Package jgromacs.data

Class Atom

java.lang.Object
jgromacs.data.Atom
All Implemented Interfaces:
Cloneable
public class Atom extends Object implements Cloneable
Objects of this class represent a single atom

  • Constructor Details

    • Atom

      public Atom()
      Constructs a new Atom object

  • Method Details

    • 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 String getName()
      Returns the name of atom
      Returns:
      Name of the atom

    • setName

      public void setName(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 String toString()
      Returns the String representation of atom
      Overrides:
      toString in class Object
      Returns:
      String representation

    • clone

      public Object clone()
      Returns an identical Atom object
      Overrides:
      clone in class Object
      Returns:
      clone of the atom

    • equals

      public boolean equals(Object other)
      Returns true if the two atoms are identical
      Overrides:
      equals in class Object
      Parameters:
      other - the other atom

    • hashCode

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