Package io.github.WeronikaJargielo.protein_interaction_finder

Class ProteinInteractionFinder

java.lang.Object

io.github.WeronikaJargielo.protein_interaction_finder.ProteinInteractionFinder

public final class ProteinInteractionFinder
extends java.lang.Object

Class for identifying all implemented interactions.

Constructor Summary

Constructors

Constructor	Description
ProteinInteractionFinder(java.lang.String pdbFilename)	Instantiates new ProteinInteractionFinder for identifying interactions in protein stored in given PDB file.

Method Summary

Modifier and Type	Method	Description
java.util.List<AminoAromaticInteraction>	findAminoAromaticInteractions()	Identify amino-aromatic interactions in protein.
java.util.List<AminoAromaticInteraction>	findAminoAromaticInteractions(AminoAromaticInteractionCriteria userDefinedCriteria)	Identify amino-aromatic interactions in protein.
java.util.List<AromaticAromaticInteraction>	findAromaticAromaticInteractions()	Identify aromatic-aromatic interactions in protein.
java.util.List<AromaticAromaticInteraction>	findAromaticAromaticInteractions(AromaticAromaticInteractionCriteria userDefinedCriteria)	Identify aromatic-aromatic interactions in protein.
java.util.List<DisulphideBridge>	findDisulphideBridges()	Identify disulphide bridges in protein.
java.util.List<DisulphideBridge>	findDisulphideBridges(DisulphideBridgeCriteria userDefinedCriteria)	Identify disulphide bridges in protein.
java.util.List<HydrophobicInteraction>	findHydrophobicInteractions()	Identify hydrophobic interactions in protein.
java.util.List<HydrophobicInteraction>	findHydrophobicInteractions(HydrophobicInteractionCriteria userDefinedCriteria)	Identify hydrophobic interactions in protein.
java.util.List<IonicInteraction>	findIonicInteractions()	Identify ionic interactions in protein.
java.util.List<IonicInteraction>	findIonicInteractions(IonicInteractionCriteria userDefinedCriteria)	Identify ionic interactions in protein.
java.util.List<HydrogenBond>	findMainMainHydrogenBonds()	Identify main chain - main chain hydrogen bonds in protein.
java.util.List<HydrogenBond>	findMainMainHydrogenBonds(HydrogenBondCriteria userDefinedCriteria)	Identify main chain - main chain hydrogen bonds in protein.
java.util.List<HydrogenBond>	findMainSideHydrogenBonds()	Identify main chain - side chain hydrogen bonds in protein.
java.util.List<HydrogenBond>	findMainSideHydrogenBonds(HydrogenBondCriteria userDefinedCriteria)	Identify main chain - side chain hydrogen bonds in protein.
java.util.List<HydrogenBond>	findSideSideHydrogenBonds()	Identify side chain - side chain hydrogen bonds in protein.
java.util.List<HydrogenBond>	findSideSideHydrogenBonds(HydrogenBondCriteria userDefinedCriteria)	Identify side chain - side chain hydrogen bonds in protein.
java.util.List<SulphurAromaticInteraction>	findSulphurAromaticInteractions()	Identify sulphur-aromatic interactions in protein.
java.util.List<SulphurAromaticInteraction>	findSulphurAromaticInteractions(SulphurAromaticInteractionCriteria userDefinedCriteria)	Identify sulphur-aromatic interactions in protein.
PdbStructureParser	getPdbStructureParser()	Returns PdbStructureParser created in constructor.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinInteractionFinder

public ProteinInteractionFinder(java.lang.String pdbFilename)
                         throws java.io.IOException,
                                org.biojava.nbio.structure.StructureException

Instantiates new ProteinInteractionFinder for identifying interactions in protein stored in given PDB file.

Parameters:

pdbFilename - Path to protein PDB file.

Throws:

java.io.IOException - Probably given PDB file does not exist.

org.biojava.nbio.structure.StructureException - Probably given PDB file is incorrectly formatted.

Method Detail

getPdbStructureParser

public PdbStructureParser getPdbStructureParser()

Returns PdbStructureParser created in constructor.

Returns:

PdbStructureParser created in constructor.

findMainMainHydrogenBonds

public java.util.List<HydrogenBond> findMainMainHydrogenBonds()

Identify main chain - main chain hydrogen bonds in protein. Found bonds satisfy default criteria.

Returns:

List of main chain - main chain hydrogen bonds satisfying default criteria.

See Also:

HydrogenBondCriteria

findMainMainHydrogenBonds

public java.util.List<HydrogenBond> findMainMainHydrogenBonds(HydrogenBondCriteria userDefinedCriteria)

Identify main chain - main chain hydrogen bonds in protein. Found bonds satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for hydrogen bond identification.

Returns:

List of main chain - main chain hydrogen bonds satisfying custom criteria.

See Also:

HydrogenBondCriteria

findSideSideHydrogenBonds

public java.util.List<HydrogenBond> findSideSideHydrogenBonds()

Identify side chain - side chain hydrogen bonds in protein. Found bonds satisfy default criteria.

Returns:

List of side chain - side chain hydrogen bonds satisfying default criteria.

