CTFR 17/652,796 CTFR 100426 DETAILED ACTION Applicant's response, filed 24 February 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application. Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Information Disclosure Statement The information disclosure statements (IDS) submitted on 2/2/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner. Claim Status Claims 1-4, 6-11, 13-17, and 19-23 are pending. Claims 5, 12, and 18 are cancelled. Claims 21-23 are newly recited. Claims 1-4, 6-11, 13-17, and 19-23 are rejected. Claim Rejections - 35 USC § 112 Response to Amendment In view of applicant’s amendments to the claims previous rejections under 35 U.S.C. 112 (b) over antecedent basis, have been withdrawn. Claim Rejections - 35 USC § 101 Response to Amendment In view of applicant’s amendments to the claims previous rejections under 35 U.S.C. 101 have been reviewed, updated, and provided below. 07-04-01 AIA 07-04 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 1-4, 6-11, 13-17, and 19-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more. The claims recite a method, system, and computer program product for generating molecular descriptors based on global structure information. This judicial exception is not integrated into a practical application because while claims 1-4, 6-11, 13-17, and 19-23 attempt to integrate the exception into a practical application, said practical application is a generically recited computer element that does not add meaningful limitations to the abstract idea as it is simply implementing the abstract idea on a computer. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the computer elements only store and retrieve information in memory as well as perform basic calculations that are known to be well-understood, routine and conventional computer functions as recognized by the decisions listed in MPEP § 2106.05(d) . Framework with which to Analyze Subject Matter Eligibility: Step 1: Are the claims directed to a category of statutory subject matter (a process, machine manufacture, or composition of matter)? [ see MPEP § 2106.03 ] Claims are directed to statutory subject matter, specifically methods (claims 1-7), a system (claims 8-14), and a CRM (claims 15-20). Step 2A Prong One: Do the claims recite a judicially recognized exception, i.e., an abstract idea, a law of nature, or a natural phenomenon? [ see MPEP § 2106.04(a) ] The claims herein recite abstract ideas. With respect to the Step 2A Prong One evaluation, the instant claims are found herein to recite abstract ideas that fall into the grouping of mental processes and mathematical concepts. The following claims recite abstract ideas (mental processes and mathematical concepts): Claims 1, 8, 15: Extracting substructures from the target molecule, generating a dictionary entry, updating the set of training data, and generating a molecular descriptor based on distance are processes of examining, identifying, and comparing/contrasting information that can be done via pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes . Generating a distance matrix corresponding to atom indexes, determining distances between atoms based on the distance matrix, and calculating a distance between pairs of substructures based on the distances between atoms are verbal articulations of mathematical processes and therefore abstract ideas, specifically mathematical concepts . Claims 2, 9, 16: The substructures being selected from the group provided is directed to the definition of the information itself, and information is an abstract idea itself, therefore the definition is an abstract idea, specifically a mental process . Claims 3, 10: The small entities comprising at least three non-hydrogen atoms is directed to the definition of the information itself, and information is an abstract idea itself, therefore the definition is an abstract idea, specifically a mental process . Claims 4, 11, 17: Determining the distances between atoms comprise a distance between atoms with a given number of bonds is a process of calculating information that can be done via pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process . Claims 6, 13, 19: The given number of bonds being six is directed to the definition of the information itself, and information is an abstract idea itself, therefore the definition is an abstract idea, specifically a mental process . Claims 7, 14, 20: Generating a molecular descriptor based on distances between the more than one pair of the substructures is a process of identifying, calculating and comparing/contrasting that can be done via pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes . Claim 21: Eliminating the set of atom indexes for the small entity from the dictionary entry is a process of comparing/contrasting and removal of data analogous to manually crossing out an entry in a physical ledger, which is an abstract idea, specifically