#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

virtual ~Processor ( )

inlinevirtual

Definition at line 49 of file processor.hh.

Processor	(	bool	bf,
		bool	at,
		bool	cn,
		bool	aa,
		bool	ch,
		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 86 of file processor.hh.

bool GetCheckBondFeasibility ( ) const

inline

Definition at line 104 of file processor.hh.

bool GetConnect ( ) const

inline

Definition at line 79 of file processor.hh.

bool GetConnectAminoAcids ( ) const

inline

Definition at line 90 of file processor.hh.

bool GetConnectHetatm ( ) const

inline

Definition at line 97 of file processor.hh.

ConopAction GetZeroOccTreatment ( ) const

inline

Definition at line 112 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 83 of file processor.hh.

void SetCheckBondFeasibility ( bool flag )

inline

Definition at line 108 of file processor.hh.

void SetConnect ( bool connect )

inline

Definition at line 76 of file processor.hh.

void SetConnectAminoAcids ( bool c )

inline

Definition at line 93 of file processor.hh.

void SetConnectHetatm ( bool c )

inline

Definition at line 100 of file processor.hh.

void SetZeroOccTreatment ( ConopAction action )

inline

Definition at line 115 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:

build-2.6/stage/include/ost/conop/processor.hh

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation