#include <mmcif_info.hh>

Public Member Functions
	MMCifInfo ()

void	AddCitation (MMCifInfoCitation citation)

void	AddAuthorsToCitation (StringRef id, std::vector< String > list, bool fault_tolerant=false)

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

void	SetMethod (String method)

const StringRef	GetMethod () const

void	SetResolution (Real res)

Real	GetResolution () const

void	SetRFree (Real r_free)

Real	GetRFree () const

void	SetRWork (Real r_work)

Real	GetRWork () const

void	AddMMCifPDBChainTr (String cif, String pdb)

String	GetMMCifPDBChainTr (String cif) const

void	AddPDBMMCifChainTr (String pdb, String cif)

String	GetPDBMMCifChainTr (String pdb) const

void	AddMMCifEntityIdTr (String cif, String ent_id)

String	GetMMCifEntityIdTr (String cif) 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)

void	SetRevisionsDateOriginal (String date)

void	AddRevision (int num, String date, String status, int major=-1, int minor=-1)

MMCifInfoRevisions	GetRevisions () const

void	AddEntityBranchLink (String chain_name, mol::AtomHandle atom1, mol::AtomHandle atom2, unsigned char bond_order)

const std::vector < MMCifInfoEntityBranchLink >	GetEntityBranchLinks () const

const std::vector < MMCifInfoEntityBranchLink >	GetEntityBranchByChain (const String &chain_name) const

const std::vector< String >	GetEntityBranchChainNames () const

const mol::ChainHandleList	GetEntityBranchChains () const

void	ConnectBranchLinks ()

	MMCifInfo ()

void	AddCitation (MMCifInfoCitation citation)

void	AddAuthorsToCitation (StringRef id, std::vector< String > list, bool fault_tolerant=false)

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

void	SetMethod (String method)

const StringRef	GetMethod () const

void	SetResolution (Real res)

Real	GetResolution () const

void	SetRFree (Real r_free)

Real	GetRFree () const

void	SetRWork (Real r_work)

Real	GetRWork () const

void	AddMMCifPDBChainTr (String cif, String pdb)

String	GetMMCifPDBChainTr (String cif) const

void	AddPDBMMCifChainTr (String pdb, String cif)

String	GetPDBMMCifChainTr (String pdb) const

void	AddMMCifEntityIdTr (String cif, String ent_id)

String	GetMMCifEntityIdTr (String cif) 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)

void	SetRevisionsDateOriginal (String date)

void	AddRevision (int num, String date, String status, int major=-1, int minor=-1)

MMCifInfoRevisions	GetRevisions () const

void	AddEntityBranchLink (String chain_name, mol::AtomHandle atom1, mol::AtomHandle atom2, unsigned char bond_order)

const std::vector < MMCifInfoEntityBranchLink >	GetEntityBranchLinks () const

const std::vector < MMCifInfoEntityBranchLink >	GetEntityBranchByChain (const String &chain_name) const

const std::vector< String >	GetEntityBranchChainNames () const

const mol::ChainHandleList	GetEntityBranchChains () const

void	ConnectBranchLinks ()

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 975 of file mmcif_info.hh.

Constructor & Destructor Documentation

MMCifInfo ( )

inline

Create an info object.

Definition at line 978 of file mmcif_info.hh.

MMCifInfo ( )

inline

Create an info object.

Definition at line 978 of file mmcif_info.hh.

Member Function Documentation

void AddAuthorsToCitation	(	StringRef	id,
		std::vector< String >	list,
		bool	fault_tolerant = `false`
	)

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,
		bool	fault_tolerant = `false`
	)

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 )

Add a biounit.

Parameters

bu	biounit to be added

void AddBioUnit ( MMCifInfoBioUnit bu )

Add a biounit.

Parameters

bu	biounit to be added

void AddCitation ( MMCifInfoCitation citation )

inline

Add an item to the list of citations.

Parameters

citation to be added

Definition at line 983 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 983 of file mmcif_info.hh.

void AddEntityBranchLink	(	String	chain_name,
		mol::AtomHandle	atom1,
		mol::AtomHandle	atom2,
		unsigned char	bond_order
	)

Add bond information for a branched entity.

Parameters

chain_name	chain the bond belongs to
atom1	first atom of the bond
atom2	second atom of the bond

void AddEntityBranchLink	(	String	chain_name,
		mol::AtomHandle	atom1,
		mol::AtomHandle	atom2,
		unsigned char	bond_order
	)

Add bond information for a branched entity.

Parameters

chain_name	chain the bond belongs to
atom1	first atom of the bond
atom2	second atom of the bond

void AddMMCifEntityIdTr	(	String	cif,
		String	ent_id
	)

Add a new mmCIF chain name / entity ID tuple.

Parameters

cif	chain name as used by the mmCIF file (label_asym_id)
ent_id	entity ID as used by the mmCIF file (label_entity_id)

void AddMMCifEntityIdTr	(	String	cif,
		String	ent_id
	)

Add a new mmCIF chain name / entity ID tuple.

Parameters

cif	chain name as used by the mmCIF file (label_asym_id)
ent_id	entity ID as used by the mmCIF file (label_entity_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 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 1098 of file mmcif_info.hh.

void AddOperation ( MMCifInfoTransOpPtr op )

inline

Add a operation.

Parameters

op	operation to be added

Definition at line 1098 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)

void AddRevision	(	int	num,
		String	date,
		String	status,
		int	major = `-1`,
		int	minor = `-1`
	)

inline

Add a revision to history.

See Also: MMCifInfoRevisions::AddRevision

Definition at line 1158 of file mmcif_info.hh.

void AddRevision	(	int	num,
		String	date,
		String	status,
		int	major = `-1`,
		int	minor = `-1`
	)

inline

Add a revision to history.