a mental process . Claim 22: The molecular descriptor being an inverse square of the average is directed to the definition of the information itself, and information is an abstract idea itself, therefore the definition is an abstract idea, specifically a mental process . Claim 23: Generating a second molecular descriptor based on distances between the atoms is a process of identifying, calculating and comparing/contrasting that can be done via pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes . Step 2A Prong Two: If the claims recite a judicial exception under prong one, then is the judicial exception integrated into a practical application? [ see MPEP § 2106.04(d) ] Because the claims do recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application. The following claims recite the following additional elements in the form of non-abstract elements: Claims 1, 8, and 15: Receiving a target molecule is an insignificant extra solution activities, specifically necessary data gathering ( See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering) , Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis) ) [ See MPEP § 2106.05(g) ]. Training a model is not clear in what the judicial exception is impacting and is therefore merely recites the idea of a solution or outcome and amount to nothing more than a recitation of the words "apply it" ( See Intellectual Ventures v. Erie Indem. Co., 850 F.3d 1315, 1331, 121 USPQ2d 1928, 1939 (Fed. Cir. 2017), Intellectual Ventures I v. Symantec Corp., 838 F.3d 1307, 1319, 120 USPQ2d 1353, 1361 (Fed. Cir. 2016) , and Affinity Labs of Texas v. DirecTV, LLC, 838 F.3d 1253, 1262-63, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) ) [ See MPEP § 2106.05(f) ] Claims 8 and 15: A system, memory, processor, computer program product, computer readable storage medium, and instructions are generic and nonspecific elements of a computer that do not improve the functioning of any computer or technology described herein [ See MPEP § 2106.04(d)(1) and MPEP § 2106.05(d) ]. Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? [ see MPEP § 2106.05 ] Because the additional claim elements do not integrate the abstract ideas into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. The claims do not recite additional elements that are sufficient to amount to significantly more than the judicial exceptions because the claims recite additional elements that are generic, conventional, nonspecific, or insignificant extra solution activity. These additional elements include: The additional element of receiving a target molecule (Conventional: Specification Paragraph [0049]) is an insignificant extra solution activity, specifically necessary data gathering ( See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering) , Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis) ) [ See MPEP § 2106.05(g) ]. Therefore, taken both individually and as a whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept. The additional element of training a model (Conventional: Basheer et al. 2000 – Page 7, Column 2, Subheading 2.6; newly cited) is not clear in what the judicial exception is impacting and is therefore merely recites the idea of a solution or outcome and amount to nothing more than a recitation of the words "apply it" (See Intellectual Ventures v. Erie Indem. Co., 850 F.3d 1315, 1331, 121 USPQ2d 1928, 1939 (Fed. Cir. 2017), Intellectual Ventures I v. Symantec Corp., 838 F.3d 1307, 1319, 120 USPQ2d 1353, 1361 (Fed. Cir. 2016), and Affinity Labs of Texas v. DirecTV, LLC, 838 F.3d 1253, 1262-63, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016)) [See MPEP § 2106.05(f)]. Therefore, taken both individually and as a whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept. The additional elements of system, memory, processor, computer program product, computer readable storage medium, and instructions are generic and nonspecific elements of a computer that are well-understood, routine and conventional within the art and therefore do not improve the functioning of any computer or technology described therein ( Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information) , Performing repetitive calculations, Flook, 437 U.S. at 594, 198 USPQ2d at 199 (recomputing or readjusting alarm limit values) , and Storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015) ) [ See § MPEP 2106.05(d)(II) ]. Therefore, taken both individually and as a whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept. Therefore, claims 1-20, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non-statutory subject matter. Response to Arguments 07-37 AIA Applicant's arguments filed 2/24/2026 have been fully considered but they are not persuasive. Applicant asserts on page 9 of the Remarks filed 2/24/2026 that the claims as amended “integrate any asserted abstract idea into a practical application by requiring concrete data