OpenStructure
Data Structures | Public Member Functions | Protected Types | Protected Member Functions
MMCifReader Class Reference

#include <mmcif_reader.hh>

Inherits StarParser, and StarParser.

Public Member Functions

 MMCifReader (std::istream &stream, mol::EntityHandle &ent_handle, const IOProfile &profile)
 
 MMCifReader (const String &filename, mol::EntityHandle &ent_handle, const IOProfile &profile)
 
void Init ()
 
void ClearState ()
 
void SetRestrictChains (const String &restrict_chains)
 
const StringGetRestrictChains () const
 
void SetAuthChainID (bool id)
 
virtual bool OnBeginData (const StringRef &data_name)
 
virtual bool OnBeginLoop (const StarLoopDesc &header)
 
virtual void OnDataRow (const StarLoopDesc &header, const std::vector< StringRef > &columns)
 
virtual void OnEndData ()
 
seq::SequenceList GetSeqRes () const
 
const MMCifInfoGetInfo ()
 
 MMCifReader (std::istream &stream, mol::EntityHandle &ent_handle, const IOProfile &profile)
 
 MMCifReader (const String &filename, mol::EntityHandle &ent_handle, const IOProfile &profile)
 
void Init ()
 
void ClearState ()
 
void SetRestrictChains (const String &restrict_chains)
 
const StringGetRestrictChains () const
 
void SetAuthChainID (bool id)
 
virtual bool OnBeginData (const StringRef &data_name)
 
virtual bool OnBeginLoop (const StarLoopDesc &header)
 
virtual void OnDataRow (const StarLoopDesc &header, const std::vector< StringRef > &columns)
 
virtual void OnEndData ()
 
seq::SequenceList GetSeqRes () const
 
const MMCifInfoGetInfo ()
 
- Public Member Functions inherited from StarParser
 StarParser (std::istream &stream, bool items_as_row=false)
 
 StarParser (const String &filename, bool items_as_row=false)
 
virtual ~StarParser ()
 
virtual void OnEndLoop ()
 
virtual void OnDataItem (const StarDataItem &item)
 
Real TryGetReal (const StringRef &data, const String &name) const
 
Real GetRealOrDefault (const StringRef &data, const String &name, Real alt, bool(*is_default)(StringRef)) const
 
float TryGetFloat (const StringRef &data, const String &name) const
 
std::pair< bool, float > TryGetFloat (const StringRef &data, const String &name, bool may_fail) const
 
int TryGetInt (const StringRef &data, const String &name) const
 
std::pair< bool, int > TryGetInt (const StringRef &data, const String &name, bool may_fail) const
 
bool TryGetBool (const StringRef &data, const String &name) const
 
String FormatDiagnostic (StarDiagType type, const String &message, int line=-1) const
 
void SetFilename (const String &filename)
 
int GetCurrentLinenum () const
 
void Parse ()
 
 StarParser (std::istream &stream, bool items_as_row=false)
 
 StarParser (const String &filename, bool items_as_row=false)
 
virtual ~StarParser ()
 
virtual void OnEndLoop ()
 
virtual void OnDataItem (const StarDataItem &item)
 
Real TryGetReal (const StringRef &data, const String &name) const
 
Real GetRealOrDefault (const StringRef &data, const String &name, Real alt, bool(*is_default)(StringRef)) const
 
float TryGetFloat (const StringRef &data, const String &name) const
 
std::pair< bool, float > TryGetFloat (const StringRef &data, const String &name, bool may_fail) const
 
int TryGetInt (const StringRef &data, const String &name) const
 
std::pair< bool, int > TryGetInt (const StringRef &data, const String &name, bool may_fail) const
 
bool TryGetBool (const StringRef &data, const String &name) const
 
String FormatDiagnostic (StarDiagType type, const String &message, int line=-1) const
 
void SetFilename (const String &filename)
 
int GetCurrentLinenum () const
 
void Parse ()
 

