Chiral configuration representation method based on mixed product
By employing a chiral configuration representation method based on the mixture product, and utilizing open-source cheminformatics databases and substructure search algorithms, the chiral product and matrix are calculated. This solves the problem that existing technologies cannot fully characterize the three-dimensional structure and chiral features of molecules, and achieves efficient and accurate characterization of molecular chirality.
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Patents(China)
- Current Assignee / Owner
- SHANGHAI JIAOTONG UNIV
- Filing Date
- 2024-04-08
- Publication Date
- 2026-08-04
AI Technical Summary
Existing chemical molecular characterization methods cannot fully represent the three-dimensional structure of molecules, especially the axial chiral configuration, and machine learning methods have failed to fully learn the chiral characteristics of molecules, resulting in insufficient characterization accuracy.
A chiral configuration representation method based on the mixing product is adopted. Asymmetric atoms and chiral axes are obtained through an open-source cheminformatics database. The chiral product and chiral matrix are calculated. Combined with substructure search and transduction discrimination algorithms, the chiral information of the molecule is characterized.
It achieves accurate characterization of atomic chirality, fills the gap in axial chirality configuration, has higher efficiency and accuracy, and can describe multiple chirality types with an accuracy of 99.79%.
Smart Images
Figure CN118136137B_ABST
Abstract
Description
Technical Field
[0001] This invention relates to the field of chemical technology, and more specifically to a method for representing chiral configurations based on the mixing product. Background Technology
[0002] The convergence of computer technology and chemistry is driving a revolution in the field. To analyze chemical molecules using methods such as artificial intelligence, they must be characterized in a way that machines can recognize. Therefore, the computer characterization of chemical molecules is fundamental to the application of computer technology in molecular science.
[0003] Currently, there are numerous methods for characterizing chemical molecules. For example, as summarized by Daniel S. Weigh et al. in their 2022 paper "A Review of Molecular Representation in the Age of Machine Learning," commonly used characterization methods include SMILES codes, ECFP molecular fingerprints, and molecular connection tables (MDLs). Simultaneously, machine learning-based methods are also being used for molecular characterization. For instance, in their 2022 paper "Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations," Connor W. Coley et al. used a neural network model to characterize atomic chirality.
[0004] However, while existing global characterization methods can describe some important information about molecules, they are not perfect, and their shortcomings are as follows:
[0005] Two-dimensional representations such as SMILES codes cannot fully represent the three-dimensional structure of molecules. In particular, while SMILES codes can describe the configuration of atomic chirality, they cannot provide an unambiguous representation of the configuration of axial chirality.
[0006] Molecular linkage tables and other characterization methods that include bonding and the three-dimensional coordinates of each atom can comprehensively characterize the three-dimensional structure of molecules, but they are not concise enough and are inefficient in use.
[0007] Machine learning-based representation methods may not be able to fully learn the chiral characteristics of molecules. As mentioned earlier, Connor W. Coley's work, using his model to classify atomic chiral configurations, achieved an accuracy of 98.5 ± 0.2%, which is not 100% accurate; and current machine learning representation methods have not yet been found to be able to represent axial chiral information.
[0008] In view of this, the present invention proposes a chiral configuration representation method based on hybrid product. Summary of the Invention
[0009] The purpose of this invention is to provide a chiral configuration representation method based on hybrid product to address the shortcomings of the prior art.
[0010] According to one aspect of the present invention, a method for representing chiral configurations based on hybrid product is provided, comprising the following steps:
[0011] S1. Based on an open-source cheminformatics database, obtain a list of all asymmetric atoms (cAtoms) within the target molecule;
[0012] S2. Traverse all asymmetric atoms in the list cAtoms and calculate their chiral product and chiral matrix;
[0013] S3. Traverse the target molecule and use the chiral axis search algorithm based on substructure search and blocking discrimination to find the chiral axis contained in the target molecule;
[0014] S4. For the chiral axes obtained in step S3, calculate their chiral product and chiral matrix;
[0015] S5. The obtained chiral matrix and chiral product, which correspond one-to-one with the asymmetric atoms and chiral axes within the molecule, are used to characterize the local representation of the chiral information of the target molecule based on the chiral matrix and chiral product.