storage and data update actions within a database”. Furthermore, applicant asserts that the generation of dictionaries and distance matrix are not well understood, routine, or conventional; specifically citing “Desjardins memo and Enfish/McRO as the claims recite a specific way to build and use data structures”. Firstly, generation of dictionaries and distance matrices are not additional elements but rather abstract ideas, as recited above, and therefore are not subject to the conventionality Step 2B of the additional elements. Second, the integration of the judicial exception into a practical application cannot be generally linking the use of a judicial exception to a particular technological environment or field of use (MPEP 2106.05(h)), adding insignificant extra-solution activity to the judicial exception (MPEP 2106.05(g)), or Merely reciting the words "apply it" (or an equivalent) with the judicial exception, or merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea (MPEP 2106.05(f)) as recited in MPEP 2106.04(d). Recitation of and direction to the Ex Parte Desjardins memo with emphasis on the improvements to technology by the applicant seems to direct the practical application to the improvement in the functioning of a computer, or improvement to other technological fields. However, 2106.05(a) states - It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception . Yet within applicant’s arguments improvements are directed to either the judicial elements (“updating the set of training data”) or additional elements that have already been found to well-understood, routine and conventional (“receiving a target molecule”). Therefore, as currently recited the claim limitations cannot be the basis for an improvement to technology and sans the selection of another viable argument for the integration of the judicial exception into a practical application, said limitations do not integrate the judicial exception into a practical application . Claim Rejections - 35 USC § 103 Response to Amendment In view of applicant’s amendments to the claims previous rejections under 35 U.S.C. 103 have been reviewed, updated, and provided below. 07-06 AIA 15-10-15 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. 07-20-aia AIA 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. 07-23-aia AIA 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. 07-21-aia AIA Claim s 1-2, 4, 7-9, 11, 14-17 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Fechner et al. (Handbook of Chemoinformatics Algorithms (2010) 101-156; previously cited), and Landrum et al. (Release (2013) 1-93; newly cited) . Claim 1 is directed to a method of generating molecular descriptors based on global structure information by computing distances between atoms in substructures of molecules. Claim 8 is directed to a system of generating molecular descriptors based on global structure information by computing distances between atoms in substructures of molecules. Claim 15 is directed to a computer program product of generating molecular descriptors based on global structure information by computing distances between atoms in substructures of molecules. Fechner et al. teaches on page 99, paragraph 3 “Molecular substructures can be regarded as connected graphs that are completely contained in the molecular graph… there are two points of view regarding substructures as descriptors. One popular approach frequently used in molecular fingerprint methods is to consider the substructure as the descriptor and its presence or frequency in a specific molecule as its value… An alternative method is to define an algorithm that generates a set of substructures for a molecule”, on page 101, paragraph 2 “The easiest way to include the topology of a molecule is to use pairs of atom types together with their intramolecular topological or geometrical distance… The interatomic distance was measured as the count of bonds on the shortest path (i.e., the topological distances)”, on page 98, paragraph 6 “Descriptors based on the distance matrix can also be defined, for example, the largest eigenvalue of the distance matrix or the unique negative eigenvalue. Combinations of those descriptors were also proposed, for example, the sum of leading eigenvalues of the distance matrix and the adjacency matrix”, and on page 129 paragraph 2 outlines the score for each substructure being defined as the equation provided which includes the database from which the structure is pulled, additionally the use of Hashing, Kabsch algorithm, kernel functions and computer pseudocode featured on pages 109-110, 113, 115-116, 119, 124, 130, 135, 137, etc. renders obvious the use of computers including but not limited to memory, processors and computer-readable mediums, reading on receiving a target molecule from a set of training data stored in a database; extracting substructures from the target molecule; generating, for each