Protected Types

enum  MMCifSecStructElement {
  MMCIF_HELIX , MMCIF_STRAND , MMCIF_TURN , MMCIF_COIL ,
  MMCIF_HELIX , MMCIF_STRAND , MMCIF_TURN , MMCIF_COIL
}
 
enum  MMCifSecStructElement {
  MMCIF_HELIX , MMCIF_STRAND , MMCIF_TURN , MMCIF_COIL ,
  MMCIF_HELIX , MMCIF_STRAND , MMCIF_TURN , MMCIF_COIL
}
 

Protected Member Functions

void TryStoreIdx (const int mapping, const String &item, const StarLoopDesc &header)
 
bool ParseAtomIdent (const std::vector< StringRef > &columns, String &auth_chain_name, String &cif_chain_name, StringRef &res_name, mol::ResNum &resnum, bool &valid_res_num, StringRef &atom_name, char &alt_loc)
 
void ParseAndAddAtom (const std::vector< StringRef > &columns)
 
void ParseEntity (const std::vector< StringRef > &columns)
 
void ParseEntityPoly (const std::vector< StringRef > &columns)
 
void ParseCitation (const std::vector< StringRef > &columns)
 
const MMCifInfoStructRefsGetStructRefs () const
 
void ParseCitationAuthor (const std::vector< StringRef > &columns)
 
void ParseStructRef (const std::vector< StringRef > &columns)
 
void ParseStructRefSeq (const std::vector< StringRef > &columns)
 
void ParseStructRefSeqDif (const std::vector< StringRef > &columns)
 
void ParseExptl (const std::vector< StringRef > &columns)
 
void ParseRefine (const std::vector< StringRef > &columns)
 
void ParsePdbxStructAssembly (const std::vector< StringRef > &columns)
 
void ParsePdbxStructAssemblyGen (const std::vector< StringRef > &columns)
 
std::vector< std::vector< String > > UnPackOperExperession (StringRef expression)
 
void StoreExpression (const char *l, const char *s, bool &is_range, int lborder, std::vector< String > &single_block)
 
void StoreRange (const char *&l, const char *s, bool &is_range, int &lborder, std::vector< String > &single_block)
 
void ParsePdbxStructOperList (const std::vector< StringRef > &columns)
 
void ParseDatabasePDBRev (const std::vector< StringRef > &columns)
 
void ParsePdbxAuditRevisionHistory (const std::vector< StringRef > &columns)
 
void ParsePdbxAuditRevisionDetails (const std::vector< StringRef > &columns)
 
void ParsePdbxDatabaseStatus (const std::vector< StringRef > &columns)
 
void ParseStruct (const std::vector< StringRef > &columns)
 
void ParseStructConf (const std::vector< StringRef > &columns)
 
void ParseStructSheetRange (const std::vector< StringRef > &columns)
 
void ParsePdbxDatabasePdbObsSpr (const std::vector< StringRef > &columns)
 
void ParsePdbxEntityBranch (const std::vector< StringRef > &columns)
 
void ParsePdbxEntityBranchLink (const std::vector< StringRef > &columns)
 
void ParseEntityPolySeq (const std::vector< StringRef > &columns)
 
void ParseEm3DReconstruction (const std::vector< StringRef > &columns)
 
MMCifSecStructElement DetermineSecStructType (const StringRef &type) const
 
void AssignSecStructure (mol::EntityHandle ent)
 
void TryStoreIdx (const int mapping, const String &item, const StarLoopDesc &header)
 
bool ParseAtomIdent (const std::vector< StringRef > &columns, String &auth_chain_name, String &cif_chain_name, StringRef &res_name, mol::ResNum &resnum, bool &valid_res_num, StringRef &atom_name, char &alt_loc)
 
void ParseAndAddAtom (const std::vector< StringRef > &columns)
 
void ParseEntity (const std::vector< StringRef > &columns)
 
void ParseEntityPoly (const std::vector< StringRef > &columns)
 
void ParseCitation (const std::vector< StringRef > &columns)
 
const MMCifInfoStructRefsGetStructRefs () const
 
void ParseCitationAuthor (const std::vector< StringRef > &columns)
 
void ParseStructRef (const std::vector< StringRef > &columns)
 
void ParseStructRefSeq (const std::vector< StringRef > &columns)
 
