Package org.biojava.nbio.structure

Interface Atom

All Superinterfaces:
Cloneable, PDBRecord, Serializable
All Known Implementing Classes:
AtomImpl
public interface Atom extends Cloneable, PDBRecord
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.
Since:
1.4
Version:
%I% %G%
Author:
Andreas Prlic, Horvath Tamas

  • 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

      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:

    • setElement

      void setElement(Element e)
      Set element of the atom name, e.g. Element.Fe
      Parameters:
      e - an Element enumeration
      See Also:

    • getElement

      Element getElement()
      Get element of the atom, e.g. Element.Ca
      Returns:
      an Element enumeration
      See Also:

    • setPDBserial

      void setPDBserial(int i)
      Set PDB atom number.
      Parameters:
      i - an int specifying the PDBserial value
      See Also:

    • getPDBserial

      int getPDBserial()
      Get PDB atom number.
      Returns:
      an int representing the PDBserial value
      See Also:

    • setCoords

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

    • getCoords

      double[] getCoords()
      Get the coordinates.
      Returns:
      a new array of doubles representing the coords value
      See Also:

    • getCoordsAsPoint3d

      javax.vecmath.Point3d getCoordsAsPoint3d()
      Get the coordinates.

      Internally the coordinates are represented as Point3d so this is recommended over getCoords()

      Returns:
      a reference to the Point3d coordinates
      See Also:

    • setX

      void setX(double x)
      Set the X coordinate.
      Parameters:
      x - a double
      See Also:

    • setY

      void setY(double y)
      Set the Y coordinate.
      Parameters:
      y - a double
      See Also:

    • setZ

      void setZ(double z)
      Set the Z coordinate.
      Parameters:
      z - a double
      See Also:

    • getX

      double getX()
      Get coordinate X.
      Returns:
      a double
      See Also:

    • getY

      double getY()
      Get coordinate Y.
      Returns:
      a double
      See Also:

    • getZ

      double getZ()
      Get coordinate Z.
      Returns:
      a double
      See Also:

    • setAltLoc

      void setAltLoc(Character c)
      Set alternate Location.
      Parameters:
      c - a Character object specifying the alt loc value
      See Also:

    • getAltLoc

      Character getAltLoc()
      Get alternate Location.
      Returns:
      a Character object representing the alt loc value. Default altLoc ('.' in mmCIF files) is represented by ' ' (space character, ascii 32).
      See Also:

    • setOccupancy

      void setOccupancy(float occupancy)
      Set occupancy.
      Parameters:
      occupancy - a float specifying the occupancy value
      See Also:

    • getOccupancy

      float getOccupancy()
      Get occupancy.
      Returns:
      a float representing the occupancy value
      See Also:

    • setTempFactor

      void setTempFactor(float temp)
      Set temp factor .
      Parameters:
      temp - a float specifying the temp factor value
      See Also:

    • getTempFactor

      float getTempFactor()
      Get temp factor.
      Returns:
      a float representing the temp factor value
      See Also:

    • 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

      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:

    • addBond

      void addBond(Bond bond)
      Add a bond
      Parameters:
      bond - to be added
      See Also:

    • 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