of the substructures, a dictionary entry containing a set of atom indexes and a corresponding substructure from the substructures generating a distance matrix for the target molecule based on atom indexes in the dictionary entries; determining distances between atoms of a first substructure and atoms of a second substructure based on the distance matrix; calculating a topological distance between the first and second substructures based on an average of the distances between the atoms; and generating a molecular descriptor for the target molecule based on the topological distance . Fechner et al. teaches on page 93, paragraph 3 “Topological indices are global features that derive information from the adjacency matrix of a molecular graph… Topological descriptors can be divided in bond-based descriptors and distance based descriptors” and on page 101, paragraph 1 “The easiest way to include the topology of a molecule is to use pairs of atom types together with their intramolecular topological or geometrical distance”, reading on the use of topological distance and distances between substructures (groups of atoms). Furthermore, Fechner et al. teaches on page 40, paragraph 4 “the inferred surface can be regarded as QSAR equation. The equation is trained by a genetic algorithm that varies the surface properties, which have been randomly assigned, in order to optimize the fit of the model’s energy equation to the target values”, for which QSAR data contains molecular descriptor data, thereby reading on updating the set of training data to include the molecular descriptor and training a model for predicting molecular properties on the updated set of training data . Landrum et al. teaches on page 31, paragraph 1 “Atom-pair descriptors are available in several different forms. The standard form is as fingerprint including counts for each bit instead of just zeros and ones. Because the space of bits that can be included in atom-pair fingerprints is huge, they are stored in a sparse manner. We can get the list of bits and their counts for each fingerprint as a dictionary”, reading on generating, for each of the substructures, a dictionary entry containing a set of atom indexes and a corresponding substructure from the substructures . It would have been obvious at the time of first filing to have modified the teachings of Fechner et al. for the method, system and computer program product of claims 1, 8 and 15 with the teachings of Landrum et al. for the storage of atom indexes and substructures as the latter existed as an opensource toolkit for cheminformatics supported by MAC/Windows/Linux with multiple parameters for controlling fingerprinting based on topology that allows for further control of the chemical folding all within a dictionary format that allows for large amounts of information stored in a sparse manner allowing for easier/faster computing. Furthermore, since the latter is computer implemented and Fechner et al. teaches computer pseudocode, it would have been obvious at the time of filing to modify the teachings of Fechner et al. for the method, system and computer program product of claims 1, 8 and 15 with a computer implementation. One would have had a reasonable expectation of success given the open-source nature of RDKit and that the pseudocode teaches the implementation of the method described for a computer. Therefore, it would have been obvious at the time of filing to modify the teachings of Fechner et al. and to be successful. Claim 2 is directed to the method of claim 1 but further specifies that the substructures are selected from the group provided. Claim 9 is directed to the system of claim 8 but further specifies that the substructures are selected from the group provided. Claim 16 is directed to the computer program product of claim 15 but further specifies that the substructures are selected from the group provided. Fechner et al. teaches on page 105, paragraph 2 “Molecular fragments are the most complex and versatile substructure types”, and on page 95, paragraph 3 “it is concluded that common requirements on complexity indices are as follows: principles of homology, reflection of branching, cyclicity, multiple edges, and heteroatoms”, reading on wherein the substructures are independently selected from the group consisting of molecular fragments, small entities, and heteroatoms . Claim 4 is directed to the method of claim 1 but further specifies that the distances comprise a distance between atoms within a given number of bonds. Claim 11 is directed to the system of claim 8 but further specifies that the distances comprise a distance between atoms within a given number of bonds. Claim 17 is directed to the computer program product of claim 15 but further specifies that the distances comprise a distance between atoms within a given number of bonds. Fechner et al. teaches on page 102, paragraph 2 “Sequences of graph