void ParseStructRefSeqDif (const std::vector< StringRef > &columns)
 
void ParseExptl (const std::vector< StringRef > &columns)
 
void ParseRefine (const std::vector< StringRef > &columns)
 
void ParsePdbxStructAssembly (const std::vector< StringRef > &columns)
 
void ParsePdbxStructAssemblyGen (const std::vector< StringRef > &columns)
 
std::vector< std::vector< String > > UnPackOperExperession (StringRef expression)
 
void StoreExpression (const char *l, const char *s, bool &is_range, int lborder, std::vector< String > &single_block)
 
void StoreRange (const char *&l, const char *s, bool &is_range, int &lborder, std::vector< String > &single_block)
 
void ParsePdbxStructOperList (const std::vector< StringRef > &columns)
 
void ParseDatabasePDBRev (const std::vector< StringRef > &columns)
 
void ParsePdbxAuditRevisionHistory (const std::vector< StringRef > &columns)
 
void ParsePdbxAuditRevisionDetails (const std::vector< StringRef > &columns)
 
void ParsePdbxDatabaseStatus (const std::vector< StringRef > &columns)
 
void ParseStruct (const std::vector< StringRef > &columns)
 
void ParseStructConf (const std::vector< StringRef > &columns)
 
void ParseStructSheetRange (const std::vector< StringRef > &columns)
 
void ParsePdbxDatabasePdbObsSpr (const std::vector< StringRef > &columns)
 
void ParsePdbxEntityBranch (const std::vector< StringRef > &columns)
 
void ParsePdbxEntityBranchLink (const std::vector< StringRef > &columns)
 
void ParseEntityPolySeq (const std::vector< StringRef > &columns)
 
void ParseEm3DReconstruction (const std::vector< StringRef > &columns)
 
MMCifSecStructElement DetermineSecStructType (const StringRef &type) const
 
void AssignSecStructure (mol::EntityHandle ent)
 

Additional Inherited Members

- Static Public Member Functions inherited from StarParser
static bool SplitLine (const StringRef &line, std::vector< StringRef > &parts, bool clear=true)
 
static bool SplitLine (const StringRef &line, std::vector< StringRef > &parts, bool clear=true)
 

Detailed Description

reader for the mmcif file format

mmcif format description/ coverage

mmcif is an instance of the STAR format to store entries of the PDB. The following data categories should be covered by this reader:

Definition at line 61 of file mmcif_reader.hh.

Member Enumeration Documentation

◆ MMCifSecStructElement [1/2]

enum MMCifSecStructElement
protected
Enumerator
MMCIF_HELIX 
MMCIF_STRAND 
MMCIF_TURN 
MMCIF_COIL 
MMCIF_HELIX 
MMCIF_STRAND 
MMCIF_TURN 
MMCIF_COIL 

Definition at line 316 of file mmcif_reader.hh.

◆ MMCifSecStructElement [2/2]

enum MMCifSecStructElement
protected
Enumerator
MMCIF_HELIX 
MMCIF_STRAND 
MMCIF_TURN 
MMCIF_COIL 
MMCIF_HELIX 
MMCIF_STRAND 
MMCIF_TURN 
MMCIF_COIL 

Definition at line 316 of file mmcif_reader.hh.

Constructor & Destructor Documentation

◆ MMCifReader() [1/4]

MMCifReader ( std::istream &  stream,
mol::EntityHandle ent_handle,
const IOProfile profile 
)

create a MMCifReader

Parameters
streaminput stream
ent_handle
profile

◆ MMCifReader() [2/4]

MMCifReader ( const String filename,
mol::EntityHandle ent_handle,
const IOProfile profile 
)

create a MMCifReader

Parameters
filenameinput file
ent_handle
profile

◆ MMCifReader() [3/4]

MMCifReader ( std::istream &  stream,
mol::EntityHandle ent_handle,
const IOProfile profile 
)

create a MMCifReader

Parameters
streaminput stream
ent_handle
profile

◆ MMCifReader() [4/4]

MMCifReader ( const String filename,
mol::EntityHandle ent_handle,
const IOProfile profile 
)

create a MMCifReader

Parameters
filenameinput file
ent_handle
profile

Member Function Documentation

◆ AssignSecStructure() [1/2]

void AssignSecStructure ( mol::EntityHandle  ent)
protected

Transform data from struct_conf entry into secondary structure.

