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

#include <PDBInfo.hh>

Inheritance diagram for core::pose::PDBInfo:

Collaboration diagram for core::pose::PDBInfo:

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	Returns true if PDBInfo is obsolete and needs updating.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...

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...

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...

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	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_

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.

Definition at line 105 of file PDBInfo.hh.

Member Typedef Documentation

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

private

Definition at line 123 of file PDBInfo.hh.

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

Definition at line 114 of file PDBInfo.hh.

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

Definition at line 116 of file PDBInfo.hh.

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

private

Definition at line 130 of file PDBInfo.hh.

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

Definition at line 113 of file PDBInfo.hh.

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

Definition at line 115 of file PDBInfo.hh.

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

Definition at line 111 of file PDBInfo.hh.

Constructor & Destructor Documentation

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

default constructor, obsolete is true

Definition at line 51 of file PDBInfo.cc.

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

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

Definition at line 64 of file PDBInfo.cc.

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

Definition at line 82 of file PDBInfo.cc.

References core::conformation::Residue::chain(), core::pose::PDBInfo::ResidueRecord::chainID, core::pose::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

Definition at line 113 of file PDBInfo.cc.

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

virtual

default destructor

Definition at line 132 of file PDBInfo.cc.

References detach_from().

Member Function Documentation

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

Definition at line 683 of file PDBInfo.cc.

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

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

Definition at line 768 of file PDBInfo.hh.

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

Definition at line 842 of file PDBInfo.hh.

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

Definition at line 591 of file PDBInfo.cc.

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

Definition at line 181 of file PDBInfo.cc.

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().

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

Definition at line 573 of file PDBInfo.hh.

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), core::pose::renumber_pdbinfo_based_on_conf_chains(), show(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

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 '^'

Definition at line 414 of file PDBInfo.cc.

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, 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

Definition at line 705 of file PDBInfo.cc.

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

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

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

Definition at line 552 of file PDBInfo.cc.

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

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

Definition at line 656 of file PDBInfo.cc.

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 protocols::loops::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

Definition at line 199 of file PDBInfo.cc.

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(), and ~PDBInfo().

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

inlinestatic

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

Definition at line 416 of file PDBInfo.hh.

Referenced by core::io::pdb::FileData::append_residue(), 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

Definition at line 1121 of file PDBInfo.hh.

References num_unrecognized_atoms_.

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

inline

Definition at line 1128 of file PDBInfo.hh.

References num_unrecognized_res_.

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

inline

remembers info about atoms not read into the pose

Definition at line 1115 of file PDBInfo.hh.

References unrecognized_atoms_.

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

inline

Definition at line 1135 of file PDBInfo.hh.

References unrecognized_res_num2name_.

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

inline

Definition at line 1142 of file PDBInfo.hh.

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.

Definition at line 542 of file PDBInfo.hh.

References header_information(), and header_information_.

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

inline

Definition at line 548 of file PDBInfo.hh.

References header_information_.

Referenced by header_information().

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

inline

Definition at line 554 of file PDBInfo.hh.

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

Definition at line 609 of file PDBInfo.hh.

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):

Definition at line 450 of file PDBInfo.cc.

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, 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)

Definition at line 747 of file PDBInfo.hh.

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)

Definition at line 827 of file PDBInfo.hh.

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

Definition at line 174 of file PDBInfo.cc.

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

Definition at line 463 of file PDBInfo.hh.

References modeltag_.

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

Definition at line 478 of file PDBInfo.hh.

References modeltag_.

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

inline

Returns the pdb name.

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

Definition at line 433 of file PDBInfo.hh.

References name_.

Referenced by 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

Definition at line 448 of file PDBInfo.hh.

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

Definition at line 361 of file PDBInfo.hh.

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

Definition at line 345 of file PDBInfo.hh.

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), 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

Definition at line 591 of file PDBInfo.hh.

References residue_rec_.

Referenced by core::pose::PDBPoseMap::fill(), core::pose::renumber_pdbinfo_based_on_conf_chains(), show(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

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

Definition at line 432 of file PDBInfo.cc.

References core::pose::PDBInfo::ResidueRecord::chainID, core::pose::PDBPoseMap::conditional_erase(), core::pose::PDBInfo::ResidueRecord::iCode, core::pose::PDBPoseMap::insert(), pdb2pose_, 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

Definition at line 315 of file PDBInfo.hh.

References obsolete_.

Referenced by 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.

Definition at line 327 of file PDBInfo.hh.

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

Definition at line 788 of file PDBInfo.hh.

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>

Definition at line 856 of file PDBInfo.hh.

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

Definition at line 212 of file PDBInfo.cc.

