RuleBasedProcessor Class Reference

#include <rule_based.hh>

Inherits Processor.

Public Member Functions
	RuleBasedProcessor (CompoundLibPtr compound_lib)
	RuleBasedProcessor (CompoundLibPtr compound_lib, bool fe, bool sh, ConopAction ur, ConopAction ua, bool bf, bool at, bool cn, bool aa, ConopAction zo)
ConopAction	GetUnkResidueTreatment () const
ConopAction	GetUnkAtomTreatment () const
bool	GetFixElement () const
void	SetFixElement (bool flag)
bool	GetStrictHydrogens () const
void	SetStrictHydrogens (bool flag)
void	SetUnkResidueTreatment (ConopAction action)
void	SetUnkAtomTreatment (ConopAction action)
virtual ProcessorPtr	Copy () const
virtual String	ToString () const
Public Member Functions inherited from Processor
DiagnosticsPtr	Process (mol::EntityHandle ent, bool log_diags=true) const
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)

Protected Member Functions
void	ProcessUnkResidue (DiagnosticsPtr diags, mol::ResidueHandle res, mol::AtomHandleList &remaining) const
void	ProcessUnkAtoms (DiagnosticsPtr diags, mol::ResidueHandle res, mol::AtomHandleList unks, mol::AtomHandleList &remaining) const
virtual void	DoProcess (DiagnosticsPtr diags, mol::EntityHandle ent) const
Protected Member Functions inherited from Processor
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

Additional Inherited Members
Static Protected Member Functions inherited from Processor
static bool	AreResiduesConsecutive (mol::ResidueHandle a, mol::ResidueHandle b)

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Detailed Description

Definition at line 37 of file rule_based.hh.

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Constructor & Destructor Documentation

RuleBasedProcessor ( CompoundLibPtr  compound_lib )

inline

Definition at line 39 of file rule_based.hh.

RuleBasedProcessor ( CompoundLibPtr  compound_lib, bool  fe, bool  sh, ConopAction  ur, ConopAction  ua, bool  bf, bool  at, bool  cn, bool  aa, ConopAction  zo  )

inline

Definition at line 45 of file rule_based.hh.

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Member Function Documentation

virtual ProcessorPtr Copy ( ) const

inlinevirtual

Implements Processor.

Definition at line 78 of file rule_based.hh.

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

protectedvirtual

Implements Processor.

bool GetFixElement ( ) const

inline

Definition at line 58 of file rule_based.hh.

bool GetStrictHydrogens ( ) const

inline

Definition at line 64 of file rule_based.hh.

ConopAction GetUnkAtomTreatment ( ) const

inline

Definition at line 54 of file rule_based.hh.

ConopAction GetUnkResidueTreatment ( ) const

inline

Definition at line 50 of file rule_based.hh.

void ProcessUnkAtoms ( DiagnosticsPtr  diags, mol::ResidueHandle  res, mol::AtomHandleList  unks, mol::AtomHandleList &  remaining  ) const

protected

void ProcessUnkResidue ( DiagnosticsPtr  diags, mol::ResidueHandle  res, mol::AtomHandleList &  remaining  ) const

protected

void SetFixElement ( bool  flag )

inline

Definition at line 61 of file rule_based.hh.

void SetStrictHydrogens ( bool  flag )

inline

Definition at line 68 of file rule_based.hh.

void SetUnkAtomTreatment ( ConopAction  action )

inline

Definition at line 75 of file rule_based.hh.

void SetUnkResidueTreatment ( ConopAction  action )

inline

Definition at line 71 of file rule_based.hh.

virtual String ToString ( ) const

virtual

Implements Processor.

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

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