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>

Inheritance diagram for core::pose::PDBPoseMap:

Collaboration diagram for core::pose::PDBPoseMap:

List of all members.

Classes
struct	ResidueKey
	sortable residue key internal to PDBPoseMap
Public Types
typedef core::Size	Size
Public Member Functions
	PDBPoseMap ()
	default constructor
	PDBPoseMap (PDBInfo const &info)
	PDBInfo constructor.
	PDBPoseMap (PDBPoseMap const &map)
	copy constructor
virtual	~PDBPoseMap ()
	default destructor
PDBPoseMap &	operator= (PDBPoseMap const &m)
	copy assignment
Size	size () const
	number of mappings
Size	find (char const chain, int const pdb_res, char const ins_code= ' ') const
	lookup pose numbering
void	insert (char const chain, int const pdb_res, char const ins_code, Size const pose_res)
	insert pdb -> pose number mapping
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
void	erase (char const chain, int const pdb_res, char const ins_code)
	forcibly remove mapping for pdb residue key
void	clear ()
	clear the current mapping data
void	fill (PDBInfo const &info)
	fill with corresponding pdb -> pose residue mapping

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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.

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Member Typedef Documentation

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

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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

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Member Function Documentation

void core::pose::PDBPoseMap::clear

(

)

[inline]

clear the current mapping data

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

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

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

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::pose::PDBInfo::pdb2pose(), and protocols::anchored_design::Anchor::read_anchorfile().

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().

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

Size core::pose::PDBPoseMap::size

(

)

const [inline]

number of mappings

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

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