Interface Atom

    • Method Detail

      • setName

        void setName​(String s)
        Set atom name, e.g. "CA".
        Parameters:
        s - a trimmed String specifying the name value
        See Also:
        getName()
      • 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:
        setName(java.lang.String)
      • setPDBserial

        void setPDBserial​(int i)
        Set PDB atom number.
        Parameters:
        i - an int specifying the PDBserial value
        See Also:
        getPDBserial()
      • 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​(Character c)
        Set alternate Location.
        Parameters:
        c - a Character object specifying the alt loc value
        See Also:
        getAltLoc()
      • setOccupancy

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

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

        List<BondgetBonds()
        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