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Public Types | Public Member Functions | Static Public Member Functions
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< 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< 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 250 of file omf.hh.

◆ GetChainData() [2/2]

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

Definition at line 250 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 246 of file omf.hh.

◆ GetResidueDefinitions() [2/2]

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

Definition at line 246 of file omf.hh.

◆ 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:
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