Constructor Detail

• ProteinModificationIdentifier

  public ProteinModificationIdentifier​()

Method Detail

• 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 java.util.Set<ModifiedCompound> getIdentifiedModifiedCompound​()

  Returns:

  a set of identified ModifiedCompounds from the last parse result.

  See Also:

  ModifiedCompound

• getUnidentifiableAtomLinkages

  public java.util.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 java.util.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,
                       java.util.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​(java.util.List<Chain> chains)

  Identify all registered modifications in chains.

  Parameters:

  chains - query Chains.

• identify

  public void identify​(Chain chain,
                       java.util.Set<ProteinModification> potentialModifications)

  Identify a set of modifications in a a chains.

  Parameters:

  chain - query Chain.

  potentialModifications - query ProteinModifications.

• identify

  public void identify​(java.util.List<Chain> chains,
                       java.util.Set<ProteinModification> potentialModifications)

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

  Parameters:

  chains - query Chains.

  potentialModifications - query ProteinModifications.