DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s Response
Applicant’s response, filed 02/02/2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Claims Status
Claims 14 and 15 are new.
Claim 11 is canceled.
Claims 1-10 and 12-15 are pending.
Claims 1-10 and 12-15 are examined.
Withdrawn Objections/Rejections
The rejection of claims 1-13 under 35 USC 112(b) of Office Action mailed 10/01/2025 is withdrawn in view of the amendments submitted.
The rejection of claim 11 under 35 USC 112(d) is moot because the claim has been canceled.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-10 and 12-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. This is a new grounds of rejection as necessitated by claim amendments.
With respect to claims 1 and 13, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-10 and 12-15 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendment.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims are directed to a process and a device.
With respect to step (2A)(1): The claims are directed to abstract ideas of mental processes and mathematical concepts.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claims 1 and 13:
selecting anyone of an addition of an atom or an atomic group to the compound structure based on the input form the user, or a deletion of an atom or an atomic group from the compound structure based on the input from the user
determining a synthetic aptitude of the modified compound structure based on a synthetic aptitude score calculated using information of the standard compound database
in a case of selecting the addition of an atom or an atomic group to the compound structure, bonding a new atom or a new atomic group to an atom selected from atoms included in the compound structure, or in a case of selecting the deletion of an atom or an atomic group from the compound structure, deleting an atom or atomic group selected from atoms or atomic groups included in the compound structure, thereby obtaining a modified compound structure
in a case where the modified compound structure has the synthetic aptitude, accepting the modification, or in a case where the modified compound structure does not have the synthetic aptitude, rejecting the modification
repeating the selection in (B) to the acceptance and the rejection in (E) until the compound structure which has undergone the acceptance or the rejection in (E) satisfies a termination condition
Mathematical concepts recited in claims 1 and 13:
wherein the synthetic aptitude score for the modified compound structure is calculated based on an appearance frequency for each number of bonds of an atomic arrangement in the modified compound structure and an appearance frequency for each number of bonds of the atomic arrangement in the standard compound database, using a function in which a synthetic aptitude score for the atomic arrangement in the modified compound structure decreases as the number of bonds and appearance frequency in the atomic arrangement of the modified compound structure increase
Dependent claims 2-10, 14, and 15 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 1, and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 2: “the compound structure input by the user is one atom or a compound”
Claim 3: “wherein the one atom is randomly selected, or selected based on an appearance frequency of atomic species appearing in the compound database”
Claim 4: “wherein, in the selection in (B), the additional of an atom or an atomic group or the deletion of an atom or an atomic group is randomly selected, or selected based on an appearance frequency of atomic species included in the compound database”
Claim 5: “wherein, in the obtaining of the modified compound structure in (C), an atom having the number of bonded atoms less than a maximum value is selected from the atoms included in the compound structure, and the new atom is bonded to the selected atom”
Claim 6: “wherein, in a case of selecting the atom having the number of bonded atoms less than the maximum value in the obtaining of the modified compound structure in (C), an atom in which the number of bonded atoms does not teach a minimum value is selected, and in a case where two or more atoms having the number of bonded atoms less than the maximum value are selected in the obtaining of the modified compound structure in (C) and the number of the bonded atoms reaches the minimum value in all of the selected atoms, an atom having a larger difference between the number of bonded atoms and the maximum value is selected from among the selected atoms”
Claim 7: “wherein, in the obtaining of the modified compound structure in (C), based on the information of the compound database, the new atom is or randomly selected from atomic species capable of bonding to the selected atom”
Claim 8: “wherein, in the obtaining of the modified compound structure in (C), in a case where an atomic arrangement capable of forming a cyclic structure appears as a result of bonding the new atom to the selected atom, the cyclic structure is formed probabilistically or randomly based on the information of the compound database”
Claim 9: “wherein, in a case of deleting an atom selected from the atoms included in the compound structure in the obtaining of the modified compound structure in (C), candidates of an atom capable of avoiding splitting the compound structure into two or more molecules are extracted, and the atom to be deleted is selected from the candidates”
Claim 10: “wherein, in the case of deleting an atom selected from the atoms included in the compound structure in the obtaining of the modified compound structure in (C), the atom to be deleted is selected form the candidates randomly or based on the information of the compound database”
Claim 14: “wherein in the selection in (B), the additional of the atom or the atomic group or the deletion of the atom or atomic group is further selected based on an appearance frequency of atomic species included in the standard compound database”
