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Public Member Functions
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:

Definition at line 983 of file mmcif_info.hh.

Constructor & Destructor Documentation

◆ MMCifInfo() [1/2]

MMCifInfo ( )
inline

Create an info object.

Definition at line 986 of file mmcif_info.hh.

◆ MMCifInfo() [2/2]

MMCifInfo ( )
inline

Create an info object.

Definition at line 986 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
ididentifier of the citation to be modified.
listlist 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
ididentifier of the citation to be modified.
listlist of authors to be added.

◆ AddBioUnit() [1/2]

void AddBioUnit ( MMCifInfoBioUnit  bu)

Add a biounit.

Parameters
bubiounit to be added

◆ AddBioUnit() [2/2]

void AddBioUnit ( MMCifInfoBioUnit  bu)

Add a biounit.

Parameters
bubiounit to be added

◆ AddCitation() [1/2]

void AddCitation ( MMCifInfoCitation  citation)
inline

Add an item to the list of citations.

Parameters
citationto be added

Definition at line 992 of file mmcif_info.hh.

◆ AddCitation() [2/2]

void AddCitation ( MMCifInfoCitation  citation)
inline

Add an item to the list of citations.

Parameters
citationto be added

Definition at line 992 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_namechain the bond belongs to
atom1first atom of the bond
atom2second 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_namechain the bond belongs to
atom1first atom of the bond
atom2second 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
cifchain name as used by the mmCIF file (label_asym_id)
ent_identity 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
cifchain name as used by the mmCIF file (label_asym_id)
ent_identity 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
cifchain name as used by the mmCIF file (label_asym_id)
pdbchain 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
cifchain name as used by the mmCIF file (label_asym_id)
pdbchain name as used in the PDB file (auth_asym_id)

◆ AddOperation() [1/2]

void AddOperation ( MMCifInfoTransOpPtr  op)
inline

Add a operation.

Parameters
opoperation to be added

Definition at line 1120 of file mmcif_info.hh.

◆ AddOperation() [2/2]

void AddOperation ( MMCifInfoTransOpPtr  op)
inline

Add a operation.

Parameters
opoperation to be added

Definition at line 1120 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
pdbchain name as used by the PDB file (auth_asym_id)
cifchain 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
pdbchain name as used by the PDB file (auth_asym_id)
cifchain 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 1180 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 1180 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 1112 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 1112 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 1007 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 1007 of file mmcif_info.hh.

◆ GetEMResolution() [1/2]

Real GetEMResolution ( ) const
inline

Get EM resolution.

Returns
EM experiment resolution

Definition at line 1043 of file mmcif_info.hh.

◆ GetEMResolution() [2/2]

Real GetEMResolution ( ) const
inline

Get EM resolution.

Returns
EM experiment resolution

Definition at line 1043 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_nameName 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_nameName 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 1020 of file mmcif_info.hh.

◆ GetMethod() [2/2]

const StringRef GetMethod ( ) const
inline

Get an experimental method.

Returns
Method description

Definition at line 1020 of file mmcif_info.hh.

◆ GetMMCifEntityIdTr() [1/2]

String GetMMCifEntityIdTr ( String  cif) const

Get the entity ID for a CIF chain name.

Parameters
cifchain 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
cifchain 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
cifchain 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
cifchain 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 1160 of file mmcif_info.hh.

◆ GetObsoleteInfo() [2/2]

MMCifInfoObsolete GetObsoleteInfo ( ) const
inline

Get information on an obsolete entries.

Returns
MMCifInfoObsolete object

Definition at line 1160 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 1128 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 1128 of file mmcif_info.hh.

◆ GetPDBMMCifChainTr() [1/2]

String GetPDBMMCifChainTr ( String  pdb) const

Get a CIF chain name for a PDB chain name.

Parameters
pdbchain 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
pdbchain 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 1033 of file mmcif_info.hh.

◆ GetResolution() [2/2]

Real GetResolution ( ) const
inline

Get resolution.

Returns
experiment resolution

Definition at line 1033 of file mmcif_info.hh.

◆ GetRevisions() [1/2]

MMCifInfoRevisions GetRevisions ( ) const
inline

Get history.

Returns
MMCifInfoRevisions

Definition at line 1189 of file mmcif_info.hh.

