#include <mmcif_info.hh>

Public Member Functions
	MMCifInfo ()
void	AddCitation (MMCifInfoCitation citation)
void	AddAuthorsToCitation (StringRef id, std::vector< String > list)
const std::vector < MMCifInfoCitation > &	GetCitations () const
void	SetMethod (String method)
const StringRef	GetMethod () const
void	SetResolution (Real res)
Real	GetResolution () const
void	AddMMCifPDBChainTr (String cif, String pdb)
String	GetMMCifPDBChainTr (String cif) const
void	AddPDBMMCifChainTr (String pdb, String cif)
String	GetPDBMMCifChainTr (String pdb) const
void	AddBioUnit (MMCifInfoBioUnit bu)
const std::vector < MMCifInfoBioUnit > &	GetBioUnits () const
void	AddOperation (MMCifInfoTransOpPtr op)
const std::vector < MMCifInfoTransOpPtr > &	GetOperations () const
void	SetStructDetails (MMCifInfoStructDetails details)
const MMCifInfoStructDetails	GetStructDetails () const
void	SetObsoleteInfo (MMCifInfoObsolete obsolete)
MMCifInfoObsolete	GetObsoleteInfo () const
const MMCifInfoStructRefs &	GetStructRefs () const
void	SetStructRefs (const MMCifInfoStructRefs &sr)
	MMCifInfo ()
void	AddCitation (MMCifInfoCitation citation)
void	AddAuthorsToCitation (StringRef id, std::vector< String > list)
const std::vector < MMCifInfoCitation > &	GetCitations () const
void	SetMethod (String method)
const StringRef	GetMethod () const
void	SetResolution (Real res)
Real	GetResolution () const
void	AddMMCifPDBChainTr (String cif, String pdb)
String	GetMMCifPDBChainTr (String cif) const
void	AddPDBMMCifChainTr (String pdb, String cif)
String	GetPDBMMCifChainTr (String pdb) const
void	AddBioUnit (MMCifInfoBioUnit bu)
const std::vector < MMCifInfoBioUnit > &	GetBioUnits () const
void	AddOperation (MMCifInfoTransOpPtr op)
const std::vector < MMCifInfoTransOpPtr > &	GetOperations () const
void	SetStructDetails (MMCifInfoStructDetails details)
const MMCifInfoStructDetails	GetStructDetails () const
void	SetObsoleteInfo (MMCifInfoObsolete obsolete)
MMCifInfoObsolete	GetObsoleteInfo () const
const MMCifInfoStructRefs &	GetStructRefs () const
void	SetStructRefs (const MMCifInfoStructRefs &sr)

Detailed Description

container class for additional information from MMCif files

annotation information

MMCif files contain loads of additional information beside coordinates. This class is set up to capture some of it. In detail, we have:

citations
biounits
transformation information from asym. unit to biounit
structure information
resolution
method

Definition at line 725 of file mmcif_info.hh.

Constructor & Destructor Documentation

MMCifInfo ( )

inline

Create an info object.

Definition at line 728 of file mmcif_info.hh.

MMCifInfo ( )

inline

Create an info object.

Definition at line 728 of file mmcif_info.hh.

Member Function Documentation

void AddAuthorsToCitation	(	StringRef	id,
		std::vector< String >	list
	)

Add a list of authors to a specific citation.

Parameters:

id	identifier of the citation to be modified.
list	list of authors to be added.

void AddAuthorsToCitation	(	StringRef	id,
		std::vector< String >	list
	)

Add a list of authors to a specific citation.

Parameters:

id	identifier of the citation to be modified.
list	list of authors to be added.

void AddBioUnit ( MMCifInfoBioUnit bu )

inline

Add a biounit.

Parameters:

bu	biounit to be added

Definition at line 802 of file mmcif_info.hh.

void AddBioUnit ( MMCifInfoBioUnit bu )

inline

Add a biounit.

Parameters:

bu	biounit to be added

Definition at line 802 of file mmcif_info.hh.

void AddCitation ( MMCifInfoCitation citation )

inline

Add an item to the list of citations.

Parameters:

citation to be added

Definition at line 733 of file mmcif_info.hh.

void AddCitation ( MMCifInfoCitation citation )

inline

Add an item to the list of citations.

Parameters:

citation to be added

Definition at line 733 of file mmcif_info.hh.

void AddMMCifPDBChainTr	(	String	cif,
		String	pdb
	)

Add a new mmCIF/ PDB chain name tuple.

Parameters:

cif	chain name as used by the mmCIF file (label_asym_id)
pdb	chain name as used in the PDB file (auth_asym_id)

void AddMMCifPDBChainTr	(	String	cif,
		String	pdb
	)

Add a new mmCIF/ PDB chain name tuple.

Parameters:

cif	chain name as used by the mmCIF file (label_asym_id)
pdb	chain name as used in the PDB file (auth_asym_id)

void AddOperation ( MMCifInfoTransOpPtr op )

inline

Add a operation.

Parameters:

op	operation to be added

Definition at line 818 of file mmcif_info.hh.

void AddOperation ( MMCifInfoTransOpPtr op )

inline

Add a operation.

Parameters:

op	operation to be added

Definition at line 818 of file mmcif_info.hh.

void AddPDBMMCifChainTr	(	String	pdb,
		String	cif
	)

Add a new PDB/ mmCIF chain name tuple.

Parameters:

pdb	chain name as used by the PDB file (auth_asym_id)
cif	chain name as used in the mmCIF file (label_asym_id)

void AddPDBMMCifChainTr	(	String	pdb,
		String	cif
	)

Add a new PDB/ mmCIF chain name tuple.

