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 and Description |
---|---|
void |
addBond(Bond bond)
Adds a bond
|
java.lang.Object |
clone()
returns and identical copy of this object .
|
java.lang.Character |
getAltLoc()
get set alternate Location.
|
java.util.List<Bond> |
getBonds()
Gets all
Bond s this atom is part of. |
double[] |
getCoords()
get the coordinates.
|
Element |
getElement()
get element of the atom, e.g.
|
java.lang.String |
getFullName()
get full name of atom e.g.
|
Group |
getGroup()
Returns the parent Group of the Atom.
|
java.lang.String |
getName()
get trimmed version of atom name, e.g.
|
double |
getOccupancy()
get occupancy.
|
Group |
getParent()
Deprecated.
replaced by
getGroup() |
java.lang.String |
getPDBline()
Deprecated.
@deprecated replaced by
PDBRecord.toPDB() |
int |
getPDBserial()
get PDB atom number.
|
double |
getTempFactor()
get set temp factor.
|
double |
getX()
Get coordinate X.
|
double |
getY()
Get coordinate Y.
|
double |
getZ()
Get coordinate Z.
|
void |
setAltLoc(java.lang.Character c)
get set alternate Location.
|
void |
setCoords(double[] c)
set the coordinates.
|
void |
setElement(Element e)
set element of the atom name, e.g.
|
void |
setFullName(java.lang.String s)
set full name of atom e.g.
|
void |
setGroup(Group parent)
Sets the back-reference to its parent Group.
|
void |
setName(java.lang.String s)
set trimmed version of atom name, e.g.
|
void |
setOccupancy(double occupancy)
set occupancy.
|
void |
setParent(Group parent)
Deprecated.
replaced by
setGroup(Group) |
void |
setPDBline(java.lang.String s)
Deprecated.
replaced by
PDBRecord.toPDB() |
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.
|
void setName(java.lang.String s)
s
- a String specifying the name valuegetName()
java.lang.String getName()
setName(java.lang.String)
void setFullName(java.lang.String s)
s
- a String specifying the full name valuegetFullName()
java.lang.String getFullName()
setFullName(java.lang.String)
void setElement(Element e)
e
- an Element enumerationgetElement()
Element getElement()
setElement(org.biojava.bio.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 setPDBline(java.lang.String s)
PDBRecord.toPDB()
s
- a String specifying the PDBline valuegetPDBline()
java.lang.String getPDBline()
PDBRecord.toPDB()
setPDBline(java.lang.String)
void setOccupancy(double occupancy)
occupancy
- a double specifying the occupancy valuegetOccupancy()
double getOccupancy()
setOccupancy(double)
void setTempFactor(double temp)
temp
- a double specifying the temp factor valuegetTempFactor()
double getTempFactor()
setTempFactor(double)
java.lang.Object clone()
void setParent(Group parent)
setGroup(Group)
parent
- the parent GroupgetParent()
void setGroup(Group parent)
parent
- the parent GroupgetGroup()
Group getParent()
getGroup()
setParent(Group)
Group getGroup()
setParent(Group)
void addBond(Bond bond)
bond
- to be addedgetBonds()