org.proteinshader.structure.visitor
Class BondGeneratorVisitor

java.lang.Object
  org.proteinshader.structure.visitor.Visitor
      org.proteinshader.structure.visitor.BondGeneratorVisitor

public class BondGeneratorVisitor
extends Visitor

Generates standard Bonds for AminoAcids and Waters.

Peptide Bonds, intra-AminoAcid Bonds, and the oxygen-hydrogen Bonds of Water are generated after calculating which Atoms are close enough to form a Bond. The algorithm for Bond prediction is given in the BondPredictor class.

Usage

structure.accept( new BondGeneratorVisitor() );

will generate AminoAcid and Water Bonds on the Structure, while

Visitor visitor = new BondGeneratorVisitor();
visitor.setMode( ResidueMode.AMINO_ACIDS );
structure.accept( visitor );

would only generate Bonds for the AminoAcids.

Note on Exception Handling

Currently, the VisitorException in the visit() method signatures is only there to satisfy the Visitor API (other Visitors such as the SFWriterVisitor do need an exception in the visit() method declaration).

Constructor Summary

BondGeneratorVisitor()
Constructs a BondGeneratorVisitor.

Method Summary

void	setAABondVisibility(VisibilityEnum visibility) Determines what visibility status the Bond generator will use when generating Bonds for AminoAcids.
void	setMinBondLength(double minBondLength) Sets the minimum Bond length value used for Bond prediction.
void	setTolerance(double tolerance) Sets the tolerance value used for Bond prediction.
void	setWaterBondVisibility(VisibilityEnum visibility) Determines what visibility status the Bond generator use when generating Bonds for Waters.
void	visit(AminoAcid aminoAcid) Uses Atom distances to generate Bonds within the AminoAcid, and also uses the memory of the last carbonyl carbon seen to check for a possible peptide Bond.
void	visit(Atom atom) Checks if the Atom is a possible Bond destination Atom for any previously seen Atoms of the same Residue, and then adds the Atom to the list of Atoms to remember.
void	visit(Bond bond) NO OPERATION: This Visitor method is not needed by the bond generator.
void	visit(Chain chain) Generates all standard Bonds (AminoAcids and Waters) for the Chain.
void	visit(Heterogen heterogen) NO OPERATION: This method is not needed because non-water heterogen bonds are given explicitly in the PDB structure entry.
void	visit(Model model) Generates all standard Bonds (AminoAcids and Waters) for the Model.
void	visit(Structure structure) Generates all standard Bonds (AminoAcids and Waters) for the Structure.
void	visit(Water water) If the Water includes hydrogen atoms, then Bonds will be created between the oxygen and each hydrogen (after checking that the Bond lengths are reasonable).

Methods inherited from class org.proteinshader.structure.visitor.Visitor

clear, includeAAHetAndWater, setDebug, setMode, setMode, setMode, setMode, setMode, setMode, setVisitSegments, visit, visit, visit, visit

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BondGeneratorVisitor

public BondGeneratorVisitor()

Constructs a BondGeneratorVisitor. The Bonds are set to Visiblity.OPAQUE by default.

The traversal logic is set so that only AminoAcids and Waters will be visited because Heterogen Bonds are given explicitly in a PDB structure entry.

Method Detail

setAABondVisibility

public void setAABondVisibility(VisibilityEnum visibility)

Determines what visibility status the Bond generator will use when generating Bonds for AminoAcids. If null is given as an argument, the visiblity will be set to VisibilityEnum.INVISIBLE.

Parameters:

visibility - the visibility status for AminoAcid Bonds.

setWaterBondVisibility

public void setWaterBondVisibility(VisibilityEnum visibility)

Determines what visibility status the Bond generator use when generating Bonds for Waters. If null is given as an argument, the visiblity will be set to VisibilityEnum.INVISIBLE.

Parameters:

visibility - the visibility status for Water Bonds.

setTolerance

public void setTolerance(double tolerance)

Sets the tolerance value used for Bond prediction.

Parameters:

tolerance - tolerance value in Angstroms.

setMinBondLength

public void setMinBondLength(double minBondLength)

Sets the minimum Bond length value used for Bond prediction.

Parameters:

minBondLength - minimum Bond length in Angstroms.

visit

public void visit(Structure structure)
           throws VisitorException

Generates all standard Bonds (AminoAcids and Waters) for the Structure.

Overrides:

visit in class Visitor

Parameters:

structure - the Structure to generate Bonds for.

Throws:

VisitorException - if an error occurs while generating Bonds.

visit

public void visit(Model model)
           throws VisitorException

Generates all standard Bonds (AminoAcids and Waters) for the Model.

Overrides:

visit in class Visitor

Parameters:

model - the Model to generate Bonds for.

Throws:

VisitorException - if an error occurs while generating Bonds.

visit

public void visit(Chain chain)
           throws VisitorException

Generates all standard Bonds (AminoAcids and Waters) for the Chain.

The distance between Atoms is checked before generating a Bond.

Overrides:

visit in class Visitor

Parameters:

chain - the Chain to generate Bonds for.

Throws:

VisitorException - if an error occurs while generating Bonds.

visit

public void visit(AminoAcid aminoAcid)
           throws VisitorException

Uses Atom distances to generate Bonds within the AminoAcid, and also uses the memory of the last carbonyl carbon seen to check for a possible peptide Bond.

Before calling on super.visit( aminoAcid ) to use its traversal logic on the Atoms of the current AminoAcid, this method will clear out the memory of any previously seen Atoms (other than the last carbonyl carbon, which needs to be remembered from one AminoAcid to the next).

Overrides:

visit in class Visitor

Parameters:

aminoAcid - the AminoAcid to generate Bonds for.

Throws:

VisitorException - if an error occurs while generating Bonds.

visit

public void visit(Heterogen heterogen)
           throws VisitorException

NO OPERATION: This method is not needed because non-water heterogen bonds are given explicitly in the PDB structure entry.

Overrides:

visit in class Visitor

Parameters:

heterogen - the Heterogen to do nothing with.

Throws:

VisitorException - will not happen.

visit

public void visit(Water water)
           throws VisitorException

If the Water includes hydrogen atoms, then Bonds will be created between the oxygen and each hydrogen (after checking that the Bond lengths are reasonable).

Before calling on super.visit( water ) to use its traversal logic on the Atoms of the current Water, this method will clear out the memory of any previously seen Atoms.

Overrides:

visit in class Visitor

Parameters:

water - the Water to generate Bonds for.

Throws:

VisitorException - if an error occurs while processing a Water.

visit

public void visit(Atom atom)
           throws VisitorException

Checks if the Atom is a possible Bond destination Atom for any previously seen Atoms of the same Residue, and then adds the Atom to the list of Atoms to remember.

In a PDB record, the hydrogen Atoms always appear after the heavier Atom that they may be bonded with. Therefore, as a minor speed optimization, hydrogen Atoms are never added to the list of Atoms to remember because they are considered only as destination Atoms, and the list of Atoms to remember are intended as potential source Atoms.

Overrides:

visit in class Visitor

Parameters:

atom - the Atom to visit.

Throws:

VisitorException - if an error occurs while processing an Atom.

visit

public void visit(Bond bond)
           throws VisitorException

NO OPERATION: This Visitor method is not needed by the bond generator.

Overrides:

visit in class Visitor

Parameters:

bond - the Bond to do nothing with.

Throws:

VisitorException - will not happen.