[0016] As a preferred technical solution of the present invention, a method for identifying chiral centers in molecules based on an open-source cheminformatics database and returning their relevant information is used to find chiral centers, and the returned results are iterated to print the atomic index and chiral label of each chiral center.
[0017] Extract a list of all asymmetric atoms, cAtoms, from the atom indices and chiral labels of the chiral centers using a list comprehension.
[0018] As a preferred embodiment of the present invention, the step of calculating the chiral product and the chiral matrix in step S2 includes:
[0019] S21. Initialize the atomic chiral product list atomProducts and the atomic chiral matrix list atomMatrix to be empty;
[0020] S22. Traverse the asymmetric atoms in the asymmetric atom list cAtoms, and obtain the neighbor list of atoms adjacent to the asymmetric atoms using the GetNeighbors method of the atom object in rdkit;
[0021] S23. Sort the atoms in the neighbor list in ascending order according to the CIP rules;
[0022] S24. For atom O in the asymmetric atom list cAtoms, define the atoms in its neighbor lists as A, B, C, and D in ascending order of CIP. Calculate the chirality matrix based on their three-dimensional coordinates. Add the chirality matrix to the atom matrix list;
[0023] S25. Calculate the determinant value CP corresponding to the chiral matrix, which is the chiral product. Add CP to the atom chiral product list atomProducts.
[0024] As a preferred embodiment of the present invention, finding the chiral axis contained in the target molecule includes the following steps:
[0025] S31. Traverse the target molecule, find the spirocyclic atom structure contained in the target molecule, and obtain the list of chiral spirocyclic atoms csAtoms;
[0026] S32. Traverse the target molecule, find the helical ring chain structure contained in the target molecule, and obtain the list of chiral helical ring chains csChains;
[0027] S33. Traverse the target molecule, search for the allene structures contained in the target molecule, and obtain a list of chiral allenes (cenes);
[0028] S34. Traverse all single bonds in the target molecule, use the blocking-rotation discrimination algorithm to find the single bonds that can be symmetrically rotated in the target molecule, and obtain the list of chiral single bonds csBonds.
[0029] S35. Summarize and save the results of steps S31, S32, S33, S34 and S35 to obtain the chiral axis of the molecule; if the result is empty, it means that the molecule does not have axial chirality.
[0030] As a preferred embodiment of the present invention, the step of calculating the chiral product and the chiral matrix in step S4 includes:
[0031] S41. For the chiral axis that is found, define the atoms at its two ends as C1 and C2 respectively. Obtain the two groups connected to C1 and define them as A1 and A2 according to the CIP rule from smallest to largest. Also, define the two groups connected to C2 as B1 and B2 according to the CIP rule from smallest to largest.
[0032] S42. Calculate the chiral matrix based on the three-dimensional coordinates of C1, A1, A2, B1, and B2.
[0033] S43. Calculate the determinant value CP corresponding to the chiral matrix as the chiral product. Similar to the result in S24, the sign of the chiral product can be used to define the configuration of the chiral axis.
[0034] According to another aspect of the present invention, an electronic device is provided, comprising: a processor and a memory, wherein the memory stores a computer program that can be called by the processor;
[0035] The processor executes the chiral configuration representation method based on hybrid product described above by calling the computer program stored in the memory.
[0036] According to another aspect of the present invention, a computer-readable storage medium is provided storing instructions that, when executed on a computer, cause the computer to perform the chiral configuration representation method based on hybrid product described above.
[0037] The technical effects and advantages provided by the present invention in the above technical solution are as follows:
[0038] This invention enables the characterization of atomic chirality and fills the gap in the characterization of axial chirality configurations. It also has potential portability, with the possibility of transferring to chirality types such as facet chirality and helical chirality. The resulting chirality matrix generally occupies less memory compared to a molecular connection table containing all atomic coordinates, thus having higher efficiency.
