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)
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 ()
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)
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 ()
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 991 of file mmcif_info.hh.

Constructor & Destructor Documentation

MMCifInfo ( )

inline

Create an info object.

Definition at line 994 of file mmcif_info.hh.

MMCifInfo ( )

inline

Create an info object.

Definition at line 994 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 1000 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 1000 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 1125 of file mmcif_info.hh.

void AddOperation ( MMCifInfoTransOpPtr  op )

inline

Add a operation.

Parameters

op	operation to be added

Definition at line 1125 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 1185 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 1185 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 1117 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 1117 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 1015 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 1015 of file mmcif_info.hh.

Real GetEMResolution ( ) const

inline

Get EM resolution.

Returns

EM experiment resolution

Definition at line 1051 of file mmcif_info.hh.

Real GetEMResolution ( ) const

inline

Get EM resolution.

Returns

EM experiment resolution

Definition at line 1051 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 MMCifEntityDesc& GetEntityDesc

(

const String &

entity_id

)

const

const MMCifEntityDesc& GetEntityDesc

(

const String &

entity_id

)

const

std::vector<String> GetEntityIds

(

)

const

std::vector<String> GetEntityIds

(

)

const

std::vector<String> GetEntityIdsOfType

(

const String &

type

)

const

std::vector<String> GetEntityIdsOfType

(

const String &

type

)

const

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns

Method description

Definition at line 1028 of file mmcif_info.hh.

const StringRef GetMethod ( ) const

inline

Get an experimental method.

Returns

Method description

Definition at line 1028 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 1165 of file mmcif_info.hh.

MMCifInfoObsolete GetObsoleteInfo ( ) const

inline

Get information on an obsolete entries.

Returns

MMCifInfoObsolete object

Definition at line 1165 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 1133 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 1133 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 1041 of file mmcif_info.hh.

Real GetResolution ( ) const

inline

Get resolution.

Returns

experiment resolution

Definition at line 1041 of file mmcif_info.hh.

MMCifInfoRevisions GetRevisions ( ) const

inline

Get history.

Returns

MMCifInfoRevisions

Definition at line 1194 of file mmcif_info.hh.

MMCifInfoRevisions GetRevisions ( ) const

inline

Get history.

Returns

MMCifInfoRevisions

Definition at line 1194 of file mmcif_info.hh.

Real GetRFree ( ) const

inline

Get R-free value.

Returns

experiment R-free value

Definition at line 1061 of file mmcif_info.hh.

Real GetRFree ( ) const

inline

Get R-free value.

Returns

experiment R-free value

Definition at line 1061 of file mmcif_info.hh.

Real GetRWork ( ) const

inline

Get R-work value.

Returns

experiment R-work value

Definition at line 1071 of file mmcif_info.hh.

Real GetRWork ( ) const

inline

Get R-work value.

Returns

experiment R-work value

Definition at line 1071 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 1149 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 1149 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 1169 of file mmcif_info.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const

inline

Definition at line 1169 of file mmcif_info.hh.

void SetEMResolution ( Real  res )

inline

Set EM resolution.

Parameters

res	EM experiment resolution

Definition at line 1046 of file mmcif_info.hh.

void SetEMResolution ( Real  res )

inline

Set EM resolution.

Parameters

res	EM experiment resolution

Definition at line 1046 of file mmcif_info.hh.

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

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

void SetMethod ( String  method )

inline

Set an experimental method.

Parameters

method

Method description

Definition at line 1023 of file mmcif_info.hh.

void SetMethod ( String  method )

inline

Set an experimental method.

Parameters

method

Method description

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 1157 of file mmcif_info.hh.

void SetObsoleteInfo ( MMCifInfoObsolete  obsolete )

inline

Add a block of information on obsolete entries.

Parameters

obsolete

Definition at line 1157 of file mmcif_info.hh.

void SetResolution ( Real  res )

inline

Set resolution.

Parameters

res	experiment resolution

Definition at line 1036 of file mmcif_info.hh.

void SetResolution ( Real  res )

inline

Set resolution.

Parameters

res	experiment resolution

Definition at line 1036 of file mmcif_info.hh.

void SetRevisionsDateOriginal ( String  date )

inline

Set date_original of revisions.

Parameters

date

Definition at line 1175 of file mmcif_info.hh.

void SetRevisionsDateOriginal ( String  date )

inline

Set date_original of revisions.

Parameters

date

Definition at line 1175 of file mmcif_info.hh.

void SetRFree ( Real  r_free )

inline

Set R-free value.

Parameters

res	experiment R-free value

Definition at line 1056 of file mmcif_info.hh.

void SetRFree ( Real  r_free )

inline

Set R-free value.

Parameters

res	experiment R-free value

Definition at line 1056 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 1066 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 1066 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 1141 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 1141 of file mmcif_info.hh.

void SetStructRefs ( const MMCifInfoStructRefs &  sr )

inline

Definition at line 1170 of file mmcif_info.hh.

void SetStructRefs ( const MMCifInfoStructRefs &  sr )

inline

Definition at line 1170 of file mmcif_info.hh.

---

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

• build-2.7-doc/stage/include/ost/io/mmcif_info.hh
• build-2.7-doc/stage/include/ost/io/mol/mmcif_info.hh