MMCifInfo Class Reference

#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	SetEMResolution (Real res)
Real	GetEMResolution () const
void	SetRFree (Real r_free)
Real	GetRFree () const
void	SetRWork (Real r_work)
Real	GetRWork () const
void	AddMMCifPDBChainTr (String cif, String pdb, bool fault_tolerant=false)
String	GetMMCifPDBChainTr (String cif) const
void	AddPDBMMCifChainTr (String pdb, String cif, bool fault_tolerant=false)
String	GetPDBMMCifChainTr (String pdb) const
void	AddMMCifEntityIdTr (String cif, String ent_id, bool fault_tolerant=false)
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, int rnum1, int rnum2, const String &aname1, const String &aname2, unsigned char bond_order)
const std::vector< MMCifInfoEntityBranchLink >	GetEntityBranchByChain (const String &chain_name) const
const std::vector< String >	GetEntityBranchChainNames () const
const MMCifEntityDesc &	GetEntityDesc (const String &entity_id) const
void	SetEntityDesc (const String &entity_id, const MMCifEntityDesc &entity_desc)
std::vector< String >	GetEntityIds () const
std::vector< String >	GetEntityIdsOfType (const String &type) const
	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	SetEMResolution (Real res)
Real	GetEMResolution () const
void	SetRFree (Real r_free)
Real	GetRFree () const
void	SetRWork (Real r_work)
Real	GetRWork () const
void	AddMMCifPDBChainTr (String cif, String pdb, bool fault_tolerant=false)
String	GetMMCifPDBChainTr (String cif) const
void	AddPDBMMCifChainTr (String pdb, String cif, bool fault_tolerant=false)
String	GetPDBMMCifChainTr (String pdb) const
void	AddMMCifEntityIdTr (String cif, String ent_id, bool fault_tolerant=false)
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, int rnum1, int rnum2, const String &aname1, const String &aname2, unsigned char bond_order)
const std::vector< MMCifInfoEntityBranchLink >	GetEntityBranchByChain (const String &chain_name) const
const std::vector< String >	GetEntityBranchChainNames () const
const MMCifEntityDesc &	GetEntityDesc (const String &entity_id) const
void	SetEntityDesc (const String &entity_id, const MMCifEntityDesc &entity_desc)
std::vector< String >	GetEntityIds () const
std::vector< String >	GetEntityIdsOfType (const String &type) 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 982 of file mmcif_info.hh.

Constructor & Destructor Documentation

MMCifInfo() [1/2]

MMCifInfo ( )

inline

Create an info object.

Definition at line 985 of file mmcif_info.hh.

MMCifInfo() [2/2]

MMCifInfo ( )

inline

Create an info object.

Definition at line 985 of file mmcif_info.hh.

Member Function Documentation

AddAuthorsToCitation() [1/2]

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.

AddAuthorsToCitation() [2/2]

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.

AddBioUnit() [1/2]

void AddBioUnit

(

MMCifInfoBioUnit

bu

)

Add a biounit.

Parameters

bu	biounit to be added

AddBioUnit() [2/2]

void AddBioUnit

(

MMCifInfoBioUnit

bu

)

Add a biounit.

Parameters

bu	biounit to be added

AddCitation() [1/2]

void AddCitation ( MMCifInfoCitation  citation )

inline

Add an item to the list of citations.

Parameters

citation

to be added

Definition at line 991 of file mmcif_info.hh.

AddCitation() [2/2]

void AddCitation ( MMCifInfoCitation  citation )

inline

Add an item to the list of citations.

Parameters

citation

to be added

Definition at line 991 of file mmcif_info.hh.

AddEntityBranchLink() [1/2]

void AddEntityBranchLink	(	String	chain_name,
		int	rnum1,
		int	rnum2,
		const String &	aname1,
		const String &	aname2,
		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

AddEntityBranchLink() [2/2]

void AddEntityBranchLink	(	String	chain_name,
		int	rnum1,
		int	rnum2,
		const String &	aname1,
		const String &	aname2,
		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

AddMMCifEntityIdTr() [1/2]

void AddMMCifEntityIdTr	(	String	cif,
		String	ent_id,
		bool	fault_tolerant = false
	)

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)

AddMMCifEntityIdTr() [2/2]

void AddMMCifEntityIdTr	(	String	cif,
		String	ent_id,
		bool	fault_tolerant = false
	)

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)

AddMMCifPDBChainTr() [1/2]

void AddMMCifPDBChainTr	(	String	cif,
		String	pdb,
		bool	fault_tolerant = false
	)

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)

AddMMCifPDBChainTr() [2/2]

void AddMMCifPDBChainTr	(	String	cif,
		String	pdb,
		bool	fault_tolerant = false
	)

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)

AddOperation() [1/2]

void AddOperation ( MMCifInfoTransOpPtr  op )

inline

Add a operation.

Parameters

op	operation to be added

Definition at line 1119 of file mmcif_info.hh.

