Interface Atom

Method Details

• setName

  void setName(String s)

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

  Parameters:

  s - a trimmed String specifying the name value

  See Also:

  • getName()

• getName

  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(Character c)

  Set alternate Location.

  Parameters:

  c - a Character object specifying the alt loc value

  See Also:

  • getAltLoc()

• getAltLoc

  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

  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

  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(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