Parameters
entEntity to assign secondary structure to

◆ AssignSecStructure() [2/2]

void AssignSecStructure ( mol::EntityHandle  ent)
protected

Transform data from struct_conf entry into secondary structure.

Parameters
entEntity to assign secondary structure to

◆ ClearState() [1/2]

void ClearState ( )

Set up a fresh instance.

◆ ClearState() [2/2]

void ClearState ( )

Set up a fresh instance.

◆ DetermineSecStructType() [1/2]

MMCifSecStructElement DetermineSecStructType ( const StringRef type) const
protected

Check whether an element was classified sheet or helix.

Parameters
typeType to be classified

◆ DetermineSecStructType() [2/2]

MMCifSecStructElement DetermineSecStructType ( const StringRef type) const
protected

Check whether an element was classified sheet or helix.

Parameters
typeType to be classified

◆ GetInfo() [1/2]

const MMCifInfo& GetInfo ( )
inline

Get additional information of the mmCIF file.

Returns
MMCitfInfo object

Definition at line 139 of file mmcif_reader.hh.

◆ GetInfo() [2/2]

const MMCifInfo& GetInfo ( )
inline

Get additional information of the mmCIF file.

Returns
MMCitfInfo object

Definition at line 139 of file mmcif_reader.hh.

◆ GetRestrictChains() [1/2]

const String& GetRestrictChains ( ) const
inline

Definition at line 92 of file mmcif_reader.hh.

◆ GetRestrictChains() [2/2]

const String& GetRestrictChains ( ) const
inline

Definition at line 92 of file mmcif_reader.hh.

◆ GetSeqRes() [1/2]

seq::SequenceList GetSeqRes ( ) const

Return sequences.

Returns
List of sequences

◆ GetSeqRes() [2/2]

seq::SequenceList GetSeqRes ( ) const

Return sequences.

Returns
List of sequences

◆ GetStructRefs() [1/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const
inlineprotected

Definition at line 206 of file mmcif_reader.hh.

◆ GetStructRefs() [2/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const
inlineprotected

Definition at line 206 of file mmcif_reader.hh.

◆ Init() [1/2]

void Init ( )

Initialise the reader.

◆ Init() [2/2]

void Init ( )

Initialise the reader.

◆ OnBeginData() [1/2]

virtual bool OnBeginData ( const StringRef data_name)
virtual

check mmcif input to be read. Substitutional function for StarParser.

Parameters
data_namevalue of the data_ tag
Returns
true, if the blockcode (PDB id) is valid, false otherwise

Reimplemented from StarParser.

◆ OnBeginData() [2/2]

virtual bool OnBeginData ( const StringRef data_name)
virtual

check mmcif input to be read. Substitutional function for StarParser.

Parameters
data_namevalue of the data_ tag
Returns
true, if the blockcode (PDB id) is valid, false otherwise

Reimplemented from StarParser.

◆ OnBeginLoop() [1/2]

virtual bool OnBeginLoop ( const StarLoopDesc header)
virtual

check if a current loop is to be parsed

Parameters
headercategories of the upcoming loop block
Returns
bool

Reimplemented from StarParser.

◆ OnBeginLoop() [2/2]

virtual bool OnBeginLoop ( const StarLoopDesc header)
virtual

check if a current loop is to be parsed

Parameters
headercategories of the upcoming loop block
Returns
bool

Reimplemented from StarParser.

◆ OnDataRow() [1/2]

virtual void OnDataRow ( const StarLoopDesc header,
const std::vector< StringRef > &  columns 
)
virtual

read a row of data

Parameters
headercategories and items
columnsdata

Reimplemented from StarParser.

◆ OnDataRow() [2/2]

virtual void OnDataRow ( const StarLoopDesc header,
const std::vector< StringRef > &  columns 
)
virtual

read a row of data

Parameters
headercategories and items
columnsdata

Reimplemented from StarParser.

