public class CathDomain extends java.lang.Object implements java.io.Serializable, StructureIdentifier
Modifier and Type | Field and Description |
---|---|
static long |
serialVersionUID |
Constructor and Description |
---|
CathDomain() |
Modifier and Type | Method and Description |
---|---|
java.lang.Integer |
getArchitectureId() |
java.lang.String |
getCATH() |
java.util.Set<java.lang.String> |
getChains()
Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
|
java.lang.Integer |
getClassId() |
java.lang.Integer |
getClassificationId(CathCategory cathCategory) |
java.lang.String |
getComment() |
java.util.Date |
getDate() |
java.lang.Integer |
getDomainCounter() |
java.lang.Integer |
getDomainId() |
java.lang.String |
getDomainName() |
java.lang.String |
getFormat() |
java.lang.Integer |
getHomologyId() |
java.lang.Integer |
getIdenticalSequenceFamilyId() |
java.lang.String |
getIdentifier()
Get the String form of this identifier.
|
java.lang.Integer |
getLength() |
java.lang.Integer |
getLikeSequenceFamilyId() |
java.lang.String |
getName() |
java.lang.Integer |
getOrthologousSequenceFamilyId() |
java.lang.String |
getPdbId()
Deprecated.
This method is poorly named; use
getThePdbId() or getPdbIdAndChain() instead |
java.lang.String |
getPdbIdAndChain()
Returns a string of the form
PDBID.CHAIN . |
java.lang.Double |
getResolution() |
java.util.List<CathSegment> |
getSegments() |
java.lang.String |
getSequence() |
java.lang.Integer |
getSequenceFamilyId() |
java.lang.String |
getSequenceHeader() |
java.lang.String |
getSOILD() |
java.lang.String |
getSource() |
java.lang.String |
getThePdbId()
Returns the PDB ID.
|
java.lang.Integer |
getTopologyId() |
java.lang.String |
getVersion() |
Structure |
loadStructure(AtomCache cache)
Loads a structure encompassing the structure identified.
|
Structure |
reduce(Structure input)
Takes a complete structure as input and reduces it to the substructure
represented by this StructureIdentifier.
|
void |
setArchitectureId(java.lang.Integer architectureId) |
void |
setCATH(java.lang.String cathCode) |
void |
setClassId(java.lang.Integer classId) |
void |
setComment(java.lang.String comment) |
void |
setDate(java.util.Date date) |
void |
setDomainCounter(java.lang.Integer domainCounter) |
void |
setDomainName(java.lang.String domainName) |
void |
setFormat(java.lang.String format) |
void |
setHomologyId(java.lang.Integer homologyId) |
void |
setIdenticalSequenceFamilyId(java.lang.Integer identicalSequenceFamilyId) |
void |
setLength(java.lang.Integer length) |
void |
setLikeSequenceFamilyId(java.lang.Integer likeSequenceFamilyId) |
void |
setName(java.lang.String name) |
void |
setOrthologousSequenceFamilyId(java.lang.Integer orthologousSequenceFamilyId) |
void |
setResolution(java.lang.Double resolution) |
void |
setSegments(java.util.List<CathSegment> segments) |
void |
setSequence(java.lang.String sequence) |
void |
setSequenceFamilyId(java.lang.Integer sequenceFamilyId) |
void |
setSequenceHeader(java.lang.String sequenceHeader) |
void |
setSOLID(java.lang.String cathCode) |
void |
setSource(java.lang.String source) |
void |
setTopologyId(java.lang.Integer topologyId) |
void |
setVersion(java.lang.String version) |
SubstructureIdentifier |
toCanonical()
Convert to a canonical SubstructureIdentifier.
|
java.lang.String |
toString() |
public static final long serialVersionUID
public java.lang.String getDomainName()
public void setDomainName(java.lang.String domainName)
@Deprecated public java.lang.String getPdbId()
getThePdbId()
or getPdbIdAndChain()
insteadPDBID.CHAIN
.
For example: 1hiv.A
.public java.lang.String getThePdbId()
public java.lang.String getPdbIdAndChain()
PDBID.CHAIN
.
For example: 1hiv.A
.public java.lang.Integer getDomainId()
public java.lang.Integer getClassId()
public void setClassId(java.lang.Integer classId)
public java.lang.Integer getArchitectureId()
public void setArchitectureId(java.lang.Integer architectureId)
public java.lang.Integer getTopologyId()
public void setTopologyId(java.lang.Integer topologyId)
public java.lang.Integer getHomologyId()
public void setHomologyId(java.lang.Integer homologyId)
public java.lang.Integer getSequenceFamilyId()
public void setSequenceFamilyId(java.lang.Integer sequenceFamilyId)
public java.lang.Integer getOrthologousSequenceFamilyId()
public void setOrthologousSequenceFamilyId(java.lang.Integer orthologousSequenceFamilyId)
public java.lang.Integer getLikeSequenceFamilyId()
public void setLikeSequenceFamilyId(java.lang.Integer likeSequenceFamilyId)
public java.lang.Integer getIdenticalSequenceFamilyId()
public void setIdenticalSequenceFamilyId(java.lang.Integer identicalSequenceFamilyId)
public java.lang.Integer getDomainCounter()
public void setDomainCounter(java.lang.Integer domainCounter)
public java.lang.Integer getLength()
public void setLength(java.lang.Integer length)
public java.lang.Double getResolution()
public void setResolution(java.lang.Double resolution)
public void setCATH(java.lang.String cathCode)
public java.lang.String getCATH()
public void setSOLID(java.lang.String cathCode)
public java.lang.String getSOILD()
public java.lang.Integer getClassificationId(CathCategory cathCategory)
public java.lang.String getFormat()
public void setFormat(java.lang.String format)
public java.lang.String getVersion()
public void setVersion(java.lang.String version)
public java.util.Date getDate()
public void setDate(java.util.Date date)
public java.lang.String getName()
public void setName(java.lang.String name)
public java.lang.String getSource()
public void setSource(java.lang.String source)
public java.lang.String getSequenceHeader()
public void setSequenceHeader(java.lang.String sequenceHeader)
public java.lang.String getSequence()
public void setSequence(java.lang.String sequence)
public java.util.List<CathSegment> getSegments()
public void setSegments(java.util.List<CathSegment> segments)
public java.lang.String getComment()
public void setComment(java.lang.String comment)
public java.lang.String toString()
toString
in class java.lang.Object
public java.util.Set<java.lang.String> getChains()
public java.lang.String getIdentifier()
StructureIdentifier
#toString()
method also return the
identifier, for consistency during serialization.getIdentifier
in interface StructureIdentifier
public SubstructureIdentifier toCanonical()
StructureIdentifier
This allows all domains to be converted to a standard format String.
toCanonical
in interface StructureIdentifier
public Structure reduce(Structure input) throws StructureException
StructureIdentifier
The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.
reduce
in interface StructureIdentifier
input
- A full structure, e.g. as loaded from the PDB. The structure
ID should match that returned by getPdbId(), if applicable.StructureException
StructureTools.getReducedStructure(Structure, String)
public Structure loadStructure(AtomCache cache) throws StructureException, java.io.IOException
StructureIdentifier
StructureIdentifier.reduce(Structure)
.
It is recommended that the most complete structure available be returned
(e.g. the full PDB) to allow processing of unselected portions where
appropriate.loadStructure
in interface StructureIdentifier
StructureException
- For errors loading and parsing the structurejava.io.IOException
- Errors reading the structure from disk