Claim 15: “wherein in the selection in (B), the additional of the atom or the atomic group or the deletion of the atom or atomic group is further selected based on an appearance frequency of atomic species included in the standard compound database”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than modeling and simulation of molecules and characterizing the synthetic abilities of the molecule.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claims 1 and 13 recite the following additional elements that are not abstract ideas:
a computer comprising a processor and a non-transitory and tangible memory, wherein the processor includes circuitry formed by combining circuit elements such as semiconductor devices, the processor being implemented by any one of, or any combination of, a CPU, a GPU, an FPGA, a PLD, or an ASIC, or being implemented on a system-on-chip (SoC), and wherein the processor performs the method by reading and executing processor-readable code recorded in the non-transitory and tangible memory
receiving, via an input device from a user, an input identifying a compound structure
accessing a standard compound database for evaluating a synthetic aptitude, and acquiring a compound structure
outputting via an output device to the user, the compound structure in a case where the compound structure satisfied the termination
The steps of receiving an input identifying a compound structure and accessing a standard compound database are directed to data gathering as they gather the data on which the judicial exceptions are performed. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)).The elements of a non-temporary and computer-readable recording medium and processor are elements of a generic computer. The claims do not describe any specific computation steps by which the computer parts perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implements these functions. The claims state nothing more than a generic computer which performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). The step of outputting the compound structure is ancillary to the judicial exceptions and thus does not integrate the judicial exceptions into a practical application.
Dependent claim 12 is directed to further generic computer elements.
None of these dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d)(I), determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claims 1 and 13: The additional elements of a computer comprising a processor and a non-transitory and tangible memory, wherein the processor includes circuitry formed by combining circuit elements such as semiconductor devices, the processor being implemented by any one of, or any combination of, a CPU, a GPU, an FPGA, a PLD, or an ASIC, or being implemented on a system-on-chip (SoC), and wherein the processor performs the method by reading and executing processor-readable code recorded in the non-transitory and tangible memory, receiving an input identifying a compound structure, accessing a standard compound database for evaluating a synthetic aptitude, and acquiring a compound structure, and outputting the compound structure in a case where the compound structure satisfied the termination do not rise to the level of significantly more than the judicial exception. The prior art Umeyama et al. (US 2010/0312538 A1, published December 2010, IDS reference) discloses that the conventional procedure for performing low molecular compound docking to target macromolecules and in silico screenings includes compound databases that store an enormous number of compounds (paragraph [0003]). With respect to the computer elements of a computer-readable medium, receiving input, outputting, etc., as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that this additional limitation is routine, well understood, and conventional in the art. This limitation does not improve the functioning of a computer, or comprise an improvement to any other technical field, it does not require or set forth a particular machine, it does not affect a transformation of matter, nor does it provide a non-conventional or unconventional step. As such, this limitation fails to rise to the level of significantly more.
With respect to claim 12: The additional element of a non-transitory and computer-readable tangible recording medium does not rise to the level of significantly more than the judicial exception. With respect to the computer-readable medium, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
In combination, the collection or generation of the data, acted upon by the judicial exception, fail to rise to the level of significantly more. The data gathering steps provide the data for the judicial exception. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
Response to Arguments
Applicant states that “the step (D) in claim 1 does describe specific computation steps, based on the description in paragraph [0057] of the present specification.” Furthermore, Applicant states that “Applicant has amended claim 1 by further reciting how the actual hardware is implemented or controlled to perform the mathematical computation steps, based on the description in paragraphs [0027] and [0028] of the present specification. Because the present invention according to claim 1, as amended, can provide the user with a compound structure having enough synthetic aptitude before the user actually tries to synthesize a chemical compound, the present invention has a practical application in which actual hardware is implemented and controlled, thereby reduce burden on the user in generating a compound structure having a desired physical property”.
It is respectfully submitted that this is not persuasive. The hardware recited in the claims can still be interpreted as a generic computer. Furthermore, an improvement of reducing burden on the user is not a practical application, as a reduced burden on a user can still be a judicial exception, e.g., an improved mental process or method or organizing human activity. Thus, the claims are directed to using a generic computer for an improved method of calculating synthetic aptitude to determine a compound structure. The claims do not recite sufficient additional elements that integrate this determination into a practical application (see MPEP 2106.04(d)). Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/E.A.S./Examiner, Art Unit 1686
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
Prosecution Insights