[0039] This invention is based on rule-based design and has strong interpretability. Validation of atomic chiral configurations on existing validation datasets achieved a 99.79% accuracy rate, which is higher than the previous method, indicating that this representation method can better describe atomic chiral characteristics. Attached Figure Description
[0040] To more clearly illustrate the technical solutions in the embodiments of this application or the prior art, the drawings used in the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments recorded in this invention. For those skilled in the art, other drawings can be obtained based on these drawings.
[0041] Figure 1 This is a flowchart of the chiral axis finding algorithm based on substructure search and resistance-rotation discrimination in the method of the present invention;
[0042] Figure 2 This is an exemplary chemical molecular diagram of the chiral configuration in the method of the present invention;
[0043] Figure 3 This is an exemplary chemical molecular diagram of the chiral configuration in the method of the present invention; Detailed Implementation
[0044] To make the objectives, technical solutions, and advantages of the embodiments of the present invention clearer, the technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only some embodiments of the present invention, not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort are within the scope of protection of the present invention.
[0045] Example 1
[0046] Please see Figure 1 As shown, the chiral configuration representation method based on hybrid product described in this embodiment includes the following steps:
[0047] S1. Based on an open-source cheminformatics database, obtain a list of all asymmetric atoms (cAtoms) within the target molecule;
[0048] Specifically, the open-source cheminformatics database can be the rdkit library, an open-source cheminformatics toolkit for analyzing and visualizing chemical data. The rdkit library uses a method to identify chiral centers in molecules and return their related information, such as the `Chem.FindMolChiralCenters` method. This involves calling the `Chem.FindMolChiralCenters` method to find chiral centers; marking the molecules corresponding to the chiral centers as target molecules; iterating through the returned results to print the atom index and chiral label of each chiral center; and extracting a list of all asymmetric atoms (`cAtoms`) from the `chiral_centers` list using a list comprehension.
[0049] It should be noted that the indices in the cAtoms list are arranged in the order of atoms in the molecular diagram. If your molecule has multiple chiral centers, the cAtoms list will contain the indices of all of these centers; if the molecule has no chiral centers, then the cAtoms list will be empty.
[0050] S2. Traverse all asymmetric atoms in the list cAtoms and calculate their chiral product and chiral matrix;
[0051] The steps in step S2 for calculating the chiral product and the chiral matrix include:
[0052] S21. Initialize the atomic chiral product list atomProducts and the atomic chiral matrix list atomMatrix to be empty;
[0053] S22. Traverse the asymmetric atoms in the asymmetric atom list cAtoms, and obtain the neighbor list of atoms adjacent to the asymmetric atoms using the GetNeighbors method of the atom object in rdkit;
[0054] S23. Sort the atoms in the neighbor list in ascending order according to the CIP rules;
[0055] S24. For atom O in the asymmetric atom list cAtoms, define the atoms in its neighbor lists as A, B, C, and D in ascending order of CIP. Calculate the chirality matrix based on their three-dimensional coordinates. Add the chirality matrix to the list of atomic chirality matrices, atomMatrix;
[0056] S25. Calculate the determinant value CP corresponding to the chiral matrix, which is the chiral product. Add CP to the atom chiral product list atomProducts.
[0057] The definitions of calculating the chiral product and the chiral matrix in step S2 are as follows:
[0058] For an asymmetric atom O, the atoms in its neighbor list are defined as A, B, C, and D in ascending order of CIP.
[0059] It should be noted that the CIP order follows the Cahn-Ingold-Prelog rule, an empirical rule in chemistry. For atoms in a molecule with different chemical environments, they are ordered according to their atomic numbers. When their atomic numbers are equal, the atoms connected to them are compared until an order is determined.
