Particle structure generation method and device, computer equipment and storage medium

Abstract

The invention relates to a particle structure generation method and device, computer equipment and a storage medium. The method comprises the following steps: acquiring a particle structure description file of a reference particle, wherein the reference particle comprises at least one part of structure of a specified particle; generating topological information and force field parameters of reference particles based on the particle structure description file; determining a first structure difference between the specified particle and the reference particle, and adjusting topological information and force field parameters of the reference particle to obtain topological information and force field parameters of the specified particle; obtaining preset structure information of the specified particle, and determining a second structure difference between a particle structure represented by the adjusted topological information of the specified particle and a structure represented by the preset structure information; correcting topological information of the specified particles according to the second structural difference; and generating a structural representation of the specified particle based on the corrected topological information of the specified particle and the force field parameter of the specified particle. By adopting the method, the structure of particles with uncommon elements and uncommon bonding modes can be generated.

Description

Technical Field

[0001] The present disclosure relates to the field of computer simulation technology, and in particular to a particle structure generation method, apparatus, computer equipment, and storage medium. Background Art

[0002] With the advancement of computer simulation technology, more and more particle simulations are being run on computers. However, traditional particle simulations, such as those for molecules or ions, are primarily designed for protein-ligand binding scenarios. In these scenarios, they are primarily used to simulate ionic compounds with common elements and common bonding patterns. Simulations of uncommon elements, ionic compounds with unusual bonding patterns, and small molecules, which are involved in other scenarios, are not possible.

[0003] Therefore, conventional techniques are currently unable to generate structures of ionic compounds with unusual elements and unusual bonding patterns, as well as small molecules. Summary of the Invention

[0004] Based on this, it is necessary to provide a particle structure generation method, device, computer equipment, and storage medium that can generate ionic compounds and small molecule structures of uncommon elements and uncommon bonding patterns to address the above technical problems.

[0005] In a first aspect, the present disclosure provides a method for generating a particle structure. The method comprises:

[0006] Obtaining a particle structure description file of a reference particle, wherein the reference particle includes at least a portion of the structure of the designated particle;

[0007] Based on the particle structure description file, generating topological information and force field parameters of the reference particle;

[0008] determining a first structural difference between the designated particle and the reference particle, and adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle;

[0009] Acquiring preset structural information of the designated particle, and determining a second structural difference between a particle structure represented by the adjusted topological information of the designated particle and a structure represented by the preset structural information;

[0010] Correcting the topological information of the designated particle according to the second structural difference;

[0011] A structural representation of the designated particle is generated based on the corrected topological information of the designated particle and the force field parameters of the designated particle.

[0012] In a second aspect, the present disclosure further provides a particle structure generating device. The device comprises:

[0013] an information acquisition module, configured to acquire a particle structure description file of a reference particle, wherein the reference particle includes at least a portion of the structure of a designated particle;

[0014] A data generation module, configured to generate topological information and force field parameters of the reference particle based on the particle structure description file;

[0015] a first data adjustment module, configured to determine a first structural difference between the designated particle and the reference particle, and adjust the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle;

[0016] a second data adjustment module, configured to obtain preset structural information of the designated particle, determine a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information; and correct the topological information of the designated particle according to the second structural difference;

[0017] A structure generation module is configured to generate a structural representation of the designated particle based on the modified topological information of the designated particle and the force field parameters of the designated particle. In a third aspect, the present disclosure further provides a computer device. The computer device includes a memory and a processor, the memory storing a computer program, and the processor executing the computer program implements the steps described in any of the methods in the above embodiments.

[0018] In a fourth aspect, the present disclosure further provides a computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, implements the steps of any of the methods in the above embodiments.

[0019] In a fifth aspect, the present disclosure further provides a computer program product, which includes a computer program that, when executed by a processor, implements the steps of any of the methods in the above embodiments.

[0020] In the aforementioned particle structure generation method, apparatus, computer device, storage medium, and computer program product, because the designated particle is typically an ionic compound or small molecule composed of uncommon elements and uncommon bonding patterns, it is not possible to directly generate the topological information and force field parameters for the designated particle. However, the reference particle contains at least a portion of the structure of the designated particle, which allows processing of the designated particle to be transformed into processing of the reference particle. Furthermore, the reference particle only needs to contain at least a portion of the structure of the designated particle, which increases the selection range of reference particles and accommodates a wider range of processing scenarios for different types of designated particles. Based on the particle structure description file of the reference particle, the topological information and force field parameters of the reference particle are generated. A first structural difference between the designated particle and the reference particle is determined, and the topological information and force field parameters of the reference particle are adjusted based on the first structural difference to obtain the topological information and force field parameters of the designated particle. Since there may be certain structural differences between the designated particle and the reference particle, the first structural difference can be used to modify the topological information and force field parameters of the reference particle, thereby changing the modified topological information and force field parameters of the reference particle to those of the designated particle. It is possible to generate topological information and force field parameters for designated particles of uncommon elements and uncommon bonding modes. In addition, since the structure of designated particles is usually a three-dimensional structure or a two-dimensional structure in space. After obtaining the topological information of designated particles, in the process of using the topological information to construct the structure of the particles, there may be a situation where the topological information is satisfied but the structure itself is wrong, and this structure will not meet the requirements. According to the preset structural information of the designated particles that is set in advance, the second structural difference between the particle structure represented by the topological information of the designated particles and the structure represented by the preset structural information is determined, and the topological information of the designated particles is further corrected using the second structural difference, so that the structure of the designated particles finally generated can meet the requirements. Finally, based on the corrected topological information of the designated particles and the force field parameters of the designated particles, a structural representation of the designated particles of uncommon elements and uncommon bonding modes can be generated. BRIEF DESCRIPTION OF THE DRAWINGS

[0021] In order to more clearly illustrate the specific embodiments of the present disclosure or the technical solutions in the prior art, the following briefly introduces the drawings required for use in the specific embodiments or the description of the prior art. Obviously, the drawings described below are some embodiments of the present disclosure. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying any creative work.

[0022] Figure 1 A flow chart of a particle structure generation method according to an embodiment;

[0023] Figure 2 A schematic diagram of a structure and a particle structure represented by preset structural information in one embodiment;

[0024] Figure 3 is a schematic diagram of a second structural difference in one embodiment;

[0025] Figure 4 is a schematic diagram of a coordinate system in one embodiment;

[0026] Figure 5 is a schematic diagram of a coordinate system and atoms in one embodiment;

[0027] Figure 6 Schematic diagram of an electrochemical reduction reaction in which EC mainly participates in one embodiment;

[0028] Figure 7 In one embodiment and Schematic diagram of the structure;

[0029] Figure 8 A schematic diagram of a process for generating a structural representation of a surrogate particle in one embodiment;

[0030] Figure 9 A schematic diagram of the structures of surrogate particles and designated particles in one embodiment;

[0031] Figure 10 is a schematic flow chart of a particle structure generation method according to another embodiment;

[0032] Figure 11 A schematic diagram of a process flow of .lmp file processing in another embodiment;

[0033] Figure 12 A diagram showing the structure of a configuration file in another embodiment;

[0034] Figure 13 is a schematic block diagram of the structure of a particle structure generating device in one embodiment;

[0035] Figure 14 Schematic diagram of the internal structure of a computer device in one embodiment. DETAILED DESCRIPTION

[0036] In order to make the purpose, technical solutions and advantages of the present disclosure more clearly understood, the present disclosure is further described in detail below with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are only used to explain the present disclosure and are not intended to limit the present disclosure.

[0037] It should be noted that the terms "first," "second," and the like in the specification and claims herein and in the accompanying drawings are used to distinguish similar objects and are not necessarily used to describe a particular order or precedence. It should be understood that the terms used in this manner are interchangeable where appropriate so that the embodiments of the present invention described herein can be implemented in an order other than those illustrated or described herein. In addition, the terms "including" and "having," as well as any variations thereof, are intended to cover non-exclusive inclusions. For example, a process, method, apparatus, product, or device comprising a series of steps or units is not necessarily limited to those steps or units explicitly listed, but may include other steps or units that are not explicitly listed or that are inherent to these processes, methods, products, or devices.

[0038] In this document, the term "and / or" simply describes a relationship between related objects, indicating that three possible relationships exist. For example, "A and / or B" could mean: A exists alone, A and B exist simultaneously, or B exists alone. Furthermore, the character " / " in this document generally indicates an "or" relationship between the related objects.

[0039] As described in the background technology, tools such as the SwissParam force field parameterization network server, LigParGen, CGenFF, CHARMM-GUI, Antechamber, Paramchem, and ATB (Automated TopologyBuilder) can be used to generate topological descriptions and force field parameters for molecules or ions. However, it should be noted that after generating the topological descriptions and force field parameters for molecules or ions, the 3T algorithm needs to be utilized for subsequent optimization processing. The 3T algorithm will call the CHARMM force field for rapid optimization to obtain a better initial structure during the subsequent generation of the initial structure of the gas-solid / liquid-solid interface. Therefore, it is necessary to select a tool compatible with the CHARMM force field to generate the topological descriptions and force field parameters for molecules or ions.

[0040] In the processing of the 3T algorithm, taking the SwissParam force field parameterization network server as an example, in order to ensure that the bond definitions in the molecule can be effectively recognized by the CHARMM force field, the molecular structure needs to be recorded in .mol2 format, and all hydrogen atoms must be included and all aromatic bonds therein must be converted into clear single bonds or double bonds. In this process, the original molecular structure will be protonated to varying degrees depending on the pH, so the converted structure will occasionally be inconsistent with the input molecule (the ion is incorrectly protonated or hydrogenated to convert it into a molecule, such as the bis(trifluoromethanesulfonyl)imide ion). will be hydrogenated to become a molecule). As a result, the initial structure generation method provided by the 3T algorithm cannot effectively handle ionic compounds or small molecules containing uncommon elements and uncommon bonding patterns.

[0041] Currently, other tools like the SwissParam force field parameterization web server are primarily used for molecular dynamics simulations in the field of computer-aided drug design (CADD). In the field of lithium batteries, however, electrolytes often contain unusual molecules or ions. Current tools do not fully support the construction of structures for these molecules or ions. Therefore, 3T cannot support lithium battery applications or the construction of structures for these unusual molecules or ions.

[0042] Therefore, in order to solve the above problems, in one embodiment, Figure 1 As shown, a particle structure generation method is provided. This embodiment uses the method applied to a terminal as an example for illustration. It is understandable that the method can also be applied to a server, and can also be applied to a system including a terminal and a server, and implemented through the interaction between the terminal and the server. In this embodiment, the method includes the following steps:

[0043] S102, obtaining a particle structure description file of a reference particle, where the reference particle includes at least a portion of the structure of a designated particle.

