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java.lang.Objectorg.biojava3.protmod.structure.ProteinModificationIdentifier
public class ProteinModificationIdentifier
Identify attachment modification in a 3-D structure.
Constructor Summary | |
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ProteinModificationIdentifier()
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Method Summary | |
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void |
destroy()
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Set<ModifiedCompound> |
getIdentifiedModifiedCompound()
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boolean |
getRecordAdditionalAttachments()
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boolean |
getRecordUnidentifiableCompounds()
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Set<StructureAtomLinkage> |
getUnidentifiableAtomLinkages()
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Set<StructureGroup> |
getUnidentifiableModifiedResidues()
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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)
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void |
setRecordAdditionalAttachments(boolean recordAdditionalAttachments)
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void |
setRecordUnidentifiableCompounds(boolean recordUnidentifiableModifiedCompounds)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinModificationIdentifier()
Method Detail |
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public void destroy()
public void setbondLengthTolerance(double bondLengthTolerance)
bondLengthTolerance
- tolerance of error (in Angstroms) of the
covalent bond length, when calculating the atom distance threshold.public void setRecordUnidentifiableCompounds(boolean recordUnidentifiableModifiedCompounds)
recordUnidentifiableAtomLinkages
- true if choosing to record unidentifiable
atoms; false, otherwise.getRecordUnidentifiableCompounds()
,
getUnidentifiableModifiedResidues()
,
getUnidentifiableAtomLinkages()
public boolean getRecordUnidentifiableCompounds()
setRecordUnidentifiableCompounds(boolean)
,
getUnidentifiableModifiedResidues()
,
getUnidentifiableAtomLinkages()
public void setRecordAdditionalAttachments(boolean recordAdditionalAttachments)
recordAdditionalAttachments
- true if choosing to record additional attachments
that are not directly attached to a modified residue.getRecordAdditionalAttachments()
public boolean getRecordAdditionalAttachments()
setRecordAdditionalAttachments(boolean)
public Set<ModifiedCompound> getIdentifiedModifiedCompound()
ModifiedCompound
s from
the last parse result.ModifiedCompound
public Set<StructureAtomLinkage> getUnidentifiableAtomLinkages()
ModifiedCompound
s from the last parse result.
Each element of the list is a array containing two atoms.StructureAtomLinkage
,
setRecordUnidentifiableCompounds(boolean)
public Set<StructureGroup> getUnidentifiableModifiedResidues()
StructureGroup
,
setRecordUnidentifiableCompounds(boolean)
,
getIdentifiedModifiedCompound()
public void identify(Structure structure)
structure
- public void identify(Structure structure, Set<ProteinModification> potentialModifications)
structure
- query Structure
.potentialModifications
- query ProteinModification
s.public void identify(Chain chain)
chain
- query Chain
.public void identify(List<Chain> chains)
chains
- query Chain
s.public void identify(Chain chain, Set<ProteinModification> potentialModifications)
chain
- query Chain
.potentialModifications
- query ProteinModification
s.public void identify(List<Chain> chains, Set<ProteinModification> potentialModifications)
chains
- query Chain
s.potentialModifications
- query ProteinModification
s.
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