Deriving fixed bond information

• US 7,805,255 B2
• Filed: 11/13/2007
• Issued: 09/28/2010
• Est. Priority Date: 02/18/1999
• Status: Expired due to Fees

• Current Assignee: Cambridgesoft Corporation (Perkinelmer Incorporated)
• Original Assignee: Cambridgesoft Corporation (Perkinelmer Incorporated)
• Inventors: Helson, Harold E.
• Primary Examiner(s): Wachsman; Hal D
• Assistant Examiner(s): Suarez; Felix E
• Application Number:
  US11/939,101
• Publication Number:
  US 20080183400A1
• Time in Patent Office: 1,050 Days
• Field of Search: 702/19, 702/20, 702/22, 702/27, 702/179, 702/182, 702/183, 395/500.05, 435/4, 435/6, 703/11
• US Class Current: 702/23
• CPC Class Codes: G16C 20/20 Identification of molecular entities, parts thereof or of chemical compositions

Abstract

Fixed bond information is derived. A fixed bond representation of a chemical structure is derived from a delocalized representation. A path is conceptually traced through the represented structure and an examination is conducted, for each atom, of each possible electronic and bonding state that is consistent with what has come before along the path. A result is found by extensively or exhaustively examining all possible states and orders in a semi-recursive procedure that is directed early towards likely answers. If there is more than one possible solution, the best solution is chosen by use of a rating function.

Claims

1. A computer-implemented method for use in deriving fixed bond information, comprising:

analyzing a delocalized representation of a chemical structure;

identifying, based on valence information, a plurality of fixed bond representation candidates for at least a portion of the chemical structure;

evaluating at least a subset of the fixed bond representation candidates;

selecting from among the plurality of fixed bond representation candidates one or more candidates based on the evaluation;

producing fixed bond information based on the selection; and

outputting the produced fixed bond information to an output device.

2. The computer-implemented method of claim 1, wherein the identifying includes tracing a path through the structure, assigning bond orders and atomic charges or radicals as the path is traced, and, when an unacceptable state is detected, backtracking the path to the last assignment that was made.

3. The computer-implemented method of claim 1, further comprising:

deriving electronic state and valence distributions information together with analyzing the delocalized representation.

4. The computer-implemented method of claim 1, further comprising:

determining, by either exhaustion or exceeding a predetermined amount of time, whether it is possible to produce a neutral, non-radical fixed bond representation of most chemical structures.

5. The computer-implemented method of claim 1, wherein when the evaluating determines that a fixed bond representation candidate cannot be improved upon, it is selected.

6. The computer-implemented method of claim 1, wherein the assigning atomic charges or radicals is performed based on electronic state and valence distribution (ESVD), and further comprising:

queuing at least a subset of the ESVDs by priority.

7. The computer-implemented method of claim 6, wherein the highest priority ESVD is assigned and the remainder of the at least a subset of the ESVDs are placed in an independent queue.

8. A method for use in deriving fixed bond information, comprising:

analyzing a delocalized representation of a chemical structure;

identifying, based on valence information, a plurality of fixed bond representation candidates for at least a portion of the chemical structure;

evaluating at least a subset of the fixed bond representation candidates;

selecting from among the plurality of fixed bond representation candidates based on the evaluation;

producing fixed bond information based on the selection;

using a precomputed collection of atom valences as a function of element, charge, radical state, and number and distribution of bonds inside and outside of a delocalized region in the delocalized representation; and

outputting the produced fixed bond information to an output device.

9. The method of claim 8, wherein the identifying includes tracing a path through the structure, assigning bond orders and atomic charges or radicals as the path is traced, and backtracking the path to the last assignment that was made, when an unacceptable state is detected.

10. The method of claim 8, wherein the collection is configured to allow additional elements and values to be added.

11. The method of claim 8, wherein the collection is configured to allow additional elements and values to be added to apply to any chemical element.

12. A computer-implemented system for deriving fixed bond information, comprising:

an analyzer configured to analyze a delocalized representation of a chemical structure;

an identifier configured to identify, based on valence information, a plurality of fixed bond representation candidates for at least a portion of the chemical structure;

an evaluator configured to evaluate at least a subset of the fixed bond representation candidates;

a selector configured to elect from among the plurality of fixed bond representation candidates based on the evaluation; and

a producer configured to produce and output fixed bond information based on the selection.

13. The computer-implemented system of claim 12, the identifier configured to identify the plurality of fixed bond representation candidates for at least a portion of the chemical structure further based on tracing a path through the structure, assigning bond orders and atomic charges or radicals as the path is traced, and, when an unacceptable state is detected, backtracking the path to the last assignment that was made.

14. Computer software, residing on a non-transitory computer-readable storage medium, comprising a set of instructions for use in a computer system to help cause the computer system to derive fixed bond information, the instructions causing the system to:

analyze a delocalized representation of a chemical structure;

identify, based on valence information, a plurality of fixed bond representation candidates for at least a portion of the chemical structure;

evaluate at least a subset of the fixed bond representation candidates;

select from among the plurality of fixed bond representation candidates based on the evaluation;

produce fixed bond information based on the selection; and

output the produced fixed bond information to an output device.

15. The computer software of claim 14, wherein the identifying includes tracing a path through the structure, assigning bond orders and atomic charges or radicals as the path is traced, and backtracking the path to the last assignment that was made, when an unacceptable state is detected.