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Public Member Functions | Protected Member Functions | Static Protected Member Functions
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)

Detailed Description

Definition at line 45 of file processor.hh.


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.


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.


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