[0060] The chirality matrix is calculated based on its three-dimensional coordinates. The determinant value CP corresponding to the chiral matrix is the chiral product. If the sign of the chiral product is positive, the corresponding chiral center is of the R configuration; if the sign of the chiral product is negative, the corresponding chiral center is of the S configuration.
[0061] Specifically, for example, such as Figure 2 The molecule shown has atomic chirality, with the C atom labeled 1 as its chiral center. The C atom is centrally asymmetric and has four adjacent atoms, arranged in descending order of CIP order: I(4) > Br(3) > Cl(2) > F(0). Based on the coordinates of the corresponding atoms, the values of the following three vectors can be calculated.
[0062] Combine these three vectors into a matrix. This is the chiral matrix of the target molecule, and the value of its determinant is called the chiral product. If the sign of the chiral product is positive, it corresponds to the R configuration; if the sign of the chiral product is negative, it corresponds to the S configuration. For the target molecule, the obtained list of chiral centers and the list of chiral matrices are as follows:
[0063] Chiral center list = [1];
[0064]
[0065] They contain information about the central chirality of the target molecule; therefore, these two lists can serve as a characterization of molecular chirality.
[0066] S3. Traverse the target molecule and use the chiral axis search algorithm based on substructure search and blocking discrimination to find the chiral axis contained in the target molecule;
[0067] The process of finding the chiral axis contained in the target molecule includes the following steps:
[0068] S31. Traverse the target molecule to find the spirocyclic atomic structure contained in the target molecule;
[0069] The step of searching for spirocyclic atoms in step S31 includes:
[0070] S311. Initialize the list of spirocyclic atoms sAtoms and the list of chiral spirocyclic atoms csAtoms to be empty;
[0071] S312. Traverse all atoms within the molecule. If an atom is shared by two rings, and all atoms connected to it are not simultaneously in these two rings, then add that atom to the list of spirocyclic atoms sAtoms.
[0072] S313. For all spirocyclic atoms in the list sAtoms, if two adjacent atoms in the same ring have different CIP orders, then the spirocyclic atom is axially chiral and is retained in the list csAtoms of chiral spirocyclic atoms.
[0073] S32. Traverse the target molecule to find the helical ring chain structure contained in the target molecule;
[0074] The step of finding the helical ring chain structure contained in the target molecule in step S32 includes:
[0075] S321. Initialize the spiro ring chain list sChains to the spiro ring atom list sAtoms, and initialize the chiral spiro ring chain list csChains to be empty;
[0076] S322. Traverse the list of spirocyclic atoms sAtoms. If two structures share a ring, combine the two structures into a whole and store it in the list of spirocyclic chains sChains. Remove duplicates from the new sChains.
[0077] S323, Repeat S322 until all structures in the helical chain list sChains do not share a ring with other structures;
[0078] S324. For all spirocyclic chain segments in the list sChains, if two atoms of each segment are connected to two distinct groups, and these four groups are not coplanar, then the spirocyclic chain segment is axially chiral and is retained in the list of chiral spirocyclic chains csChains.
[0079] S33. Based on an open-source cheminformatics toolkit, traverse the target molecule to find the allene structure contained in the target molecule;
[0080] The step of finding the allene structure contained in the target molecule in step S33 includes:
[0081] S331. Initialize the allene list enes to contain all double bonds within the molecule, and initialize the chiral allene list cenes to be empty;
[0082] S332. Traverse all structures in the allene list enes. If a structure shares atoms with other elements in the list, merge the two into a larger new structure and store the new structure in place of the original structure in the allene list enes.
[0083] S333, Repeat the operation in S32 until no element in the allene list enes shares an atom with any other element;
[0084] S334. For all allene fragments in the allene list enes, if the two adjacent atoms connected to each of its end atoms are not the same, and the adjacent atoms connected to the two end atoms are not coplanar, then the allene fragment is axially chiral and is retained in the chiral allene list cenes.
