#include <mmcif_reader.hh>

Inherits StarParser, and StarParser.

Data Structures
struct	MMCifBioUAssembly
struct	MMCifEntityDesc
struct	MMCifHSEntry

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 String &	GetRestrictChains () 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 MMCifInfo &	GetInfo ()
	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 String &	GetRestrictChains () 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 MMCifInfo &	GetInfo ()
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_HELIX, MMCIF_STRAND, MMCIF_TURN }
enum	MMCifSecStructElement { MMCIF_HELIX, MMCIF_STRAND, MMCIF_TURN, MMCIF_HELIX, MMCIF_STRAND, MMCIF_TURN }

Protected Member Functions
void	TryStoreIdx (const int mapping, const String &item, const StarLoopDesc &header)
bool	IsValidPDBIdent (const StringRef &pdbid)
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 MMCifInfoStructRefs &	GetStructRefs () const
String	ConvertSEQRES (const String &seqres, conop::CompoundLibPtr 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	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)
MMCifSecStructElement	DetermineSecStructType (const StringRef &type) const
void	AssignSecStructure (mol::EntityHandle ent)
void	TryStoreIdx (const int mapping, const String &item, const StarLoopDesc &header)
bool	IsValidPDBIdent (const StringRef &pdbid)
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 MMCifInfoStructRefs &	GetStructRefs () const
String	ConvertSEQRES (const String &seqres, conop::CompoundLibPtr 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	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)
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:

atom_site
entity
entity_poly
citation
citation_author
exptl
refine
pdbx_struct_assembly
pdbx_struct_assembly_gen
pdbx_struct_oper_list
struct
struct_conf
struct_sheet_range
pdbx_database_PDB_obs_spr
database_PDB_rev

Definition at line 59 of file mmcif_reader.hh.

Member Enumeration Documentation

enum MMCifSecStructElement

protected

Enumerator:

MMCIF_HELIX
MMCIF_STRAND
MMCIF_TURN
MMCIF_HELIX
MMCIF_STRAND
MMCIF_TURN

Definition at line 317 of file mmcif_reader.hh.

enum MMCifSecStructElement

protected

Enumerator:

MMCIF_HELIX
MMCIF_STRAND
MMCIF_TURN
MMCIF_HELIX
MMCIF_STRAND
MMCIF_TURN

Definition at line 317 of file mmcif_reader.hh.

Constructor & Destructor Documentation

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

create a MMCifReader

Parameters:

stream input stream

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

create a MMCifReader

Parameters:

filename input file

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

create a MMCifReader

Parameters:

stream input stream

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

create a MMCifReader

Parameters:

filename input file

Member Function Documentation

void AssignSecStructure ( mol::EntityHandle ent )

protected

Transform data from struct_conf entry into secondary structure.

Parameters:

ent	Entity to assign secondary structure to

void AssignSecStructure ( mol::EntityHandle ent )

protected

Transform data from struct_conf entry into secondary structure.

Parameters:

ent	Entity 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::CompoundLibPtr	compound_lib
	)

protected

convert the seqres data item to canonical form.

The seqres sequence lists non-standard residues in paranthesis. 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::CompoundLibPtr	compound_lib
	)

protected

convert the seqres data item to canonical form.

The seqres sequence lists non-standard residues in paranthesis. 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:

type	Type to be classified

MMCifSecStructElement DetermineSecStructType ( const StringRef & type ) const

protected

Check whether an element was classified sheet or helix.

Parameters:

type	Type to be classified

const MMCifInfo& GetInfo ( )

inline

Get additional information of the mmCIF file.

Returns:: MMCitfInfo object

Definition at line 161 of file mmcif_reader.hh.

const MMCifInfo& GetInfo ( )

inline

Get additional information of the mmCIF file.

Returns:: MMCitfInfo object

Definition at line 161 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 153 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 153 of file mmcif_reader.hh.

const String& GetRestrictChains ( ) const

inline

Definition at line 96 of file mmcif_reader.hh.

const String& GetRestrictChains ( ) const

inline

Definition at line 96 of file mmcif_reader.hh.

seq::SequenceList GetSeqRes ( ) const

inline

Return sequences.

Returns:: List of sequences

Definition at line 138 of file mmcif_reader.hh.

seq::SequenceList GetSeqRes ( ) const

inline

Return sequences.

Returns:: List of sequences

Definition at line 138 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.

Parameters:

loc	Location of the file

void Init ( )

Initialise the reader.

Parameters:

loc	Location of the file

bool IsValidPDBIdent ( const StringRef & pdbid )

protected

Check a PDB id to be of length 4 and start with a digit.

Parameters:

pdbid putative PDB id

Returns:: true for a valid id, false otherwise

bool IsValidPDBIdent ( const StringRef & pdbid )

protected

Check a PDB id to be of length 4 and start with a digit.

