Package org.biojava.bio.structure
Interface Atom
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- All Known Implementing Classes:
AtomImpl
public interface Atom
A simple interface for an Atom. The coordinates can be accessed via thegetCoords()
, or thegetX()
,getY()
,getZ()
methods. There are a few additional methods here to provide some PDB specific information.- Since:
- 1.4
- Version:
- %I% %G%
- Author:
- Andreas Prlic, Horvath Tamas
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.Object
clone()
returns and identical copy of this object .java.lang.Character
getAltLoc()
get set alternate Location.double[]
getCoords()
get the coordinates.java.lang.String
getFullName()
get full name of atom e.g.java.lang.String
getName()
get trimmed version of atom name, e.g.double
getOccupancy()
get occupancy.Group
getParent()
Returns the parent Group of the Atom.java.lang.String
getPDBline()
store the whole line.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
setFullName(java.lang.String s)
set full name of atom e.g.void
setName(java.lang.String s)
set trimmed version of atom name, e.g.void
setOccupancy(double occupancy)
set occupancy.void
setParent(Group parent)
Sets the back-reference to its parent Group.void
setPDBline(java.lang.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.
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Method Detail
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setName
void setName(java.lang.String s)
set trimmed version of atom name, e.g. "CA".- Parameters:
s
- a String specifying the name value- See Also:
getName()
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getName
java.lang.String getName()
get trimmed version of atom name, e.g. "CA".- Returns:
- a String representing the name value
- See Also:
setName(java.lang.String)
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setFullName
void setFullName(java.lang.String s)
set full name of atom e.g. " CA ".- Parameters:
s
- a String specifying the full name value- See Also:
getFullName()
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getFullName
java.lang.String getFullName()
get full name of atom e.g. " CA ".- Returns:
- a String representing the full name value
- See Also:
setFullName(java.lang.String)
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setPDBserial
void setPDBserial(int i)
set PDB atom number.- Parameters:
i
- an int specifying the PDBserial value- See Also:
getPDBserial()
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getPDBserial
int getPDBserial()
get PDB atom number.- Returns:
- an int representing the PDBserial value
- See Also:
setPDBserial(int)
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setCoords
void setCoords(double[] c)
set the coordinates.- Parameters:
c
- an array of doubles specifying the coords value- See Also:
getCoords()
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getCoords
double[] getCoords()
get the coordinates.- Returns:
- an array of doubles representing the coords value
- See Also:
setCoords(double[])
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setX
void setX(double x)
Set the X coordinate.- Parameters:
x
- a double- See Also:
getX()
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setY
void setY(double y)
Set the Y coordinate.- Parameters:
y
- a double- See Also:
getY()
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setZ
void setZ(double z)
Set the Z coordinate.- Parameters:
z
- a double- See Also:
getZ()
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getX
double getX()
Get coordinate X.- Returns:
- a double
- See Also:
setX(double)
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getY
double getY()
Get coordinate Y.- Returns:
- a double
- See Also:
setY(double)
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getZ
double getZ()
Get coordinate Z.- Returns:
- a double
- See Also:
setZ(double)
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setAltLoc
void setAltLoc(java.lang.Character c)
get set alternate Location.- Parameters:
c
- a Character object specifying the alt loc value- See Also:
getAltLoc()
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getAltLoc
java.lang.Character getAltLoc()
get set alternate Location.- Returns:
- a Character object representing the alt loc value
- See Also:
setAltLoc(java.lang.Character)
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setPDBline
void setPDBline(java.lang.String s)
store the whole line.- Parameters:
s
- a String specifying the PDBline value- See Also:
getPDBline()
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getPDBline
java.lang.String getPDBline()
store the whole line.- Returns:
- a String representing the PDBline value
- See Also:
setPDBline(java.lang.String)
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setOccupancy
void setOccupancy(double occupancy)
set occupancy.- Parameters:
occupancy
- a double specifying the occupancy value- See Also:
getOccupancy()
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getOccupancy
double getOccupancy()
get occupancy.- Returns:
- a double representing the occupancy value
- See Also:
setOccupancy(double)
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setTempFactor
void setTempFactor(double temp)
get set temp factor .- Parameters:
temp
- a double specifying the temp factor value- See Also:
getTempFactor()
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getTempFactor
double getTempFactor()
get set temp factor.- Returns:
- a double representing the temp factor value
- See Also:
setTempFactor(double)
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clone
java.lang.Object clone()
returns and identical copy of this object .- Returns:
- and identical copy of this object
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setParent
void setParent(Group parent)
Sets the back-reference to its parent Group.- Parameters:
parent
- the parent Group- See Also:
getParent()
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getParent
Group getParent()
Returns the parent Group of the Atom. returns null if the referenced object is not Group- Returns:
- Group the parent Group of the Atom, or null
- See Also:
setParent(Group)
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