Method Detail

• setName

  void setName​(java.lang.String s)

  Set atom name, e.g. "CA".

  Parameters:

  s - a trimmed String specifying the name value

  See Also:

  getName()

• getName

  java.lang.String getName​()

  Get atom name, e.g. "CA". Beware that some PDB atom names are ambiguous (e.g. CA, which means C-alpha or Calcium), the ambiguity can simply be resolved by also checking the element with getElement()

  Returns:

  a trimmed String representing the name value

  See Also:

  setName(java.lang.String)

• setElement

  void setElement​(Element e)

  Set element of the atom name, e.g. Element.Fe

  Parameters:

  e - an Element enumeration

  See Also:

  getElement()

• getElement

  Element getElement​()

  Get element of the atom, e.g. Element.Ca

  Returns:

  an Element enumeration

  See Also:

  setElement(org.biojava.nbio.structure.Element)

• setPDBserial

  void setPDBserial​(int i)

  Set PDB atom number.

  Parameters:

  i - an int specifying the PDBserial value

  See Also:

  getPDBserial()

• getPDBserial

  int getPDBserial​()

  Get PDB atom number.

  Returns:

  an int representing the PDBserial value

  See Also:

  setPDBserial(int)

• setCoords

  void setCoords​(double[] c)

  Set the coordinates.

  Parameters:

  c - an array of doubles specifying the coords value

  See Also:

  getCoords()

• getCoords

  double[] getCoords​()

  Get the coordinates.

  Returns:

  an array of doubles representing the coords value

  See Also:

  setCoords(double[])

• setX

  void setX​(double x)

  Set the X coordinate.

  Parameters:

  x - a double

  See Also:

  getX()

• setY

  void setY​(double y)

  Set the Y coordinate.

  Parameters:

  y - a double

  See Also:

  getY()

• setZ

  void setZ​(double z)

  Set the Z coordinate.

  Parameters:

  z - a double

  See Also:

  getZ()

• getX

  double getX​()

  Get coordinate X.

  Returns:

  a double

  See Also:

  setX(double)

• getY

  double getY​()

  Get coordinate Y.

  Returns:

  a double

  See Also:

  setY(double)

• getZ

  double getZ​()

  Get coordinate Z.

  Returns:

  a double

  See Also:

  setZ(double)

• setAltLoc

  void setAltLoc​(java.lang.Character c)

  Set alternate Location.

  Parameters:

  c - a Character object specifying the alt loc value

  See Also:

  getAltLoc()

• getAltLoc

  java.lang.Character getAltLoc​()

  Get alternate Location.

  Returns:

  a Character object representing the alt loc value

  See Also:

  setAltLoc(java.lang.Character)

• setOccupancy

  void setOccupancy​(float occupancy)

  Set occupancy.

  Parameters:

  occupancy - a float specifying the occupancy value

  See Also:

  getOccupancy()

• getOccupancy

  float getOccupancy​()

  Get occupancy.

  Returns:

  a float representing the occupancy value

  See Also:

  setOccupancy(float)

• setTempFactor

  void setTempFactor​(float temp)

  Set temp factor .

  Parameters:

  temp - a float specifying the temp factor value

  See Also:

  getTempFactor()

• getTempFactor

  float getTempFactor​()

  Get temp factor.

  Returns:

  a float representing the temp factor value

  See Also:

  setTempFactor(float)

• clone

  java.lang.Object clone​()

  Return an identical copy of this object .

  Returns:

  an identical copy of this object

• setGroup

  void setGroup​(Group parent)

  Set the back-reference to its parent Group.

  Parameters:

  parent - the parent Group

  See Also:

  getGroup()

• getGroup

  Group getGroup​()

  Return 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:

  setGroup(Group)

• addBond

  void addBond​(Bond bond)

  Add a bond

  Parameters:

  bond - to be added

  See Also:

  getBonds()

• getBonds

  java.util.List<Bond> getBonds​()

  Get all Bonds this atom is part of.

  Returns:

  a list of Bonds or null if no bonds exist for this Atom

• setBonds

  void setBonds​(java.util.List<Bond> bonds)

  Sets the bonds

  Parameters:

  bonds -

• hasBond

  boolean hasBond​(Atom other)

  Test if another atom has a bond to this atom

  Parameters:

  other -

  Returns:

• getCharge

  short getCharge​()

  Get the charge of this atom

  Returns:

  a the integer charge.

• setCharge

  void setCharge​(short charge)

  Set the charge of this atom