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

Definition at line 232 of file PDBInfo.cc.

References detach_from(), obsolete(), core::conformation::signals::IdentityEvent::position, replace_res(), 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.

Definition at line 266 of file PDBInfo.cc.

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

Definition at line 142 of file PDBInfo.cc.

References 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

Definition at line 630 of file PDBInfo.hh.

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

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

inline

Returns the internally maintained PDBPoseMap.

example(s):

Definition at line 894 of file PDBInfo.hh.

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

Definition at line 401 of file PDBInfo.cc.

References 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

Definition at line 615 of file PDBInfo.cc.

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

Definition at line 717 of file PDBInfo.cc.

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

Definition at line 493 of file PDBInfo.hh.

References remarks_.

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

Definition at line 511 of file PDBInfo.hh.

References remarks_.

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

inline

Sets the pdb remarks to <in>

example(s):

Member Data Documentation

core::conformation::Conformation const* core::pose::PDBInfo::conf_

private

Conformation being observed, NULL if not attached.

Definition at line 1218 of file PDBInfo.hh.

Referenced by attach_to(), detach_from(), and is_observing().

io::pdb::HeaderInformationOP core::pose::PDBInfo::header_information_

private

header information

Definition at line 1203 of file PDBInfo.hh.

Referenced by header_information(), and operator=().

String core::pose::PDBInfo::modeltag_

private

model tag for multi-model pdbs

Definition at line 1199 of file PDBInfo.hh.

Referenced by modeltag(), and operator=().

String core::pose::PDBInfo::name_

private

name of pdb/structure

Definition at line 1195 of file PDBInfo.hh.

Referenced by name(), and operator=().

core::Size core::pose::PDBInfo::num_unrecognized_atoms_

private

Definition at line 1227 of file PDBInfo.hh.

Referenced by add_unrecognized_atom(), get_num_unrecognized_atoms(), and operator=().

core::Size core::pose::PDBInfo::num_unrecognized_res_

private

Definition at line 1226 of file PDBInfo.hh.

Referenced by add_unrecognized_atom(), get_num_unrecognized_res(), and operator=().

bool core::pose::PDBInfo::obsolete_

private

indicates object is out of sync with reference (e.g. parent Pose)

control boolean prevents PDB emitter access if info out of sync

Definition at line 1191 of file PDBInfo.hh.

Referenced by obsolete(), and operator=().

PDBPoseMap core::pose::PDBInfo::pdb2pose_

private

maps PDB chain,residue -> internal residue numbering

Definition at line 1214 of file PDBInfo.hh.

Referenced by append_res(), chain(), copy(), delete_res(), icode(), number(), operator=(), pdb2pose(), prepend_res(), rebuild_pdb2pose(), and set_resinfo().

Remarks core::pose::PDBInfo::remarks_

private

pdb remarks

Definition at line 1206 of file PDBInfo.hh.

Referenced by operator=(), remarks(), and tighten_memory().

ResidueRecords core::pose::PDBInfo::residue_rec_

private

residue records in internal rosetta numbering from 1 .. n

Definition at line 1210 of file PDBInfo.hh.

Referenced by alt_loc(), append_res(), chain(), check_residue_records_size(), copy(), delete_res(), icode(), is_het(), natoms(), nres(), number(), occupancy(), operator=(), PDBInfo(), pose2pdb(), prepend_res(), replace_res(), resize_atom_records(), resize_residue_records(), set_chains(), set_icodes(), set_numbering(), set_resinfo(), temperature(), and tighten_memory().

utility::vector1< UnrecognizedAtomRecord > core::pose::PDBInfo::unrecognized_atoms_

private

information about unrecognized residues

Definition at line 1223 of file PDBInfo.hh.

Referenced by add_unrecognized_atom(), get_unrecognized_atoms(), and operator=().

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

private

Definition at line 1224 of file PDBInfo.hh.

Referenced by add_unrecognized_atom(), get_unrecognized_res_name(), and operator=().

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

private

Definition at line 1225 of file PDBInfo.hh.

Referenced by add_unrecognized_atom(), get_unrecognized_res_size(), and operator=().

The documentation for this class was generated from the following files:

src/core/pose/PDBInfo.hh
src/core/pose/PDBInfo.cc

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

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

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

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

void core::pose::PDBInfo::set_resinfo	(	Size const	res,
		char const	chain_id,
		int const	pdb_res,
		char const	ins_code = `' '`
	)

[in]	res	residue in pose numbering
[in]	chain_id	pdb chain id
[in]	pdb_res	residue in pdb numbering
[in]	ins_code	pdb insertion code

Classes

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