Parameters:

pdbid putative PDB id

Returns:: true for a valid id, false otherwise

virtual bool OnBeginData ( const StringRef & data_name )

virtual

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

Parameters:

data_name value 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_name value 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:

header categories 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:

header categories 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:

header	categories and items
columns	data

Reimplemented from StarParser.

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

virtual

read a row of data

Parameters:

header	categories and items
columns	data

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:

columns data row

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

protected

Fetch atom information and store it.

Parameters:

columns data 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]	columns	data row
[out]	chain_name	takes atom_site.label_asym_id or, if auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
[out]	res_name	fetches atom_site.label_comp_id
[out]	resnum	gets atom_site.label_seq_id if available, consecutive numbers, otherwise
[out]	valid_res_num	shows if we have a valid residue number or if we have to invent our own
[out]	atom_name	corresponds to label_atom_id
[out]	alt_loc	gets 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]	columns	data row
[out]	chain_name	takes atom_site.label_asym_id or, if auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
[out]	res_name	fetches atom_site.label_comp_id
[out]	resnum	gets atom_site.label_seq_id if available, consecutive numbers, otherwise
[out]	valid_res_num	shows if we have a valid residue number or if we have to invent our own
[out]	atom_name	corresponds to label_atom_id
[out]	alt_loc	gets first letter of atom_site.label_alt_id

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

protected

Fetch mmCIF citation information.

Parameters:

columns data row

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

protected

Fetch mmCIF citation information.

Parameters:

columns data row

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

protected

Fetch mmCIF citation_author information.

Parameters:

columns data row

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

protected

Fetch mmCIF citation_author information.

Parameters:

columns data row

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

protected

Fetch mmCIF database_PDB_rev information.

Parameters:

columns data row

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

protected

Fetch mmCIF database_PDB_rev information.

Parameters:

columns data row

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

protected

Fetch mmCIF entity information.

Parameters:

columns data row

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

protected

Fetch mmCIF entity information.

Parameters:

columns data row

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

protected

Fetch mmCIF entity_poly information.

Parameters:

columns data row

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

protected

Fetch mmCIF entity_poly information.

Parameters:

columns data row

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

protected

Fetch mmCIF exptl information.

Parameters:

columns data row

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

protected

Fetch mmCIF exptl information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_database_PDB_obs_spr information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_database_PDB_obs_spr information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_struct_assembly information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_struct_assembly information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_struct_assembly_gen information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_struct_assembly_gen information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_struct_oper_list information.

Parameters:

columns data row

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

protected

Fetch mmCIF pdbx_struct_oper_list information.

Parameters:

columns data row

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

protected

Fetch mmCIF refine information.

Parameters:

columns data row

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

protected

Fetch mmCIF refine information.

Parameters:

columns data row

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

protected

Fetch mmCIF struct information.

Parameters:

columns data row

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

protected

Fetch mmCIF struct information.

Parameters:

columns data row

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

protected

Fetch mmCIF struct_conf (secondary structure) information.

Parameters:

columns data row

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

protected

Fetch mmCIF struct_conf (secondary structure) information.

Parameters:

columns data 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:

columns data row

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

protected

Fetch mmCIF struct_sheet_range (beta sheets) information.

Parameters:

columns data row

void SetAuthChainID ( bool id )

inline

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

Parameters:

id	enable (true) or disable (false) reading of auth_chain_id.

Definition at line 105 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:

id	enable (true) or disable (false) reading of auth_chain_id.

Definition at line 105 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:

flag	True for reading canonical sequences.

Definition at line 91 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:

flag	True for reading canonical sequences.

Definition at line 91 of file mmcif_reader.hh.

void SetReadSeqRes ( bool flag )

inline

Toggle reading of SEQRES.

Parameters:

flag	True enables, False disables reading SEQRES

Definition at line 145 of file mmcif_reader.hh.

void SetReadSeqRes ( bool flag )

inline

Toggle reading of SEQRES.

Parameters:

flag	True enables, False disables reading SEQRES

Definition at line 145 of file mmcif_reader.hh.

void SetRestrictChains ( const String & restrict_chains )

Set names of restricted chains for the reader.

Parameters:

restrict_chains chain name

void SetRestrictChains ( const String & restrict_chains )

Set names of restricted chains for the reader.

Parameters:

restrict_chains chain 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:

mapping	position the item index is stored at
item	exact item name to fetch
header	loop header to pull index from

Definition at line 170 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:

mapping	position the item index is stored at
item	exact item name to fetch
header	loop header to pull index from

Definition at line 170 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:

stage/include/ost/io/mmcif_reader.hh
stage/include/ost/io/mol/mmcif_reader.hh

Data Structures

Public Member Functions

Protected Types

Protected Member Functions

Additional Inherited Members

Detailed Description

mmcif format description/ coverage

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation