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.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()
The unique identifier, using the following formal specification:
name := pdbID
| pdbID '.' chainID
| pdbID '.' range
| scopID
range := '('?
|
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.util.List<java.lang.String> |
getRanges()
Returns a list of ranges of the form described in
StructureIdentifier.getIdentifier() . |
java.util.List<ResidueRange> |
getResidueRanges()
Returns the list of
ResidueRanges that this StructureIdentifier defines. |
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() |
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) |
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()
PDBID.CHAIN
.
For example: 1hiv.A
.getPdbId
in interface StructureIdentifier
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.lang.String getIdentifier()
StructureIdentifier
name := pdbID | pdbID '.' chainID | pdbID '.' range | scopID range := '('? range (',' range)? ')'? | chainID | chainID '_' resNum '-' resNum pdbID := [0-9][a-zA-Z0-9]{3} chainID := [a-zA-Z0-9] scopID := 'd' pdbID [a-z_][0-9_] cathID := pdbID [A-Z][0-9]{2} resNum := [-+]?[0-9]+[A-Za-z]?For example:
1TIM #whole structure 1tim #same as above 4HHB.C #single chain 3AA0.A,B #two chains d2bq6a1 #SCOP domain 1cukA01 #CATH domain 4GCR.A_1-40 #substructure 3iek.A_17-28,A_56-294,A_320-377 #substructure of 3 disjoint partsMore options may be added to the specification at a future time.
getIdentifier
in interface StructureIdentifier
public java.util.List<ResidueRange> getResidueRanges()
StructureIdentifier
ResidueRanges
that this StructureIdentifier defines.
This is a unique representation.getResidueRanges
in interface StructureIdentifier
public java.util.List<java.lang.String> getRanges()
StructureIdentifier
StructureIdentifier.getIdentifier()
. For example:
getRanges().get(0): 'A' getRanges().get(1): 'B_5-100'This is a unique representation.
getRanges
in interface StructureIdentifier