Builder Class Reference

#include <builder.hh>

Inherited by HeuristicBuilder, and RuleBasedBuilder.

Public Member Functions
	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 bool	IsResidueComplete (const mol::ResidueHandle &rh)
virtual mol::ResidueKey	IdentifyResidue (const mol::ResidueHandle &rh)
virtual void	FillResidueProps (mol::ResidueHandle residue)
virtual void	FillAtomProps (mol::AtomHandle atom)
virtual void	ConnectAtomsOfResidue (mol::ResidueHandle rh)
virtual void	ConnectResidueToPrev (mol::ResidueHandle rh, mol::ResidueHandle prev)
virtual void	ConnectResidueToNext (mol::ResidueHandle rh, mol::ResidueHandle next)
virtual void	AssignTorsions (mol::ChainHandle ch)
virtual void	AssignTorsionsToResidue (mol::ResidueHandle residue)
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

Static Public Member Functions
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

abstract builder interface

A builder serves several purposes:

• knows how to connect atoms of residues based on their name
• is able to identify as residue based on its name
• knows whether a residue has all required atoms
• assigns named torsions to residues
• knows when to connect two consecutive residues.

The exact behaviour for a builder is implementation-specific. While some builders implement sophisticated checks to identity residues, other builders may only perform a name lookup. For two specific implementations of builders, HeuristicBuilder and RuleBasedBuilder.

Custom builders can be registered with Conopology::RegisterBuilder(). The default builder is set with Conopology::SetDefaultBuilder(). Since all entity loaders make use of the default builder to infer connectivity of the atoms, changing the default builder can largely affect the loading behaviour.

Definition at line 54 of file builder.hh.

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Constructor & Destructor Documentation

Builder ( )

inline

Definition at line 57 of file builder.hh.

virtual ~Builder ( )

virtual

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Member Function Documentation

static bool AreResiduesConsecutive ( const mol::ResidueHandle &  r1, const mol::ResidueHandle &  r2  )

static

whether the r1 and r2 have consecutive residue numbers

void AssignBackBoneTorsionsToResidue

(

mol::ResidueHandle

res

)

assign Backbone torsions to single residue

virtual void AssignTorsions ( mol::ChainHandle  ch )

virtual

assign named torsions to a complete chain

Reimplemented in RuleBasedBuilder, and HeuristicBuilder.

virtual void AssignTorsionsToResidue ( mol::ResidueHandle  residue )

virtual

assign named torsions to single residue

Reimplemented in HeuristicBuilder, and RuleBasedBuilder.

virtual void CheckResidueCompleteness ( const mol::ResidueHandle &  rh )

virtual

verify that the given residue has all atoms it is supposed to have based on its key

Reimplemented in RuleBasedBuilder.

virtual void CompleteAtoms ( mol::ResidueHandle  rh )

virtual

add any missing atoms to the residue based on its key, with coordinates set to zero

Reimplemented in RuleBasedBuilder.

virtual void ConnectAtomsOfResidue ( mol::ResidueHandle  rh )

virtual

connect atoms of one residue

Connects atoms of residue based on residue and atom name. This method does not establish inter-residue bonds. To connect atoms that belong to different residues, use ConnectResidueToPrev(), or ConnectResidueToNext().

Reimplemented in HeuristicBuilder, and RuleBasedBuilder.

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

virtual

See also:

ConnectResidueToPrev

Reimplemented in HeuristicBuilder, and RuleBasedBuilder.

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

virtual

connect atoms of residue to previous

The order of the parameters is important. In case of a polypeptide chain, the residues are thought to be ordered from N- to C- terminus.

See also:

ConnectResidueToNext

Reimplemented in HeuristicBuilder.

void DistanceBasedConnect

(

mol::AtomHandle

atom

)

|brief Connect atom with all atoms for whith IsBondFeasible() and AreResiduesConsecutive() returns true

virtual bool DoesPeptideBondExist ( const mol::AtomHandle &  n, const mol::AtomHandle &  c  )

virtual

Check if peptide bond is formed between the two atoms.

This method is called by ConnectResidueWithNext() after making sure that both residues participating in the peptide bond are peptide linking components.

By default, IsBondFeasible() is used to check whether the two atoms form a peptide bond.

virtual void FillAtomProps ( mol::AtomHandle  atom )

virtual

Reimplemented in HeuristicBuilder, and RuleBasedBuilder.

virtual void FillResidueProps ( mol::ResidueHandle  residue )

virtual

Assign (correct) residue properties.

Assign chemical class of the residue and one letter code.

Reimplemented in RuleBasedBuilder, and HeuristicBuilder.

bool GetBondFeasibilityCheck ( ) const

inline

Get bond feasibility check flag.

Definition at line 151 of file builder.hh.

Dialect GetDialect ( ) const

inline

Definition at line 69 of file builder.hh.

bool GetStrictHydrogenMode ( ) const

inline

Definition at line 67 of file builder.hh.

static String GuessAtomElement ( const String &  atom_name, bool  hetatm  )

static

guess element of atom based on name and hetatm flag

void GuessChemClass

(

mol::ResidueHandle

res

)

guess and assign chemical class of residue based on atoms and connectivity

virtual mol::ResidueKey IdentifyResidue ( const mol::ResidueHandle &  rh )

virtual

attempt to identify the residue based on its atoms, and return a suggestion for the proper residue key

Reimplemented in RuleBasedBuilder.

virtual bool IsBondFeasible ( const mol::AtomHandle &  atom_a, const mol::AtomHandle &  atom_b  )

virtual

Overloadable hook to check if bond between to atoms is feasible.

The default implementation uses a distance-based check to check if the two atoms should be connected. The atoms are connected if they are in the range of 0.8 to 1.2 times their van-der-WAALS radius.

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 in RuleBasedBuilder, and HeuristicBuilder.

void SetBondFeasibilityCheck ( bool  b_feas_flag )

inline

Set bond feasibility check flag.

Definition at line 148 of file builder.hh.

virtual void SetDialect ( Dialect  dialect )

inlinevirtual

Reimplemented in RuleBasedBuilder.

Definition at line 64 of file builder.hh.

virtual void SetStrictHydrogenMode ( bool  strict )

inlinevirtual

Definition at line 66 of file builder.hh.

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

• stage/include/ost/conop/builder.hh