java.io.Serializable
, PDBRecord
public class DBRef extends java.lang.Object implements PDBRecord, java.io.Serializable
Constructor | Description |
---|---|
DBRef() |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
getChainId() |
The chain ID of the corresponding chain.
|
java.lang.String |
getDatabase() |
The database of the db-ref.
|
java.lang.String |
getDbAccession() |
Sequence database accession code.
|
java.lang.String |
getDbIdCode() |
Sequence database identification code.
|
int |
getDbSeqBegin() |
Initial sequence number of the
database seqment.
|
int |
getDbSeqEnd() |
Ending sequence position of the database segment.
|
java.lang.Long |
getId() |
Get the ID used by Hibernate.
|
char |
getIdbnsBegin() |
Insertion code of initial residue of the segment, if PDB is the
reference.
|
char |
getIdbnsEnd() |
Insertion code of the ending
residue of the segment, if PDB is
the reference.
|
java.lang.String |
getIdCode() |
get the idCode for this entry
|
char |
getInsertBegin() |
Initial insertion code of the PDB sequence segment.
|
char |
getInsertEnd() |
Ending insertion code of the PDB sequence segment.
|
Structure |
getParent() |
Get the structure object that this DBRef relates to.
|
int |
getSeqBegin() |
Initial sequence number of the PDB sequence segment.
|
int |
getSeqEnd() |
Ending sequence number of the PDB sequence segment.
|
void |
setChainId(java.lang.String chainId) |
The chain ID of the corresponding chain.
|
void |
setDatabase(java.lang.String database) |
Specifies the database value.
|
void |
setDbAccession(java.lang.String dbAccession) |
Sequence database accession code.
|
void |
setDbIdCode(java.lang.String dbIdCode) |
Sequence database identification code.
|
void |
setDbSeqBegin(int dbSeqBegin) |
Initial sequence number of the
database seqment.
|
void |
setDbSeqEnd(int dbSeqEnd) |
The begin of the sequence position in the database
|
void |
setId(java.lang.Long id) |
Set the ID used by Hibernate.
|
void |
setIdbnsBegin(char idbnsBegin) |
Insertion code of initial residue of the segment, if PDB is the
reference.
|
void |
setIdbnsEnd(char idbnsEnd) |
Insertion code of the ending
residue of the segment, if PDB is
the reference.
|
void |
setIdCode(java.lang.String idCode) |
Set the idCode for this entry.
|
void |
setInsertBegin(char insertBegin) |
Initial insertion code of the PDB sequence segment.
|
void |
setInsertEnd(char insertEnd) |
Ending insertion code of the PDB sequence segment.
|
void |
setParent(Structure s) |
Set the structure object that this DBRef relates to.
|
void |
setSeqBegin(int seqbegin) |
Initial sequence number of the PDB sequence segment.
|
void |
setSeqEnd(int seqEnd) |
Ending sequence number of the PDB sequence segment.
|
java.lang.String |
toPDB() |
Convert the DBRef object to a DBREF record as it is used in PDB files
|
void |
toPDB(java.lang.StringBuffer buf) |
Append the PDB representation of this DBRef to the provided StringBuffer
|
java.lang.String |
toString() |
String representation of a DBRef.
|
public java.lang.Long getId()
setId(Long)
public void setId(java.lang.Long id)
id
- the id assigned by HibernategetId()
public void setParent(Structure s)
s
- a structure objectgetParent()
public Structure getParent()
setParent(Structure)
public java.lang.String toPDB()
public void toPDB(java.lang.StringBuffer buf)
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String getIdCode()
setIdCode(String)
public void setIdCode(java.lang.String idCode)
idCode
- the idCode for this entrygetIdCode()
public java.lang.String getChainId()
public void setChainId(java.lang.String chainId)
chainId
- the ID of the corresponding chaingetChainId()
public java.lang.String getDatabase()
Database name database (code in columns 27 - 32) ---------------------------------------------------------- GenBank GB Protein Data Bank PDB Protein Identification Resource PIR SWISS-PROT SWS TREMBL TREMBL UNIPROT UNP
setDatabase(String)
public void setDatabase(java.lang.String database)
database
- the databasegetDatabase()
public java.lang.String getDbAccession()
setDbAccession(String)
public void setDbAccession(java.lang.String dbAccession)
dbAccession
- the dbAccessiongetDbAccession()
public java.lang.String getDbIdCode()
setDbIdCode(String)
public void setDbIdCode(java.lang.String dbIdCode)
dbIdCode
- identification codegetDbIdCode()
public int getDbSeqBegin()
setDbSeqBegin(int)
public void setDbSeqBegin(int dbSeqBegin)
dbSeqBegin
- a sequence positiongetDbSeqBegin()
public int getDbSeqEnd()
setDbSeqEnd(int)
public void setDbSeqEnd(int dbSeqEnd)
dbSeqEnd
- sequence positiongetDbSeqEnd()
public char getIdbnsBegin()
setIdbnsBegin(char)
public void setIdbnsBegin(char idbnsBegin)
idbnsBegin
- insertion codegetIdbnsBegin()
public char getIdbnsEnd()
setIdbnsEnd(char)
public void setIdbnsEnd(char idbnsEnd)
idbnsEnd
- the insertion codesetIdbnsEnd(char)
public char getInsertBegin()
setInsertBegin(char)
public void setInsertBegin(char insertBegin)
insertBegin
- getInsertBegin()
public char getInsertEnd()
setInsertEnd(char)
public void setInsertEnd(char insertEnd)
insertEnd
- insertEndgetInsertEnd()
public int getSeqBegin()
setSeqBegin(int)
public void setSeqBegin(int seqbegin)
seqbegin
- start seq. positiongetSeqBegin()
public int getSeqEnd()
getSeqEnd()
public void setSeqEnd(int seqEnd)
seqEnd
- sequence end positionsetSeqEnd(int)