Interface Atom

  • All Known Implementing Classes:
    AtomImpl

    public interface Atom
    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 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.
    • Method Detail

      • 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()
      • 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)
      • 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()
      • 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)
      • 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)
        get set alternate Location.
        Parameters:
        c - a Character object specifying the alt loc value
        See Also:
        getAltLoc()
      • getAltLoc

        java.lang.Character getAltLoc()
        get set alternate Location.
        Returns:
        a Character object representing the alt loc value
        See Also:
        setAltLoc(java.lang.Character)
      • setPDBline

        void setPDBline​(java.lang.String s)
        store the whole line.
        Parameters:
        s - a String specifying the PDBline value
        See Also:
        getPDBline()
      • getPDBline

        java.lang.String getPDBline()
        store the whole line.
        Returns:
        a String representing the PDBline value
        See Also:
        setPDBline(java.lang.String)
      • setOccupancy

        void setOccupancy​(double occupancy)
        set occupancy.
        Parameters:
        occupancy - a double specifying the occupancy value
        See Also:
        getOccupancy()
      • getOccupancy

        double getOccupancy()
        get occupancy.
        Returns:
        a double representing the occupancy value
        See Also:
        setOccupancy(double)
      • setTempFactor

        void setTempFactor​(double temp)
        get set temp factor .
        Parameters:
        temp - a double specifying the temp factor value
        See Also:
        getTempFactor()
      • getTempFactor

        double getTempFactor()
        get set temp factor.
        Returns:
        a double representing the temp factor value
        See Also:
        setTempFactor(double)
      • clone

        java.lang.Object clone()
        returns and identical copy of this object .
        Returns:
        and identical copy of this object
      • setParent

        void setParent​(Group parent)
        Sets the back-reference to its parent Group.
        Parameters:
        parent - the parent Group
        See Also:
        getParent()
      • 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)