vertices are divided into two classes: a walk is according to Borgwardt a nonalternating sequence of vertices and edges such that ei = bond(vi, vi+1)”, page 105, paragraph 4 “Molecular fingerprints are a common method to combine the presence or absence of different substructures in a molecule into one molecular descriptor” and page 106, paragraph 6 “A popular hashed fingerprint implementation is the Daylight Chemical Information Fingerprint, which is calculated by enumerating the set of labeled paths shorter than a specified number of bonds in a molecule”, reading on wherein the at least one of the distances between the atoms comprises a distance between atoms within a given number of bonds . Claim 7 is directed to the method of claim 1 but further specifies generating a molecular descriptor that based on the distances between more than one pair of the substructures. Claim 14 is directed to the system of claim 8 but further specifies generating a molecular descriptor that based on the distances between more than one pair of the substructures. Claim 20 is directed to the computer program product of claim 15 but further specifies generating a molecular descriptor that based on the distances between more than one pair of the substructures. Fechner et al. teaches on page 105, paragraph 4 “Molecular fingerprints are a common method to combine the presence or absence of different substructures in a molecule into one molecular descriptor” and page 106, paragraph 6 “A popular hashed fingerprint implementation is the Daylight Chemical Information Fingerprint, which is calculated by enumerating the set of labeled paths shorter than a specified number of bonds in a molecule”, reading on generating a molecular descriptor based on distances between more than one pair of the substructures . Claim 21 is directed to the method of claim 1 but further specifies the filtering of atom indexes from the dictionary if a small entity is found among them. Landrum et al. teaches on page 25, under Substructure Searching “Substructure matching can be done using query molecules built from SMARTS. Those are the atom indices in m, ordered as patt‘s atoms. This can be used to easily filter lists of molecules”, it would have been obvious to a person skilled in the art to implement filtering based upon substructure (small entity) within the proposed method of storing information (dictionaries), thereby reading on in response to determining that a set of atom indexes for a substructure contains a set of atom indexes for a small entity, eliminating the set of atom indexes for the small entity from the dictionary entry corresponding to the substructure . Claim 23 is directed to the method of claim 1 but further specifies generation of a second molecular descriptor. Fechner et al. teaches on page 90, paragraph 1 “In the case of molecular structures, the chosen description of the same compound would certainly differ if a specific pharmaceutical target affinity or its experimental synthesis should be described. For this reason, literally thousands of molecular descriptors have been proposed covering all properties of interest”, and on page 93, paragraph 4 “Topological descriptors can be divided in bond-based descriptors and distance-based descriptors. Whereas the first give information on how the atoms in a molecular graph are connected, the latter are based on the topological distance”. It would have been obvious to a person skilled in the art to calculate multiple molecular descriptors as Fechner et al. teaches the existence of not only multiple descriptors, but multiple descriptors for similar concepts such as distance, thereby reading on generating a second molecular descriptor based on at least one of the distances between the atoms . 07-22-aia AIA Claim s 3 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Fechner et al. (Handbook of Chemoinformatics Algorithms (2010) 101-156; previously cited) and Landrum et al. (Release (2013) 1-93; newly cited) as applied to claim s 1-2, 4, 7-9, 11, 14-17 and 20 above, and further in view of Hu et al. (Future Sci OA. (2020) 1-9; previously cited) . Claim 3 is directed to the method of claim 2 and thus claim 1, but further specifies that the small entities comprise at least 3 non-hydrogen atoms. Claim 10 is directed to the system of claim 9 and thus claim 8, but further specifies that the small entities comprise at least 3 non-hydrogen atoms. Fechner et al. and Landrum et al. teach the method of claim 1, system of claim 8 and computer program product of claim 15 as previously described. Fechner et al. and Landrum et al. do not teach that the small entities comprise at least 3 non-hydrogen atoms. Hu et al. teaches on page 4, paragraph 1 “the following size restrictions were applied to obtain a core and substituent fragment. The number of nonhydrogen atoms of the core fragment was required to be at least twice as large as the