Parameters:

pdb	chain name as used by the PDB file (auth_asym_id)
cif	chain name as used in the mmCIF file (label_asym_id)

const std::vector<MMCifInfoBioUnit>& GetBioUnits ( ) const

inline

Get the list of biounits stored in an info object.

Returns:: vector of MMCifInfoBioUnit objects

Definition at line 810 of file mmcif_info.hh.

const std::vector<MMCifInfoBioUnit>& GetBioUnits ( ) const

inline

Get the list of biounits stored in an info object.

Returns:: vector of MMCifInfoBioUnit objects

Definition at line 810 of file mmcif_info.hh.

const std::vector<MMCifInfoCitation>& GetCitations ( ) const

inline

Get the list of citations stored in an info object.

Returns:: vector of MMCifInfoCitation objects

Definition at line 747 of file mmcif_info.hh.

const std::vector<MMCifInfoCitation>& GetCitations ( ) const

inline

Get the list of citations stored in an info object.

Returns:: vector of MMCifInfoCitation objects

Definition at line 747 of file mmcif_info.hh.

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns:: Method description

Definition at line 760 of file mmcif_info.hh.

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns:: Method description

Definition at line 760 of file mmcif_info.hh.

String GetMMCifPDBChainTr ( String cif ) const

Get a PDB chain name for a CIF chain name.

Parameters:

cif	chain name as used by the mmCIF file (label_asym_id)

Returns:: chain name as used in the PDB file (auth_asym_id)

String GetMMCifPDBChainTr ( String cif ) const

Get a PDB chain name for a CIF chain name.

Parameters:

cif	chain name as used by the mmCIF file (label_asym_id)

Returns:: chain name as used in the PDB file (auth_asym_id)

MMCifInfoObsolete GetObsoleteInfo ( ) const

inline

Get information on an obsolete entries.

Returns:: MMCifInfoObsolete object

Definition at line 858 of file mmcif_info.hh.

MMCifInfoObsolete GetObsoleteInfo ( ) const

inline

Get information on an obsolete entries.

Returns:: MMCifInfoObsolete object

Definition at line 858 of file mmcif_info.hh.

const std::vector<MMCifInfoTransOpPtr>& GetOperations ( ) const

inline

Get the list of operations stored in an info object.

Returns:: vector of MMCifInfoTransOp objects

Definition at line 826 of file mmcif_info.hh.

const std::vector<MMCifInfoTransOpPtr>& GetOperations ( ) const

inline

Get the list of operations stored in an info object.

Returns:: vector of MMCifInfoTransOp objects

Definition at line 826 of file mmcif_info.hh.

String GetPDBMMCifChainTr ( String pdb ) const

Get a CIF chain name for a PDB chain name.

Parameters:

pdb	chain name as used by the mmCIF file (auth_asym_id)

Returns:: chain name as used in the PDB file (label_asym_id)

String GetPDBMMCifChainTr ( String pdb ) const

Get a CIF chain name for a PDB chain name.

Parameters:

pdb	chain name as used by the mmCIF file (auth_asym_id)

Returns:: chain name as used in the PDB file (label_asym_id)

Real GetResolution ( ) const

inline

Get resolution.

Returns:: experiment resolution

Definition at line 773 of file mmcif_info.hh.

Real GetResolution ( ) const

inline

Get resolution.

Returns:: experiment resolution

Definition at line 773 of file mmcif_info.hh.

const MMCifInfoStructDetails GetStructDetails ( ) const

inline

Get the list of details about structures.

Returns:: vector of MMCifInfoStructDetails objects

Definition at line 842 of file mmcif_info.hh.

const MMCifInfoStructDetails GetStructDetails ( ) const

inline

Get the list of details about structures.

Returns:: vector of MMCifInfoStructDetails objects

Definition at line 842 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 862 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 862 of file mmcif_info.hh.

void SetMethod ( String method )

inline

Set an experimental method.

Parameters:

method Method description

Definition at line 755 of file mmcif_info.hh.

void SetMethod ( String method )

inline

Set an experimental method.

Parameters:

method Method description

Definition at line 755 of file mmcif_info.hh.

void SetObsoleteInfo ( MMCifInfoObsolete obsolete )

inline

Add a block of information on obsolete entries.

Parameters:

obsolete

Definition at line 850 of file mmcif_info.hh.

void SetObsoleteInfo ( MMCifInfoObsolete obsolete )

inline

Add a block of information on obsolete entries.

Parameters:

obsolete

Definition at line 850 of file mmcif_info.hh.

void SetResolution ( Real res )

inline

Set resolution.

Parameters:

res	experiment resolution

Definition at line 768 of file mmcif_info.hh.

void SetResolution ( Real res )

inline

Set resolution.

Parameters:

res	experiment resolution

Definition at line 768 of file mmcif_info.hh.

void SetStructDetails ( MMCifInfoStructDetails details )

inline

Add a set of structure details.

Parameters:

details info block to be added

Definition at line 834 of file mmcif_info.hh.

void SetStructDetails ( MMCifInfoStructDetails details )

inline

Add a set of structure details.

Parameters:

details info block to be added

Definition at line 834 of file mmcif_info.hh.

void SetStructRefs ( const MMCifInfoStructRefs & sr )

inline

Definition at line 863 of file mmcif_info.hh.

void SetStructRefs ( const MMCifInfoStructRefs & sr )

inline

Definition at line 863 of file mmcif_info.hh.

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

stage/include/ost/io/mmcif_info.hh
stage/include/ost/io/mol/mmcif_info.hh

Public Member Functions

Detailed Description

annotation information

Constructor & Destructor Documentation

Member Function Documentation