[0044] Among them, the designated particles in some embodiments of the present disclosure may be molecules or ions with uncommon bonding patterns, or molecules or ions composed of uncommon elements. For example, bonding patterns may include: covalent bond: a bond formed by two non-metal atoms by sharing electrons, such as the bond between hydrogen atoms in a hydrogen molecule, ionic bond: a bond formed by the mutual attraction between positive and negative charges, such as the bond between sodium ions and chloride ions in sodium chloride, metallic bond: a bond formed by metal atoms sharing electron clouds, such as the bond between metal atoms in metals, etc. In some embodiments of the present disclosure, common bonding patterns may be Bonding patterns between elements related to life sciences, such as 、 、 、 For example, in the embodiment of the present disclosure, common elements can be In some embodiments of the present disclosure, uncommon elements may be, for example, 、 、 、 It is understood that in some embodiments of the present disclosure, particles that cannot use traditional tools to generate topological descriptions and force field parameters can all be designated particles. In addition, in some embodiments of the present disclosure, uncommon bonding modes mainly refer to some bonding types that cannot be supported and processed by SwissParam, LigParaGen tools or some other tools. Designated particles may include, for example: carbonate , dioxalatoborate ion , or oxygen molecules. The reference particle usually contains at least part of the structure of the specified particle. For example, the specified particle is an oxygen molecule , then the reference particle can be a water molecule , carbon dioxide molecules , or it could be a hydrogen peroxide molecule . In some embodiments of the present disclosure, the particle structure description file can be a SMILES file or a file in .xyz format. The SMILES (Simplified molecular-input line-entry system) file is a simplified molecular linear input specification, which is a specification that uses AScII strings to clearly describe molecular structures. SMILES strings are currently the main representation method for storing molecular topological structures. They can be easily converted into two-dimensional graphics or generate three-dimensional structures of molecules. They are often used as molecular input representations for machine learning algorithms that process molecules.

[0045] Specifically, for a given particle, due to its inherent bonding pattern or elemental issues, traditional methods cannot generate an accurate structure. Instead, a reference particle can be identified. This reference particle contains at least a portion of the structure of the given particle. This allows the processing of the given particle to be transformed into processing the reference particle. When processing the reference particle, the particle structure description file for the reference particle must first be obtained.

[0046] In some exemplary embodiments, the reference particles may be determined by converting ions or free radicals into neutral molecules by adding hydrogen or halogen on a designated particle, thereby determining the reference particles.

[0047] S104: Generate topological information and force field parameters of the reference particle based on the particle structure description file.

[0048] Topological information can include atomic positions, velocities, types, interatomic bonds, angles, dihedral angles, and other descriptive information. Force field parameters are typically used to describe the interaction forces, bond lengths, bond angles, dihedral angles, charges, polarization, dipole moments, and other parameters between atoms within a molecule. These can be used to calculate molecular energy and structure and perform molecular dynamics.

[0049] Specifically, the topological information and force field parameters of the reference particles can be generated according to the particle structure description file.

[0050] In some exemplary embodiments, since some embodiments of the present disclosure may also involve the processing of ions, the particle structure description file can be input into the LigParGen force field parameterization network server with added ion support to generate the topological information and force field parameters of the reference particle. LigParGen can generate topological descriptions and OPLS-AA force field parameters for organic small molecules or ions, and can be compatible with the CHARMM force field. The SMILES file of the reference particle can be input into LigParGen to generate the topological information and force field parameters of the reference particle. The topological information and force field parameters of the generated reference particle can be recorded in different file formats. If you want to use the topological information and force field parameters for other processing operations later, such as molecular dynamics, the topological information and force field parameters of the reference particle can be stored in the .lmp format. The .lmp format file can include: the position, velocity, type, bonds between atoms, angles, dihedral angles and other topological descriptions of the reference particle and the force field parameters of the reference particle. The information in the .lmp format file can be parsed later, and then the data object of the molecule or ion can be constructed based on the information in the .lmp format file.

[0051] In other exemplary embodiments, if the reference particles in the embodiments of the present disclosure are not ions but only molecules, other tools such as CGenFF, CHARMM-GUI, Antechamber, Paramchem, ATB (Automated Topology Builder) and other tools can also be used to generate topological descriptions and force field parameters of the reference particles.

[0052] S106 , determining a first structural difference between the designated particle and the reference particle, adjusting the topological information and force field parameters of the reference particle according to the first structural difference, and obtaining the topological information and force field parameters of the designated particle.

[0053] Since both the designated particle and the reference particle are composed of atoms, the first structural difference may generally include atoms in the reference particle that are different from those in the designated particle (atoms that need to be deleted or modified).

[0054] Specifically, because the reference particle contains at least a portion of the structure of the designated particle, there will be differences in the structures of the reference particle and the designated particle. A first structural difference between the reference particle and the designated particle can be determined. This first structural difference is then used to adjust the topological information and force field parameters of the reference particle, thereby obtaining the topological information and force field parameters of the designated particle.

[0055] In some exemplary embodiments, for example, the designated particles are oxygen molecules. , the reference particle is nitric acid , then the first structural difference between the reference particle and the specified particle can be hydrogen atoms, A nitrogen atom and a Oxygen atoms. hydrogen atoms, A nitrogen atom and a The oxygen atoms are used to adjust the topological information and force field parameters of the reference particle to obtain the topological information and force field parameters of the specified particle. For example, the specified particle is , the reference particle is , the first structural difference can be Atoms and Atoms can be based on , to adjust the topological information and force field parameters of the reference particle to obtain the topological information and force field parameters of the specified particle.

[0056] S108 , obtaining preset structural information of the designated particle, and determining a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information.

[0057] The preset structural information may generally be information corresponding to the correct structure of a specified particle, and the second structural difference may generally be a difference in the order, position, spatial relationship, bond length, etc. of atoms in the particle.

[0058] Specifically, in order to accurately obtain the structure of the specified particle, the topological information of the specified particle may be further modified. Preset structural information of the specified particle is obtained, and a second structural difference between the particle structure represented by the topological information of the specified particle and the structure represented by the preset structural information is determined.

[0059] In some exemplary embodiments, Figure 2 As shown, if the structure represented by the preset structure information of the specified particle is a three-dimensional spatial structure, such as Figure 2 The structure shown in B1, The bond angle between atoms is 120 degrees. Although the topological information also mentions 3 Atom, three The bond angle between atoms is also 120 degrees, but the Figure 2 The structure shown in A1 is a planar structure. The atomic structure difference is the second structural difference between the particle structure represented by the topological information of the specified particle and the structure represented by the preset structure information.

