MMCifReader Class Reference

reader for the mmcif file format More...

#include <mmcif_reader.hh>

Inherits ost::io::StarParser, and ost::io::StarParser.

Data Structures
struct	MMCifBioUAssembly
struct	MMCifEntityDesc
struct	MMCifHSEntry
struct	MMCifPSAEntry
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 ()
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	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)
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	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)
MMCifSecStructElement	DetermineSecStructType (const StringRef &type) const
void	AssignSecStructure (mol::EntityHandle ent)

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 337 of file mmcif_reader.hh.

enum MMCifSecStructElement [protected]

Enumerator:

MMCIF_HELIX
MMCIF_STRAND
MMCIF_TURN
MMCIF_HELIX
MMCIF_STRAND
MMCIF_TURN

Definition at line 337 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
	ent_handle
	profile

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

create a MMCifReader

Parameters:

	filename	input file
	ent_handle
	profile

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

create a MMCifReader

Parameters:

	stream	input stream
	ent_handle
	profile

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

create a MMCifReader

Parameters:

	filename	input file
	ent_handle
	profile

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 165 of file mmcif_reader.hh.

const MMCifInfo& GetInfo ( ) [inline]

Get additional information of the mmCIF file.

Returns:: MMCitfInfo object

Definition at line 165 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 157 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 157 of file mmcif_reader.hh.

const String& GetRestrictChains ( ) const [inline]

Definition at line 100 of file mmcif_reader.hh.

const String& GetRestrictChains ( ) const [inline]

Definition at line 100 of file mmcif_reader.hh.

seq::SequenceList GetSeqRes ( ) const [inline]

Return sequences.

Returns:: List of sequences

Definition at line 142 of file mmcif_reader.hh.

seq::SequenceList GetSeqRes ( ) const [inline]

Return sequences.

Returns:: List of sequences

Definition at line 142 of file mmcif_reader.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const [inline, protected]

Definition at line 239 of file mmcif_reader.hh.

const MMCifInfoStructRefs& GetStructRefs ( ) const [inline, protected]

Definition at line 239 of file mmcif_reader.hh.

void Init ( )

Initialise the reader.

void Init ( )

Initialise the reader.

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]`	auth_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]`	cif_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]`	auth_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]`	cif_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 ParsePdbxAuditRevisionDetails ( const std::vector< StringRef > & columns ) [protected]

Fetch mmCIF pdbx_audit_revision_details information.

Parameters:

columns

data row

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

Fetch mmCIF pdbx_audit_revision_details information.

Parameters:

columns

data row

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

Fetch mmCIF pdbx_audit_revision_history information.

Parameters:

columns

data row

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

Fetch mmCIF pdbx_audit_revision_history 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 ParsePdbxDatabaseStatus ( const std::vector< StringRef > & columns ) [protected]

Fetch mmCIF pdbx_database_status information.

Parameters:

columns

data row

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

Fetch mmCIF pdbx_database_status 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 109 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 109 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 95 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 95 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 149 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 149 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
	)			`[inline, protected]`

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 174 of file mmcif_reader.hh.

void TryStoreIdx	(	const int	mapping,
		const String &	item,
		const StarLoopDesc &	header
	)			`[inline, protected]`

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 174 of file mmcif_reader.hh.

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

MMCifReader Class Reference

Data Structures

Public Member Functions

Protected Types

Protected Member Functions

Detailed Description

mmcif format description/ coverage

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation