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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)
 
void SetReadCanonicalSeqRes (bool flag)
 
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
 
void SetReadSeqRes (bool flag)
 
bool GetReadSeqRes () 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)
 
void SetReadCanonicalSeqRes (bool flag)
 
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
 
void SetReadSeqRes (bool flag)
 
bool GetReadSeqRes () 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
 
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
 
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
 
String ConvertSEQRES (const String &seqres, conop::CompoundLibBasePtr compound_lib)
 
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
 
String ConvertSEQRES (const String &seqres, conop::CompoundLibBasePtr compound_lib)
 
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

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

Definition at line 352 of file mmcif_reader.hh.

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

Definition at line 352 of file mmcif_reader.hh.

Constructor & Destructor Documentation

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

create a MMCifReader

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

create a MMCifReader

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

create a MMCifReader

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

create a MMCifReader

Parameters
filenameinput file
ent_handle
profile

Member Function Documentation

void AssignSecStructure ( mol::EntityHandle  ent)
protected

Transform data from struct_conf entry into secondary structure.

Parameters
entEntity to assign secondary structure to
void AssignSecStructure ( mol::EntityHandle  ent)
protected

Transform data from struct_conf entry into secondary structure.

Parameters
entEntity to assign secondary structure to
void ClearState ( )

Set up a fresh instance.

void ClearState ( )

Set up a fresh instance.

String ConvertSEQRES ( const String seqres,
conop::CompoundLibBasePtr  compound_lib 
)
protected

convert the seqres data item to canonical form.

The seqres sequence lists non-standard residues in parenthesis. For proper handling of our sequence classes, these need to be converted to one-letter-codes. Ideally, we would use the canonical SEQRES. This is not possible, however, since the PDB assigns multiple one letter codes to some of the residues. To be consistent, we have to do the conversion on our own.

String ConvertSEQRES ( const String seqres,
conop::CompoundLibBasePtr  compound_lib 
)
protected

convert the seqres data item to canonical form.

The seqres sequence lists non-standard residues in parenthesis. For proper handling of our sequence classes, these need to be converted to one-letter-codes. Ideally, we would use the canonical SEQRES. This is not possible, however, since the PDB assigns multiple one letter codes to some of the residues. To be consistent, we have to do the conversion on our own.

MMCifSecStructElement DetermineSecStructType ( const StringRef type) const
protected

Check whether an element was classified sheet or helix.

Parameters
typeType to be classified
MMCifSecStructElement DetermineSecStructType ( const StringRef type) const
protected

Check whether an element was classified sheet or helix.

Parameters
typeType to be classified
const MMCifInfo& GetInfo ( )
inline

Get additional information of the mmCIF file.

Returns
MMCitfInfo object

Definition at line 167 of file mmcif_reader.hh.

const MMCifInfo& GetInfo ( )
inline

Get additional information of the mmCIF file.

Returns
MMCitfInfo object

Definition at line 167 of file mmcif_reader.hh.

bool GetReadSeqRes ( ) const
inline

Check if reading of SEQRES is enabled.

Returns
True if reading of SEQRES is enabled

Definition at line 159 of file mmcif_reader.hh.

bool GetReadSeqRes ( ) const
inline

Check if reading of SEQRES is enabled.

Returns
True if reading of SEQRES is enabled

Definition at line 159 of file mmcif_reader.hh.

const String& GetRestrictChains ( ) const
inline

Definition at line 102 of file mmcif_reader.hh.

const String& GetRestrictChains ( ) const
inline

Definition at line 102 of file mmcif_reader.hh.

seq::SequenceList GetSeqRes ( ) const
inline

Return sequences.

Returns
List of sequences

Definition at line 144 of file mmcif_reader.hh.

seq::SequenceList GetSeqRes ( ) const
inline

Return sequences.

Returns
List of sequences

Definition at line 144 of file mmcif_reader.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const
inlineprotected

Definition at line 234 of file mmcif_reader.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const
inlineprotected

Definition at line 234 of file mmcif_reader.hh.

void Init ( )

Initialise the reader.

void Init ( )

Initialise the reader.

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.

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.

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.

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.

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.

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.

virtual void OnEndData ( )
virtual

Finalise parsing.

Reimplemented from StarParser.

virtual void OnEndData ( )
virtual

Finalise parsing.

Reimplemented from StarParser.

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

Fetch atom information and store it.

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

Fetch atom information and store it.

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

Fetch mmCIF citation information.

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

Fetch mmCIF citation information.

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

Fetch mmCIF citation_author information.

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

Fetch mmCIF citation_author information.

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

Fetch mmCIF database_PDB_rev information.

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

Fetch mmCIF database_PDB_rev information.

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

Fetch mmCIF entity_poly_seq information.

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

Fetch mmCIF entity_poly_seq information.

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

Fetch mmCIF entity information.

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

Fetch mmCIF entity information.

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

Fetch mmCIF entity_poly information.

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

Fetch mmCIF entity_poly information.

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

Fetch mmCIF entity_poly_seq information.

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

Fetch mmCIF entity_poly_seq information.

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

Fetch mmCIF exptl information.

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

Fetch mmCIF exptl information.

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

Fetch mmCIF pdbx_audit_revision_details information.

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

Fetch mmCIF pdbx_audit_revision_details information.

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

Fetch mmCIF pdbx_audit_revision_history information.

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

Fetch mmCIF pdbx_audit_revision_history information.

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

Fetch mmCIF pdbx_database_PDB_obs_spr information.

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

Fetch mmCIF pdbx_database_PDB_obs_spr information.

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

Fetch mmCIF pdbx_database_status information.

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

Fetch mmCIF pdbx_database_status information.

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

Fetch mmCIF pdbx_entity_branch information.

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

Fetch mmCIF pdbx_entity_branch information.

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

Fetch mmCIF pdbx_entity_branch_link information.

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

Fetch mmCIF pdbx_entity_branch_link information.

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

Fetch mmCIF pdbx_struct_assembly information.

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

Fetch mmCIF pdbx_struct_assembly information.

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

Fetch mmCIF pdbx_struct_assembly_gen information.

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

Fetch mmCIF pdbx_struct_assembly_gen information.

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

Fetch mmCIF pdbx_struct_oper_list information.

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

Fetch mmCIF pdbx_struct_oper_list information.

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

Fetch mmCIF refine information.

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

Fetch mmCIF refine information.

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

Fetch mmCIF struct information.

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

Fetch mmCIF struct information.

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

Fetch mmCIF struct_conf (secondary structure) information.

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

Fetch mmCIF struct_conf (secondary structure) information.

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

\ brief parse a row in the struct_ref category

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

\ brief parse a row in the struct_ref category

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

parse row in the struct_ref_seq category

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

parse row in the struct_ref_seq category

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

parse row in the struct_ref_seq_dif category

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

parse row in the struct_ref_seq_dif category

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

Fetch mmCIF struct_sheet_range (beta sheets) information.

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

Fetch mmCIF struct_sheet_range (beta sheets) information.

Parameters
columnsdata row
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 111 of file mmcif_reader.hh.

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 111 of file mmcif_reader.hh.

void SetReadCanonicalSeqRes ( bool  flag)
inline

Toggle reading of canonical sequence residues (entity_poly.pdbx_seq_one_letter_code_can instead of entity_poly.pdbx_seq_one_letter_code). This flag is exclusive.

Parameters
flagTrue for reading canonical sequences.

Definition at line 97 of file mmcif_reader.hh.

void SetReadCanonicalSeqRes ( bool  flag)
inline

Toggle reading of canonical sequence residues (entity_poly.pdbx_seq_one_letter_code_can instead of entity_poly.pdbx_seq_one_letter_code). This flag is exclusive.

Parameters
flagTrue for reading canonical sequences.

Definition at line 97 of file mmcif_reader.hh.

void SetReadSeqRes ( bool  flag)
inline

Toggle reading of SEQRES.

Parameters
flagTrue enables, False disables reading SEQRES

Definition at line 151 of file mmcif_reader.hh.

void SetReadSeqRes ( bool  flag)
inline

Toggle reading of SEQRES.

Parameters
flagTrue enables, False disables reading SEQRES

Definition at line 151 of file mmcif_reader.hh.

void SetRestrictChains ( const String restrict_chains)

Set names of restricted chains for the reader.

Parameters
restrict_chainschain name
void SetRestrictChains ( const String restrict_chains)

Set names of restricted chains for the reader.

Parameters
restrict_chainschain name
void StoreExpression ( const char *  l,
const char *  s,
bool &  is_range,
int  lborder,
std::vector< String > &  single_block 
)
protected
void StoreExpression ( const char *  l,
const char *  s,
bool &  is_range,
int  lborder,
std::vector< String > &  single_block 
)
protected
void StoreRange ( const char *&  l,
const char *  s,
bool &  is_range,
int &  lborder,
std::vector< String > &  single_block 
)
protected
void StoreRange ( const char *&  l,
const char *  s,
bool &  is_range,
int &  lborder,
std::vector< String > &  single_block 
)
protected
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 176 of file mmcif_reader.hh.

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 176 of file mmcif_reader.hh.

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

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