Class 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.