[0085] S34. Based on an open-source cheminformatics toolkit, all single bonds in the molecule are traversed, and a rotational resistance discrimination algorithm is used to find single bonds in the molecule that are difficult to rotate.
[0086] The steps of the blocking / rotation discrimination algorithm in step S34 include:
[0087] S341. Initialize the outer ring single-key list sBonds, the small-to-medium ring single-key list rBonds, and the chiral single-key list csBonds to be empty;
[0088] S342. For all single bonds within a molecule, if the smallest ring containing it has fewer than 12 atoms, add it to the list of small and medium ring single bonds (rBonds); if it is not in a ring or the smallest ring containing it has more than 12 atoms, add it to the list of external ring single bonds (sBonds).
[0089] S343. For all single bonds in the list of single bonds outside the ring sBonds, obtain the atoms A and B at their two ends, set the scope of consideration n, and initialize the lists of adjacent atoms of A and B as aNeighbour and bNeighbour, respectively.
[0090] S344. Taking the atoms A and B at both ends as the center, extend n atoms outward in the opposite direction of the other end and add them to the lists aNeighbour and bNeighbour respectively.
[0091] S345. For each pair consisting of an atom in the aNeighbour list and an atom in the bNeighbour list, calculate the sum of the atomic radii rSum and the planar distance pDistance. If there exists a pair of atoms such that the difference between pDistance and rSum is greater than zero, then the single bond under consideration has the characteristic of resisted transformation and is added to the list of resisted single bonds.
[0092] S346. Combine the list of single-key resistors and the list of single-key small and medium rings sBonds to form the list of single-key resistors rlBonds;
[0093] S347. For all single bonds in the list of chiral single bonds in rlBonds, if each of its two ends is connected to two groups with different CIP sequences and these four groups are not coplanar, then the single bond has axial chirality and is added to the list of chiral single bonds in csBonds.
[0094] S35. The obtained list of chiral spirocyclic atoms (csAtoms), chiral spirocyclic chains (csChains), chiral allenes (cenes), and chiral single bonds (csBonds) are the results of finding the intramolecular chiral axis.
[0095] S4. For the chiral axes obtained in step S3, calculate their chiral product and chiral matrix;
[0096] It should be noted that, since axial chirality and central chirality have different asymmetries, the definitions of the chirality product and chirality matrix here are different from those of central chirality in S2. For detailed definitions, please refer to S41 and S42.
[0097] The steps in step S4 for calculating the chiral product and the chiral matrix include:
[0098] S41. For the chiral axis that is found, define the atoms at its two ends as C1 and C2 respectively. Obtain the two groups connected to C1 and define them as A1 and A2 according to the CIP rule from smallest to largest. Also, define the two groups connected to C2 as B1 and B2 according to the CIP rule from smallest to largest.
[0099] S42. Calculate the chiral matrix based on the three-dimensional coordinates of C1, A1, A2, B1, and B2.
[0100] S43. Calculate the determinant value CP corresponding to the chiral matrix as the chiral product. Similar to the result in S24, the sign of the chiral product can be used to define the configuration of the chiral axis.
[0101] S5. The obtained chiral matrix and chiral product, which correspond one-to-one with the asymmetric atoms and chiral axes within the molecule, are used to characterize the chiral information of the target molecule.
[0102] For example, for Figure 3 The molecule shown has axial chirality, with its chiral axis being the single bond formed by atoms numbered 7 and 8. Let A be defined as... i The atom with subscript i is shown in the diagram. Using the method described in the previously mentioned patent, "Chiral Axis Search Algorithm Based on Substructure Search and Restriction Discrimination," the chiral axes in the molecule, namely A7 and A8, can be found. Then, for the groups connected at both ends of the axis, the following matrix can be calculated based on the three-dimensional coordinates of the atoms using the method in S4. The chiral matrix of the target molecule is given by a matrix whose determinant is called the chiral product. The sign of the chiral product corresponds to the two enantiomers of the target molecule. For the target molecule, the resulting list of chiral centers and the list of chiral matrices are as follows:
[0103] Chiral center list = [[7,8]];
[0104]
[0105] Molecular chirality information is characterized based on lists of chiral centers and lists of chiral matrices.