◆ GetRevisions() [2/2]

MMCifInfoRevisions GetRevisions ( ) const
inline

Get history.

Returns
MMCifInfoRevisions

Definition at line 1189 of file mmcif_info.hh.

◆ GetRFree() [1/2]

Real GetRFree ( ) const
inline

Get R-free value.

Returns
experiment R-free value

Definition at line 1053 of file mmcif_info.hh.

◆ GetRFree() [2/2]

Real GetRFree ( ) const
inline

Get R-free value.

Returns
experiment R-free value

Definition at line 1053 of file mmcif_info.hh.

◆ GetRWork() [1/2]

Real GetRWork ( ) const
inline

Get R-work value.

Returns
experiment R-work value

Definition at line 1063 of file mmcif_info.hh.

◆ GetRWork() [2/2]

Real GetRWork ( ) const
inline

Get R-work value.

Returns
experiment R-work value

Definition at line 1063 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 1144 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 1144 of file mmcif_info.hh.

◆ GetStructRefs() [1/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const
inline

Definition at line 1164 of file mmcif_info.hh.

◆ GetStructRefs() [2/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const
inline

Definition at line 1164 of file mmcif_info.hh.

◆ SetEMResolution() [1/2]

void SetEMResolution ( Real  res)
inline

Set EM resolution.

Parameters
resEM experiment resolution

Definition at line 1038 of file mmcif_info.hh.

◆ SetEMResolution() [2/2]

void SetEMResolution ( Real  res)
inline

Set EM resolution.

Parameters
resEM experiment resolution

Definition at line 1038 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
methodMethod description

Definition at line 1015 of file mmcif_info.hh.

◆ SetMethod() [2/2]

void SetMethod ( String  method)
inline

Set an experimental method.

Parameters
methodMethod description

Definition at line 1015 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 1152 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 1152 of file mmcif_info.hh.

◆ SetResolution() [1/2]

void SetResolution ( Real  res)
inline

Set resolution.

Parameters
resexperiment resolution

Definition at line 1028 of file mmcif_info.hh.

◆ SetResolution() [2/2]

void SetResolution ( Real  res)
inline

Set resolution.

Parameters
resexperiment resolution

Definition at line 1028 of file mmcif_info.hh.

◆ SetRevisionsDateOriginal() [1/2]

void SetRevisionsDateOriginal ( String  date)
inline

Set date_original of revisions.

Parameters
date

Definition at line 1170 of file mmcif_info.hh.

◆ SetRevisionsDateOriginal() [2/2]

void SetRevisionsDateOriginal ( String  date)
inline

Set date_original of revisions.

Parameters
date

Definition at line 1170 of file mmcif_info.hh.

◆ SetRFree() [1/2]

void SetRFree ( Real  r_free)
inline

Set R-free value.

Parameters
resexperiment R-free value

Definition at line 1048 of file mmcif_info.hh.

◆ SetRFree() [2/2]

void SetRFree ( Real  r_free)
inline

Set R-free value.

Parameters
resexperiment R-free value

Definition at line 1048 of file mmcif_info.hh.

◆ SetRWork() [1/2]

void SetRWork ( Real  r_work)
inline

Set R-work value.

Parameters
r_workexperiment R-work value

Definition at line 1058 of file mmcif_info.hh.

◆ SetRWork() [2/2]

void SetRWork ( Real  r_work)
inline

Set R-work value.

Parameters
r_workexperiment R-work value

Definition at line 1058 of file mmcif_info.hh.

◆ SetStructDetails() [1/2]

void SetStructDetails ( MMCifInfoStructDetails  details)
inline

Add a set of structure details.

Parameters
detailsinfo block to be added

Definition at line 1136 of file mmcif_info.hh.

◆ SetStructDetails() [2/2]

void SetStructDetails ( MMCifInfoStructDetails  details)
inline

Add a set of structure details.

Parameters
detailsinfo block to be added

Definition at line 1136 of file mmcif_info.hh.

◆ SetStructRefs() [1/2]

void SetStructRefs ( const MMCifInfoStructRefs &  sr)
inline

Definition at line 1165 of file mmcif_info.hh.

◆ SetStructRefs() [2/2]

void SetStructRefs ( const MMCifInfoStructRefs &  sr)
inline

Definition at line 1165 of file mmcif_info.hh.

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