org.biojava3.protmod.structure
Class ProteinModificationIdentifier

java.lang.Object
  extended by org.biojava3.protmod.structure.ProteinModificationIdentifier

public class ProteinModificationIdentifier
extends Object

Identify attachment modification in a 3-D structure.

Since:
3.0
Author:
Jianjiong Gao

Constructor Summary
ProteinModificationIdentifier()
           
 
Method Summary
 void destroy()
           
 Set<ModifiedCompound> getIdentifiedModifiedCompound()
           
 boolean getRecordAdditionalAttachments()
           
 boolean getRecordUnidentifiableCompounds()
           
 Set<StructureAtomLinkage> getUnidentifiableAtomLinkages()
           
 Set<StructureGroup> getUnidentifiableModifiedResidues()
           
 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(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(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 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:
recordUnidentifiableAtomLinkages - 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.