OMF Class Reference

#include <omf.hh>

Public Types
enum	OMFOption {   DEFAULT_PEPLIB = 1 , AVG_BFACTORS = 2 , ROUND_BFACTORS = 4 , SKIP_SS = 8 ,   INFER_PEP_BONDS = 16 , DEFAULT_PEPLIB = 1 , AVG_BFACTORS = 2 , ROUND_BFACTORS = 4 ,   SKIP_SS = 8 , INFER_PEP_BONDS = 16 }
enum	OMFOption {   DEFAULT_PEPLIB = 1 , AVG_BFACTORS = 2 , ROUND_BFACTORS = 4 , SKIP_SS = 8 ,   INFER_PEP_BONDS = 16 , DEFAULT_PEPLIB = 1 , AVG_BFACTORS = 2 , ROUND_BFACTORS = 4 ,   SKIP_SS = 8 , INFER_PEP_BONDS = 16 }

Public Member Functions
bool	OptionSet (OMFOption opt) const
void	ToFile (const String &fn) const
String	ToString () const
ost::mol::EntityHandle	GetAU () const
ost::mol::EntityHandle	GetEntity () const
ost::mol::EntityHandle	GetAUChain (const String &name) const
ost::mol::EntityHandle	GetEntityChain (const String &name) const
OMFPtr	ToAssembly (const std::vector< std::vector< String > > &au_chains, const std::vector< std::vector< geom::Mat4 > > &transformations, const std::vector< std::vector< std::vector< String > > > &bu_chains) const
void	Trace (const String &cname, const String &aname, std::vector< int > &rnums, geom::Vec3List &pos) const
int	GetVersion () const
Real	GetMaxError () const
String	GetName () const
std::vector< String >	GetChainNames () const
const geom::Vec3List &	GetPositions (const String &cname) const
const std::vector< Real > &	GetBFactors (const String &cname) const
std::vector< Real >	GetAvgBFactors (const String &cname) const
const std::vector< Real > &	GetOccupancies (const String &cname) const
String	GetSequence (const String &cname) const
const std::vector< int > &	GetRNums (const String &cname) const
const std::vector< ResidueDefinition > &	GetResidueDefinitions () const
ChainDataPtr	GetChainData (const std::string &cname) const
bool	OptionSet (OMFOption opt) const
void	ToFile (const String &fn) const
String	ToString () const
ost::mol::EntityHandle	GetAU () const
ost::mol::EntityHandle	GetEntity () const
ost::mol::EntityHandle	GetAUChain (const String &name) const
ost::mol::EntityHandle	GetEntityChain (const String &name) const
OMFPtr	ToAssembly (const std::vector< std::vector< String > > &au_chains, const std::vector< std::vector< geom::Mat4 > > &transformations, const std::vector< std::vector< std::vector< String > > > &bu_chains) const
void	Trace (const String &cname, const String &aname, std::vector< int > &rnums, geom::Vec3List &pos) const
int	GetVersion () const
Real	GetMaxError () const
String	GetName () const
std::vector< String >	GetChainNames () const
const geom::Vec3List &	GetPositions (const String &cname) const
const std::vector< Real > &	GetBFactors (const String &cname) const
std::vector< Real >	GetAvgBFactors (const String &cname) const
const std::vector< Real > &	GetOccupancies (const String &cname) const
String	GetSequence (const String &cname) const
const std::vector< int > &	GetRNums (const String &cname) const
const std::vector< ResidueDefinition > &	GetResidueDefinitions () const
ChainDataPtr	GetChainData (const std::string &cname) const

Static Public Member Functions
static OMFPtr	FromEntity (const ost::mol::EntityHandle &ent, Real max_error=0.0, uint8_t options=0)
static OMFPtr	FromFile (const String &fn)
static OMFPtr	FromString (const String &s)
static int	GetCurrentOMFVersion ()
static OMFPtr	FromEntity (const ost::mol::EntityHandle &ent, Real max_error=0.0, uint8_t options=0)
static OMFPtr	FromFile (const String &fn)
static OMFPtr	FromString (const String &s)
static int	GetCurrentOMFVersion ()

Detailed Description

Definition at line 180 of file omf.hh.

Member Enumeration Documentation

OMFOption [1/2]

enum OMFOption

Enumerator
DEFAULT_PEPLIB
AVG_BFACTORS
ROUND_BFACTORS
SKIP_SS
INFER_PEP_BONDS
DEFAULT_PEPLIB
AVG_BFACTORS
ROUND_BFACTORS
SKIP_SS
INFER_PEP_BONDS

Definition at line 184 of file omf.hh.

OMFOption [2/2]

enum OMFOption

Enumerator
DEFAULT_PEPLIB
AVG_BFACTORS
ROUND_BFACTORS
SKIP_SS
INFER_PEP_BONDS
DEFAULT_PEPLIB
AVG_BFACTORS
ROUND_BFACTORS
SKIP_SS
INFER_PEP_BONDS

Definition at line 184 of file omf.hh.

Member Function Documentation

FromEntity() [1/2]

static OMFPtr FromEntity ( const ost::mol::EntityHandle &  ent, Real  max_error = 0.0, uint8_t  options = 0  )

static

FromEntity() [2/2]

static OMFPtr FromEntity ( const ost::mol::EntityHandle &  ent, Real  max_error = 0.0, uint8_t  options = 0  )

static

FromFile() [1/2]

static OMFPtr FromFile ( const String &  fn )

static

FromFile() [2/2]

static OMFPtr FromFile ( const String &  fn )

static

FromString() [1/2]

static OMFPtr FromString ( const String &  s )

static

FromString() [2/2]

static OMFPtr FromString ( const String &  s )

static

GetAU() [1/2]

ost::mol::EntityHandle GetAU

(

)

const

GetAU() [2/2]

ost::mol::EntityHandle GetAU

(

)

const

GetAUChain() [1/2]

ost::mol::EntityHandle GetAUChain

(

const String &

name

)

const

GetAUChain() [2/2]

ost::mol::EntityHandle GetAUChain

(

const String &

name

)

const

GetAvgBFactors() [1/2]

std::vector<Real> GetAvgBFactors

(

const String &

cname

)

const

GetAvgBFactors() [2/2]

std::vector<Real> GetAvgBFactors

(

const String &

cname

)

const

GetBFactors() [1/2]

const std::vector<Real>& GetBFactors

(

const String &

cname

)

const

GetBFactors() [2/2]

const std::vector<Real>& GetBFactors

(

const String &

cname

)

const

GetChainData() [1/2]

ChainDataPtr GetChainData ( const std::string &  cname ) const

inline

Definition at line 252 of file omf.hh.

GetChainData() [2/2]

ChainDataPtr GetChainData ( const std::string &  cname ) const

inline

Definition at line 252 of file omf.hh.

GetChainNames() [1/2]

std::vector<String> GetChainNames

(

)

const

GetChainNames() [2/2]

std::vector<String> GetChainNames

(

)

const

GetCurrentOMFVersion() [1/2]

static int GetCurrentOMFVersion ( )

inlinestatic

Definition at line 224 of file omf.hh.

GetCurrentOMFVersion() [2/2]

static int GetCurrentOMFVersion ( )

inlinestatic

Definition at line 224 of file omf.hh.

GetEntity() [1/2]

ost::mol::EntityHandle GetEntity ( ) const

inline

Definition at line 205 of file omf.hh.

GetEntity() [2/2]

ost::mol::EntityHandle GetEntity ( ) const

inline

Definition at line 205 of file omf.hh.

GetEntityChain() [1/2]

ost::mol::EntityHandle GetEntityChain ( const String &  name ) const

inline

Definition at line 211 of file omf.hh.

GetEntityChain() [2/2]

ost::mol::EntityHandle GetEntityChain ( const String &  name ) const

inline

Definition at line 211 of file omf.hh.

GetMaxError() [1/2]

Real GetMaxError ( ) const

inline

Definition at line 226 of file omf.hh.

GetMaxError() [2/2]

Real GetMaxError ( ) const

inline

Definition at line 226 of file omf.hh.

GetName() [1/2]

String GetName ( ) const

inline

Definition at line 231 of file omf.hh.

GetName() [2/2]

String GetName ( ) const

inline

Definition at line 231 of file omf.hh.

GetOccupancies() [1/2]

const std::vector<Real>& GetOccupancies

(

const String &

cname

)

const

GetOccupancies() [2/2]

const std::vector<Real>& GetOccupancies

(

const String &

cname

)

const

GetPositions() [1/2]

const geom::Vec3List& GetPositions

(

const String &

cname

)

const

GetPositions() [2/2]

const geom::Vec3List& GetPositions

(

const String &

cname

)

const

GetResidueDefinitions() [1/2]

const std::vector<ResidueDefinition>& GetResidueDefinitions ( ) const

inline

Definition at line 248 of file omf.hh.

GetResidueDefinitions() [2/2]

const std::vector<ResidueDefinition>& GetResidueDefinitions ( ) const

inline

Definition at line 248 of file omf.hh.

GetRNums() [1/2]

const std::vector<int>& GetRNums

(

const String &

cname

)

const

GetRNums() [2/2]

const std::vector<int>& GetRNums

(

const String &

cname

)

const

GetSequence() [1/2]

String GetSequence

(

const String &

cname

)

const

GetSequence() [2/2]

String GetSequence

(

const String &

cname

)

const

GetVersion() [1/2]

int GetVersion ( ) const

inline

Definition at line 222 of file omf.hh.

GetVersion() [2/2]

int GetVersion ( ) const

inline

Definition at line 222 of file omf.hh.

OptionSet() [1/2]

bool OptionSet ( OMFOption  opt ) const

inline

Definition at line 187 of file omf.hh.

OptionSet() [2/2]

bool OptionSet ( OMFOption  opt ) const

inline

Definition at line 187 of file omf.hh.

ToAssembly() [1/2]

OMFPtr ToAssembly	(	const std::vector< std::vector< String > > &	au_chains,
		const std::vector< std::vector< geom::Mat4 > > &	transformations,
		const std::vector< std::vector< std::vector< String > > > &	bu_chains
	)		const

ToAssembly() [2/2]

OMFPtr ToAssembly	(	const std::vector< std::vector< String > > &	au_chains,
		const std::vector< std::vector< geom::Mat4 > > &	transformations,
		const std::vector< std::vector< std::vector< String > > > &	bu_chains
	)		const

ToFile() [1/2]

void ToFile

(

const String &

fn

)

const

ToFile() [2/2]

void ToFile

(

const String &

fn

)

const

ToString() [1/2]

String ToString

(

)

const

ToString() [2/2]

String ToString

(

)

const

Trace() [1/2]

void Trace	(	const String &	cname,
		const String &	aname,
		std::vector< int > &	rnums,
		geom::Vec3List &	pos
	)		const

Trace() [2/2]

void Trace	(	const String &	cname,
		const String &	aname,
		std::vector< int > &	rnums,
		geom::Vec3List &	pos
	)		const

---

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

• build-2.10/stage/include/ost/io/mol/omf.hh