OpenStructure
Public Member Functions | Protected Member Functions | Static Protected Member Functions
Processor Class Referenceabstract

#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, bool ch, 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 GetConnectHetatm () const
 
void SetConnectHetatm (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

◆ ~Processor()

virtual ~Processor ( )
inlinevirtual

Definition at line 49 of file processor.hh.

◆ Processor() [1/2]

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

Definition at line 69 of file processor.hh.

◆ Processor() [2/2]

Processor ( )
inline

Definition at line 72 of file processor.hh.

Member Function Documentation

◆ AreResiduesConsecutive()

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

◆ BeginProcessing()

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

Definition at line 53 of file processor.hh.

◆ ConnectAtomsOfResidue()

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

◆ ConnectResidues()

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

◆ Copy()

virtual ProcessorPtr Copy ( ) const
pure virtual

Implemented in RuleBasedProcessor, and HeuristicProcessor.

◆ DistanceBasedConnect()

void DistanceBasedConnect ( mol::AtomHandle  atom) const
protected

◆ DoProcess()

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

Implemented in RuleBasedProcessor, and HeuristicProcessor.

◆ EndProcessing()

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

Definition at line 55 of file processor.hh.

◆ FillResidueProps()

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

◆ GetAssignTorsions()

bool GetAssignTorsions ( ) const
inline

Definition at line 86 of file processor.hh.

◆ GetCheckBondFeasibility()

bool GetCheckBondFeasibility ( ) const
inline

Definition at line 104 of file processor.hh.

◆ GetConnect()

bool GetConnect ( ) const
inline

Definition at line 79 of file processor.hh.

◆ GetConnectAminoAcids()

bool GetConnectAminoAcids ( ) const
inline

Definition at line 90 of file processor.hh.

◆ GetConnectHetatm()

bool GetConnectHetatm ( ) const
inline

Definition at line 97 of file processor.hh.

◆ GetZeroOccTreatment()

ConopAction GetZeroOccTreatment ( ) const
inline

Definition at line 112 of file processor.hh.

◆ HasUnknownAtoms()

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

◆ LocateAtom()

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

◆ OptionsToString()

String OptionsToString ( ) const
protected

◆ Process()

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

◆ ReorderAtoms()

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

◆ SetAssignTorsions()

void SetAssignTorsions ( bool  flag)
inline

Definition at line 83 of file processor.hh.

◆ SetCheckBondFeasibility()

void SetCheckBondFeasibility ( bool  flag)
inline

Definition at line 108 of file processor.hh.

◆ SetConnect()

void SetConnect ( bool  connect)
inline

Definition at line 76 of file processor.hh.

◆ SetConnectAminoAcids()

void SetConnectAminoAcids ( bool  c)
inline

Definition at line 93 of file processor.hh.

◆ SetConnectHetatm()

void SetConnectHetatm ( bool  c)
inline

Definition at line 100 of file processor.hh.

◆ SetZeroOccTreatment()

void SetZeroOccTreatment ( ConopAction  action)
inline

Definition at line 115 of file processor.hh.

◆ ToString()

virtual String ToString ( ) const
pure virtual

Implemented in RuleBasedProcessor, and HeuristicProcessor.

The documentation for this class was generated from the following file:
Generated by doxygen 1.9.1