public class AtomImpl extends java.lang.Object implements Atom, java.io.Serializable, PDBRecord
Constructor and Description |
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AtomImpl() |
Modifier and Type | Method and Description |
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void |
addBond(Bond bond)
Add a bond
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java.lang.Object |
clone()
returns and identical copy of this object .
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java.lang.Character |
getAltLoc()
get alternate Location.
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java.util.List<Bond> |
getBonds()
Get all
Bond s this atom is part of. |
double[] |
getCoords()
Get the coordinates.
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Element |
getElement()
Get element of the atom, e.g.
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Group |
getGroup()
Return the parent Group of the Atom.
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long |
getId()
Get the Hibernate database ID.
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java.lang.String |
getName()
Get atom name, e.g.
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double |
getOccupancy()
Get occupancy.
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int |
getPDBserial()
Get PDB atom number.
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double |
getTempFactor()
Get temp factor.
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double |
getX()
Get coordinate X.
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double |
getY()
Get coordinate Y.
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double |
getZ()
Get coordinate Z.
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void |
setAltLoc(java.lang.Character c)
set alternate Location.
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void |
setCoords(double[] c)
Set the coordinates.
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void |
setElement(Element e)
Set element of the atom name, e.g.
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void |
setGroup(Group parent)
Set the back-reference to its parent Group.
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void |
setId(long id)
Set the Hibernate database ID.
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void |
setName(java.lang.String s)
Set atom name, e.g.
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void |
setOccupancy(double occu)
Set occupancy.
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void |
setPDBserial(int i)
Set PDB atom number.
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void |
setTempFactor(double temp)
Set temp factor .
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void |
setX(double x)
Set the X coordinate.
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void |
setY(double y)
Set the Y coordinate.
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void |
setZ(double z)
Set the Z coordinate.
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java.lang.String |
toPDB()
Returns a PDB file like representation of this record.
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void |
toPDB(java.lang.StringBuffer buf)
Appends a PDB file like representation of this record to the provided StringBuffer.
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java.lang.String |
toString()
string representation.
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public long getId()
setId(long)
public void setId(long id)
id
- the hibernate idgetId()
public void setName(java.lang.String s)
setName
in interface Atom
s
- a trimmed String specifying the name valueAtom.getName()
public java.lang.String getName()
Atom.getElement()
getName
in interface Atom
Atom.setName(java.lang.String)
public void setPDBserial(int i)
setPDBserial
in interface Atom
i
- an int specifying the PDBserial valueAtom.getPDBserial()
public int getPDBserial()
getPDBserial
in interface Atom
Atom.setPDBserial(int)
public void setCoords(double[] c)
setCoords
in interface Atom
c
- an array of doubles specifying the coords valueAtom.getCoords()
public double[] getCoords()
getCoords
in interface Atom
Atom.setCoords(double[])
public void setX(double x)
Atom
setX
in interface Atom
x
- a doubleAtom.getX()
public void setY(double y)
Atom
setY
in interface Atom
y
- a doubleAtom.getY()
public void setZ(double z)
Atom
setZ
in interface Atom
z
- a doubleAtom.getZ()
public double getX()
getX
in interface Atom
Atom.setX(double)
public double getY()
getY
in interface Atom
Atom.setY(double)
public double getZ()
getZ
in interface Atom
Atom.setZ(double)
public void setAltLoc(java.lang.Character c)
setAltLoc
in interface Atom
c
- a Character object specifying the alt loc valuegetAltLoc()
public java.lang.Character getAltLoc()
getAltLoc
in interface Atom
setAltLoc(java.lang.Character)
public java.lang.String toString()
toString
in class java.lang.Object
public void setOccupancy(double occu)
Atom
setOccupancy
in interface Atom
occu
- a double specifying the occupancy valueAtom.getOccupancy()
public double getOccupancy()
Atom
getOccupancy
in interface Atom
Atom.setOccupancy(double)
public void setTempFactor(double temp)
Atom
setTempFactor
in interface Atom
temp
- a double specifying the temp factor valueAtom.getTempFactor()
public double getTempFactor()
Atom
getTempFactor
in interface Atom
Atom.setTempFactor(double)
public java.lang.Object clone()
public void setGroup(Group parent)
setGroup
in interface Atom
parent
- the parent GroupAtom.getGroup()
public Group getGroup()
getGroup
in interface Atom
Atom.setGroup(Group)
public Element getElement()
Element.Ca
getElement
in interface Atom
Atom.setElement(org.biojava.nbio.structure.Element)
public void setElement(Element e)
Element.Fe
setElement
in interface Atom
e
- an Element enumerationAtom.getElement()
public java.lang.String toPDB()
PDBRecord
public void toPDB(java.lang.StringBuffer buf)
PDBRecord
public java.util.List<Bond> getBonds()
Atom
Bond
s this atom is part of.public void addBond(Bond bond)
Atom
addBond
in interface Atom
bond
- to be addedAtom.getBonds()