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

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