◆ OnEndData() [1/2]

virtual void OnEndData ( )
virtual

Finalise parsing.

Reimplemented from StarParser.

◆ OnEndData() [2/2]

virtual void OnEndData ( )
virtual

Finalise parsing.

Reimplemented from StarParser.

◆ ParseAndAddAtom() [1/2]

void ParseAndAddAtom ( const std::vector< StringRef > &  columns)
protected

Fetch atom information and store it.

Parameters
columnsdata row

◆ ParseAndAddAtom() [2/2]

void ParseAndAddAtom ( const std::vector< StringRef > &  columns)
protected

Fetch atom information and store it.

Parameters
columnsdata row

◆ ParseAtomIdent() [1/2]

bool ParseAtomIdent ( const std::vector< StringRef > &  columns,
String auth_chain_name,
String cif_chain_name,
StringRef res_name,
mol::ResNum resnum,
bool &  valid_res_num,
StringRef atom_name,
char &  alt_loc 
)
protected

fetch values identifying atoms

Parameters
[in]columnsdata row
[out]auth_chain_nametakes atom_site.label_asym_id or, if auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
[out]cif_chain_name
[out]res_namefetches atom_site.label_comp_id
[out]resnumgets atom_site.label_seq_id if available, consecutive numbers, otherwise
[out]valid_res_numshows if we have a valid residue number or if we have to invent our own
[out]atom_namecorresponds to label_atom_id
[out]alt_locgets first letter of atom_site.label_alt_id

◆ ParseAtomIdent() [2/2]

bool ParseAtomIdent ( const std::vector< StringRef > &  columns,
String auth_chain_name,
String cif_chain_name,
StringRef res_name,
mol::ResNum resnum,
bool &  valid_res_num,
StringRef atom_name,
char &  alt_loc 
)
protected

fetch values identifying atoms

Parameters
[in]columnsdata row
[out]auth_chain_nametakes atom_site.label_asym_id or, if auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
[out]cif_chain_name
[out]res_namefetches atom_site.label_comp_id
[out]resnumgets atom_site.label_seq_id if available, consecutive numbers, otherwise
[out]valid_res_numshows if we have a valid residue number or if we have to invent our own
[out]atom_namecorresponds to label_atom_id
[out]alt_locgets first letter of atom_site.label_alt_id

◆ ParseCitation() [1/2]

void ParseCitation ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF citation information.

Parameters
columnsdata row

◆ ParseCitation() [2/2]

void ParseCitation ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF citation information.

Parameters
columnsdata row

◆ ParseCitationAuthor() [1/2]

void ParseCitationAuthor ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF citation_author information.

Parameters
columnsdata row

◆ ParseCitationAuthor() [2/2]

void ParseCitationAuthor ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF citation_author information.

Parameters
columnsdata row

◆ ParseDatabasePDBRev() [1/2]

void ParseDatabasePDBRev ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF database_PDB_rev information.

Parameters
columnsdata row

◆ ParseDatabasePDBRev() [2/2]

void ParseDatabasePDBRev ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF database_PDB_rev information.

Parameters
columnsdata row

◆ ParseEm3DReconstruction() [1/2]

void ParseEm3DReconstruction ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity_poly_seq information.

Parameters
columnsdata row

◆ ParseEm3DReconstruction() [2/2]

void ParseEm3DReconstruction ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity_poly_seq information.

Parameters
columnsdata row

◆ ParseEntity() [1/2]

void ParseEntity ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity information.

Parameters
columnsdata row

◆ ParseEntity() [2/2]

void ParseEntity ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity information.

Parameters
columnsdata row

◆ ParseEntityPoly() [1/2]

void ParseEntityPoly ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity_poly information.

Parameters
columnsdata row

◆ ParseEntityPoly() [2/2]

void ParseEntityPoly ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity_poly information.

Parameters
columnsdata row

◆ ParseEntityPolySeq() [1/2]

void ParseEntityPolySeq ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity_poly_seq information.

Parameters
columnsdata row

◆ ParseEntityPolySeq() [2/2]

void ParseEntityPolySeq ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF entity_poly_seq information.

