Package org.biojava.bio.structure
Class AtomImpl
- java.lang.Object
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- org.biojava.bio.structure.AtomImpl
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Constructor Summary
Constructors Constructor Description AtomImpl()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.Object
clone()
returns and identical copy of this object .java.lang.Character
getAltLoc()
get alternate Location.double[]
getCoords()
get the coordinates as a double[3] array .java.lang.String
getFullName()
get full name of atom e.g.long
getId()
Get the Hibernate database ID.java.lang.String
getName()
Gets this object's name.double
getOccupancy()
get occupancy.Group
getParent()
Returns the parent Group of the Atom.java.lang.String
getPDBline()
get the whole line .int
getPDBserial()
get PDB atom number.double
getTempFactor()
get set temp factor.double
getX()
Get the X coordinate.double
getY()
Get the Y coordinate.double
getZ()
Get the Z coordinate.void
setAltLoc(java.lang.Character c)
set alternate Location.void
setCoords(double[] c)
the coordinates.void
setFullName(java.lang.String s)
set full name of atom e.g.void
setId(long id)
Set the Hibernate database ID.void
setName(java.lang.String s)
trimmed version of atom name, e.g.void
setOccupancy(double occu)
set occupancy.void
setParent(Group parent)
Sets the back-reference to its parent Group.void
setPDBline(java.lang.String s)
store the whole line.void
setPDBserial(int i)
set PDB atom number.void
setTempFactor(double temp)
get set temp factor .void
setX(double x)
Set the X coordinate.void
setY(double y)
Set the Y coordinate.void
setZ(double z)
Set the Z coordinate.java.lang.String
toString()
string representation.
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Method Detail
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getId
public long getId()
Get the Hibernate database ID.- Returns:
- the id
- See Also:
setId(long)
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setId
public void setId(long id)
Set the Hibernate database ID.- Parameters:
id
- the hibernate id- See Also:
getId()
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setName
public void setName(java.lang.String s)
trimmed version of atom name, e.g. "CA"
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getName
public java.lang.String getName()
Gets this object's name.- Specified by:
getName
in interfaceAtom
- Returns:
- a String representing the name value
- See Also:
setName(java.lang.String)
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setFullName
public void setFullName(java.lang.String s)
set full name of atom e.g. " CA " .- Specified by:
setFullName
in interfaceAtom
- Parameters:
s
- a String specifying the full name value- See Also:
getFullName()
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getFullName
public java.lang.String getFullName()
get full name of atom e.g. " CA ".- Specified by:
getFullName
in interfaceAtom
- Returns:
- a String representing the full name value
- See Also:
setFullName(java.lang.String)
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setPDBserial
public void setPDBserial(int i)
set PDB atom number.- Specified by:
setPDBserial
in interfaceAtom
- Parameters:
i
- an int specifying the PDBserial value- See Also:
getPDBserial()
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getPDBserial
public int getPDBserial()
get PDB atom number.- Specified by:
getPDBserial
in interfaceAtom
- Returns:
- an int representing the PDBserial value
- See Also:
setPDBserial(int)
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setCoords
public void setCoords(double[] c)
the coordinates.- Specified by:
setCoords
in interfaceAtom
- Parameters:
c
- an array of doubles specifying the coords value- See Also:
getCoords()
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getCoords
public double[] getCoords()
get the coordinates as a double[3] array .- Specified by:
getCoords
in interfaceAtom
- Returns:
- an array of doubles representing the coords value
- See Also:
setCoords(double[])
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setX
public void setX(double x)
Description copied from interface:Atom
Set the X coordinate.- Specified by:
setX
in interfaceAtom
- Parameters:
x
- a double- See Also:
Atom.getX()
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setY
public void setY(double y)
Description copied from interface:Atom
Set the Y coordinate.- Specified by:
setY
in interfaceAtom
- Parameters:
y
- a double- See Also:
Atom.getY()
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setZ
public void setZ(double z)
Description copied from interface:Atom
Set the Z coordinate.- Specified by:
setZ
in interfaceAtom
- Parameters:
z
- a double- See Also:
Atom.getZ()
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getX
public double getX()
Get the X coordinate.- Specified by:
getX
in interfaceAtom
- Returns:
- a double
- See Also:
setX(double)
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getY
public double getY()
Get the Y coordinate.- Specified by:
getY
in interfaceAtom
- Returns:
- a double
- See Also:
setY(double)
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getZ
public double getZ()
Get the Z coordinate.- Specified by:
getZ
in interfaceAtom
- Returns:
- a double
- See Also:
setZ(double)
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setAltLoc
public void setAltLoc(java.lang.Character c)
set alternate Location.- Specified by:
setAltLoc
in interfaceAtom
- Parameters:
c
- a Character object specifying the alt loc value- See Also:
getAltLoc()
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getAltLoc
public java.lang.Character getAltLoc()
get alternate Location.- Specified by:
getAltLoc
in interfaceAtom
- Returns:
- a Character object representing the alt loc value
- See Also:
setAltLoc(java.lang.Character)
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setPDBline
public void setPDBline(java.lang.String s)
store the whole line.- Specified by:
setPDBline
in interfaceAtom
- Parameters:
s
- a String specifying the PDBline value- See Also:
getPDBline()
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getPDBline
public java.lang.String getPDBline()
get the whole line .- Specified by:
getPDBline
in interfaceAtom
- Returns:
- a String representing the PDBline value
- See Also:
setPDBline(java.lang.String)
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toString
public java.lang.String toString()
string representation.- Overrides:
toString
in classjava.lang.Object
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setOccupancy
public void setOccupancy(double occu)
Description copied from interface:Atom
set occupancy.- Specified by:
setOccupancy
in interfaceAtom
- Parameters:
occu
- a double specifying the occupancy value- See Also:
Atom.getOccupancy()
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getOccupancy
public double getOccupancy()
Description copied from interface:Atom
get occupancy.- Specified by:
getOccupancy
in interfaceAtom
- Returns:
- a double representing the occupancy value
- See Also:
Atom.setOccupancy(double)
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setTempFactor
public void setTempFactor(double temp)
Description copied from interface:Atom
get set temp factor .- Specified by:
setTempFactor
in interfaceAtom
- Parameters:
temp
- a double specifying the temp factor value- See Also:
Atom.getTempFactor()
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getTempFactor
public double getTempFactor()
Description copied from interface:Atom
get set temp factor.- Specified by:
getTempFactor
in interfaceAtom
- Returns:
- a double representing the temp factor value
- See Also:
Atom.setTempFactor(double)
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clone
public java.lang.Object clone()
returns and identical copy of this object .
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setParent
public void setParent(Group parent)
Description copied from interface:Atom
Sets the back-reference to its parent Group.- Specified by:
setParent
in interfaceAtom
- Parameters:
parent
- the parent Group- See Also:
Atom.getParent()
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getParent
public Group getParent()
Description copied from interface:Atom
Returns the parent Group of the Atom. returns null if the referenced object is not Group- Specified by:
getParent
in interfaceAtom
- Returns:
- Group the parent Group of the Atom, or null
- See Also:
Atom.setParent(Group)
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