Enhancing structure diagram generation through use of symmetry

• US 7,912,689 B1
• Filed: 02/11/2000
• Issued: 03/22/2011
• Est. Priority Date: 02/11/1999
• Status: Expired due to Fees

• Current Assignee: Cambridgesoft Corporation (Perkinelmer Incorporated)
• Original Assignee: Cambridgesoft Corporation (Perkinelmer Incorporated)
• Inventors: Helson, Harold E.
• Primary Examiner(s): JONES, HUGH M
• Application Number:
  US09/502,133
• Time in Patent Office: 4,057 Days
• Field of Search: 703/12,11,9,5,6,2,1
• US Class Current: 703/12
• CPC Class Codes: G16C 20/80 Data visualisation

Abstract

A method and a system are provided for enhancing structure diagram generation (“SDG”). In SDG, aesthetic two-dimensional (“2-D”) coordinates for use in a diagrammatic representation (“diagram”) of a molecule are derived from a connection table for the molecule. SDG may also improve the aesthetic qualities of a chemical structure diagram having existing coordinates, if available. SDG is enhanced by expressing the symmetry present in the molecule, by making use of symmetry in the 2-D dynamics used to lay out rings and chains, by construction of bridges using an open polygon method together with a potential function, and by an elegant approach to the relative positioning of molecules (“free rectangle method”).

Claims

1. A computer-implemented method for use in deriving a chemical structure diagram, comprising:

identifying, from a connection table for a chemical structure, an instance of chemical structural symmetry in the chemical structure;

wherein the instance of chemical structural symmetry includes chemically symmetrically equivalent atoms and bonds;

determining an arrangement of the chemically symmetrically equivalent atoms and bonds to provide a visually symmetric expression of the identified chemical structural symmetry in the chemical structure diagram;

laying out the chemically symmetrically equivalent atoms and bonds in the chemical structure diagram in a two-dimensional pictorial representation of the chemical structure in accordance with the determined arrangement and outputting the pictorial representation of the chemical structure.

outputting a representation of chemical structure.

2. The method of claim 1, wherein the identified instance of chemical structural symmetry is based on rotational symmetry.

3. The method of claim 1, wherein the identified instance of chemical structural symmetry is based on reflective symmetry.

4. The method of claim 1, wherein the identified instance of chemical structural symmetry is based on inversive symmetry.

5. The method of claim 1, further comprising:

basing the identification of an instance of chemical structural symmetry on sterochemistry.

6. The method of claim 1, further comprising:

basing the identification of an instance of chemical structural symmetry on rotational symmetry, reflective symmetry, and stereochemistry.

7. The method of claim 1, further comprising:

basing the identification of an instance of chemical structural symmetry on double bond stereochemistry.

8. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

determining a pivot point for the instance of chemical structural symmetry.

9. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

determining a graph-theoretic center for the instance of chemical structural symmetry

10. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

determining a symmetric order for the instance of chemical structural symmetry.

11. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

determining whether an atom belongs to the identified instance of chemical structural symmetry.

12. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

determining whether a bond belongs to the identified instance of chemical structural symmetry.

13. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

in the event the identified instance of chemical structural symmetry is reflective, selecting a position for at least one of the chemically symmetrically equivalent atoms and bonds on an opposite side of a mirror line.

14. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

in the event the identified instance of chemical structural symmetry is rotative, selecting a position for at least one of the chemically symmetrically equivalent atoms and bonds based on a pivot point.

15. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

rotating the chemical structure diagram so that a mirror plane in the chemical structure diagram is horizontal.

16. The method of claim 1, the determining an arrangement of the chemically symmetrically equivalent atoms and bonds further comprising:

rotating the chemical structure diagram so that a mirror plane in the chemical structure diagram is vertical.

17. A computer-readable storage medium encoded with a set of instructions for use in a computer system to cause the computer system to derive a chemical structure diagram, the instructions causing the system to:

identify, from a connection table for a chemical structure, an instance of chemical structural symmetry in the chemical structure, wherein the instance of chemical structural symmetry includes symmetrically equivalent atoms and bonds;

determine an arrangement of the chemically symmetrically equivalent atoms and bonds to provide a visually symmetric expression of the identified chemical structural symmetry in the chemical structure diagram;

lay out the chemically symmetrically equivalent atoms and bonds in the chemical structure diagram in a two-dimensional pictorial representation of the chemical structure in accordance with the determined arrangement and output the pictorial representation of the chemical structure.

18. A computer-implemented method for use in deriving a chemical structure diagram, comprising:

identifying an instance of chemical structural symmetry in the chemical structure;

wherein the instance of chemical structural symmetry includes symmetrically equivalent atoms and bonds;

determining an arrangement of the chemically symmetrically equivalent atoms and bonds to provide a visually symmetric expression of the identified chemical symmetry in the chemical structure diagram;

laying out the chemically symmetrically equivalent atoms and bonds in the chemical structure diagram in a two-dimensional pictorial representation of the chemical structure in accordance with the determined arrangement and outputting the pictorial representation of the chemical structure.

19. The method of claim 18, wherein the identified instance of chemical structural symmetry is based on rotational symmetry.

20. The method of claim 18, wherein the identified instance of chemical structural symmetry is based on reflective symmetry.

21. The method of claim 18, wherein the identified instance of chemical structural symmetry is based on inversive symmetry.

22. The method of claim 18, further comprising:

basing the identification of an instance of chemical structural symmetry on stereochemistry.

23. The method of claim 18, further comprising:

basing the identification of an instance of chemical structural symmetry on rotational symmetry, reflective symmetry, and stereochemistry.

24. The method of claim 18, further comprising:

basing the identification of an instance of chemical structural symmetry on double bond stereochemistry.

25. A computer-readable storage medium encoded with a set of instructions to cause a system to derive a chemical structure diagram, the instructions causing the system to:

identify an instance of chemical structural symmetry in the chemical structure, wherein the instance of chemical structural symmetry includes chemically symmetrically equivalent atoms and bonds;

determine an arrangement of the chemically symmetrically equivalent atoms and bonds to provide a visually symmetric expression of the identified chemical symmetry in the chemical structure diagram;

lay out the chemically symmetrically equivalent atoms and bonds in the chemical structure diagram in a two-dimensional pictorial representation of the chemical structure in accordance with the determined arrangement and output the pictorial representation of the chemical structure.