[0060] In addition, if Figure 3 As shown, if the structure represented by the preset structure information of the specified particle is a planar structure, such as Figure 3 The structure shown in A2, wherein The bond length between an atom and the atoms it is connected to is a. The structure formed in the topological information is as follows Figure 3 The structure shown in B2, one of The bond length between the atom and the atom it is connected to is 2a, so the bond length between the atom it is connected to is 2a An atom is a second structural difference between the particle structure represented by the topological information of a specified particle and the structure represented by the preset structural information. It is understood that the above is merely illustrative, and in actual applications, more cases of second structural differences may exist. Those skilled in the art can flexibly determine the second structural difference based on the actual application scenario.

[0061] S110: Modify the topological information of the designated particle according to the second structural difference.

[0062] Specifically, after determining the second structural difference, the second structural difference can be used to further correct the topological information of the specified particle.

[0063] In some exemplary embodiments, continue with Figure 2 The second structural difference is explained as an example. Figure 2 After the second structural difference of the O atoms in the A1 and B1 structures is detected, in order to eliminate the difference, the topological information of the specified particle can be adjusted using the second structural difference. For example, constraints on the coordinates of each O atom can be added to the topological information so that the particle structure represented by the revised topological information is the same as the structure represented by the preset structural information.

[0064] by Figure 3 Taking the second structural difference as an example, the bond length connected to each O atom is adjusted in the topological information, and the bond length is adjusted to a. In this way, the bond length connected to each O atom in the particle structure represented by the revised topological information is a. At this time, the particle structure represented by the revised topological information is the same as the structure represented by the preset structure information.

[0065] S112 : Generate a structural representation of the designated particle based on the corrected topological information of the designated particle and the force field parameters of the designated particle.

[0066] The structural representation may be structural information corresponding to the structure, or may be a specific structure. In some embodiments of the present disclosure, the structural representation refers to a specific structural model.

[0067] Specifically, a Python particle data object can be constructed based on the corrected topological information of the specified particles and the force field parameters of the specified particles. The Python particle data object can be an initial structural model. Packmol and the Python particle data object are then used to generate a structural representation containing a variety of different specified particles. Packmol is a program for generating molecular packing. It can automatically arrange a group of molecules into a stable molecular set for use in molecular simulations, protein-lipid interaction studies, solution model construction, etc. Packmol can handle various types of molecules, including atoms, ions, proteins, and nucleic acids. It can generate a molecular packing structure with the desired density, spacing, and geometric constraints based on the parameters provided by the user (which can be topological information and force field parameters in some embodiments of the present disclosure).

[0068] In the above embodiment, since the designated particle is typically an ionic compound or small molecule composed of an uncommon element and an uncommon bonding pattern, it is impossible to directly generate the topological information and force field parameters for the designated particle. However, the reference particle contains at least a portion of the structure of the designated particle, which allows processing of the designated particle to be converted to processing of the reference particle. Furthermore, the reference particle only needs to contain at least a portion of the structure of the designated particle, which increases the selection range of reference particles and meets a wider range of processing scenarios for different types of designated particles. Based on the particle structure description file of the reference particle, the topological information and force field parameters of the reference particle are generated. A first structural difference between the designated particle and the reference particle is determined, and the topological information and force field parameters of the reference particle are adjusted based on the first structural difference to obtain the topological information and force field parameters of the designated particle. Since there may be certain structural differences between the designated particle and the reference particle, the first structural difference can be used to modify the topological information and force field parameters of the reference particle, thereby changing the modified topological information and force field parameters of the reference particle to those of the designated particle. This allows the generation of topological information and force field parameters for designated particles composed of uncommon elements and uncommon bonding patterns. In addition, since the structure of the specified particle is usually a three-dimensional structure or a two-dimensional structure in space. After obtaining the topological information of the specified particle, in the process of using the topological information to construct the structure of the particle, a situation may occur where the topological information is satisfied but the structure itself is wrong, and this structure will not meet the requirements. According to the preset structural information of the specified particle that is set in advance, the second structural difference between the particle structure represented by the topological information of the specified particle and the structure represented by the preset structural information is determined, and the topological information of the specified particle is further corrected using the second structural difference, so that the structure of the specified particle finally generated can meet the requirements. Ultimately, based on the corrected topological information of the specified particle and the force field parameters of the specified particle, a structural representation of the specified particle of uncommon elements and uncommon bonding modes can be generated.

[0069] In one embodiment, under normal circumstances, the reference particle can contain the entire structure of the specified particle, so that only some atoms in the reference particle need to be deleted to obtain the specified particle. In this case, the first structural difference contains the atoms that need to be deleted in the reference particle. If the specified particle is , the reference particle can be , the atom that needs to be deleted is a Atom. If the reference particle is , the atom that needs to be deleted is a Atom and a The step of adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle includes:

[0070] The topological information and force field parameters of the atoms to be deleted in the reference particle are determined.

[0071] Specifically, the atoms to be deleted are determined according to the first structural difference, the topological information associated with the atoms to be deleted is determined in the topological information of the reference particle, and the force field parameters associated with the atoms to be deleted are determined in the force field parameters of the reference particle.

[0072] The topological information of the atom to be deleted is deleted from the topological information of the reference particle, and the force field parameters of the atom to be deleted are deleted from the force field parameters of the reference particle to obtain the topological information and force field parameters of the designated particle.

[0073] Specifically, after determining the topological information of the atom to be deleted, the topological information of the atom to be deleted can be deleted from the topological information of the reference particle. The topological information of the designated particle is obtained. After determining the force field parameters of the atom to be deleted, the force field parameters of the atom to be deleted can be deleted from the force field parameters of the reference particle to obtain the force field parameters of the designated particle.

