Interface Atom

  • All Superinterfaces:
    java.lang.Cloneable, PDBRecord
    All Known Implementing Classes:
    AtomImpl

    public interface Atom
    extends java.lang.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 Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void addBond​(Bond bond)
      Add a bond
      java.lang.Object clone()
      Return an identical copy of this object .
      java.lang.Character getAltLoc()
      Get alternate Location.
      java.util.List<Bond> getBonds()
      Get all Bonds this atom is part of.
      short getCharge()
      Get the charge of this atom
      double[] getCoords()
      Get the coordinates.
      Element getElement()
      Get element of the atom, e.g.
      Group getGroup()
      Return the parent Group of the Atom.
      java.lang.String getName()
      Get atom name, e.g.
      float getOccupancy()
      Get occupancy.
      int getPDBserial()
      Get PDB atom number.
      float getTempFactor()
      Get temp factor.
      double getX()
      Get coordinate X.
      double getY()
      Get coordinate Y.
      double getZ()
      Get coordinate Z.
      boolean hasBond​(Atom other)
      Test if another atom has a bond to this atom
      void setAltLoc​(java.lang.Character c)
      Set alternate Location.
      void setBonds​(java.util.List<Bond> bonds)
      Sets the bonds
      void setCharge​(short charge)
      Set the charge of this atom
      void setCoords​(double[] c)
      Set the coordinates.
      void setElement​(Element e)
      Set element of the atom name, e.g.
      void setGroup​(Group parent)
      Set the back-reference to its parent Group.
      void setName​(java.lang.String s)
      Set atom name, e.g.
      void setOccupancy​(float occupancy)
      Set occupancy.
      void setPDBserial​(int i)
      Set PDB atom number.
      void setTempFactor​(float temp)
      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 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()
      • 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