Interface ICrystal

All Superinterfaces:
Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener
All Known Implementing Classes:
Crystal, Crystal, DebugCrystal

public interface ICrystal extends IAtomContainer
Class representing a molecular crystal. The crystal is described with molecules in fractional coordinates and three cell axes: a,b and c.

The crystal is designed to store only the asymetric atoms. Though this is not enforced, it is assumed by all methods.

Source code:
main
Belongs to CDK module:
interfaces
Keywords:
crystal
  • Method Details

    • add

      void add(IAtomContainer container)
      Adds the atoms in the AtomContainer as cell content. Symmetry related atoms should not be added unless P1 space group is used.
      Specified by:
      add in interface IAtomContainer
      Parameters:
      container - The molecule to add
    • addAtom

      void addAtom(IAtom atom)
      Adds the atom to the crystal. Symmetry related atoms should not be added unless P1 space group is used.
      Specified by:
      addAtom in interface IAtomContainer
      Parameters:
      atom - the atom to add
    • setA

      void setA(javax.vecmath.Vector3d newAxis)
      Sets the A unit cell axes in carthesian coordinates in a eucledian space.
      Parameters:
      newAxis - the new A axis
      See Also:
    • getA

      javax.vecmath.Vector3d getA()
      Gets the A unit cell axes in carthesian coordinates as a three element double array.
      Returns:
      a Vector3D representing the A axis
      See Also:
    • setB

      void setB(javax.vecmath.Vector3d newAxis)
      Sets the B unit cell axes in carthesian coordinates.
      Parameters:
      newAxis - the new B axis
      See Also:
    • getB

      javax.vecmath.Vector3d getB()
      Gets the B unit cell axes in carthesian coordinates as a three element double array.
      Returns:
      a Vector3D representing the B axis
      See Also:
    • setC

      void setC(javax.vecmath.Vector3d newAxis)
      Sets the C unit cell axes in carthesian coordinates.
      Parameters:
      newAxis - the new C axis
      See Also:
    • getC

      javax.vecmath.Vector3d getC()
      Gets the C unit cell axes in carthesian coordinates as a three element double array.
      Returns:
      a Vector3D representing the C axis
      See Also:
    • getSpaceGroup

      String getSpaceGroup()
      Gets the space group of this crystal.
      Returns:
      the space group of this crystal structure
      See Also:
    • setSpaceGroup

      void setSpaceGroup(String group)
      Sets the space group of this crystal.
      Parameters:
      group - the space group of this crystal structure
      See Also:
    • getZ

      Integer getZ()
      Gets the number of asymmetric parts in the unit cell.
      Returns:
      the number of assymetric parts in the unit cell
      See Also:
    • setZ

      void setZ(Integer value)
      Sets the number of assymmetric parts in the unit cell.
      Parameters:
      value - the number of assymetric parts in the unit cell
      See Also:
    • clone

      Returns a deep clone of this IChemObject.
      Specified by:
      clone in interface IAtomContainer
      Specified by:
      clone in interface IChemObject
      Returns:
      Object the clone of this IChemObject.
      Throws:
      CloneNotSupportedException - if the IChemObject cannot be cloned