Package org.biojava.nbio.structure.cath
Class CathDomain
- java.lang.Object
-
- org.biojava.nbio.structure.cath.CathDomain
-
- All Implemented Interfaces:
java.io.Serializable
,StructureIdentifier
public class CathDomain extends java.lang.Object implements java.io.Serializable, StructureIdentifier
A class which represents a single CATH domain.- See Also:
- Serialized Form
-
-
Field Summary
Fields Modifier and Type Field Description static long
serialVersionUID
-
Constructor Summary
Constructors Constructor Description CathDomain()
-
Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method 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; usegetThePdbId()
orgetPdbIdAndChain()
insteadjava.lang.String
getPdbIdAndChain()
Returns a string of the formPDBID.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()
-
-
-
Field Detail
-
serialVersionUID
public static final long serialVersionUID
- See Also:
- Constant Field Values
-
-
Method Detail
-
getDomainName
public java.lang.String getDomainName()
-
setDomainName
public void setDomainName(java.lang.String domainName)
-
getPdbId
@Deprecated public java.lang.String getPdbId()
Deprecated.This method is poorly named; usegetThePdbId()
orgetPdbIdAndChain()
insteadReturns a string of the formPDBID.CHAIN
. For example:1hiv.A
.
-
getThePdbId
public java.lang.String getThePdbId()
Returns the PDB ID.
-
getPdbIdAndChain
public java.lang.String getPdbIdAndChain()
Returns a string of the formPDBID.CHAIN
. For example:1hiv.A
.
-
getDomainId
public java.lang.Integer getDomainId()
-
getClassId
public java.lang.Integer getClassId()
-
setClassId
public void setClassId(java.lang.Integer classId)
-
getArchitectureId
public java.lang.Integer getArchitectureId()
-
setArchitectureId
public void setArchitectureId(java.lang.Integer architectureId)
-
getTopologyId
public java.lang.Integer getTopologyId()
-
setTopologyId
public void setTopologyId(java.lang.Integer topologyId)
-
getHomologyId
public java.lang.Integer getHomologyId()
-
setHomologyId
public void setHomologyId(java.lang.Integer homologyId)
-
getSequenceFamilyId
public java.lang.Integer getSequenceFamilyId()
-
setSequenceFamilyId
public void setSequenceFamilyId(java.lang.Integer sequenceFamilyId)
-
getOrthologousSequenceFamilyId
public java.lang.Integer getOrthologousSequenceFamilyId()
-
setOrthologousSequenceFamilyId
public void setOrthologousSequenceFamilyId(java.lang.Integer orthologousSequenceFamilyId)
-
getLikeSequenceFamilyId
public java.lang.Integer getLikeSequenceFamilyId()
-
setLikeSequenceFamilyId
public void setLikeSequenceFamilyId(java.lang.Integer likeSequenceFamilyId)
-
getIdenticalSequenceFamilyId
public java.lang.Integer getIdenticalSequenceFamilyId()
-
setIdenticalSequenceFamilyId
public void setIdenticalSequenceFamilyId(java.lang.Integer identicalSequenceFamilyId)
-
getDomainCounter
public java.lang.Integer getDomainCounter()
-
setDomainCounter
public void setDomainCounter(java.lang.Integer domainCounter)
-
getLength
public java.lang.Integer getLength()
-
setLength
public void setLength(java.lang.Integer length)
-
getResolution
public java.lang.Double getResolution()
-
setResolution
public void setResolution(java.lang.Double resolution)
-
setCATH
public void setCATH(java.lang.String cathCode)
-
getCATH
public java.lang.String getCATH()
-
setSOLID
public void setSOLID(java.lang.String cathCode)
-
getSOILD
public java.lang.String getSOILD()
-
getClassificationId
public java.lang.Integer getClassificationId(CathCategory cathCategory)
-
getFormat
public java.lang.String getFormat()
-
setFormat
public void setFormat(java.lang.String format)
-
getVersion
public java.lang.String getVersion()
-
setVersion
public void setVersion(java.lang.String version)
-
getDate
public java.util.Date getDate()
-
setDate
public void setDate(java.util.Date date)
-
getName
public java.lang.String getName()
-
setName
public void setName(java.lang.String name)
-
getSource
public java.lang.String getSource()
-
setSource
public void setSource(java.lang.String source)
-
getSequenceHeader
public java.lang.String getSequenceHeader()
-
setSequenceHeader
public void setSequenceHeader(java.lang.String sequenceHeader)
-
getSequence
public java.lang.String getSequence()
-
setSequence
public void setSequence(java.lang.String sequence)
-
getSegments
public java.util.List<CathSegment> getSegments()
-
setSegments
public void setSegments(java.util.List<CathSegment> segments)
-
getComment
public java.lang.String getComment()
-
setComment
public void setComment(java.lang.String comment)
-
toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
-
getChains
public 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.
-
getIdentifier
public java.lang.String getIdentifier()
Description copied from interface:StructureIdentifier
Get the String form of this identifier. It is recommended that the#toString()
method also return the identifier, for consistency during serialization.- Specified by:
getIdentifier
in interfaceStructureIdentifier
- Returns:
- The String form of this identifier
-
toCanonical
public SubstructureIdentifier toCanonical()
Description copied from interface:StructureIdentifier
Convert to a canonical SubstructureIdentifier.This allows all domains to be converted to a standard format String.
- Specified by:
toCanonical
in interfaceStructureIdentifier
- Returns:
- A SubstructureIdentifier equivalent to this
-
reduce
public Structure reduce(Structure input) throws StructureException
Description copied from interface:StructureIdentifier
Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.
- Specified by:
reduce
in interfaceStructureIdentifier
- Parameters:
input
- A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.- Returns:
- Throws:
StructureException
- See Also:
StructureTools.getReducedStructure(Structure, String)
-
loadStructure
public Structure loadStructure(AtomCache cache) throws StructureException, java.io.IOException
Description copied from interface:StructureIdentifier
Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input toStructureIdentifier.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.- Specified by:
loadStructure
in interfaceStructureIdentifier
- Returns:
- A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
- Throws:
StructureException
- For errors loading and parsing the structurejava.io.IOException
- Errors reading the structure from disk
-
-