java.lang.Cloneable
, PDBRecord
AtomImpl
public interface Atom extends java.lang.Cloneable, PDBRecord
getCoords()
, or the
getX()
, getY()
, getZ()
methods.
There are a few additional methods here to provide some PDB specific information.Modifier and Type | Method | Description |
---|---|---|
void |
addBond(Bond bond) |
Add a bond
|
java.lang.Object |
clone() |
Return an identical copy of this object .
|
java.lang.Character |
getAltLoc() |
Get alternate Location.
|
java.util.List<Bond> |
getBonds() |
Get all
Bond s this atom is part of. |
short |
getCharge() |
Get the charge of this atom
|
double[] |
getCoords() |
Get the coordinates.
|
Element |
getElement() |
Get element of the atom, e.g.
|
Group |
getGroup() |
Return the parent Group of the Atom.
|
java.lang.String |
getName() |
Get atom name, e.g.
|
float |
getOccupancy() |
Get occupancy.
|
int |
getPDBserial() |
Get PDB atom number.
|
float |
getTempFactor() |
Get temp factor.
|
double |
getX() |
Get coordinate X.
|
double |
getY() |
Get coordinate Y.
|
double |
getZ() |
Get coordinate Z.
|
boolean |
hasBond(Atom other) |
Test if another atom has a bond to this atom
|
void |
setAltLoc(java.lang.Character c) |
Set alternate Location.
|
void |
setBonds(java.util.List<Bond> bonds) |
Sets the bonds
|
void |
setCharge(short charge) |
Set the charge of this atom
|
void |
setCoords(double[] c) |
Set the coordinates.
|
void |
setElement(Element e) |
Set element of the atom name, e.g.
|
void |
setGroup(Group parent) |
Set the back-reference to its parent Group.
|
void |
setName(java.lang.String s) |
Set atom name, e.g.
|
void |
setOccupancy(float occupancy) |
Set occupancy.
|
void |
setPDBserial(int i) |
Set PDB atom number.
|
void |
setTempFactor(float temp) |
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.
|
void setName(java.lang.String s)
s
- a trimmed String specifying the name valuegetName()
java.lang.String getName()
getElement()
setName(java.lang.String)
void setElement(Element e)
Element.Fe
e
- an Element enumerationgetElement()
Element getElement()
Element.Ca
setElement(org.biojava.nbio.structure.Element)
void setPDBserial(int i)
i
- an int specifying the PDBserial valuegetPDBserial()
int getPDBserial()
setPDBserial(int)
void setCoords(double[] c)
c
- an array of doubles specifying the coords valuegetCoords()
double[] getCoords()
setCoords(double[])
void setX(double x)
x
- a doublegetX()
void setY(double y)
y
- a doublegetY()
void setZ(double z)
z
- a doublegetZ()
double getX()
setX(double)
double getY()
setY(double)
double getZ()
setZ(double)
void setAltLoc(java.lang.Character c)
c
- a Character object specifying the alt loc valuegetAltLoc()
java.lang.Character getAltLoc()
setAltLoc(java.lang.Character)
void setOccupancy(float occupancy)
occupancy
- a float specifying the occupancy valuegetOccupancy()
float getOccupancy()
setOccupancy(float)
void setTempFactor(float temp)
temp
- a float specifying the temp factor valuegetTempFactor()
float getTempFactor()
setTempFactor(float)
java.lang.Object clone()
void setGroup(Group parent)
parent
- the parent GroupgetGroup()
Group getGroup()
setGroup(Group)
void addBond(Bond bond)
bond
- to be addedgetBonds()
java.util.List<Bond> getBonds()
Bond
s this atom is part of.Bond
s or null if no bonds exist for this Atomvoid setBonds(java.util.List<Bond> bonds)
bonds
- boolean hasBond(Atom other)
other
- short getCharge()
void setCharge(short charge)