Package org.biojava.nbio.protmod.structure

Class ProteinModificationIdentifier

java.lang.Object

org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

public class ProteinModificationIdentifier
extends Object

Identify attachment modification in a 3-D structure.

Since:

3.0

Author:

Jianjiong Gao

Constructor Summary

Constructors

Constructor	Description
ProteinModificationIdentifier()

Method Summary

Modifier and Type	Method	Description
void	destroy()
Set<ModifiedCompound>	getIdentifiedModifiedCompound()
boolean	getRecordAdditionalAttachments()
boolean	getRecordUnidentifiableCompounds()
Set<StructureAtomLinkage>	getUnidentifiableAtomLinkages()
Set<StructureGroup>	getUnidentifiableModifiedResidues()
void	identify(List<Chain> chains)	Identify all registered modifications in chains.
void	identify(List<Chain> chains, Set<ProteinModification> potentialModifications)	Identify a set of modifications in a a list of chains.
void	identify(Chain chain)	Identify all registered modifications in a chain.
void	identify(Chain chain, Set<ProteinModification> potentialModifications)	Identify a set of modifications in a a chains.
void	identify(Structure structure)	Identify all registered modifications in a structure.
void	identify(Structure structure, Set<ProteinModification> potentialModifications)	Identify a set of modifications in a structure.
void	setbondLengthTolerance(double bondLengthTolerance)
void	setRecordAdditionalAttachments(boolean recordAdditionalAttachments)
void	setRecordUnidentifiableCompounds(boolean recordUnidentifiableModifiedCompounds)

Methods inherited from class java.lang.Object

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

Constructor Details

ProteinModificationIdentifier

public ProteinModificationIdentifier()

Method Details

destroy

public void destroy()

setbondLengthTolerance

public void setbondLengthTolerance(double bondLengthTolerance)

Parameters:

bondLengthTolerance - tolerance of error (in Angstroms) of the covalent bond length, when calculating the atom distance threshold.

setRecordUnidentifiableCompounds

public void setRecordUnidentifiableCompounds(boolean recordUnidentifiableModifiedCompounds)

Parameters:

recordUnidentifiableModifiedCompounds - true if choosing to record unidentifiable atoms; false, otherwise.

See Also:

• getRecordUnidentifiableCompounds()
• getUnidentifiableModifiedResidues()
• getUnidentifiableAtomLinkages()

getRecordUnidentifiableCompounds

public boolean getRecordUnidentifiableCompounds()

Returns:

true if choosing to record unidentifiable atoms; false, otherwise.

See Also:

• setRecordUnidentifiableCompounds(boolean)
• getUnidentifiableModifiedResidues()
• getUnidentifiableAtomLinkages()

setRecordAdditionalAttachments

public void setRecordAdditionalAttachments(boolean recordAdditionalAttachments)

Parameters:

recordAdditionalAttachments - true if choosing to record additional attachments that are not directly attached to a modified residue.

See Also:

• getRecordAdditionalAttachments()

getRecordAdditionalAttachments

public boolean getRecordAdditionalAttachments()

Returns:

true if choosing to record additional attachments that are not directly attached to a modified residue.

See Also:

• setRecordAdditionalAttachments(boolean)

getIdentifiedModifiedCompound

public Set<ModifiedCompound> getIdentifiedModifiedCompound()

Returns:

a set of identified ModifiedCompounds from the last parse result.

See Also:

• ModifiedCompound

getUnidentifiableAtomLinkages

public Set<StructureAtomLinkage> getUnidentifiableAtomLinkages()

Returns:

a set of atom linkages, which represent the atom bonds that were not covered by the identified ModifiedCompounds from the last parse result. Each element of the list is a array containing two atoms.

See Also:

• StructureAtomLinkage
• setRecordUnidentifiableCompounds(boolean)

getUnidentifiableModifiedResidues

public Set<StructureGroup> getUnidentifiableModifiedResidues()

Returns:

a set of modified residues that were not covered by the identified ModifiedCompounds from the last parse result.

See Also:

• StructureGroup
• setRecordUnidentifiableCompounds(boolean)
• getIdentifiedModifiedCompound()

identify

public void identify(Structure structure)

Identify all registered modifications in a structure.

Parameters:

structure -

identify

public void identify(Structure structure,
 Set<ProteinModification> potentialModifications)

Identify a set of modifications in a structure.

Parameters:

structure - query Structure.

potentialModifications - query ProteinModifications.

identify

public void identify(Chain chain)

Identify all registered modifications in a chain.

Parameters:

chain - query Chain.

identify

public void identify(List<Chain> chains)

Identify all registered modifications in chains.

Parameters:

chains - query Chains.

identify

public void identify(Chain chain,
 Set<ProteinModification> potentialModifications)

Identify a set of modifications in a a chains.

Parameters:

chain - query Chain.

potentialModifications - query ProteinModifications.

identify

public void identify(List<Chain> chains,
 Set<ProteinModification> potentialModifications)

Identify a set of modifications in a a list of chains.

Parameters:

chains - query Chains.

potentialModifications - query ProteinModifications.