[0106] Example 2
[0107] For the parts not described in detail in this embodiment, please refer to the description in Embodiment 1. This embodiment provides an electronic device, including: a processor and a memory, wherein the memory stores a computer program that can be called by the processor;
[0108] The processor executes the chiral configuration representation method based on hybrid product by calling the computer program stored in the memory.
[0109] The electronic device can vary considerably depending on its configuration or performance. It may include one or more Central Processing Units (CPUs) and one or more memories, wherein the memory stores at least one computer program, which is loaded and executed by the processor to implement the chiral configuration representation method based on hybrid product provided in the various method embodiments described above. The electronic device may also include other components for implementing device functions; for example, it may have wired or wireless network interfaces and input / output interfaces for input / output. Further details regarding the embodiments described in this application are omitted here.
[0110] This embodiment also provides a computer-readable storage medium having an erasable and rewritable computer program stored thereon;
[0111] When the computer program is run on a computer device, the computer device executes the chiral configuration representation method based on hybrid product described above.
[0112] In an exemplary embodiment, a computer-readable storage medium is also provided, such as a memory including at least one computer program, which is executable by a processor to perform the chiral configuration representation method based on hybrid product in the above embodiments. For example, the computer-readable storage medium can be a read-only memory (ROM), a random access memory (RAM), a compact disc read-only memory (CD-ROM), magnetic tape, floppy disk, and optical data storage device, etc.
[0113] In an exemplary embodiment, a computer program product or computer program is also provided, comprising one or more lines of program code stored in a computer-readable storage medium. One or more processors of an electronic device are capable of reading the one or more lines of program code from the computer-readable storage medium, and the one or more processors execute the one or more lines of program code, enabling the electronic device to perform the chiral configuration representation method based on hybrid product described above.
[0114] It should be understood that in the various embodiments of this application, the order of the above-mentioned processes does not imply the order of execution. The execution order of each process should be determined by its function and internal logic, and should not constitute any limitation on the implementation process of the embodiments of this application.
[0115] It should be understood that determining B based on A does not mean determining B solely based on A; it also means determining B based on A and / or other information.
[0116] Those skilled in the art will understand that all or part of the steps of the above embodiments can be implemented by hardware or by a program instructing related hardware. The program can be stored in a computer-readable storage medium, such as a read-only memory, a disk, or an optical disk.
[0117] The above description is only an optional embodiment of this application and is not intended to limit this application. Any modifications, equivalent substitutions, improvements, etc., made within the spirit and principles of this application should be included within the protection scope of this application.
[0118] In the several embodiments provided by this invention, it should be understood that the disclosed systems, apparatuses, and methods can be implemented in other ways. For example, the apparatus embodiments described above are merely illustrative; for instance, the division of units is only one method, and in actual implementation, there may be other division methods. For example, multiple units or components may be combined or integrated into another system, or some features may be ignored or not executed. Furthermore, the coupling or direct coupling or communication connection shown or discussed may be through some interfaces; the indirect coupling or communication connection between apparatuses or units may be electrical, mechanical, or other forms.
[0119] The units described as separate components may or may not be physically separate. The components shown as units may or may not be physical units; that is, they may be located in one place or distributed across multiple network units. Some or all of the units can be selected to achieve the purpose of this embodiment according to actual needs.
[0120] In addition, the functional units in the various embodiments of the present invention can be integrated into one processing unit, or each unit can exist physically separately, or two or more units can be integrated into one unit.
[0121] The above description is merely a specific embodiment of this application, but the scope of protection of this application is not limited thereto. Any variations or substitutions that can be easily conceived by those skilled in the art within the scope of the technology disclosed in this application should be included within the scope of protection of this application. Therefore, the scope of protection of this application should be determined by the scope of the claims.
