Interface Atom

  • All Superinterfaces:
    java.lang.Cloneable, PDBRecord, java.io.Serializable
    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 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()
      • 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:
        getCoords()
      • 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. Default altLoc ('.' in mmCIF files) is represented by ' ' (space character, ascii 32).
        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