Parameters
columnsdata row

◆ ParseExptl() [1/2]

void ParseExptl ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF exptl information.

Parameters
columnsdata row

◆ ParseExptl() [2/2]

void ParseExptl ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF exptl information.

Parameters
columnsdata row

◆ ParsePdbxAuditRevisionDetails() [1/2]

void ParsePdbxAuditRevisionDetails ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_audit_revision_details information.

Parameters
columnsdata row

◆ ParsePdbxAuditRevisionDetails() [2/2]

void ParsePdbxAuditRevisionDetails ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_audit_revision_details information.

Parameters
columnsdata row

◆ ParsePdbxAuditRevisionHistory() [1/2]

void ParsePdbxAuditRevisionHistory ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_audit_revision_history information.

Parameters
columnsdata row

◆ ParsePdbxAuditRevisionHistory() [2/2]

void ParsePdbxAuditRevisionHistory ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_audit_revision_history information.

Parameters
columnsdata row

◆ ParsePdbxDatabasePdbObsSpr() [1/2]

void ParsePdbxDatabasePdbObsSpr ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_database_PDB_obs_spr information.

Parameters
columnsdata row

◆ ParsePdbxDatabasePdbObsSpr() [2/2]

void ParsePdbxDatabasePdbObsSpr ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_database_PDB_obs_spr information.

Parameters
columnsdata row

◆ ParsePdbxDatabaseStatus() [1/2]

void ParsePdbxDatabaseStatus ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_database_status information.

Parameters
columnsdata row

◆ ParsePdbxDatabaseStatus() [2/2]

void ParsePdbxDatabaseStatus ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_database_status information.

Parameters
columnsdata row

◆ ParsePdbxEntityBranch() [1/2]

void ParsePdbxEntityBranch ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_entity_branch information.

Parameters
columnsdata row

◆ ParsePdbxEntityBranch() [2/2]

void ParsePdbxEntityBranch ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_entity_branch information.

Parameters
columnsdata row

◆ ParsePdbxEntityBranchLink() [1/2]

void ParsePdbxEntityBranchLink ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_entity_branch_link information.

Parameters
columnsdata row

◆ ParsePdbxEntityBranchLink() [2/2]

void ParsePdbxEntityBranchLink ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_entity_branch_link information.

Parameters
columnsdata row

◆ ParsePdbxStructAssembly() [1/2]

void ParsePdbxStructAssembly ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_struct_assembly information.

Parameters
columnsdata row

◆ ParsePdbxStructAssembly() [2/2]

void ParsePdbxStructAssembly ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_struct_assembly information.

Parameters
columnsdata row

◆ ParsePdbxStructAssemblyGen() [1/2]

void ParsePdbxStructAssemblyGen ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_struct_assembly_gen information.

Parameters
columnsdata row

◆ ParsePdbxStructAssemblyGen() [2/2]

void ParsePdbxStructAssemblyGen ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_struct_assembly_gen information.

Parameters
columnsdata row

◆ ParsePdbxStructOperList() [1/2]

void ParsePdbxStructOperList ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_struct_oper_list information.

Parameters
columnsdata row

◆ ParsePdbxStructOperList() [2/2]

void ParsePdbxStructOperList ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF pdbx_struct_oper_list information.

Parameters
columnsdata row

◆ ParseRefine() [1/2]

void ParseRefine ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF refine information.

Parameters
columnsdata row

◆ ParseRefine() [2/2]

void ParseRefine ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF refine information.

Parameters
columnsdata row

◆ ParseStruct() [1/2]

void ParseStruct ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF struct information.

Parameters
columnsdata row

◆ ParseStruct() [2/2]

void ParseStruct ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF struct information.

Parameters
columnsdata row

◆ ParseStructConf() [1/2]

void ParseStructConf ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF struct_conf (secondary structure) information.

Parameters
columnsdata row

◆ ParseStructConf() [2/2]

void ParseStructConf ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF struct_conf (secondary structure) information.