number of nonhydrogen atoms comprising the substituent fragment. In addition, the size of the substituent was restricted to at most 13 nonhydrogen atoms”, and on page 2, paragraph 2 “For formally defining ACs, molecular similarity and potency difference criteria must be specified. Similarity can be calculated on the basis of chemical descriptors and numerical similarity metrics (descriptor-based/numerical similarity) or on the basis of substructure relationships (substructure-based similarity)”, reading on wherein the small entities comprise at least three non-hydrogen atoms . It would have been obvious at the time of filing to modify the teachings of Fechner et al. for the method and system of claims 1 and 8, with the teachings of Hu et al. for using a number of nonhydrogen atoms to define a substituent/fragment/small entity as this allowed for Hu et al. to obtain higher identification of activity curves (Hu et al. page 7, paragraph 5) which are tied to molecular descriptors (Hu et al. page 2 paragraph 2). One would have had a reasonable expectation of success given that this would merely be a change in the categorization of data to be used. Therefore, it would have been obvious at the time of filing to modify the teachings of each and to be successful . 07-22-aia AIA Claim 22 is rejected under 35 U.S.C. 103 as being unpatentable over Fechner et al. (Handbook of Chemoinformatics Algorithms (2010) 101-156; previously cited) and Landrum et al. (Release (2013) 1-93; newly cited) as applied to claim s 1-2, 4, 7-9, 11, 14-17 and 20 above, and further in view of Randic et al. (Journal of Chemical Information and Computer Sciences (2001) 575-581; previously cited) . Claim 22 is directed to the method of claim 1 but further specifies calculating an average distance between atoms and calculating an inverse square of the average distance. Fechner et al. and Landrum et al. teach the method of claim 1, system of claim 8 and computer program product of claim 15 as previously described. Additionally on page 99, paragraph 2 Fechner et al. teaches “Weighted Holistic Invariant Molecular (WHIM) descriptors are 3D descriptors that capture information regarding size, shape, symmetry, and atom distribution. A principal component analysis (PCA) is performed on the centered coordinates of a molecule using a weighted covariance matrix. The weighted covariance matrix is obtained by applying a weighting scheme of the general form: where sjk is the weighted covariance between the jth and kth atomic coordinates. |A| is the total number of atoms, wi is the ith weight, qij and qik are the ith and kth coordinates, and ¯qk is the corresponding average value”, reading on when more than two atoms from the pair of the substructures are within the given number of bonds, calculating an average distance between the more than two atoms . Fechner et al. and Landrum et al. do not teach calculating an inverse square of the average distance. Randic et al. teaches on page 576, column 2, paragraph 3 “The distance matrix has an apparent conceptual disadvantage: One expects that as the distance between atoms in a molecule increases the role of more distant neighbors will decrease. But in the row sums of the distance matrix more distant neighbors make larger contributions. One way to deal with this was introduction of the inverse distance matrix by Plavsˇic´ et al. and Ivanciuc et al. An alternative route is to consider “reversed” weights, giving to the shortest distances the larger weight” and page 577, column 1, paragraph 2 “The reversed distance matrix leads to a topological index for which we use symbol 1/J. Hence, we will designate the variable analogue of 1/J as 1/J*. At the bottom of Table 4 we gave the expression for 1/J* illustrated on 2-pentanol. Additional variable indices can be similarly constructed from the reciprocal distance matrix, the reciprocal square distance matrix, and the hyper-Wiener matrix”, reading on calculating an inverse square of the average distance . It would have been obvious at the time of filing to modify the teachings of Fechner et al. for the method and system of claims 1 and 8, with the teachings of Randic et al. for the use of an inverse distance matrix and square distance matrix to counter more distant neighbors making larger contributions. One would have had a reasonable expectation of success given that it is merely substituting one component of a method with another, the standard distance matrix with an inverse and squared distance. Therefore, it would have been obvious at the time of filing to modify the teachings of each and to be successful . 