See Also: MMCifInfoRevisions::AddRevision

Definition at line 1158 of file mmcif_info.hh.

void ConnectBranchLinks ( )

Connect all atoms listed as links for branched entities.

void ConnectBranchLinks ( )

Connect all atoms listed as links for branched entities.

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 1090 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 1090 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 998 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 998 of file mmcif_info.hh.

const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchByChain ( const String & chain_name ) const

Check if a chain is a branched entity and return it.

Parameters

chain_name Name of the chain to check

const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchByChain ( const String & chain_name ) const

Check if a chain is a branched entity and return it.

Parameters

chain_name Name of the chain to check

const std::vector<String> GetEntityBranchChainNames ( ) const

Get the names of all chains of branched entities.

const std::vector<String> GetEntityBranchChainNames ( ) const

Get the names of all chains of branched entities.

const mol::ChainHandleList GetEntityBranchChains ( ) const

Get the all chains of branched entities.

const mol::ChainHandleList GetEntityBranchChains ( ) const

Get the all chains of branched entities.

const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchLinks ( ) const

Get all links for all branched entities.

const std::vector<MMCifInfoEntityBranchLink> GetEntityBranchLinks ( ) const

Get all links for all branched entities.

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns: Method description

Definition at line 1011 of file mmcif_info.hh.

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns: Method description

Definition at line 1011 of file mmcif_info.hh.

String GetMMCifEntityIdTr ( String cif ) const

Get the entity ID for a CIF chain name.

Parameters

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

Returns: entity ID as used by the mmCIF file (label_entity_id)

String GetMMCifEntityIdTr ( String cif ) const

Get the entity ID for a CIF chain name.

Parameters

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

Returns: entity ID as used by the mmCIF file (label_entity_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)

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 1138 of file mmcif_info.hh.

MMCifInfoObsolete GetObsoleteInfo ( ) const

inline

Get information on an obsolete entries.

Returns: MMCifInfoObsolete object

Definition at line 1138 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 1106 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 1106 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 1024 of file mmcif_info.hh.

Real GetResolution ( ) const

inline

Get resolution.

Returns: experiment resolution

Definition at line 1024 of file mmcif_info.hh.

MMCifInfoRevisions GetRevisions ( ) const

inline

Get history.

Returns: MMCifInfoRevisions

Definition at line 1167 of file mmcif_info.hh.

MMCifInfoRevisions GetRevisions ( ) const

inline

Get history.

Returns: MMCifInfoRevisions

Definition at line 1167 of file mmcif_info.hh.

Real GetRFree ( ) const

inline

Get R-free value.

Returns: experiment R-free value

Definition at line 1034 of file mmcif_info.hh.

Real GetRFree ( ) const

inline

Get R-free value.

Returns: experiment R-free value

Definition at line 1034 of file mmcif_info.hh.

Real GetRWork ( ) const

inline

Get R-work value.

Returns: experiment R-work value

Definition at line 1044 of file mmcif_info.hh.

Real GetRWork ( ) const

inline

Get R-work value.

Returns: experiment R-work value

Definition at line 1044 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 1122 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 1122 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 1142 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 1142 of file mmcif_info.hh.

void SetMethod ( String method )

inline

Set an experimental method.

Parameters

method Method description

Definition at line 1006 of file mmcif_info.hh.

void SetMethod ( String method )

inline

Set an experimental method.

Parameters

method Method description

Definition at line 1006 of file mmcif_info.hh.

void SetObsoleteInfo ( MMCifInfoObsolete obsolete )

inline

Add a block of information on obsolete entries.

Parameters

obsolete

Definition at line 1130 of file mmcif_info.hh.

void SetObsoleteInfo ( MMCifInfoObsolete obsolete )

inline

Add a block of information on obsolete entries.

Parameters

obsolete

Definition at line 1130 of file mmcif_info.hh.

void SetResolution ( Real res )

inline

Set resolution.

Parameters

res	experiment resolution

Definition at line 1019 of file mmcif_info.hh.

void SetResolution ( Real res )

inline

Set resolution.

Parameters

res	experiment resolution

Definition at line 1019 of file mmcif_info.hh.

void SetRevisionsDateOriginal ( String date )

inline

Set date_original of revisions.

Parameters

date

Definition at line 1148 of file mmcif_info.hh.

void SetRevisionsDateOriginal ( String date )

inline

Set date_original of revisions.

Parameters

date

Definition at line 1148 of file mmcif_info.hh.

void SetRFree ( Real r_free )

inline

Set R-free value.

Parameters

res	experiment R-free value

Definition at line 1029 of file mmcif_info.hh.

void SetRFree ( Real r_free )

inline

Set R-free value.

Parameters

res	experiment R-free value

Definition at line 1029 of file mmcif_info.hh.

void SetRWork ( Real r_work )

inline

Set R-work value.

Parameters

r_work experiment R-work value

Definition at line 1039 of file mmcif_info.hh.

void SetRWork ( Real r_work )

inline

Set R-work value.

Parameters

r_work experiment R-work value

Definition at line 1039 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 1114 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 1114 of file mmcif_info.hh.

void SetStructRefs ( const MMCifInfoStructRefs & sr )

inline

Definition at line 1143 of file mmcif_info.hh.

void SetStructRefs ( const MMCifInfoStructRefs & sr )

inline

Definition at line 1143 of file mmcif_info.hh.

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

build-2.6/stage/include/ost/io/mmcif_info.hh
build-2.6/stage/include/ost/io/mol/mmcif_info.hh

Public Member Functions

Detailed Description

annotation information

Constructor & Destructor Documentation

Member Function Documentation