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java.lang.Objectorg.biojava.bio.structure.AtomImpl
public class AtomImpl
Implementation of an Atom of a PDB file. currently the coordinates of an atom are represented by a doubl[3] array.
Constructor Summary | |
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AtomImpl()
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Method Summary | |
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Object |
clone()
returns and identical copy of this object . |
Character |
getAltLoc()
get alternate Location. |
double[] |
getCoords()
get the coordinates as a double[3] array . |
String |
getFullName()
get full name of atom e.g. |
String |
getName()
Gets this object's name. |
double |
getOccupancy()
get occupancy. |
Group |
getParent()
Returns the parent Group of the Atom returns null if the referenced object is not Group |
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(Character c)
set alternate Location. |
void |
setCoords(double[] c)
the coordinates. |
void |
setFullName(String s)
set full name of atom e.g. |
void |
setName(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(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 |
String |
toString()
string representation. |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public AtomImpl()
Method Detail |
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public void setName(String s)
setName
in interface Atom
s
- a String specifying the name valuegetName()
public String getName()
getName
in interface Atom
setName(java.lang.String)
public void setFullName(String s)
setFullName
in interface Atom
s
- a String specifying the full name valuegetFullName()
public String getFullName()
getFullName
in interface Atom
setFullName(java.lang.String)
public void setPDBserial(int i)
setPDBserial
in interface Atom
i
- an int specifying the PDBserial valuegetPDBserial()
public int getPDBserial()
getPDBserial
in interface Atom
setPDBserial(int)
public void setCoords(double[] c)
setCoords
in interface Atom
c
- an array of doubles specifying the coords valuegetCoords()
public double[] getCoords()
getCoords
in interface Atom
setCoords(double[])
public void setX(double x)
Atom
setX
in interface Atom
x
- a doublepublic void setY(double y)
Atom
setY
in interface Atom
y
- a doublepublic void setZ(double z)
Atom
setZ
in interface Atom
z
- a doublepublic double getX()
getX
in interface Atom
public double getY()
getY
in interface Atom
public double getZ()
getZ
in interface Atom
public void setAltLoc(Character c)
setAltLoc
in interface Atom
c
- a Character object specifying the alt loc valuegetAltLoc()
public Character getAltLoc()
getAltLoc
in interface Atom
setAltLoc(java.lang.Character)
public void setPDBline(String s)
setPDBline
in interface Atom
s
- a String specifying the PDBline valuegetPDBline()
public String getPDBline()
getPDBline
in interface Atom
setPDBline(java.lang.String)
public String toString()
toString
in class 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 Object clone()
clone
in interface Atom
clone
in class Object
public void setParent(Group parent)
Atom
setParent
in interface Atom
parent
- the parent Grouppublic Group getParent()
Atom
getParent
in interface Atom
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