[0074] In some exemplary embodiments, if the reference particle is , specify the particle as , you need to delete the atom as one Atom. The topological information of the reference particle includes: a Atom and two The topological information corresponding to the atom, the force field parameters of the reference particle include: a Atom and two The force field parameters such as bonds and bond angles corresponding to atoms, and for more complex molecules, information such as dihedral angles and improper angles will also be included. The topological information of the atoms to be deleted is 1 The topological information and force field parameters associated with atoms. Therefore, you can delete a The topological information corresponding to the atom, the remaining one Atom and a The topological information corresponding to the atom can be the specified particle You can delete a reference particle's force field parameters. The force field parameters corresponding to the atom, the remaining one Atom and a The force field parameters corresponding to the atom, the remaining force field parameters can be used as the specified particle force field parameters.

[0075] In this embodiment, when the first structural difference contains atoms that need to be deleted in the reference particle, the topological information of the atoms to be deleted and the force field parameters of the atoms to be deleted can be directly deleted. By deleting, the topological information and force field parameters of the specified particle can be quickly obtained. In addition, for application scenarios where the structure of a specified particle needs to be generated urgently, since only the information needs to be deleted, there is no need to modify or adjust the information and parameters, which can greatly improve efficiency. And for some beginners who have no experience in operation and processing, they only need to delete the information, which reduces the difficulty of operation and processing.

[0076] In one embodiment, in some scenarios, if a reference particle containing the entire structure of a specified particle cannot be found, a reference particle containing a portion of the structure of the specified particle can be found. , and the reference particle can be At this point, the first structural difference between the reference particle and the specified particle is Atoms and Atom. The replaced atom in the first structural difference can be atom, the replaced atom in the reference particle is The step of adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle includes:

[0077] The topological information and force field parameters of the replaced atoms in the reference particle and the topological information and force field parameters of the replaced atoms are determined.

[0078] Specifically, the replaced atom in the reference particle is determined based on the first structural difference, the topological information associated with the replaced atom is determined in the topological information of the reference particle, and the force field parameters associated with the replaced atom are determined in the force field parameters of the reference particle. The topological information and force field parameters of the replaced atom can also be determined. The topological information and force field parameters of the replaced atom can be predetermined. They can be determined based on some algorithms or based on the experience of those skilled in the art. In some embodiments of the present disclosure, there is no limitation on how the topological information and force field parameters of the replaced atom are determined.

[0079] The topological information of the replaced atom is adjusted to the topological information of the replaced atom, and the force field parameters of the replaced atom are adjusted to the force field parameters of the replaced atom, so as to obtain the topological information and force field parameters of the designated particle.

[0080] Specifically, the topological information of the replaced atom can be adjusted to the topological information of the replaced atom from the topological information of the reference particle, and the force field parameters of the replaced atom can be adjusted to the force field parameters of the replaced atom from the force field parameters of the reference particle.

[0081] In some exemplary embodiments, for example, a particle is specified as , and the reference particle can be The atoms replaced in the first structural difference can be atom, the replaced atom in the reference particle is Atoms. First, we can determine the The topological information and force field parameters associated with the atoms are then determined. The topological information and force field parameters associated with atoms. The associated topological information of the atoms and the force field parameters are adjusted to The topological information and force field parameters associated with the atoms. The topological information and force field parameters of the adjusted reference particle are The topological information and force field parameters associated with atoms and three The topological information and force field parameters corresponding to the atom, so the topological information and force field parameters of the adjusted reference particle can be regarded as the topological information and force field parameters of the specified particle.

[0082] In this embodiment, by adjusting the topological information and force field parameters of the atom to be replaced to the topological information and force field parameters of the replaced atom, even if a reference particle containing the entire structure of the specified particle cannot be found, the topological information and force field parameters of the specified particle can be obtained by adjusting the topological information and force field parameters to the replaced atom.

[0083] In one embodiment, as mentioned in the above embodiments, deleting the topological information and force field parameters of certain atoms can greatly improve efficiency. In some scenarios, deleting the topological information and force field parameters of two atoms and adjusting the topological information and force field parameters of one atom at the same time is faster than adjusting the topological information and force field parameters of three atoms by deletion. Therefore, in some scenarios, if the first reference particle can obtain the specified particle by deleting and modifying the atoms, the second reference particle can only obtain the specified particle by modifying the atoms. The first reference particle needs to be selected for processing. At this time, the first structural difference includes: atoms that need to be deleted in the reference particle, atoms to be replaced, and atoms to be replaced in the reference particle. The topological information and force field parameters of the reference particle are adjusted according to the first structural difference to obtain the topological information and force field parameters of the specified particle, including:

[0084] Determining the topological information and force field parameters of the atom to be deleted in the reference particle, the topological information and force field parameters of the atom to be replaced, and the topological information and force field parameters of the replaced atom;

[0085] Specifically, the atoms to be deleted are determined according to the first structural difference, the topological information associated with the atoms to be deleted is determined in the topological information of the reference particle, and the force field parameters associated with the atoms to be deleted are determined in the force field parameters of the reference particle. The atoms to be replaced in the reference particle are determined according to the first structural difference, and the associated topological information and force field parameters of the replaced atoms are determined in the topological information of the reference particle. The topological information and force field parameters of the replaced atoms can also be determined. How to determine the topological information and force field parameters of the replaced atoms can be referred to the above embodiment, which will not be repeated here.

[0086] The topological information of the atom to be deleted is deleted from the topological information of the reference particle, and the topological information of the replaced atom is adjusted to the topological information of the replaced atom to obtain the topological information of the designated particle.

[0087] Specifically, the topological information of the atom to be deleted is deleted from the topological information of the reference particle. At the same time, the topological information of the atom to be replaced is adjusted from the topological information of the reference particle to the topological information of the replaced atom. The topological information of the reference particle obtained after the deletion and replacement can be the topological information of the designated particle.

[0088] The reference information of the atom to be deleted is deleted from the force field parameters of the reference particle, and the force field parameters of the replaced atom are adjusted to the force field parameters of the replaced atom to obtain the force field parameters of the designated particle.

