one of resize_atom_records() afterwards if necessary.

Warning: Do not use this method for ins/del of residues, as it leaves the data state inconsistent. See append_res/prepend_res/delete_res for that type of functionality.

References rebuild_pdb2pose(), and residue_rec_.

void core::pose::PDBInfo::set_chains ( char const id )

Sets all residue chain ids to the character <id>

set all residue chain IDs to a single character

References rebuild_pdb2pose(), and residue_rec_.

Referenced by core::io::pdb::build_pose_as_is1(), core::io::silent::SilentStruct::residue_numbers_into_pose(), and set_chains().

template<typename CharIterator >

void core::pose::PDBInfo::set_chains	(	CharIterator const &	begin,
		CharIterator const &	end
	)

inline

Sets the residue chain ids from some char container, iterator version.

Warning: This function does not check if number of elements within span of iterators exceeds number of residues currently defined in object. User must ensure this independently.

References core::sequence::end, rebuild_pdb2pose(), and residue_rec_.

template<typename CharContainer >

void core::pose::PDBInfo::set_chains ( CharContainer const & c )

inline

Sets the residue chain ids from some char container, e.g. utility::vector1.

Container must have const .size(), .begin() and .end() iterator access methods.

Warning: This function checks for size first and will cause failure if size of container does not match number of residues currently defined in object.

References check_residue_records_size(), residue_rec_, and set_chains().

void core::pose::PDBInfo::set_crystinfo ( CrystInfo crystinfoin )

inline

Sets the pdb crystinfo.

References crystinfo_.

Referenced by core::io::pdb::build_pose_as_is1().

template<typename CharIterator >

void core::pose::PDBInfo::set_icodes	(	CharIterator const &	begin,
		CharIterator const &	end
	)

inline

Sets the insertion codes from some char container, iterator version.

Warning: This function does not check if number of elements within span of iterators exceeds number of residues currently defined in object. User must ensure this independently.

References core::sequence::end, rebuild_pdb2pose(), and residue_rec_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_icodes().

template<typename CharContainer >

void core::pose::PDBInfo::set_icodes ( CharContainer const & c )

inline

Sets the insertion codes from some char container, e.g. utility::vector1.

Container must have const .size(), .begin() and .end() iterator access methods.

Warning: This function checks for size first and will cause failure if size of container does not match number of residues currently defined in object.

References check_residue_records_size(), residue_rec_, and set_icodes().

template<typename IntIterator >

void core::pose::PDBInfo::set_numbering	(	IntIterator const &	begin,
		IntIterator const &	end
	)

inline

Sets the pdb sequence residue numbering from some int container, iterator version.

Warning: This function does not check if number of elements within span of iterators exceeds number of residues currently defined in object. User must ensure this independently.

References core::sequence::end, rebuild_pdb2pose(), and residue_rec_.

Referenced by core::io::pdb::build_pose_as_is1(), core::io::silent::SilentStruct::residue_numbers_into_pose(), and set_numbering().

template<typename IntContainer >

void core::pose::PDBInfo::set_numbering ( IntContainer const & c )

inline

Sets the pdb sequence residue numbering from some int container, e.g. utility::vector1.

Container must have const .size(), .begin() and .end() iterator access methods.

Warning: This function checks for size first and will cause failure if size of container does not match number of residues currently defined in object.

References check_residue_records_size(), residue_rec_, and set_numbering().