07-22-aia AIA Claim s 6, 13, and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Fechner et al. (Handbook of Chemoinformatics Algorithms (2010) 101-156; previously cited) and Landrum et al. (Release (2013) 1-93; newly cited) as applied to claim s 1-2, 4, 7-9, 11, 14-17 and 20 above, and further in view of Mauri et al. (Ecotoxicological QSARs. (2020) 801-820; previously cited) . Claim 6 is directed to the method of claim 4 and thus claim 1, but further specifies that the given number of bonds be six. Claim 13 is directed to the system of claim 11 and thus claim 8, but further specifies that the given number of bonds be six. Claim 19 is directed to the computer program product of claim 17 and thus claim 15, but further specifies that the given number of bonds be six. Fechner et al. and Landrum et al. teach the method of claim 1, system of claim 8 and computer program product of claim 15 as previously described. Fechner et al. and Landrum et al. do not teach that the given number of bonds be six. Mauri et al. teaches on page 802, paragraph 9 “Extended-connectivity fingerprints and path fingerprints can be tuned, not only with respect to the fingerprint size, fragment type, and dimensions, but even by defining atom and bond parameters considered during fragment identifications (e.g., atom type, aromaticity, the number of attached hydrogens, connectivity)”, on page 804, paragraph 2 “A molecule, or even a single fragment, can be represented in different ways; e.g., aromatic rings can be represented either in aromatic (i.e., conjugated bonds) or in Kekule´ form (i.e., bond configuration double-single-double)”, and on page809, paragraph 5 “Therefore, the resulting descriptors include chemical structure information, such as atom connections, bond orders, branching, and the aromaticity, but cannot necessarily be directly correlated to a chemical or toxicological aspect”; for which an aromatic possesses at least six carbon bonds and a total of 15 bonds, which reads on wherein the given number of bonds is six bonds . It would have been obvious at the time of filing to modify the teachings of Fechner et al. for the method and system of claims 1 and 8, with the teachings of Mauri et al. for the use of aromatic structures as the latter points out “The majority of the descriptors present in literature have not been proposed in order to identify a specific chemical or physicochemical feature, such as the molecular weight or the presence of a well-defined chemical structure, but they are typically a mathematical manipulation of different representations of the chemical graph. Therefore, the resulting descriptors include chemical structure information, such as atom connections, bond orders, branching, and the aromaticity…”. One would have a reasonable expectation of success given that both the tool presented in Mauri et al. and the teachings of Fechner et al. are geared to the same application using the same data and would merely require a simple substitution in methods. Therefore, it would have been obvious at the time of filing to have modified the teachings of each and to be successful . Response to Arguments 07-37 AIA Applicant's arguments filed 2/24/2026 have been fully considered but they are not persuasive. Applicant asserts on pages 10-11 of the Remarks filed 2/24/2026 that the newly amended claim limitations are not taught by the previously cited prior art. Examiner agrees that previously cited references do not read upon the totality of the independent claim limitations and has subsequently provided new recited references to cure said deficiencies. Conclusion 07-40 AIA 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 KEENAN NEIL ANDERSON-FEARS whose telephone number is (571)272-0108. The examiner can normally be reached M-Th, alternate F, 8-5. 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, Karlheinz Skowronek can be reached at 571-272-9047 . 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. /K.N.A./Examiner, Art Unit 1687 /OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685 Application/Control Number: 17/652,796 Page 2 Art Unit: 1687 Application/Control Number: 17/652,796 Page 3 Art Unit: 1687 Application/Control Number: 17/652,796 Page 4 Art Unit: 1687 Application/Control Number: 17/652,796 Page 5 Art Unit: 1687 Application/Control Number: 17/652,796 Page 6 Art Unit: 1687 Application/Control Number: 17/652,796 Page 7 Art Unit: 1687 Application/Control Number: 17/652,796 Page 8 Art Unit: 1687 Application/Control Number: 17/652,796 Page 9 Art Unit: 1687 Application/Control Number: 17/652,796 Page 10 Art Unit: 1687 Application/Control Number: 17/652,796 Page 11 Art Unit: 1687 Application/Control Number: 17/652,796 Page 12 Art Unit: 1687 Application/Control Number: 17/652,796 Page 13 Art Unit: 1687 Application/Control Number: 17/652,796 Page 14 Art Unit: 1687 Application/Control Number: 17/652,796 Page 15 Art Unit: 1687 Application/Control Number: 17/652,796 Page 16 Art Unit: 1687 Application/Control Number: 17/652,796 Page 17 Art Unit: 1687 Application/Control Number: 17/652,796 Page 18 Art Unit: 1687 Application/Control Number: 17/652,796 Page 19 Art Unit: 1687
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