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Public Member Functions | Protected Member Functions
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, bool ch, 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, 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)
 

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,
bool  ch,
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: