MMCifInfo Class Reference

container class for additional information from MMCif files More...

#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	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)
MMCifInfoRevisions	GetRevisions () const
	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	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)
MMCifInfoRevisions	GetRevisions () const

---

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 869 of file mmcif_info.hh.

---

Constructor & Destructor Documentation

MMCifInfo

(

)

[inline]

Create an info object.

Definition at line 872 of file mmcif_info.hh.

MMCifInfo

(

)

[inline]

Create an info object.

Definition at line 872 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

)

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 877 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 877 of file mmcif_info.hh.

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 991 of file mmcif_info.hh.

void AddOperation

(

MMCifInfoTransOpPtr

op

)

[inline]

Add a operation.

Parameters:

op

operation to be added

Definition at line 991 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
	)			[inline]

Add a revision to history.

Parameters:

	num	unique identifier
	date	date of revision
	status	status of the revision

Definition at line 1054 of file mmcif_info.hh.

void AddRevision	(	int	num,
		String	date,
		String	status
	)			[inline]

Add a revision to history.

Parameters:

	num	unique identifier
	date	date of revision
	status	status of the revision

Definition at line 1054 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 983 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 983 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 891 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 891 of file mmcif_info.hh.

const StringRef GetMethod

(

)

const [inline]

Get an experimental method.

Returns:

Method description

Definition at line 904 of file mmcif_info.hh.

const StringRef GetMethod

(

)

const [inline]

Get an experimental method.

Returns:

Method description

Definition at line 904 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 1031 of file mmcif_info.hh.

MMCifInfoObsolete GetObsoleteInfo

(

)

const [inline]

Get information on an obsolete entries.

Returns:

MMCifInfoObsolete object

Definition at line 1031 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 999 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 999 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 917 of file mmcif_info.hh.

Real GetResolution

(

)

const [inline]

Get resolution.

Returns:

experiment resolution

Definition at line 917 of file mmcif_info.hh.

MMCifInfoRevisions GetRevisions

(

)

const [inline]

Get history.

Returns:

MMCifInfoRevisions

Definition at line 1062 of file mmcif_info.hh.

MMCifInfoRevisions GetRevisions

(

)

const [inline]

Get history.

Returns:

MMCifInfoRevisions

Definition at line 1062 of file mmcif_info.hh.

Real GetRFree

(

)

const [inline]

Get R-free value.

Returns:

experiment R-free value

Definition at line 927 of file mmcif_info.hh.

Real GetRFree

(

)

const [inline]

Get R-free value.

Returns:

experiment R-free value

Definition at line 927 of file mmcif_info.hh.

Real GetRWork

(

)

const [inline]

Get R-work value.

Returns:

experiment R-work value

Definition at line 937 of file mmcif_info.hh.

Real GetRWork

(

)

const [inline]

Get R-work value.

Returns:

experiment R-work value

Definition at line 937 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 1015 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 1015 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs

(

)

const [inline]

Definition at line 1035 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs

(

)

const [inline]

Definition at line 1035 of file mmcif_info.hh.

void SetMethod

(

String

method

)

[inline]

Set an experimental method.

Parameters:

method

Method description

Definition at line 899 of file mmcif_info.hh.

void SetMethod

(

String

method

)

[inline]

Set an experimental method.

Parameters:

method

Method description

Definition at line 899 of file mmcif_info.hh.

void SetObsoleteInfo

(

MMCifInfoObsolete

obsolete

)

[inline]

Add a block of information on obsolete entries.

Parameters:

obsolete

Definition at line 1023 of file mmcif_info.hh.

void SetObsoleteInfo

(

MMCifInfoObsolete

obsolete

)

[inline]

Add a block of information on obsolete entries.

Parameters:

obsolete

Definition at line 1023 of file mmcif_info.hh.

void SetResolution

(

Real

res

)

[inline]

Set resolution.

Parameters:

res

experiment resolution

Definition at line 912 of file mmcif_info.hh.

void SetResolution

(

Real

res

)

[inline]

Set resolution.

Parameters:

res

experiment resolution

Definition at line 912 of file mmcif_info.hh.

void SetRevisionsDateOriginal

(

String

date

)

[inline]

Set date_original of revisions.

Parameters:

date

Definition at line 1041 of file mmcif_info.hh.

void SetRevisionsDateOriginal

(

String

date

)

[inline]

Set date_original of revisions.

Parameters:

date

Definition at line 1041 of file mmcif_info.hh.

void SetRFree

(

Real

r_free

)

[inline]

Set R-free value.

Parameters:

res

experiment R-free value

Definition at line 922 of file mmcif_info.hh.

void SetRFree

(

Real

r_free

)

[inline]

Set R-free value.

Parameters:

res

experiment R-free value

Definition at line 922 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 932 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 932 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 1007 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 1007 of file mmcif_info.hh.

void SetStructRefs

(

const MMCifInfoStructRefs &

sr

)

[inline]

Definition at line 1036 of file mmcif_info.hh.

void SetStructRefs

(

const MMCifInfoStructRefs &

sr

)

[inline]

Definition at line 1036 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