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. Claim Status Claims 1-5 are pending. Priority This application is a which foreign priority to application no. 2022-10118, filed 01/26/2022. The instant application has the effective filing date of 26 January 2022. Information Disclosure Statement The information disclosure statement s (IDS) submitted on 10/03/2022 and 6/22/2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner. Drawings The drawings, submitted on 10/03/2022, are objected to by the examiner for improper amino acid sequence disclosures in fig ures 2 A and 5 A , as detailed below . Nucleotide and/or Amino Acid Sequence Disclosures REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES Items 1) and 2) provide general guidance related to requirements for sequence disclosures. 37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted: In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying: the name of the ASCII text file; ii) the date of creation; and iii) the size of the ASCII text file in bytes; In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying: the name of the ASCII text file; the date of creation; and the size of the ASCII text file in bytes; In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended). When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form ( CRF ) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824. If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical. If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical. Specific deficiencies and the required response to this Office Action are as follows: Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”. Required response - Applicant must provide: A "Sequence Listing" part of the disclosure; together with An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2) ; A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3). If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide: A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and A statement according to item 2) a) or b) above. Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Required response – Applicant must provide: Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers; AND/OR A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. 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 appl icant regards as his invention. Claim s 1, 4, and 5 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 for the following reasons. Claim s 1, 4, and 5 recite “specifying an optional first type and optional second type,” “specifying on e or a plurality of first atomic groups classified into the first type …, ” and “calculating a number… between the first atomic group,” wherein it is unclear which limitations are optional, as they all appear to use information derived from the optional limitation. To overcome this rejection, please clarify which limitations in the instant claims are optional . 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 1-5 are rejected under U.S.C 101 because the claimed invention is directed to abstract ideas without significantly more, as detailed in the analysis below. Eligibility Step 1: Subject matter eligibility evaluation in accordance with MPEP § 2106: Claims 1-3 are directed to a statutory category ( product ). Claim 4 is directed to a statutory category ( method ). Claim 5 is directed to a statutory category ( apparatus ). Therefore, in accordance with MPEP § 2106.03 all claims have patent eligible subject matter. [Eligibility Step 1: YES] Eligibility Step 2A : This step determines whether a claim is directed to a judicial exception in accordance with MPEP § 2106. Eligibility Step 2A -- Prong One: Limitations are analyzed to determine if the claims recite any concepts that could equate to a judicial exception (i.e. abstract idea, law of nature, or natural phenomenon). Possible judicial exceptions are explored below. Recitations of Judicial Exceptions: Claims 1, 4, and 5: specifying one or a plurality of first atomic groups classified into the first type and one or a plurality of second atomic groups classified into the second type out of the plurality of atomic groups, on the basis of the structure specifying information; (mental process) calculating, on the basis of the structure specifying information, a number of pairs of the first atomic group and the second atomic group in which a mutual distance in the sequence between the first atomic group and the second atomic group is a predetermined distance (mental process, mathematical concept) Claim 2: calculating the distance in the direction specified by the direction specifying information. (mathematical concept) Step 2A – Prong One A nalysis: Limitations that recite mental determinations of data that require no more than the human mind and pen/paper fall into the mental process grouping of abstract ideas. Limitations that recite mathematical calculations and formulas, such as distance, fall into the mathematical concepts grouping of abstract ideas Eligibility Step 2A – Prong Two: A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. If the claim contains no additional claim elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)). Eligibility Step 2B : Claim elements are probed for inventive concept equating to significantly more than the judicial exception (MPEP 2106.04(II)). Additional Elements within the claimed invention include: Claim 1: A non-transitory computer-readable recording medium ; causing a computer to execute processing Claim 4: c alculation method implemented by a computer, Claim 5: calculation apparatus comprising: a memory; and a processor coupled to the memory, the processor being configured to perform processing, The elements above recite generic computer components or implementations. When viewed separately or in the context of a whole claimed invention they merely act as tools to apply the judicial exceptions in a generic comput ing environment without resulting in an improvement to technology. Elements of this nature do not integrate the judicial exceptions into practical application per Enfish , LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016). [Eligibility Step 2A – Prong Two: YES] Elements of this nature are further found to be well-understood, routine , and conventional per FairWarning IP, LLC v. Iatric Sys., 839 F.3d 1089, 1095, 120 USPQ2d 1293, 1296 (Fed. Cir. 2016) for accelerating a process of analyzing data when the increased speed comes solely from the capabilities of a general-purpose computer and TLI Communications, 823 F.3d at 612-13, 118 USPQ2d at 1747-48 for gathering and analyzing information using conventional techniques. [Eligibility Step 2B : NO] Additional Elements that may be categorized differently include: Claims 1, 4, and 5: r eceiving structure specifying information that specifies a type of each of a plurality of atomic groups and a sequence of the plurality of atomic groups regarding a cyclic molecule in which the plurality of atomic groups classified into a plurality of types is cyclically sequenced; and specifying an optional first type and an optional second type in the plurality of types . Claim 2: receiving direction specifying information that specifies either a first direction along a cycle