AddOperation() [2/2]

void AddOperation ( MMCifInfoTransOpPtr  op )

inline

Add a operation.

Parameters

op	operation to be added

Definition at line 1119 of file mmcif_info.hh.

AddPDBMMCifChainTr() [1/2]

void AddPDBMMCifChainTr	(	String	pdb,
		String	cif,
		bool	fault_tolerant = false
	)

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)

AddPDBMMCifChainTr() [2/2]

void AddPDBMMCifChainTr	(	String	pdb,
		String	cif,
		bool	fault_tolerant = false
	)

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)

AddRevision() [1/2]

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 1179 of file mmcif_info.hh.

AddRevision() [2/2]

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 1179 of file mmcif_info.hh.

GetBioUnits() [1/2]

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 1111 of file mmcif_info.hh.

GetBioUnits() [2/2]

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 1111 of file mmcif_info.hh.

GetCitations() [1/2]

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 1006 of file mmcif_info.hh.

GetCitations() [2/2]

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 1006 of file mmcif_info.hh.

GetEMResolution() [1/2]

Real GetEMResolution ( ) const

inline

Get EM resolution.

Returns

EM experiment resolution

Definition at line 1042 of file mmcif_info.hh.

GetEMResolution() [2/2]

Real GetEMResolution ( ) const

inline

Get EM resolution.

Returns

EM experiment resolution

Definition at line 1042 of file mmcif_info.hh.

GetEntityBranchByChain() [1/2]

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

GetEntityBranchByChain() [2/2]

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

GetEntityBranchChainNames() [1/2]

const std::vector<String> GetEntityBranchChainNames

(

)

const

Get the names of all chains of branched entities.

GetEntityBranchChainNames() [2/2]

const std::vector<String> GetEntityBranchChainNames

(

)

const

Get the names of all chains of branched entities.

GetEntityDesc() [1/2]

const MMCifEntityDesc& GetEntityDesc

(

const String &

entity_id

)

const

GetEntityDesc() [2/2]

const MMCifEntityDesc& GetEntityDesc

(

const String &

entity_id

)

const

GetEntityIds() [1/2]

std::vector<String> GetEntityIds

(

)

const

GetEntityIds() [2/2]

std::vector<String> GetEntityIds

(

)

const

GetEntityIdsOfType() [1/2]

std::vector<String> GetEntityIdsOfType

(

const String &

type

)

const

GetEntityIdsOfType() [2/2]

std::vector<String> GetEntityIdsOfType

(

const String &

type

)

const

GetMethod() [1/2]

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns

Method description

Definition at line 1019 of file mmcif_info.hh.

GetMethod() [2/2]

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns

Method description

Definition at line 1019 of file mmcif_info.hh.

GetMMCifEntityIdTr() [1/2]

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)

GetMMCifEntityIdTr() [2/2]

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)

GetMMCifPDBChainTr() [1/2]

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)

GetMMCifPDBChainTr() [2/2]

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)

GetObsoleteInfo() [1/2]

MMCifInfoObsolete GetObsoleteInfo ( ) const

inline

Get information on an obsolete entries.

Returns

MMCifInfoObsolete object

Definition at line 1159 of file mmcif_info.hh.

GetObsoleteInfo() [2/2]

MMCifInfoObsolete GetObsoleteInfo ( ) const

inline

Get information on an obsolete entries.

Returns

MMCifInfoObsolete object

Definition at line 1159 of file mmcif_info.hh.

GetOperations() [1/2]

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 1127 of file mmcif_info.hh.

GetOperations() [2/2]

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 1127 of file mmcif_info.hh.

GetPDBMMCifChainTr() [1/2]

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)

GetPDBMMCifChainTr() [2/2]

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)

GetResolution() [1/2]

Real GetResolution ( ) const

inline

Get resolution.

Returns

experiment resolution

Definition at line 1032 of file mmcif_info.hh.

GetResolution() [2/2]

Real GetResolution ( ) const

inline

Get resolution.

Returns

experiment resolution

Definition at line 1032 of file mmcif_info.hh.

GetRevisions() [1/2]

MMCifInfoRevisions GetRevisions ( ) const

inline

Get history.

Returns

MMCifInfoRevisions

Definition at line 1188 of file mmcif_info.hh.

GetRevisions() [2/2]

MMCifInfoRevisions GetRevisions ( ) const

inline

Get history.

Returns

MMCifInfoRevisions

Definition at line 1188 of file mmcif_info.hh.

GetRFree() [1/2]

Real GetRFree ( ) const

inline

Get R-free value.

Returns

experiment R-free value

Definition at line 1052 of file mmcif_info.hh.

GetRFree() [2/2]

Real GetRFree ( ) const

inline

Get R-free value.

Returns

experiment R-free value

Definition at line 1052 of file mmcif_info.hh.

GetRWork() [1/2]

Real GetRWork ( ) const

inline

Get R-work value.

