Public Member Functions | Protected Member Functions
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)
< detail::ConnResEntry, bool > 
LookupResEntry (const mol::ResidueKey &key)
virtual void FillAtomProps (mol::AtomHandle atom)
- 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)

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)

Detailed Description

Definition at line 77 of file heuristic_builder.hh.

Constructor & Destructor Documentation

virtual ~HeuristicBuilder ( )

Member Function Documentation

virtual void AssignTorsions ( mol::ChainHandle  ch)

assign named torsions to a complete chain

Reimplemented from Builder.

virtual void AssignTorsionsToResidue ( mol::ResidueHandle  residue)

assign named torsions to single residue

Reimplemented from Builder.

virtual void ConnectAtomsOfResidue ( mol::ResidueHandle  rh)

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

connect to next residue in chain.

Reimplemented from Builder.

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

connect to previous residue in chain.

Reimplemented from Builder.

virtual void FillAtomProps ( mol::AtomHandle  atom)

Reimplemented from Builder.

virtual void FillResidueProps ( mol::ResidueHandle  residue)

Assign (correct) residue properties.

Assign chemical class of the residue and one letter code.

Reimplemented from Builder.

virtual bool IsResidueComplete ( const mol::ResidueHandle rh)

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

Add hydrogen flag

Reimplemented from Builder.

std::pair<detail::ConnResEntry,bool> LookupResEntry ( const mol::ResidueKey key)

get connectivity table for residues

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