Processor Class Reference

#include <processor.hh>

Inherited by HeuristicProcessor, and RuleBasedProcessor.

Public Member Functions
DiagnosticsPtr	Process (mol::EntityHandle ent, bool log_diags=true) const
virtual ProcessorPtr	Copy () const =0
virtual	~Processor ()
	Processor (bool bf, bool at, bool cn, bool aa, ConopAction zo)
	Processor ()
void	SetConnect (bool connect)
bool	GetConnect () const
void	SetAssignTorsions (bool flag)
bool	GetAssignTorsions () const
bool	GetConnectAminoAcids () const
void	SetConnectAminoAcids (bool c)
bool	GetCheckBondFeasibility () const
void	SetCheckBondFeasibility (bool flag)
ConopAction	GetZeroOccTreatment () const
void	SetZeroOccTreatment (ConopAction action)
virtual String	ToString () const =0

Protected Member Functions
virtual void	DoProcess (DiagnosticsPtr diags, mol::EntityHandle ent) const =0
virtual bool	BeginProcessing (DiagnosticsPtr diags, mol::EntityHandle ent) const
virtual bool	EndProcessing (DiagnosticsPtr diags, mol::EntityHandle ent) const
bool	HasUnknownAtoms (mol::ResidueHandle residue, CompoundPtr compound, bool strict_hydrogens) const
void	ReorderAtoms (mol::ResidueHandle residue, CompoundPtr compound, bool fix_element) const
void	FillResidueProps (mol::ResidueHandle residue, CompoundPtr compound) const
void	ConnectAtomsOfResidue (mol::ResidueHandle residue, CompoundPtr compound, bool strict_hydrogens) const
void	ConnectResidues (mol::ResidueHandle residue, mol::ResidueHandle next) const
void	DistanceBasedConnect (mol::AtomHandle atom) const
mol::AtomHandle	LocateAtom (const mol::AtomHandleList &, int ordinal) const
String	OptionsToString () const

Static Protected Member Functions
static bool	AreResiduesConsecutive (mol::ResidueHandle a, mol::ResidueHandle b)

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Detailed Description

Definition at line 45 of file processor.hh.

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Constructor & Destructor Documentation

virtual ~Processor ( )

inlinevirtual

Definition at line 49 of file processor.hh.

Processor ( bool  bf, bool  at, bool  cn, bool  aa, ConopAction  zo  )

inline

Definition at line 69 of file processor.hh.

Processor ( )

inline

Definition at line 72 of file processor.hh.

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Member Function Documentation

static bool AreResiduesConsecutive ( mol::ResidueHandle  a, mol::ResidueHandle  b  )

staticprotected

virtual bool BeginProcessing ( DiagnosticsPtr  diags, mol::EntityHandle  ent  ) const

inlineprotectedvirtual

Definition at line 53 of file processor.hh.

void ConnectAtomsOfResidue ( mol::ResidueHandle  residue, CompoundPtr  compound, bool  strict_hydrogens  ) const

protected

void ConnectResidues ( mol::ResidueHandle  residue, mol::ResidueHandle  next  ) const

protected

virtual ProcessorPtr Copy ( ) const

pure virtual

Implemented in RuleBasedProcessor, and HeuristicProcessor.

void DistanceBasedConnect ( mol::AtomHandle  atom ) const

protected

virtual void DoProcess ( DiagnosticsPtr  diags, mol::EntityHandle  ent  ) const

protectedpure virtual

Implemented in RuleBasedProcessor, and HeuristicProcessor.

virtual bool EndProcessing ( DiagnosticsPtr  diags, mol::EntityHandle  ent  ) const

inlineprotectedvirtual

Definition at line 55 of file processor.hh.

void FillResidueProps ( mol::ResidueHandle  residue, CompoundPtr  compound  ) const

protected

bool GetAssignTorsions ( ) const

inline

Definition at line 85 of file processor.hh.

bool GetCheckBondFeasibility ( ) const

inline

Definition at line 95 of file processor.hh.

bool GetConnect ( ) const

inline

Definition at line 79 of file processor.hh.

bool GetConnectAminoAcids ( ) const

inline

Definition at line 89 of file processor.hh.

ConopAction GetZeroOccTreatment ( ) const

inline

Definition at line 105 of file processor.hh.

bool HasUnknownAtoms ( mol::ResidueHandle  residue, CompoundPtr  compound, bool  strict_hydrogens  ) const

protected

mol::AtomHandle LocateAtom ( const mol::AtomHandleList &  , int  ordinal  ) const

protected

String OptionsToString ( ) const

protected

DiagnosticsPtr Process	(	mol::EntityHandle	ent,
		bool	log_diags = true
	)		const

void ReorderAtoms ( mol::ResidueHandle  residue, CompoundPtr  compound, bool  fix_element  ) const

protected

void SetAssignTorsions ( bool  flag )

inline

Definition at line 82 of file processor.hh.

void SetCheckBondFeasibility ( bool  flag )

inline

Definition at line 100 of file processor.hh.

void SetConnect ( bool  connect )

inline

Definition at line 75 of file processor.hh.

void SetConnectAminoAcids ( bool  c )

inline

Definition at line 92 of file processor.hh.

void SetZeroOccTreatment ( ConopAction  action )

inline

Definition at line 109 of file processor.hh.

virtual String ToString ( ) const

pure virtual

Implemented in RuleBasedProcessor, and HeuristicProcessor.

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

• stage/include/ost/conop/processor.hh