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 MMCifInfoStructRefsGetStructRefs () 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 MMCifInfoStructRefsGetStructRefs () 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:

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:
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