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public interface Atom
A simple interface for an Atom.
The coordinates can be accessed via the
getCoords()
, or the
getX()
, getY()
, getZ()
methods.
There are a few additional methods here to provide some PDB specific information.
Method Summary | |
---|---|
Object |
clone()
returns and identical copy of this object . |
Character |
getAltLoc()
get set alternate Location. |
double[] |
getCoords()
get the coordinates. |
Element |
getElement()
get element of the atom, e.g. |
String |
getFullName()
get full name of atom e.g. |
Group |
getGroup()
Returns the parent Group of the Atom. |
String |
getName()
get trimmed version of atom name, e.g. |
double |
getOccupancy()
get occupancy. |
Group |
getParent()
Deprecated. replaced by getGroup() |
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(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(String s)
set full name of atom e.g. |
void |
setGroup(Group parent)
Sets the back-reference to its parent Group. |
void |
setName(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(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. |
Methods inherited from interface org.biojava.bio.structure.PDBRecord |
---|
toPDB, toPDB |
Method Detail |
---|
void setName(String s)
s
- a String specifying the name valuegetName()
String getName()
setName(java.lang.String)
void setFullName(String s)
s
- a String specifying the full name valuegetFullName()
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(Character c)
c
- a Character object specifying the alt loc valuegetAltLoc()
Character getAltLoc()
setAltLoc(java.lang.Character)
void setPDBline(String s)
PDBRecord.toPDB()
s
- a String specifying the PDBline valuegetPDBline()
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)
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)
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