Claims
1. A chiral configuration representation method based on mixed product, characterized in that, Includes the following steps: S1. Based on an open-source cheminformatics database, obtain a list of all asymmetric atoms (cAtoms) within the target molecule; S2. Traverse all asymmetric atoms in the list cAtoms and calculate their chiral product and chiral matrix; S3. Traverse the target molecule and use the chiral axis search algorithm based on substructure search and blocking discrimination to find the chiral axis contained in the target molecule; The process of finding the chiral axis contained in the target molecule includes the following steps: S31. Traverse the target molecule, find the spirocyclic atom structure contained in the target molecule, and obtain the list of chiral spirocyclic atoms csAtoms; S32. Traverse the target molecule, find the helical ring chain structure contained in the target molecule, and obtain the list of chiral helical ring chains csChains; S33. Traverse the target molecule, search for the allene structures contained in the target molecule, and obtain a list of chiral allenes (cenes); S34. Traverse all single bonds in the target molecule, use the blocking-rotation discrimination algorithm to find the single bonds that can be symmetrically rotated in the target molecule, and obtain the list of chiral single bonds csBonds. S35. Summarize and save the results of steps S31, S32, S33 and S34 to obtain the chiral axis of the molecule; if the result is empty, it means that the molecule does not have axial chirality. S4. For the chiral axes obtained in step S3, calculate their chiral product and chiral matrix; S5. The obtained chiral matrix and chiral product, which correspond one-to-one with the asymmetric atoms and chiral axes within the molecule, are used to characterize the local representation of the chiral information of the target molecule based on the chiral matrix and chiral product.
2. The chiral configuration representation method based on hybrid product according to claim 1, characterized in that: A method based on open-source cheminformatics databases is used to identify chiral centers in molecules and return their related information. The method then searches for chiral centers and iterates through the returned results to print the atomic index and chiral label of each chiral center. Extract a list of all asymmetric atoms, cAtoms, from the atom indices and chiral labels of the chiral centers using a list comprehension.
3. The chiral configuration representation method based on hybrid product according to claim 1, characterized in that: The steps in step S2 for calculating the chiral product and the chiral matrix include: S21. Initialize the atomic chiral product list atomProducts and the atomic chiral matrix list atomMatrix to be empty; S22. Traverse the asymmetric atoms in the asymmetric atom list cAtoms, and obtain the neighbor list of atoms adjacent to the asymmetric atoms using the GetNeighbors method of the atom object in rdkit; S23. Sort the atoms in the neighbor list in ascending order according to the CIP rules; S24. For atom O in the asymmetric atom list cAtoms, define the atoms in its neighbor lists as A, B, C, and D in ascending order of CIP. Calculate the chirality matrix based on their three-dimensional coordinates. Add the chirality matrix to the atom matrix list; S25. Calculate the determinant value CP corresponding to the chiral matrix, which is the chiral product. Add CP to the atom chiral product list atomProducts.
4. The chiral configuration representation method based on hybrid product according to claim 1, characterized in that: The steps in step S4 for calculating the chiral product and the chiral matrix include: S41. For the chiral axis found, define its two end atoms as follows: and To obtain and Two connected groups are defined according to the CIP rule from smallest to largest as follows: and and with Two connected groups are defined according to the CIP rule from smallest to largest as follows: and ; S42, according to , , , and The chirality matrix is calculated from the three-dimensional coordinates. ; S43. Calculate the determinant value CP corresponding to the chiral matrix as the chiral product. Similar to the result in S24, the sign of the chiral product can be used to define the configuration of the chiral axis.
5. An electronic device, characterized in that: include: A processor and a memory, wherein the memory stores a computer program that can be called by the processor; The processor executes the chiral configuration representation method based on hybrid product as described in any one of claims 1-4 by calling the computer program stored in the memory.
6. A computer-readable storage medium, characterized in that: The system stores instructions that, when executed on a computer, cause the computer to perform the chiral configuration representation method based on hybrid product as described in any one of claims 1-4.