of the cyclic molecule or a second direction along the cycle opposite to the first direction; Claim 3: wherein each of the plurality of atomic groups is an amino acid, and the cyclic molecule is a cyclic peptide. The elements above recite mere data gathering activities necessary to complete the judicial exceptions , when viewed separately or in the context of the whole claimed invention. Elements of this nature fail to integrate the judicial exceptions into practical application per MPEP 2106.05(g). [Eligibility Step 2A – Prong Two: YES] Such data gathering activities that obtain data, based on types of information and availability of information for further analysis are considered well- understood, routine, and conventional per Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1354-55, 119 USPQ2d 1739, 1742 (Fed. Cir. 2016) and Williamson et al. (Chemical Society Revs. Vol. 21; 1992) , which reviews determinants of cyclic peptide structure from NMR. [Eligibility Step 2B : NO] As such, claims 1- 5 are directed to judicial exceptions without significantly more and are rejected under 35 U.S.C 101. Claim Rejections - 35 USC § 102 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis ( i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale , or otherwise available to the public before the effective filing date of the claimed invention. (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. Claim s 1 and 3-5 are r ejected under 35 U . S . C 102(a)(2) as being anticipated by Floudas et al. (20030036093). Claims 1, 4, and 5 are directed to a computer readable medium, method, and apparatus that store a feature amount calculation program and receive a sequence of a cyclic molecule , along with structural information regarding how groups of atoms within the molecule are classified. Claim 3 is directed to the groups of atoms, representing amino acids; and the cyclic molecule representing a cyclic peptide. Floudas et al. describes a four-stage approach for predicting polypeptide structure. Floudas et al. teaches test ing a global optimization algorithm on Compstatin , a synthetic 13-residue ( ICVVQDWGUHRCT ) cyclic peptide (disulfide bridge between the Cys.sup.2 and Cys.sup.12 residues) that binds to C3 , inhibits complement activation [0390], and has undergone two-dimensional NMR techniques to yield backbone sequential restraints [0390]. Therefore, the method includes obtaining information regarding a cyclic peptide’s sequence, structural information, and amino acid types. Claims 1, 4, and 5 are directed to further receiving information pertaining optional first and second classifications ; and at least one group of atoms that can be classified into each classification, based on the structural information . Floudas et al. teaches that i n the hydrophobic residue-based superstructure and its mathematical model , all residues not belonging to helices are first classified as hydrophobic, bridge, turn , or other residues [0015]. Claims 1, 4, and 5 are further directed to calculating a number of times where the distance between the first and second group of atoms in a sequence is a predetermined amount. Floudas et al. further teaches identif ying beta. sheets and disulfide bridges through a novel superstructure-based mathematical framework [0014], including hydrophobic residue-based superstructure , which encompasses all potential contacts between pairs of hydrophobic residues [0014] with restrictions that include: ( i ) the formation of at least one contact in which no less than seven residues that fall between the contacting residues ( i and j) [0018]. Floudas et al. further teaches applying the residue-to residue contact formulation to the residues classified according to their position in the sequence in a two-stage iteration; and identif ying disulfide bonding pairs and antiparallel .beta. sheet s in the first iteration and additional single residue-to-residue contacts in the second [0355]. Floudas et al. further teaches the resulting mathematical models are Integer Linear Programming (ILP) problem s which can be solved to global optimality [0015] using CPLEX [0199 and claim 14]. Therefore, the method described by Floudas et al. teaches use of CPLEX software , stored on a computer readable medium, executed by processors of a computing environment (apparatus). Claim Rejections - 35 USC § 103 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis ( i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action: A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made. The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness . Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Floudas et al. (20030036093 A1) , as applied to claim 1 above, in view of Imanishi ( Advances in Polymer Science ; Vol 20 ; Springer ; 2005) . Floudas et al. teaches a n algorithm that receives structural and sequence information regarding a cyclic molecule and identifies residues with a predetermined distance between them. Claim 2 is directed to the computer readable medium further receiv ing information that specifies one of the following: a first direction along the cycle of the cyclic molecule or a second direction along the cycle opposite to the first direction ; and calculating the distance in the direction specified by the information. Floudas et al. teaches deriv ing lower and upper bounds on the (. phi.,. psi .) dihedral angles of the secondary structure residues , the distances between pairs of contacts of hydrophobic residues [0024] ; and comput ing main energy contributions as the sum of terms for each atom pair ( i,j ) whose interatomic distance is a function of at least one dihedral angle [0076] . Floudas et al. does not explicitly teach receiving the direction along or opposite the cycle of the molecule. Imanishi describes syntheses, conformation, and reactions of cyclic peptides. Imanishi shows three dihedral angles in a peptide unit , where the angle is positive if clockwise , and negative if anit clockwise (page 12, column 1). Therefore Floudas et al. teaches using information regarding the dihedral angles to calculate the distance between hydrophobic residues. Though Floudas et al. does not explicitly specify receiving information regarding the direction of the cycle of the molecule s , one of ordinary skill in the art could reasonably include the sign ( positive or negative ) of dihedral angles , as taught by Imanishi , with in the calculation to consider the clockwise or counterclockwise direction of the cyclic molecule s to yield a predictable result . Conclusion No claims are currently allowed. Correspondence Any inquiry concerning this communication or earlier communications from the examiner should be directed to Milana Thompson whose telephone number is FILLIN "Phone number" \* MERGEFORMAT (571) 272-8740 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT Monday - Friday, 9:00-6:00 ET . 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, FILLIN "SPE Name?" \* MERGEFORMAT Karlheinz Skowronek can be reached at FILLIN "SPE Phone?" \* MERGEFORMAT (571) 272-1113 . 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. / M.K.T ./ Examiner, Art Unit 1687 /Karlheinz R. Skowronek/ Supervisory Patent Examiner, Art Unit 1687