Returns

experiment R-work value

Definition at line 1062 of file mmcif_info.hh.

GetRWork() [2/2]

Real GetRWork ( ) const

inline

Get R-work value.

Returns

experiment R-work value

Definition at line 1062 of file mmcif_info.hh.

GetStructDetails() [1/2]

const MMCifInfoStructDetails GetStructDetails ( ) const

inline

Get the list of details about structures.

Returns

vector of MMCifInfoStructDetails objects

Definition at line 1143 of file mmcif_info.hh.

GetStructDetails() [2/2]

const MMCifInfoStructDetails GetStructDetails ( ) const

inline

Get the list of details about structures.

Returns

vector of MMCifInfoStructDetails objects

Definition at line 1143 of file mmcif_info.hh.

GetStructRefs() [1/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 1163 of file mmcif_info.hh.

GetStructRefs() [2/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 1163 of file mmcif_info.hh.

SetEMResolution() [1/2]

void SetEMResolution ( Real  res )

inline

Set EM resolution.

Parameters

res	EM experiment resolution

Definition at line 1037 of file mmcif_info.hh.

SetEMResolution() [2/2]

void SetEMResolution ( Real  res )

inline

Set EM resolution.

Parameters

res	EM experiment resolution

Definition at line 1037 of file mmcif_info.hh.

SetEntityDesc() [1/2]

void SetEntityDesc	(	const String &	entity_id,
		const MMCifEntityDesc &	entity_desc
	)

SetEntityDesc() [2/2]

void SetEntityDesc	(	const String &	entity_id,
		const MMCifEntityDesc &	entity_desc
	)

SetMethod() [1/2]

void SetMethod ( String  method )

inline

Set an experimental method.

Parameters

method

Method description

Definition at line 1014 of file mmcif_info.hh.

SetMethod() [2/2]

void SetMethod ( String  method )

inline

Set an experimental method.

Parameters

method

Method description

Definition at line 1014 of file mmcif_info.hh.

SetObsoleteInfo() [1/2]

void SetObsoleteInfo ( MMCifInfoObsolete  obsolete )

inline

Add a block of information on obsolete entries.

Parameters

obsolete

Definition at line 1151 of file mmcif_info.hh.

SetObsoleteInfo() [2/2]

void SetObsoleteInfo ( MMCifInfoObsolete  obsolete )

inline

Add a block of information on obsolete entries.

Parameters

obsolete

Definition at line 1151 of file mmcif_info.hh.

SetResolution() [1/2]

void SetResolution ( Real  res )

inline

Set resolution.

Parameters

res	experiment resolution

Definition at line 1027 of file mmcif_info.hh.

SetResolution() [2/2]

void SetResolution ( Real  res )

inline

Set resolution.

Parameters

res	experiment resolution

Definition at line 1027 of file mmcif_info.hh.

SetRevisionsDateOriginal() [1/2]

void SetRevisionsDateOriginal ( String  date )

inline

Set date_original of revisions.

Parameters

date

Definition at line 1169 of file mmcif_info.hh.

SetRevisionsDateOriginal() [2/2]

void SetRevisionsDateOriginal ( String  date )

inline

Set date_original of revisions.

Parameters

date

Definition at line 1169 of file mmcif_info.hh.

SetRFree() [1/2]

void SetRFree ( Real  r_free )

inline

Set R-free value.

Parameters

res	experiment R-free value

Definition at line 1047 of file mmcif_info.hh.

SetRFree() [2/2]

void SetRFree ( Real  r_free )

inline

Set R-free value.

Parameters

res	experiment R-free value

Definition at line 1047 of file mmcif_info.hh.

SetRWork() [1/2]

void SetRWork ( Real  r_work )

inline

Set R-work value.

Parameters

r_work

experiment R-work value

Definition at line 1057 of file mmcif_info.hh.

SetRWork() [2/2]

void SetRWork ( Real  r_work )

inline

Set R-work value.

Parameters

r_work

experiment R-work value

Definition at line 1057 of file mmcif_info.hh.

SetStructDetails() [1/2]

void SetStructDetails ( MMCifInfoStructDetails  details )

inline

Add a set of structure details.

Parameters

details

info block to be added

Definition at line 1135 of file mmcif_info.hh.

SetStructDetails() [2/2]

void SetStructDetails ( MMCifInfoStructDetails  details )

inline

Add a set of structure details.

Parameters

details

info block to be added

Definition at line 1135 of file mmcif_info.hh.

SetStructRefs() [1/2]

void SetStructRefs ( const MMCifInfoStructRefs &  sr )

inline

Definition at line 1164 of file mmcif_info.hh.

SetStructRefs() [2/2]

void SetStructRefs ( const MMCifInfoStructRefs &  sr )

inline

Definition at line 1164 of file mmcif_info.hh.

---

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

• build-2.8-doc/stage/include/ost/io/mmcif_info.hh