Package jgromacs.data

Class Atom

  • All Implemented Interfaces:
    java.lang.Cloneable

    public class Atom
    extends java.lang.Object
    implements java.lang.Cloneable
    Objects of this class represent a single atom
    • Constructor Detail

      • Atom

        public Atom()
        Constructs a new Atom object
    • Method Detail

      • getAtomType

        public AtomType getAtomType()
        Returns the type of atom
        Returns:
        Type of the atom
      • getIndex

        public int getIndex()
        Returns the index of atom
        Returns:
        Index of the atom
      • setIndex

        public void setIndex​(int index)
        Sets the index of atom
        Parameters:
        index - index of the atom
      • getName

        public java.lang.String getName()
        Returns the name of atom
        Returns:
        Name of the atom
      • setName

        public void setName​(java.lang.String name)
        Sets the name of atom
        Parameters:
        name - name of the atom
      • setAtomType

        public void setAtomType​(AtomType atomType)
        Sets the type of atom
        Parameters:
        atomType - type of the atom
      • getCoordinates

        public Point3D getCoordinates()
        Returns the coordinates of atom
        Returns:
        Coordinates of atom
      • setCoordinates

        public void setCoordinates​(Point3D coordinates)
        Sets the coordinates of atom
        Parameters:
        coordinates - coordinates of the atom
      • getXCoordinate

        public double getXCoordinate()
        Returns the X coordinate of atom
        Returns:
        X coordinate of atom
      • setXCoordinate

        public void setXCoordinate​(double x)
        Sets the X coordinate of atom
        Parameters:
        x - X coordinate of the atom
      • getYCoordinate

        public double getYCoordinate()
        Returns the Y coordinate of atom
        Returns:
        Y coordinate of atom
      • setYCoordinate

        public void setYCoordinate​(double y)
        Sets the Y coordinate of atom
        Parameters:
        y - Y coordinate of the atom
      • getZCoordinate

        public double getZCoordinate()
        Returns the Z coordinate of atom
        Returns:
        Z coordinate of atom
      • setZCoordinate

        public void setZCoordinate​(double z)
        Sets the Z coordinate of atom
        Parameters:
        z - Z coordinate of the atom
      • getOccupancy

        public double getOccupancy()
        Returns the occupancy of atom
        Returns:
        occupancy of atom
      • setOccupancy

        public void setOccupancy​(double occupancy)
        Sets the occupancy of atom
        Parameters:
        occupancy - occupancy of the atom
      • getBvalue

        public double getBvalue()
        Returns the B-value of atom
        Returns:
        B-value of atom
      • setBvalue

        public void setBvalue​(double bvalue)
        Sets the B-value of atom
        Parameters:
        bvalue - B-value of the atom
      • isHydrogenAtom

        public boolean isHydrogenAtom()
        Returns true if the atom is a Hydrogen
      • isHeavyAtom

        public boolean isHeavyAtom()
        Returns true if it is a heavy atom (not hydrogen)
      • isAlphaCarbon

        public boolean isAlphaCarbon()
        Returns true if it is an alpha carbon atom
      • isCTerminalCarbon

        public boolean isCTerminalCarbon()
        Returns true if it is a C-terminal carbon atom
      • isBetaCarbon

        public boolean isBetaCarbon()
        Returns true if it is a beta carbon atom
      • isGammaCarbon

        public boolean isGammaCarbon()
        Returns true if it is a gamma carbon atom
      • isDeltaCarbon

        public boolean isDeltaCarbon()
        Returns true if it is a delta carbon atom
      • isEpsilonCarbon

        public boolean isEpsilonCarbon()
        Returns true if it is an epsilon carbon atom
      • isZetaCarbon

        public boolean isZetaCarbon()
        Returns true if it is a zeta carbon atom
      • isCarbonylOxygen

        public boolean isCarbonylOxygen()
        Returns true if it is a carbonyl oxygen atom
      • isTerminalOxygen

        public boolean isTerminalOxygen()
        Returns true if it is a terminal oxygen atom
      • isNTerminalNitrogen

        public boolean isNTerminalNitrogen()
        Returns true if it is an N-terminal nitrogen atom
      • isBackboneAtom

        public boolean isBackboneAtom()
        Returns true if it is a backbone atom
      • isMainChainAtom

        public boolean isMainChainAtom()
        Returns true if it is a main chain atom
      • isMainChainHydrogenAtom

        public boolean isMainChainHydrogenAtom()
        Returns true if it is a main chain hydrogen atom
      • isMainChainPlusHAtom

        public boolean isMainChainPlusHAtom()
        Returns true if it is a main chain or hydrogen atom
      • isMainChainPlusCbAtom

        public boolean isMainChainPlusCbAtom()
        Returns true if it is a main chain or beta carbon atom
      • isSideChainAtom

        public boolean isSideChainAtom()
        Returns true if it is a side chain atom
      • isSideChainMinusHAtom

        public boolean isSideChainMinusHAtom()
        Returns true if it is a side chain atom but not hydrogen
      • distance

        public double distance​(Atom other)
        Returns the Euclidean distance between this atom and another atom
        Parameters:
        other - another atom
        Returns:
        distance between atoms
      • toString

        public java.lang.String toString()
        Returns the String representation of atom
        Overrides:
        toString in class java.lang.Object
        Returns:
        String representation
      • clone

        public java.lang.Object clone()
        Returns an identical Atom object
        Overrides:
        clone in class java.lang.Object
        Returns:
        clone of the atom
      • equals

        public boolean equals​(java.lang.Object other)
        Returns true if the two atoms are identical
        Overrides:
        equals in class java.lang.Object
        Parameters:
        other - the other atom
      • hashCode

        public int hashCode()
        Returns hash code
        Overrides:
        hashCode in class java.lang.Object