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 (  )  [inline, virtual]

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 
) [static, protected]
virtual bool BeginProcessing ( DiagnosticsPtr  diags,
mol::EntityHandle  ent 
) const [inline, protected, virtual]

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 HeuristicProcessor, and RuleBasedProcessor.

void DistanceBasedConnect ( mol::AtomHandle  atom  )  const [protected]
virtual void DoProcess ( DiagnosticsPtr  diags,
mol::EntityHandle  ent 
) const [protected, pure virtual]

Implemented in HeuristicProcessor, and RuleBasedProcessor.

virtual bool EndProcessing ( DiagnosticsPtr  diags,
mol::EntityHandle  ent 
) const [inline, protected, virtual]

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 HeuristicProcessor, and RuleBasedProcessor.


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