Parameters
columnsdata row

◆ ParseStructRef() [1/2]

void ParseStructRef ( const std::vector< StringRef > &  columns)
protected

\ brief parse a row in the struct_ref category

◆ ParseStructRef() [2/2]

void ParseStructRef ( const std::vector< StringRef > &  columns)
protected

\ brief parse a row in the struct_ref category

◆ ParseStructRefSeq() [1/2]

void ParseStructRefSeq ( const std::vector< StringRef > &  columns)
protected

parse row in the struct_ref_seq category

◆ ParseStructRefSeq() [2/2]

void ParseStructRefSeq ( const std::vector< StringRef > &  columns)
protected

parse row in the struct_ref_seq category

◆ ParseStructRefSeqDif() [1/2]

void ParseStructRefSeqDif ( const std::vector< StringRef > &  columns)
protected

parse row in the struct_ref_seq_dif category

◆ ParseStructRefSeqDif() [2/2]

void ParseStructRefSeqDif ( const std::vector< StringRef > &  columns)
protected

parse row in the struct_ref_seq_dif category

◆ ParseStructSheetRange() [1/2]

void ParseStructSheetRange ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF struct_sheet_range (beta sheets) information.

Parameters
columnsdata row

◆ ParseStructSheetRange() [2/2]

void ParseStructSheetRange ( const std::vector< StringRef > &  columns)
protected

Fetch mmCIF struct_sheet_range (beta sheets) information.

Parameters
columnsdata row

◆ SetAuthChainID() [1/2]

void SetAuthChainID ( bool  id)
inline

Enable or disable reading of auth_chain_id instead aof label_chain id (default)

Parameters
idenable (true) or disable (false) reading of auth_chain_id.

Definition at line 101 of file mmcif_reader.hh.

◆ SetAuthChainID() [2/2]

void SetAuthChainID ( bool  id)
inline

Enable or disable reading of auth_chain_id instead aof label_chain id (default)

Parameters
idenable (true) or disable (false) reading of auth_chain_id.

Definition at line 101 of file mmcif_reader.hh.

◆ SetRestrictChains() [1/2]

void SetRestrictChains ( const String restrict_chains)

Set names of restricted chains for the reader.

Parameters
restrict_chainschain name

◆ SetRestrictChains() [2/2]

void SetRestrictChains ( const String restrict_chains)

Set names of restricted chains for the reader.

Parameters
restrict_chainschain name

◆ StoreExpression() [1/2]

void StoreExpression ( const char *  l,
const char *  s,
bool &  is_range,
int  lborder,
std::vector< String > &  single_block 
)
protected

◆ StoreExpression() [2/2]

void StoreExpression ( const char *  l,
const char *  s,
bool &  is_range,
int  lborder,
std::vector< String > &  single_block 
)
protected

◆ StoreRange() [1/2]

void StoreRange ( const char *&  l,
const char *  s,
bool &  is_range,
int &  lborder,
std::vector< String > &  single_block 
)
protected

◆ StoreRange() [2/2]

void StoreRange ( const char *&  l,
const char *  s,
bool &  is_range,
int &  lborder,
std::vector< String > &  single_block 
)
protected

◆ TryStoreIdx() [1/2]

void TryStoreIdx ( const int  mapping,
const String item,
const StarLoopDesc header 
)
inlineprotected

Store an item index from loop header in preparation for reading a row. Throws an exception if the item does not exist.

Parameters
mappingposition the item index is stored at
itemexact item name to fetch
headerloop header to pull index from

Definition at line 148 of file mmcif_reader.hh.

◆ TryStoreIdx() [2/2]

void TryStoreIdx ( const int  mapping,
const String item,
const StarLoopDesc header 
)
inlineprotected

Store an item index from loop header in preparation for reading a row. Throws an exception if the item does not exist.

Parameters
mappingposition the item index is stored at
itemexact item name to fetch
headerloop header to pull index from

Definition at line 148 of file mmcif_reader.hh.

◆ UnPackOperExperession() [1/2]

std::vector<std::vector<String> > UnPackOperExperession ( StringRef  expression)
protected

◆ UnPackOperExperession() [2/2]

std::vector<std::vector<String> > UnPackOperExperession ( StringRef  expression)
protected

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