See Also:

HydrogenBondCriteria

findSideSideHydrogenBonds

public java.util.List<HydrogenBond> findSideSideHydrogenBonds(HydrogenBondCriteria userDefinedCriteria)

Identify side chain - side chain hydrogen bonds in protein. Found bonds satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for hydrogen bond identification.

Returns:

List of side chain - side chain hydrogen bonds satisfying custom criteria.

See Also:

HydrogenBondCriteria

findMainSideHydrogenBonds

public java.util.List<HydrogenBond> findMainSideHydrogenBonds()

Identify main chain - side chain hydrogen bonds in protein. Found bonds satisfy default criteria.

Returns:

List of main chain - side chain hydrogen bonds satisfying default criteria.

See Also:

HydrogenBondCriteria

findMainSideHydrogenBonds

public java.util.List<HydrogenBond> findMainSideHydrogenBonds(HydrogenBondCriteria userDefinedCriteria)

Identify main chain - side chain hydrogen bonds in protein. Found bonds satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for hydrogen bond identification.

Returns:

List of main chain - side chain hydrogen bonds satisfying custom criteria.

See Also:

HydrogenBondCriteria

findDisulphideBridges

public java.util.List<DisulphideBridge> findDisulphideBridges()

Identify disulphide bridges in protein. Found bridges satisfy default criteria.

Returns:

List of disulphide bridges satisfying default criteria.

See Also:

DisulphideBridgeCriteria

findDisulphideBridges

public java.util.List<DisulphideBridge> findDisulphideBridges(DisulphideBridgeCriteria userDefinedCriteria)

Identify disulphide bridges in protein. Found bridges satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for disulphide bridges identification.

Returns:

List of disulphide bridges satisfying custom criteria.

See Also:

DisulphideBridgeCriteria

findSulphurAromaticInteractions

public java.util.List<SulphurAromaticInteraction> findSulphurAromaticInteractions()

Identify sulphur-aromatic interactions in protein. Found interactions satisfy default criteria.

Returns:

List of sulphur-aromatic interactions satisfying default criteria.

See Also:

SulphurAromaticInteractionCriteria

findSulphurAromaticInteractions

public java.util.List<SulphurAromaticInteraction> findSulphurAromaticInteractions(SulphurAromaticInteractionCriteria userDefinedCriteria)

Identify sulphur-aromatic interactions in protein. Found interactions satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for sulphur-aromatic interactions identification.

Returns:

List of sulphur-aromatic interactions satisfying custom criteria.

See Also:

SulphurAromaticInteractionCriteria

findAminoAromaticInteractions

public java.util.List<AminoAromaticInteraction> findAminoAromaticInteractions()

Identify amino-aromatic interactions in protein. Found interactions satisfy default criteria.

Returns:

List of amino-aromatic interactions satisfying default criteria.

See Also:

AminoAromaticInteractionCriteria

findAminoAromaticInteractions

public java.util.List<AminoAromaticInteraction> findAminoAromaticInteractions(AminoAromaticInteractionCriteria userDefinedCriteria)

Identify amino-aromatic interactions in protein. Found interactions satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for amino-aromatic interactions identification.

Returns:

List of amino-aromatic interactions satisfying custom criteria.

See Also:

AminoAromaticInteractionCriteria

findAromaticAromaticInteractions

public java.util.List<AromaticAromaticInteraction> findAromaticAromaticInteractions()

Identify aromatic-aromatic interactions in protein. Found interactions satisfy default criteria.

Returns:

List of aromatic-aromatic interactions satisfying default criteria.

See Also:

AromaticAromaticInteractionCriteria

findAromaticAromaticInteractions

public java.util.List<AromaticAromaticInteraction> findAromaticAromaticInteractions(AromaticAromaticInteractionCriteria userDefinedCriteria)

Identify aromatic-aromatic interactions in protein. Found interactions satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for aromatic-aromatic interactions identification.

Returns:

List of aromatic-aromatic interactions satisfying custom criteria.

See Also:

AromaticAromaticInteractionCriteria

findIonicInteractions

public java.util.List<IonicInteraction> findIonicInteractions()

Identify ionic interactions in protein. Found interactions satisfy default criteria.

Returns:

List of ionic interactions satisfying default criteria.

See Also:

IonicInteractionCriteria

findIonicInteractions

public java.util.List<IonicInteraction> findIonicInteractions(IonicInteractionCriteria userDefinedCriteria)

Identify ionic interactions in protein. Found interactions satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for ionic interactions identification.

Returns:

List of ionic interactions satisfying custom criteria.

See Also:

IonicInteractionCriteria

findHydrophobicInteractions

public java.util.List<HydrophobicInteraction> findHydrophobicInteractions()

Identify hydrophobic interactions in protein. Found interactions satisfy default criteria.

Returns:

List of hydrophobic interactions satisfying default criteria.

See Also:

HydrophobicInteractionCriteria

findHydrophobicInteractions

public java.util.List<HydrophobicInteraction> findHydrophobicInteractions(HydrophobicInteractionCriteria userDefinedCriteria)

Identify hydrophobic interactions in protein. Found interactions satisfy custom criteria.

Parameters:

userDefinedCriteria - Custom criteria that will be used for hydrophobic interactions identification.

Returns:

List of hydrophobic interactions satisfying custom criteria.

See Also:

HydrophobicInteractionCriteria