public class EcodDomain extends java.lang.Object implements java.io.Serializable, java.lang.Cloneable, StructureIdentifier
For detailed explanation about the ECOD information see the original article at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
Cheng H, Schaeffer RD, Liao Y, et al. ECOD: An Evolutionary Classification of Protein Domains. Elofsson A, ed. PLoS Computational Biology. 2014;10(12):e1003926.
Constructor and Description |
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EcodDomain()
Default constructor with all null properties
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EcodDomain(EcodDomain o) |
EcodDomain(java.lang.Long uid,
java.lang.String domainId,
java.lang.Boolean manual,
java.lang.Integer xGroup,
java.lang.Integer hGroup,
java.lang.Integer tGroup,
java.lang.Integer fGroup,
java.lang.String pdbId,
java.lang.String chainId,
java.lang.String range,
java.lang.String architectureName,
java.lang.String xGroupName,
java.lang.String hGroupName,
java.lang.String tGroupName,
java.lang.String fGroupName,
java.lang.Long assemblyId,
java.util.Set<java.lang.String> ligands) |
EcodDomain(java.lang.Long uid,
java.lang.String domainId,
java.lang.Boolean manual,
java.lang.Integer xGroup,
java.lang.Integer hGroup,
java.lang.Integer tGroup,
java.lang.Integer fGroup,
java.lang.String pdbId,
java.lang.String chainId,
java.lang.String range,
java.lang.String seqId,
java.lang.String architectureName,
java.lang.String xGroupName,
java.lang.String hGroupName,
java.lang.String tGroupName,
java.lang.String fGroupName,
java.lang.Long assemblyId,
java.util.Set<java.lang.String> ligands) |
EcodDomain(java.lang.String domainId) |
Modifier and Type | Method and Description |
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protected java.lang.Object |
clone() |
boolean |
equals(java.lang.Object obj) |
java.lang.String |
getArchitectureName() |
java.lang.Long |
getAssemblyId() |
java.lang.String |
getChainId() |
java.lang.String |
getDomainId() |
java.lang.Integer |
getFGroup() |
java.lang.String |
getFGroupName() |
java.lang.Integer |
getHGroup() |
java.lang.String |
getHGroupName() |
java.lang.String |
getIdentifier()
Get the String form of this identifier.
|
java.util.Set<java.lang.String> |
getLigands() |
java.lang.Boolean |
getManual() |
java.lang.String |
getPdbId() |
java.lang.String |
getRange()
Get the range of this domain, in PDB residue numbers (mmCif's
_pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).
|
java.util.List<ResidueRange> |
getResidueRanges() |
java.lang.String |
getSeqIdRange()
Get the range of this domain, in 1-based residue indices (mmCif's
_pdbx_poly_seq_scheme.seq_id)
Note that
getRange() is used when constructing the domain. |
java.lang.Integer |
getTGroup() |
java.lang.String |
getTGroupName() |
java.lang.Long |
getUid() |
java.lang.Integer |
getXGroup() |
java.lang.String |
getXGroupName() |
int |
hashCode() |
Structure |
loadStructure(AtomCache cache)
Loads a structure encompassing the structure identified.
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Structure |
reduce(Structure input)
Takes a complete structure as input and reduces it to the substructure
represented by this StructureIdentifier.
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void |
setArchitectureName(java.lang.String architectureName) |
void |
setAssemblyId(java.lang.Long assemblyId) |
void |
setChainId(java.lang.String chainId) |
void |
setDomainId(java.lang.String domainId) |
void |
setFGroup(java.lang.Integer fGroup) |
void |
setFGroupName(java.lang.String fGroupName) |
void |
setGroupName(java.lang.String tGroupName) |
void |
setHGroup(java.lang.Integer hGroup) |
void |
setHGroupName(java.lang.String hGroupName) |
void |
setLigands(java.util.Set<java.lang.String> ligands) |
void |
setManual(java.lang.Boolean manual) |
void |
setPdbId(java.lang.String pdbId) |
void |
setRange(java.lang.String range) |
void |
setSeqIdRange(java.lang.String seqIdRange) |
void |
setTGroup(java.lang.Integer tGroup) |
void |
setUid(java.lang.Long uid) |
void |
setXGroup(java.lang.Integer xGroup) |
void |
setXGroupName(java.lang.String xGroupName) |
SubstructureIdentifier |
toCanonical()
Convert to a canonical SubstructureIdentifier.
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java.lang.String |
toString() |
public EcodDomain()
public EcodDomain(java.lang.Long uid, java.lang.String domainId, java.lang.Boolean manual, java.lang.Integer xGroup, java.lang.Integer hGroup, java.lang.Integer tGroup, java.lang.Integer fGroup, java.lang.String pdbId, java.lang.String chainId, java.lang.String range, java.lang.String architectureName, java.lang.String xGroupName, java.lang.String hGroupName, java.lang.String tGroupName, java.lang.String fGroupName, java.lang.Long assemblyId, java.util.Set<java.lang.String> ligands)
public EcodDomain(java.lang.Long uid, java.lang.String domainId, java.lang.Boolean manual, java.lang.Integer xGroup, java.lang.Integer hGroup, java.lang.Integer tGroup, java.lang.Integer fGroup, java.lang.String pdbId, java.lang.String chainId, java.lang.String range, java.lang.String seqId, java.lang.String architectureName, java.lang.String xGroupName, java.lang.String hGroupName, java.lang.String tGroupName, java.lang.String fGroupName, java.lang.Long assemblyId, java.util.Set<java.lang.String> ligands)
public EcodDomain(java.lang.String domainId)
public EcodDomain(EcodDomain o)
protected java.lang.Object clone() throws java.lang.CloneNotSupportedException
clone
in class java.lang.Object
java.lang.CloneNotSupportedException
public java.lang.Long getUid()
public void setUid(java.lang.Long uid)
public java.lang.String getDomainId()
public void setDomainId(java.lang.String domainId)
public java.lang.Boolean getManual()
public void setManual(java.lang.Boolean manual)
public java.lang.Integer getXGroup()
public void setXGroup(java.lang.Integer xGroup)
public java.lang.Integer getHGroup()
public void setHGroup(java.lang.Integer hGroup)
public java.lang.Integer getTGroup()
public void setTGroup(java.lang.Integer tGroup)
public java.lang.Integer getFGroup()
public void setFGroup(java.lang.Integer fGroup)
public java.lang.String getPdbId()
public void setPdbId(java.lang.String pdbId)
public java.lang.String getChainId()
public void setChainId(java.lang.String chainId)
public java.lang.String getRange()
public void setRange(java.lang.String range)
public java.lang.String getSeqIdRange()
getRange()
is used when constructing the domain.public void setSeqIdRange(java.lang.String seqIdRange)
public java.lang.String getArchitectureName()
public void setArchitectureName(java.lang.String architectureName)
public java.lang.String getXGroupName()
public void setXGroupName(java.lang.String xGroupName)
public java.lang.String getHGroupName()
public void setHGroupName(java.lang.String hGroupName)
public java.lang.String getTGroupName()
public void setGroupName(java.lang.String tGroupName)
public java.lang.String getFGroupName()
public void setFGroupName(java.lang.String fGroupName)
public java.lang.Long getAssemblyId()
public void setAssemblyId(java.lang.Long assemblyId)
public java.util.Set<java.lang.String> getLigands()
public void setLigands(java.util.Set<java.lang.String> ligands)
public java.lang.String toString()
toString
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public java.lang.String getIdentifier()
StructureIdentifier
#toString()
method also return the
identifier, for consistency during serialization.getIdentifier
in interface StructureIdentifier
public java.util.List<ResidueRange> getResidueRanges()
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