Package org.biojava.nbio.structure

Class AtomImpl

java.lang.Object
org.biojava.nbio.structure.AtomImpl
All Implemented Interfaces:
Serializable, Cloneable, Atom, PDBRecord
public class AtomImpl extends Object implements Atom, Serializable, PDBRecord
Implementation of an Atom of a PDB file. currently the coordinates of an atom are represented by a double[3] array.
Since:
1.4
Version:
%I% %G%
Author:
Andreas Prlic
See Also:

  • Field Details

    • BONDS_INITIAL_CAPACITY

      public static final int BONDS_INITIAL_CAPACITY
      The inital capacity of the bonds list. Most atoms have a maximum of 3 heavy atom neighbors.
      See Also:

  • Constructor Details

    • AtomImpl

      public AtomImpl()

  • Method Details

    • setName

      public void setName(String s)
      Set atom name, e.g. "CA".
      Specified by:
      setName in interface Atom
      Parameters:
      s - a trimmed String specifying the name value
      See Also:

    • getName

      public 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 Atom.getElement()
      Specified by:
      getName in interface Atom
      Returns:
      a trimmed String representing the name value
      See Also:

    • setPDBserial

      public void setPDBserial(int i)
      Set PDB atom number.
      Specified by:
      setPDBserial in interface Atom
      Parameters:
      i - an int specifying the PDBserial value
      See Also:

    • getPDBserial

      public int getPDBserial()
      Get PDB atom number.
      Specified by:
      getPDBserial in interface Atom
      Returns:
      an int representing the PDBserial value
      See Also:

    • setCoords

      public void setCoords(double[] c)
      Set the coordinates.
      Specified by:
      setCoords in interface Atom
      Parameters:
      c - an array of doubles specifying the coords value
      See Also:

    • getCoords

      public double[] getCoords()
      Get the coordinates.
      Specified by:
      getCoords in interface Atom
      Returns:
      an array of doubles representing the coords value
      See Also:

    • setX

      public void setX(double x)
      Description copied from interface: Atom
      Set the X coordinate.
      Specified by:
      setX in interface Atom
      Parameters:
      x - a double
      See Also:

    • setY

      public void setY(double y)
      Description copied from interface: Atom
      Set the Y coordinate.
      Specified by:
      setY in interface Atom
      Parameters:
      y - a double
      See Also:

    • setZ

      public void setZ(double z)
      Description copied from interface: Atom
      Set the Z coordinate.
      Specified by:
      setZ in interface Atom
      Parameters:
      z - a double
      See Also:

    • getX

      public double getX()
      Get coordinate X.
      Specified by:
      getX in interface Atom
      Returns:
      a double
      See Also:

    • getY

      public double getY()
      Get coordinate Y.
      Specified by:
      getY in interface Atom
      Returns:
      a double
      See Also:

    • getZ

      public double getZ()
      Get coordinate Z.
      Specified by:
      getZ in interface Atom
      Returns:
      a double
      See Also:

    • setAltLoc

      public void setAltLoc(Character c)
      Set alternate Location.
      Specified by:
      setAltLoc in interface Atom
      Parameters:
      c - a Character object specifying the alt loc value
      See Also:

    • getAltLoc

      public Character getAltLoc()
      Get alternate Location.
      Specified by:
      getAltLoc in interface Atom
      Returns:
      a Character object representing the alt loc value
      See Also:

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • setOccupancy

      public void setOccupancy(float occu)
      Description copied from interface: Atom
      Set occupancy.
      Specified by:
      setOccupancy in interface Atom
      Parameters:
      occu - a float specifying the occupancy value
      See Also:

    • getOccupancy

      public float getOccupancy()
      Description copied from interface: Atom
      Get occupancy.
      Specified by:
      getOccupancy in interface Atom
      Returns:
      a float representing the occupancy value
      See Also:

    • setTempFactor

      public void setTempFactor(float temp)
      Description copied from interface: Atom
      Set temp factor .
      Specified by:
      setTempFactor in interface Atom
      Parameters:
      temp - a float specifying the temp factor value
      See Also:

    • getTempFactor

      public float getTempFactor()
      Description copied from interface: Atom
      Get temp factor.
      Specified by:
      getTempFactor in interface Atom
      Returns:
      a float representing the temp factor value
      See Also:

    • clone

      public Object clone()
      returns and identical copy of this object .
      Specified by:
      clone in interface Atom
      Overrides:
      clone in class Object
      Returns:
      and identical copy of this object

    • setGroup

      public void setGroup(Group parent)
      Set the back-reference to its parent Group.
      Specified by:
      setGroup in interface Atom
      Parameters:
      parent - the parent Group
      See Also:

    • getGroup

      public Group getGroup()
      Return the parent Group of the Atom. returns null if the referenced object is not Group
      Specified by:
      getGroup in interface Atom
      Returns:
      Group the parent Group of the Atom, or null
      See Also:

    • getElement

      public Element getElement()
      Get element of the atom, e.g. Element.Ca
      Specified by:
      getElement in interface Atom
      Returns:
      an Element enumeration
      See Also:

    • setElement

      public void setElement(Element e)
      Set element of the atom name, e.g. Element.Fe
      Specified by:
      setElement in interface Atom
      Parameters:
      e - an Element enumeration
      See Also:

    • toPDB

      public String toPDB()
      Description copied from interface: PDBRecord
      Returns a PDB file like representation of this record.
      Specified by:
      toPDB in interface PDBRecord
      Returns:
      a String providing a PDB file like representation of the record.

    • toPDB

      public void toPDB(StringBuffer buf)
      Description copied from interface: PDBRecord
      Appends a PDB file like representation of this record to the provided StringBuffer.
      Specified by:
      toPDB in interface PDBRecord

    • getBonds

      public List<Bond> getBonds()
      Get all Bonds this atom is part of.
      Specified by:
      getBonds in interface Atom
      Returns:
      a list of Bonds or null if no bonds exist for this Atom

    • hasBond

      public boolean hasBond(Atom other)
      Test if another atom has a bond to this atom
      Specified by:
      hasBond in interface Atom
      Returns:

    • setBonds

      public void setBonds(List<Bond> bonds)
      Sets the bonds
      Specified by:
      setBonds in interface Atom

    • addBond

      public void addBond(Bond bond)
      Description copied from interface: Atom
      Add a bond
      Specified by:
      addBond in interface Atom
      Parameters:
      bond - to be added
      See Also:

    • getCharge

      public short getCharge()
      Description copied from interface: Atom
      Get the charge of this atom
      Specified by:
      getCharge in interface Atom
      Returns:
      a the integer charge.

    • setCharge

      public void setCharge(short inputCharge)
      Description copied from interface: Atom
      Set the charge of this atom
      Specified by:
      setCharge in interface Atom