#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)

Detailed Description

Definition at line 37 of file rule_based.hh.

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 46 of file rule_based.hh.

Member Function Documentation

virtual ProcessorPtr Copy ( ) const

inlinevirtual

Implements Processor.

Definition at line 84 of file rule_based.hh.

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

protectedvirtual

Implements Processor.

bool GetFixElement ( ) const

inline

Definition at line 64 of file rule_based.hh.

bool GetStrictHydrogens ( ) const

inline

Definition at line 70 of file rule_based.hh.

ConopAction GetUnkAtomTreatment ( ) const

inline

Definition at line 60 of file rule_based.hh.

ConopAction GetUnkResidueTreatment ( ) const

inline

Definition at line 56 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 67 of file rule_based.hh.

void SetStrictHydrogens ( bool flag )

inline

Definition at line 74 of file rule_based.hh.

void SetUnkAtomTreatment ( ConopAction action )

inline

Definition at line 81 of file rule_based.hh.

void SetUnkResidueTreatment ( ConopAction action )

inline

Definition at line 77 of file rule_based.hh.

virtual String ToString ( ) const

virtual

Implements Processor.

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

stage/include/ost/conop/rule_based.hh

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation