#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 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_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 MMCifInfoStructRefs &	GetStructRefs () 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 MMCifInfoStructRefs &	GetStructRefs () 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:

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
pdbx_entity_branch
pdbx_entity_branch_link

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 352 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 352 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

stream	input stream
ent_handle
profile

◆ MMCifReader() [2/4]

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

create a MMCifReader

Parameters

filename	input file
ent_handle
profile

◆ MMCifReader() [3/4]

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

create a MMCifReader

Parameters

stream	input stream
ent_handle
profile

◆ MMCifReader() [4/4]

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

create a MMCifReader

Parameters

filename	input 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

ent	Entity to assign secondary structure to

◆ AssignSecStructure() [2/2]

void AssignSecStructure ( mol::EntityHandle ent )

protected

Transform data from struct_conf entry into secondary structure.

Parameters

ent	Entity 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.

◆ ConvertSEQRES() [1/2]

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.

◆ ConvertSEQRES() [2/2]

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.

◆ DetermineSecStructType() [1/2]

MMCifSecStructElement DetermineSecStructType ( const StringRef & type ) const

protected

Check whether an element was classified sheet or helix.

Parameters

type	Type to be classified

◆ DetermineSecStructType() [2/2]

MMCifSecStructElement DetermineSecStructType ( const StringRef & type ) const

protected

Check whether an element was classified sheet or helix.

Parameters

type	Type to be classified

◆ GetInfo() [1/2]

const MMCifInfo& GetInfo ( )

inline

Get additional information of the mmCIF file.

Returns: MMCitfInfo object

Definition at line 167 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 167 of file mmcif_reader.hh.

◆ GetReadSeqRes() [1/2]

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.

◆ GetReadSeqRes() [2/2]

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.

◆ GetRestrictChains() [1/2]

const String& GetRestrictChains ( ) const

inline

Definition at line 102 of file mmcif_reader.hh.

◆ GetRestrictChains() [2/2]

const String& GetRestrictChains ( ) const

inline

Definition at line 102 of file mmcif_reader.hh.

◆ GetSeqRes() [1/2]

seq::SequenceList GetSeqRes ( ) const

inline

Return sequences.

Returns: List of sequences

Definition at line 144 of file mmcif_reader.hh.

◆ GetSeqRes() [2/2]

seq::SequenceList GetSeqRes ( ) const

inline

Return sequences.

Returns: List of sequences

Definition at line 144 of file mmcif_reader.hh.

◆ GetStructRefs() [1/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const

inlineprotected

Definition at line 234 of file mmcif_reader.hh.

◆ GetStructRefs() [2/2]

const MMCifInfoStructRefs& GetStructRefs ( ) const

inlineprotected

Definition at line 234 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_name value 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_name value 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

header categories 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

header categories 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

header	categories and items
columns	data

Reimplemented from StarParser.

◆ OnDataRow() [2/2]

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.

◆ 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

columns data row

◆ ParseAndAddAtom() [2/2]

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

protected

Fetch atom information and store it.

Parameters

columns data 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]	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

◆ 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]	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

◆ ParseCitation() [1/2]

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

protected

Fetch mmCIF citation information.

Parameters

columns data row

◆ ParseCitation() [2/2]

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

protected

Fetch mmCIF citation information.

Parameters

columns data row

◆ ParseCitationAuthor() [1/2]

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

protected

Fetch mmCIF citation_author information.

Parameters

columns data row

◆ ParseCitationAuthor() [2/2]

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

protected

Fetch mmCIF citation_author information.

Parameters

columns data row

◆ ParseDatabasePDBRev() [1/2]

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

protected

Fetch mmCIF database_PDB_rev information.

Parameters

columns data row

◆ ParseDatabasePDBRev() [2/2]

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

protected

Fetch mmCIF database_PDB_rev information.

Parameters

columns data row

◆ ParseEm3DReconstruction() [1/2]

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

protected

Fetch mmCIF entity_poly_seq information.

Parameters

columns data row

◆ ParseEm3DReconstruction() [2/2]

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

protected

Fetch mmCIF entity_poly_seq information.

Parameters

columns data row

◆ ParseEntity() [1/2]

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

protected

Fetch mmCIF entity information.

Parameters

columns data row

◆ ParseEntity() [2/2]

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

protected

Fetch mmCIF entity information.

Parameters

columns data row

◆ ParseEntityPoly() [1/2]

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

protected

Fetch mmCIF entity_poly information.

Parameters

columns data row

◆ ParseEntityPoly() [2/2]

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

protected

Fetch mmCIF entity_poly information.

Parameters

columns data row

◆ ParseEntityPolySeq() [1/2]

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

protected

Fetch mmCIF entity_poly_seq information.

Parameters

columns data row

◆ ParseEntityPolySeq() [2/2]

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

protected

Fetch mmCIF entity_poly_seq information.

Parameters

columns data row

◆ ParseExptl() [1/2]

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

protected

Fetch mmCIF exptl information.

Parameters

columns data row

◆ ParseExptl() [2/2]

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

protected

Fetch mmCIF exptl information.

Parameters

columns data row

◆ ParsePdbxAuditRevisionDetails() [1/2]

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

protected

Fetch mmCIF pdbx_audit_revision_details information.

Parameters

columns data row

◆ ParsePdbxAuditRevisionDetails() [2/2]

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

protected

Fetch mmCIF pdbx_audit_revision_details information.

Parameters

columns data row

◆ ParsePdbxAuditRevisionHistory() [1/2]

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

protected

Fetch mmCIF pdbx_audit_revision_history information.

Parameters

columns data row

◆ ParsePdbxAuditRevisionHistory() [2/2]

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

protected

Fetch mmCIF pdbx_audit_revision_history information.

Parameters

columns data row

◆ ParsePdbxDatabasePdbObsSpr() [1/2]

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

protected

Fetch mmCIF pdbx_database_PDB_obs_spr information.

Parameters

columns data row

◆ ParsePdbxDatabasePdbObsSpr() [2/2]

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

protected

Fetch mmCIF pdbx_database_PDB_obs_spr information.

Parameters

columns data row

◆ ParsePdbxDatabaseStatus() [1/2]

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

protected

Fetch mmCIF pdbx_database_status information.

Parameters

columns data row

◆ ParsePdbxDatabaseStatus() [2/2]

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

protected

Fetch mmCIF pdbx_database_status information.

Parameters

columns data row

◆ ParsePdbxEntityBranch() [1/2]

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

protected

Fetch mmCIF pdbx_entity_branch information.

Parameters

columns data row

◆ ParsePdbxEntityBranch() [2/2]

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

protected

Fetch mmCIF pdbx_entity_branch information.

Parameters

columns data row

◆ ParsePdbxEntityBranchLink() [1/2]

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

protected

Fetch mmCIF pdbx_entity_branch_link information.

Parameters

columns data row

◆ ParsePdbxEntityBranchLink() [2/2]

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

protected

Fetch mmCIF pdbx_entity_branch_link information.

Parameters

columns data row

◆ ParsePdbxStructAssembly() [1/2]

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

protected

Fetch mmCIF pdbx_struct_assembly information.

Parameters

columns data row

◆ ParsePdbxStructAssembly() [2/2]

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

protected

Fetch mmCIF pdbx_struct_assembly information.

Parameters

columns data row

◆ ParsePdbxStructAssemblyGen() [1/2]

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

protected

Fetch mmCIF pdbx_struct_assembly_gen information.

Parameters

columns data row

◆ ParsePdbxStructAssemblyGen() [2/2]

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

protected

Fetch mmCIF pdbx_struct_assembly_gen information.

Parameters

columns data row

◆ ParsePdbxStructOperList() [1/2]

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

protected

Fetch mmCIF pdbx_struct_oper_list information.

Parameters

columns data row

◆ ParsePdbxStructOperList() [2/2]

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

protected

Fetch mmCIF pdbx_struct_oper_list information.

Parameters

columns data row

◆ ParseRefine() [1/2]

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

protected

Fetch mmCIF refine information.

Parameters

columns data row

◆ ParseRefine() [2/2]

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

protected

Fetch mmCIF refine information.

Parameters

columns data row

◆ ParseStruct() [1/2]

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

protected

Fetch mmCIF struct information.

Parameters

columns data row

◆ ParseStruct() [2/2]

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

protected

Fetch mmCIF struct information.

Parameters

columns data row

◆ ParseStructConf() [1/2]

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

protected

Fetch mmCIF struct_conf (secondary structure) information.

Parameters

columns data row

◆ ParseStructConf() [2/2]

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

protected

Fetch mmCIF struct_conf (secondary structure) information.

Parameters

columns data 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

columns data row

◆ ParseStructSheetRange() [2/2]

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

protected

Fetch mmCIF struct_sheet_range (beta sheets) information.

Parameters

columns data row

◆ SetAuthChainID() [1/2]

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 111 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

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

Definition at line 111 of file mmcif_reader.hh.

◆ SetReadCanonicalSeqRes() [1/2]

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 97 of file mmcif_reader.hh.

◆ SetReadCanonicalSeqRes() [2/2]

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 97 of file mmcif_reader.hh.

◆ SetReadSeqRes() [1/2]

void SetReadSeqRes ( bool flag )

inline

Toggle reading of SEQRES.

Parameters

flag	True enables, False disables reading SEQRES

Definition at line 151 of file mmcif_reader.hh.

◆ SetReadSeqRes() [2/2]

void SetReadSeqRes ( bool flag )

inline

Toggle reading of SEQRES.

Parameters

flag	True enables, False disables reading SEQRES

Definition at line 151 of file mmcif_reader.hh.

◆ SetRestrictChains() [1/2]

void SetRestrictChains ( const String & restrict_chains )

Set names of restricted chains for the reader.

Parameters

restrict_chains chain name

◆ SetRestrictChains() [2/2]

void SetRestrictChains ( const String & restrict_chains )

Set names of restricted chains for the reader.

Parameters

restrict_chains chain 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

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

Definition at line 176 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

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

Definition at line 176 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:

build-dev-doc/stage/include/ost/io/mmcif_reader.hh

Public Member Functions

Protected Types

Protected Member Functions

Additional Inherited Members

Detailed Description

mmcif format description/ coverage

Member Enumeration Documentation

◆ MMCifSecStructElement [1/2]

◆ MMCifSecStructElement [2/2]

Constructor & Destructor Documentation

◆ MMCifReader() [1/4]

◆ MMCifReader() [2/4]

◆ MMCifReader() [3/4]

◆ MMCifReader() [4/4]

Member Function Documentation

◆ AssignSecStructure() [1/2]

◆ AssignSecStructure() [2/2]

◆ ClearState() [1/2]

◆ ClearState() [2/2]

◆ ConvertSEQRES() [1/2]

◆ ConvertSEQRES() [2/2]

◆ DetermineSecStructType() [1/2]

◆ DetermineSecStructType() [2/2]

◆ GetInfo() [1/2]

◆ GetInfo() [2/2]

◆ GetReadSeqRes() [1/2]

◆ GetReadSeqRes() [2/2]

◆ GetRestrictChains() [1/2]

◆ GetRestrictChains() [2/2]

◆ GetSeqRes() [1/2]

◆ GetSeqRes() [2/2]

◆ GetStructRefs() [1/2]

◆ GetStructRefs() [2/2]

◆ Init() [1/2]

◆ Init() [2/2]

◆ OnBeginData() [1/2]

◆ OnBeginData() [2/2]

◆ OnBeginLoop() [1/2]

◆ OnBeginLoop() [2/2]

◆ OnDataRow() [1/2]

◆ OnDataRow() [2/2]

◆ OnEndData() [1/2]

◆ OnEndData() [2/2]

◆ ParseAndAddAtom() [1/2]

◆ ParseAndAddAtom() [2/2]

◆ ParseAtomIdent() [1/2]

◆ ParseAtomIdent() [2/2]

◆ ParseCitation() [1/2]

◆ ParseCitation() [2/2]

◆ ParseCitationAuthor() [1/2]

◆ ParseCitationAuthor() [2/2]

◆ ParseDatabasePDBRev() [1/2]

◆ ParseDatabasePDBRev() [2/2]

◆ ParseEm3DReconstruction() [1/2]

◆ ParseEm3DReconstruction() [2/2]

◆ ParseEntity() [1/2]

◆ ParseEntity() [2/2]

◆ ParseEntityPoly() [1/2]

◆ ParseEntityPoly() [2/2]

◆ ParseEntityPolySeq() [1/2]

◆ ParseEntityPolySeq() [2/2]

◆ ParseExptl() [1/2]

◆ ParseExptl() [2/2]

◆ ParsePdbxAuditRevisionDetails() [1/2]

◆ ParsePdbxAuditRevisionDetails() [2/2]

◆ ParsePdbxAuditRevisionHistory() [1/2]

◆ ParsePdbxAuditRevisionHistory() [2/2]

◆ ParsePdbxDatabasePdbObsSpr() [1/2]

◆ ParsePdbxDatabasePdbObsSpr() [2/2]

◆ ParsePdbxDatabaseStatus() [1/2]

◆ ParsePdbxDatabaseStatus() [2/2]

◆ ParsePdbxEntityBranch() [1/2]

◆ ParsePdbxEntityBranch() [2/2]

◆ ParsePdbxEntityBranchLink() [1/2]

◆ ParsePdbxEntityBranchLink() [2/2]

◆ ParsePdbxStructAssembly() [1/2]

◆ ParsePdbxStructAssembly() [2/2]

◆ ParsePdbxStructAssemblyGen() [1/2]

◆ ParsePdbxStructAssemblyGen() [2/2]

◆ ParsePdbxStructOperList() [1/2]