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:

Classes
struct	no_segID_comp
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...
	~PDBPoseMap () override
	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=' ', std::string const &segmentID=" ") const
	lookup pose numbering More...
void	insert (char const chain, int const pdb_res, char const ins_code, std::string const &segmentID, Size const pose_res)
	insert pdb -> pose number mapping More...
bool	conditional_erase (char const chain, int const pdb_res, char const ins_code, std::string const &segmentID, 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, std::string const &segmentID=" ")
	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::VirtualBase	Super

Private Attributes
std::map< ResidueKey, Size >	pdb2pose_
	maps ResidueKey -> Pose internal numbering More...
std::map< ResidueKey, Size, no_segID_comp >	pdb2pose_noSegmentIDs_

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.

Warning

danpf.nosp@m.@uw..nosp@m.edu – In order to avoid breaking workflows I added a secondary map that tracks the map<ResidueKey, Size> without the segmentID field being checked. This is sort of a strange if you use segmentIDs, but if you don't you won't notice any differences.

Member Typedef Documentation

Size

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

Super

typedef utility::VirtualBase core::pose::PDBPoseMap::Super

private

Constructor & Destructor Documentation

PDBPoseMap() [1/3]

core::pose::PDBPoseMap::PDBPoseMap

(

)

default constructor

PDBPoseMap() [2/3]

core::pose::PDBPoseMap::PDBPoseMap

(

PDBInfo const &

info

)

PDBInfo constructor.

References fill().

PDBPoseMap() [3/3]

core::pose::PDBPoseMap::PDBPoseMap ( PDBPoseMap const &  map )

default

copy constructor

~PDBPoseMap()

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

overridedefault

default destructor

Member Function Documentation

clear()

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

inline

clear the current mapping data

References pdb2pose_, and pdb2pose_noSegmentIDs_.

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

conditional_erase()

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

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_, and pdb2pose_noSegmentIDs_.

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

erase()

void core::pose::PDBPoseMap::erase	(	char const	chain,
		int const	pdb_res,
		char const	ins_code,
		std::string const &	segmentID = "    "
	)

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_, and pdb2pose_noSegmentIDs_.

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

fill()

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(), core::pose::PDBInfo::number(), and core::pose::PDBInfo::segmentID().

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

find()

Size core::pose::PDBPoseMap::find	(	char const	chain,
		int const	pdb_res,
		char const	ins_code = ' ',
		std::string const &	segmentID = "    "
	)		const

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

Warning

this will default to return the no-segmentID version if we can't find it!

References pdb2pose_, and pdb2pose_noSegmentIDs_.

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::motifs::bpdefs2map(), protocols::motifs::defs2allowedtypes(), protocols::motifs::defs2map(), protocols::motifs::defs2vector(), protocols::motifs::make_dna_mutations(), core::pose::PDBInfo::pdb2pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), and protocols::anchored_design::Anchor::read_anchorfile().

insert()

void core::pose::PDBPoseMap::insert	(	char const	chain,
		int const	pdb_res,
		char const	ins_code,
		std::string const &	segmentID,
		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(), pdb2pose_, and pdb2pose_noSegmentIDs_.

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().

operator=()

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

(

PDBPoseMap const &

m

)

copy assignment

References pdb2pose_, and pdb2pose_noSegmentIDs_.

size()

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

inline

number of mappings

References pdb2pose_.

Member Data Documentation

pdb2pose_

std::map< ResidueKey, Size > core::pose::PDBPoseMap::pdb2pose_

private

maps ResidueKey -> Pose internal numbering

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

pdb2pose_noSegmentIDs_

std::map< ResidueKey, Size, no_segID_comp> core::pose::PDBPoseMap::pdb2pose_noSegmentIDs_

private

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

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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