Builder Class Reference

abstract builder interface More...

#include <builder.hh>

Inherited by HeuristicBuilder, and RuleBasedBuilder.

Public Member Functions
virtual	~Builder ()
virtual void	CompleteAtoms (const mol::ResidueHandle &rh)
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 (const mol::ResidueHandle &rh)
virtual void	ConnectResidueToPrev (const mol::ResidueHandle &rh, const mol::ResidueHandle &prev)
virtual void	ConnectResidueToNext (const mol::ResidueHandle &rh, const mol::ResidueHandle &next)
virtual void	AssignTorsions (const mol::ChainHandle &ch)
virtual void	AssignTorsionsToResidue (const mol::ResidueHandle &residue)
void	AssignBackBoneTorsionsToResidue (const 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	DistanceBasedConnect (const mol::AtomHandle &atom)
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 50 of file builder.hh.

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Constructor & Destructor Documentation

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

(

const mol::ResidueHandle &

res

)

assign Backbone torsions to single residue

virtual void AssignTorsions

(

const mol::ChainHandle &

ch

)

[virtual]

assign named torsions to a complete chain

Reimplemented in HeuristicBuilder, and RuleBasedBuilder.

virtual void AssignTorsionsToResidue

(

const 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

(

const 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

(

const 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	(	const mol::ResidueHandle &	rh,
		const mol::ResidueHandle &	next
	)			[virtual]

See also:

ConnectResidueToPrev

Reimplemented in HeuristicBuilder, and RuleBasedBuilder.

virtual void ConnectResidueToPrev	(	const mol::ResidueHandle &	rh,
		const 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

(

const 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 HeuristicBuilder, and RuleBasedBuilder.

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

guess element of atom based on name and hetatm flag

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 HeuristicBuilder, and RuleBasedBuilder.

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

• stage/include/ost/conop/builder.hh