core::pose::PDBPoseMap Class Reference

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...

#include <PDBPoseMap.hh>

Classes
struct	ResidueKey
	sortable residue key internal to PDBPoseMap More...

Public Types
typedef core::Size	Size

Public Member Functions
	PDBPoseMap ()
	default constructor More...
	PDBPoseMap (PDBInfo const &info)
	PDBInfo constructor. More...
	PDBPoseMap (PDBPoseMap const &map)
	copy constructor More...
virtual	~PDBPoseMap ()
	default destructor More...
PDBPoseMap &	operator= (PDBPoseMap const &m)
	copy assignment More...
Size	size () const
	number of mappings More...
Size	find (char const chain, int const pdb_res, char const ins_code= ' ') const
	lookup pose numbering More...
void	insert (char const chain, int const pdb_res, char const ins_code, Size const pose_res)
	insert pdb -> pose number mapping More...
bool	conditional_erase (char const chain, int const pdb_res, char const ins_code, Size const pose_res)
	remove mapping for pdb residue key only if Pose residue matches More...
void	erase (char const chain, int const pdb_res, char const ins_code)
	forcibly remove mapping for pdb residue key More...
void	clear ()
	clear the current mapping data More...
void	fill (PDBInfo const &info)
	fill with corresponding pdb -> pose residue mapping More...

Private Types
typedef utility::pointer::ReferenceCount	Super
typedef std::map< ResidueKey, Size >	Pdb2Pose

Private Attributes
Pdb2Pose	pdb2pose_
	maps ResidueKey -> Pose internal numbering More...

Detailed Description

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.

Member Typedef Documentation

typedef std::map< ResidueKey, Size > core::pose::PDBPoseMap::Pdb2Pose

private

typedef core::Size core::pose::PDBPoseMap::Size

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

private

Constructor & Destructor Documentation

core::pose::PDBPoseMap::PDBPoseMap

(

)

default constructor

core::pose::PDBPoseMap::PDBPoseMap

(

PDBInfo const &

info

)

PDBInfo constructor.

References fill().

core::pose::PDBPoseMap::PDBPoseMap

(

PDBPoseMap const &

map

)

copy constructor

core::pose::PDBPoseMap::~PDBPoseMap ( )

virtual

default destructor

Member Function Documentation

void core::pose::PDBPoseMap::clear ( )

inline

clear the current mapping data

References pdb2pose_.

Referenced by core::pose::PDBInfo::rebuild_pdb2pose().

bool core::pose::PDBPoseMap::conditional_erase ( char const  chain, int const  pdb_res, char const  ins_code, Size const  pose_res  )

inline

remove mapping for pdb residue key only if Pose residue matches

Parameters

[in]	chain	chain id
[in]	pdb_res	pdb residue numbering
[in]	ins_code	insertion code, use ' ' if no insertion code
[in]	pose_res	the mapped Pose residue

Returns

true if key-value pair erase, false otherwise

References pdb2pose_.

Referenced by core::pose::PDBInfo::chain(), core::pose::PDBInfo::icode(), core::pose::PDBInfo::number(), and core::pose::PDBInfo::set_resinfo().

void core::pose::PDBPoseMap::erase ( char const  chain, int const  pdb_res, char const  ins_code  )

inline

forcibly remove mapping for pdb residue key

Parameters

[in]	chain	chain id
[in]	pdb_res	pdb residue numbering
[in]	ins_code	insertion code, use ' ' if no insertion code

References pdb2pose_.

Referenced by core::pose::PDBInfo::copy(), and core::pose::PDBInfo::delete_res().

void core::pose::PDBPoseMap::fill

(

PDBInfo const &

info

)

fill with corresponding pdb -> pose residue mapping

Note

does not clear any currently existing mapping data

References core::pose::PDBInfo::chain(), core::pose::PDBInfo::icode(), insert(), core::pose::PDBInfo::nres(), and core::pose::PDBInfo::number().

Referenced by PDBPoseMap(), and core::pose::PDBInfo::rebuild_pdb2pose().

Size core::pose::PDBPoseMap::find ( char const  chain, int const  pdb_res, char const  ins_code = ' '  ) const

inline

lookup pose numbering

Parameters

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

Returns

pose numbering for residue, returns 0 if not found

References pdb2pose_.

Referenced by core::pose::PDBInfo::pdb2pose().

void core::pose::PDBPoseMap::insert	(	char const	chain,
		int const	pdb_res,
		char const	ins_code,
		Size const	pose_res
	)

insert pdb -> pose number mapping

Parameters

[in]	chain	chain id
[in]	pdb_res	pdb residue numbering
[in]	ins_code	insertion code, use ' ' if no insertion code
[in]	pose_res	pose numbering for residue

Remarks

if the chain is equal to the PDBInfo's empty record character, the insertion will be skipped

References core::pose::PDBInfo::empty_record(), and pdb2pose_.

Referenced by core::pose::PDBInfo::append_res(), core::pose::PDBInfo::chain(), core::pose::PDBInfo::copy(), core::pose::PDBInfo::delete_res(), fill(), core::pose::PDBInfo::icode(), core::pose::PDBInfo::number(), core::pose::PDBInfo::prepend_res(), and core::pose::PDBInfo::set_resinfo().

PDBPoseMap & core::pose::PDBPoseMap::operator=

(

PDBPoseMap const &

m

)

copy assignment

References pdb2pose_.

Size core::pose::PDBPoseMap::size ( ) const

inline

number of mappings

References pdb2pose_.

Member Data Documentation

Pdb2Pose core::pose::PDBPoseMap::pdb2pose_

private

maps ResidueKey -> Pose internal numbering

Referenced by clear(), conditional_erase(), erase(), find(), insert(), operator=(), and size().

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

• symlinks/rosetta/src/core/pose/PDBPoseMap.hh
• symlinks/rosetta/src/core/pose/PDBPoseMap.cc