HeuristicBuilder Class Reference

#include <heuristic_builder.hh>

Inherits Builder.

Public Member Functions
	HeuristicBuilder ()
virtual	~HeuristicBuilder ()
virtual void	AssignTorsions (mol::ChainHandle ch)
virtual void	ConnectAtomsOfResidue (mol::ResidueHandle rh)
virtual bool	IsResidueComplete (const mol::ResidueHandle &rh)
virtual void	ConnectResidueToPrev (mol::ResidueHandle rh, mol::ResidueHandle prev)
virtual void	AssignTorsionsToResidue (mol::ResidueHandle residue)
virtual void	FillResidueProps (mol::ResidueHandle residue)
virtual void	ConnectResidueToNext (mol::ResidueHandle rh, mol::ResidueHandle next)
std::pair < detail::ConnResEntry, bool >	LookupResEntry (const mol::ResidueKey &key)
virtual void	FillAtomProps (mol::AtomHandle atom)
const detail::ConnResEntry &	DefaultPeptide () const
const detail::ConnResEntry &	DefaultNucleotide () const
Public Member Functions inherited from Builder
	Builder ()
virtual	~Builder ()
virtual void	CompleteAtoms (mol::ResidueHandle rh)
virtual void	SetDialect (Dialect dialect)
virtual void	SetStrictHydrogenMode (bool strict)
bool	GetStrictHydrogenMode () const
Dialect	GetDialect () const
virtual void	CheckResidueCompleteness (const mol::ResidueHandle &rh)
virtual mol::ResidueKey	IdentifyResidue (const mol::ResidueHandle &rh)
void	AssignBackBoneTorsionsToResidue (mol::ResidueHandle res)
virtual bool	DoesPeptideBondExist (const mol::AtomHandle &n, const mol::AtomHandle &c)
virtual bool	IsBondFeasible (const mol::AtomHandle &atom_a, const mol::AtomHandle &atom_b)
void	GuessChemClass (mol::ResidueHandle res)
void	DistanceBasedConnect (mol::AtomHandle atom)
void	SetBondFeasibilityCheck (bool b_feas_flag)
bool	GetBondFeasibilityCheck () const

Protected Member Functions
void	ConnectivityFromAtomNames (const mol::ResidueHandle &res, detail::ConnResEntry &centry, mol::AtomHandleList &unknown_atoms)

Additional Inherited Members
Static Public Member Functions inherited from Builder
static String	GuessAtomElement (const String &atom_name, bool hetatm)
static bool	AreResiduesConsecutive (const mol::ResidueHandle &r1, const mol::ResidueHandle &r2)

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Detailed Description

Definition at line 77 of file heuristic_builder.hh.

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Constructor & Destructor Documentation

HeuristicBuilder

(

)

virtual ~HeuristicBuilder ( )

virtual

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Member Function Documentation

virtual void AssignTorsions ( mol::ChainHandle  ch )

virtual

assign named torsions to a complete chain

Reimplemented from Builder.

virtual void AssignTorsionsToResidue ( mol::ResidueHandle  residue )

virtual

assign named torsions to single residue

Reimplemented from Builder.

virtual void ConnectAtomsOfResidue ( mol::ResidueHandle  rh )

virtual

connect by using information in the heuristic connectivity table.

Reimplemented from Builder.

void ConnectivityFromAtomNames ( const mol::ResidueHandle &  res, detail::ConnResEntry &  centry, mol::AtomHandleList &  unknown_atoms  )

protected

virtual void ConnectResidueToNext ( mol::ResidueHandle  rh, mol::ResidueHandle  next  )

virtual

connect to next residue in chain.

Reimplemented from Builder.

virtual void ConnectResidueToPrev ( mol::ResidueHandle  rh, mol::ResidueHandle  prev  )

virtual

connect to previous residue in chain.

Reimplemented from Builder.

const detail::ConnResEntry& DefaultNucleotide ( ) const

inline

Definition at line 113 of file heuristic_builder.hh.

const detail::ConnResEntry& DefaultPeptide ( ) const

inline

Definition at line 112 of file heuristic_builder.hh.

virtual void FillAtomProps ( mol::AtomHandle  atom )

virtual

Reimplemented from Builder.

virtual void FillResidueProps ( mol::ResidueHandle  residue )

virtual

Assign (correct) residue properties.

Assign chemical class of the residue and one letter code.

Reimplemented from Builder.

virtual bool IsResidueComplete ( const mol::ResidueHandle &  rh )

virtual

Check whether the residue has all atoms it is supposed to have.

Todo:

Add hydrogen flag

Reimplemented from Builder.

std::pair<detail::ConnResEntry,bool> LookupResEntry

(

const mol::ResidueKey &

key

)

get connectivity table for residues

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

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