[0089] Specifically, the force field parameters of the atom to be deleted are deleted from the force field parameters of the reference particle, and at the same time, the force field parameters of the atom to be replaced are adjusted to the force field parameters of the replaced atom from the force field parameters of the reference particle. The force field parameters of the reference particle obtained after deletion and replacement can be the force field parameters of the specified particle.

[0090] In this embodiment, by deleting and modifying the topological information and force field parameters of the atoms, when no reference particle containing the entire structure of the specified particle can be found, compared with the method of only adjusting the topological information and force field parameters of the atoms, the deletion process is simple to operate and can improve processing efficiency.

[0091] In one embodiment, when the preset structure information includes the preset sequence information of atoms, the preset sequence information of atoms is usually the order in which the atoms are arranged according to the spatial position relationship. For example, propanol , the preset order information of its atoms is atom, atom, atom, atom, atom, atom, atom, atom, atom, atom, atom, atom.

[0092] The determining of a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information includes:

[0093] Determine the particle structure represented by the adjusted topological information of the designated particle.

[0094] Specifically, a model may be constructed or simulated according to the topological information of the designated particle to determine the particle structure represented by the adjusted topological information of the designated particle.

[0095] According to the sequence information of the atoms in the particle structure and the preset sequence information of the atoms, atoms having different sequence information are determined.

[0096] The sequence information may generally be the relative position information between atoms, such as which atoms are between certain atoms and which atom is after a certain atom.

[0097] Specifically, after determining the particle structure, the sequence information of each atom in the designated particle can be determined based on the particle structure. The sequence information of each atom in the designated particle is then compared with the preset sequence information of the atom to determine the atoms with different sequence information.

[0098] According to the atoms having different sequence information, a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information is determined.

[0099] Specifically, after determining the atoms with different sequence information, the second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information is determined based on the atoms with different sequence information.

[0100] Furthermore, modifying the topological information of the designated particle based on the second structural difference includes: determining the topological information of the atoms in the designated particle whose order information differs based on the atoms whose order information differs; and modifying the topological information of the atoms whose order information differs. For example, the order of the atoms whose order information differs may be added to the topological information to ensure that the order of the atoms in the particle structure represented by the modified topological information of the designated particle is consistent with the preset order information.

[0101] In some exemplary embodiments, when isomers appear, i.e., they have the same atomic type and the same number of atoms but different structures, in such cases, although the topological information and force field parameters of the specified particle are obtained. For example, the specified particle is a propanol molecule. , and the topological information of the specified particle obtained after adjustment forms isopropanol Although isopropyl alcohol and propanol have the same number of atoms and the same type of atoms, their final structures are different. Therefore, the particle structure represented by the adjusted topological information is incorrect. It is also necessary to adjust according to the preset structural information, which can include the order of each atom in the specified particle. If the particle structure represented by the topological information of the specified particle obtained after adjustment is isopropyl alcohol, the order of each atom is as follows: atom, atom, atom, atom, atom, atom, atom, atom, atom, atom, atom, Atom. Specify the actual structure of the particle as propanol, and the preset sequence information is: atom, atom, atom, atom, atom, atom, atom, atom, atom, atom, atom, Atoms. The atoms with different order information are atom, atom, atom, atom, atoms. Therefore, the second structural difference is: atom, atom, atom, atom, Atom. When the second structure difference is used to correct the topological information, it is necessary to constrain atom, atom, atom, atom, The position relationship of the atoms, the above atom, atom, atom, atom, The position relationship of the atoms is adjusted to: atom, atom, atom, atom, It will be appreciated that the above is for illustration only.

[0102] In this embodiment, the preset order information of atoms can be used to accurately determine the difference in particle structure represented by the topological information of the specified particle currently adjusted. Subsequently, the topological information of the specified particle is corrected using the second structural difference to ensure the accuracy of the final structure.

[0103] In one embodiment, when the preset structural information includes preset spatial coordinate information of atoms. The preset spatial coordinate information can be the coordinate information of each atom of the specified particle in the actual three-dimensional space. Through the preset spatial coordinate information, the relative position relationship of each atom, the distance between each atom and other information can be accurately determined. The second structural difference between the particle structure represented by the topological information of the specified particle obtained by the adjustment and the structure represented by the preset structural information includes:

[0104] Determine the particle structure represented by the adjusted topological information of the designated particle.

[0105] Specifically, a model may be constructed or simulated according to the topological information of the designated particle to determine the particle structure represented by the adjusted topological information of the designated particle.

[0106] Coordinate difference information of each atom is calculated according to the spatial coordinate information of each atom in the particle structure and the preset spatial coordinate information of the atom.

[0107] According to the coordinate difference information of each atom, a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information is determined.

[0108] Specifically, a coordinate system can be created based on the particle structure. Usually, the created coordinate system is the same as the coordinate system corresponding to the preset spatial coordinate information of the atom, which makes it easy to compare the differences in coordinate information. Figure 4 As shown, the preset spatial coordinate information of the atom is based on the A atom (other atoms are not shown) in the specified particle as the origin of the coordinate system, the A1 direction of the A atom is the x-axis, the A2 direction of the A atom perpendicular to the A1 direction is the y-axis, and the A3 direction perpendicular to the A2 direction is the z-axis. In the particle structure, it is also based on the A atom as the origin of the coordinate system. The A1 direction of the A atom is the x-axis, the A2 direction of the A atom is the y-axis, and the A3 direction is the z-axis to establish a coordinate system to determine the spatial coordinate information of each atom in the particle structure. Since the coordinate systems are the same, the difference between the spatial coordinate information of each atom in the particle structure and the preset spatial coordinates of the atom can be compared, and the coordinate difference information of each atom can be calculated. Based on the coordinate difference information of each atom, the second structural difference between the particle structure represented by the adjusted topological information of the specified particle and the structure represented by the preset structural information can be determined.

[0109] In some exemplary embodiments, Figure 5 As shown, Figure 5 Where A is the coordinate system and atomic diagram corresponding to the preset spatial coordinate information of the atom. The preset spatial coordinate information of the atom x1 can be (0, 0, a), the preset spatial coordinate information of the atom x2 can be (0, a, 0), and the preset spatial coordinate information of the atom x3 can be (a, 0, 0). a is the bond length. In addition, since the atomic coordinates of the coordinate origin are all (0, 0, 0), they can be omitted from the statistics. Figure 5 In Figure B, the coordinate diagram corresponding to the particle structure represented by the topological information of a specified particle is shown. Here, the spatial coordinate information of atom x1 is (0, 0, a), the atomic coordinates of x2 are (-a, 0, 0), and the atomic coordinates of x3 are (a, 0, 0). Therefore, the coordinate difference between atoms x1 and x3 can be 0. The coordinate difference between atoms x2 can be (a, a, 0). The second structural difference can be the coordinate difference between atoms x2 (a, a, 0).

[0110] In this embodiment, the spatial coordinate information of each atom in the particle structure and the preset spatial coordinate information of the atom can be used to accurately determine the second structural difference of the particle structure represented by the topological information of the specified particle adjusted in three-dimensional space. The second structural difference is then used to correct the topological information of the specified particle, which can ensure the accuracy of the structure of the specified particle finally obtained.

[0111] In a specific application scenario, ethylene carbonate (ethylene carbonate), a typical component of the electrolyte of lithium-ion batteries, ) molecules as an example. Figure 6 As shown, The electrochemical reduction reaction in which the main participants are involved. When it is desired to determine the further reaction behavior of the product obtained from this reaction in the electrolyte, it is necessary to construct a and The solid-liquid interface structure (in this embodiment, the solid-liquid interface structure is constructed However, it is difficult for either SwissParam or LigParGen to effectively parameterize this ionic structure, that is, it is impossible to generate topological information and force field parameters. , it is necessary to determine a reference particle that contains at least part of its structure. If the reference particle is Since the ions are processed, the LigParGen tool needs to be selected for processing. The SMILES file of the particle is input into the LigParGen tool and output by the LigParGen tool. The topological information and force field parameters of the particles, due to Particles and The number and type of atoms in are the same, so there is no need to delete the topological information. Figure 7 Shown, showing and structure. and The structure is different, so it is necessary to The structure of The topological information of the particles is adjusted so that the adjusted The structure represented by the topological information of the particle is The force field parameters can also be modified. The modified force field parameters will make The geometry can be kept constant in subsequent further reaction simulations. As shown in Table 1 The force field parameters are shown in the table. The force field parameters can be modified according to Relevant literature or some algorithms are adjusted.

[0112] Table 1 Force field parameter table

[0113]

[0114] In Table 1, the modified parameters are underlined. In addition, it should be noted that since the ultimate purpose of the force field parameters in Table 1 is to generate the structure of a specified particle, the force field parameters adjusted in Table 1 cannot be applied to other aspects, such as classical force fields.

[0115] In one embodiment, after obtaining the corrected topological information and force field parameters of a specified particle, these information, along with some other particle-related parameters, can be input into the 3T algorithm to generate a structural representation of the specified particle. The 3T algorithm, known as the Tiered Tensor Transform (TTT), is an efficient multi-scale structural energy minimization algorithm that can generate physically plausible structures with DFT-level accuracy, thereby generating multiple different structural conformers. The 3T multi-scale structural transformation algorithm can make it easier for the system to escape local energy minima. Consequently, it is easier to reach lower-energy structural conformations with fewer computational iterations than other methods that rely solely on atomic-level optimization. Density Functional Theory (DFT): Density Functional Theory is a computational quantum mechanical modeling method used in physics, chemistry, and materials science to study the electronic structure (primarily the ground state) of many-body systems, particularly atoms, molecules, and condensed matter. Using this theory, properties of multi-electron systems can be determined using functionals (functions of functions). In DFT, these functionals are functions of spatially correlated electron density. The specific processing process of the 3T algorithm is described below. The structure representation of the specified particle is generated based on the modified topological information of the specified particle and the force field parameters of the specified particle, including:

[0116] A lattice description file of the designated particle is obtained, and a lattice structure representation of the designated particle is constructed according to the lattice description file of the designated particle.

[0117] The lattice description file can be a file that stores the surface structure of a specified particle. The surface structure is recorded as a POSCAR file in VASP format, containing atomic coordinates and lattice periodicity information. A POSCAR file in VASP format is a text file format used to describe crystal structures and is an input file format used by the Vienna Ab initio Simulation Package (VASP) software. A POSCAR file contains information such as lattice periodicity, atomic species, and atomic coordinates, defining the crystal geometry. This file format is a simple ASCII text format that is easy to edit and parse and can be used by a variety of software and tools. Lattice periodicity information refers to the periodic nature of the atomic or ionic arrangement in a crystal. Crystals are composed of atoms or ions, which are arranged according to a specific pattern to form a lattice structure. Lattice periodicity information describes the periodic distribution of atoms or ions in a specified particle, including information such as the lattice constant, unit cell, lattice points, and crystal structure. The lattice constant refers to the distance between adjacent unit cells in the crystal lattice of a specified particle and can be obtained by measuring the crystal's diffraction pattern or calculating the unit cell parameters of the specified particle. A unit cell is the smallest repeating unit of a given particle, consisting of a set of lattice points on the given particle and the atoms or ions adjacent to them. Lattice points are the locations of atoms or ions within a given particle. Atoms or ions within a given particle typically occupy lattice points within the unit cell, which can be simple points, face-centered, or body-centered. The lattice structure is represented as a Python surface data object, which contains parameters such as atomic elements, coordinates, periodic lattice structure, and force field information.

[0118] Specifically, it retrieves the lattice description file for a specified particle, converts it into a Python surface data object, and constructs a lattice structure representation of the particle. Additionally, it retrieves Lennard-Jones and partial charge force field information (which only contains coarse atomic pair interactions). Lennard-Jones is a model for describing the potential energy of intermolecular interactions. Based on the Lennard-Jones, partial charge force field information, and lattice description file, a lattice structure representation of the specified particle is constructed.

[0119] An object structure representation of the designated particle is constructed according to the corrected topological information of the designated particle and the force field parameters of the designated particle.

[0120] The object structure representing the specified particle can be a Python molecular data object. A Python Molecular Data Object (MDO) is a data structure used to represent the structure and properties of a molecule. It can contain information such as atomic elements, coordinates, bond connectivity, charge, electronic state, rotatable bonds, and force field parameters.

[0121] Specifically, a Python molecular data object can be constructed according to the corrected topological information of the specified particle and the force field parameters of the specified particle.

[0122] The object structure representation and the lattice structure representation of the specified particle are combined to generate a structure representation of the specified particle.

[0123] Specifically, the object structure representation and the lattice structure representation of the specified particle can be combined into a 3T PyTorch model, and the 3T PyTorch model obtained by the combination is the structural representation of the specified particle.

[0124] In this embodiment, a crystal core structure representation is constructed by using a lattice description file. The use of the lattice structure representation can better simulate the arrangement and interaction of molecules in the lattice, thereby ensuring the reliability and stability of the generated specified particle structure.

[0125] In one embodiment, there are also some application scenarios, such as finding a reference particle that contains at least a portion of the structure of a specified particle, but due to the reasons of at least a portion of the structure of the specified particle itself, it is impossible to generate the topological information and force field parameters of the reference particle. For example, currently only For molecules with a structure of , it is impossible to generate topological information and force field parameters using traditional technologies. Or, in the process of determining the reference particles, many types of reference particles have been determined, but it is still impossible to find a reference particle that can generate topological information and force field parameters. In view of the above situation, when the force field parameters of the reference particles cannot be generated based on the particle structure description file, the method further includes:

[0126] Determine a surrogate particle with the same topological structure as the designated particle, wherein the atoms contained in the surrogate particle are of different types from at least a portion of the atoms contained in the designated particle. For example, the designated particle is , then the substitute particle can be If the specified particle is , then the substitute particle can be In some embodiments of the present disclosure, a substitute particle is a particle that can generate topological information and force field parameters. It should be noted that if the substitute particle found cannot generate topological information and force field parameters, the search for substitute particles can continue until a substitute particle that can generate topological information and force field parameters is found.

[0127] Specifically, the various properties of chemical elements are periodic. Elements in the same family usually have similar properties and bonding forms. Some uncommon types of atoms can also easily find similar replacements in adjacent families. Taking advantage of this feature, substitute particles with the same structure as the specified particle can be determined by replacing elements of the same family / similar elements. In addition, in addition to the same family / similar replacement of more critical atoms in the specified particle and the replacement particle, they should also have the same number of atoms, topological structure, relative arrangement order of atoms, and as similar bond order as possible. The above requirements can ensure that the substitute particle is as similar as possible to the specified particle and ensure the correctness of subsequent structural replacement. Because the main replacement method requires replacing the atoms in the specified particle, the more unique the key atoms replaced in the specified particle, the better. The preferred solution is that the atoms or ions in the substitute particle are of a different type from the atoms or ions in the specified particle.

[0128] In some exemplary embodiments, it is impossible to generate oxygen molecules by conventional methods. .because in Key length and in The key lengths are similar, so here you can use replace .Although The rotatable nature of a single bond The keys are different, but basically it does not affect Therefore, determine the geometry of yes A reasonable stand-in particle for a molecule.

[0129] A structure file of a surrogate particle is obtained, and topological information and force field parameters of the surrogate particle are generated according to the structure file.

[0130] Among them, the structure file can be a file that describes the structure of the substitute particle. The structure file can be a SMILES file or a file in .xyz format. The .xyz format is a file format used to represent three-dimensional coordinate data. In the field of chemistry, the .xyz format is commonly used to store the geometric structure information of molecules. Each file usually contains three parts: the first line is the number of atoms, followed by a line of comments, and then the information of each atom, including the atom name and its coordinates in three-dimensional space. This format is simple and easy to understand and is suitable for storing structural information of small molecules or ions.

[0131] Specifically, a structure file of a surrogate particle can be obtained. Based on the structure file, the topological information and force field parameters of the surrogate particle are generated. In some exemplary embodiments, if the surrogate particle is an ion, the structure file can generally be a SMILES file, and LigParGen can be used to generate the topological information and force field parameters of the surrogate particle. If the surrogate particle is a molecule, the structure file can be a file in .xyz format, and SwissParam or other types of processing tools (e.g., CGenFF, Antechamber, Paramchem, etc.) can be used to generate the topological information and force field parameters of the surrogate particle.

[0132] According to the topological information and force field parameters of the substitute particles, the structural representation of the substitute particles is generated.

[0133] Specifically, based on the topological information of the surrogate particle, its topological structure is constructed, including the atomic connectivity and chemical bond types. Based on the force field parameters, the interaction energy between the surrogate particle's atoms, including bond energy, angular energy, and dihedral energy, is calculated. Molecular dynamics simulation software (such as GROMACS, LAMMPS, etc.) or quantum chemistry calculation software (such as Gaussian, VASP, etc.) is used to simulate or calculate the surrogate particle under given force field parameters. The simulation or calculation results can be used to generate a structural representation of the surrogate particle, including information such as atomic coordinates, bond lengths, bond angles, and dihedral angles. Alternatively, a Python particle data object can be constructed based on the surrogate particle's topological information and force field parameters, and then a structural representation of the surrogate particle can be generated using Packmol. It will be appreciated that those skilled in the art may also choose other methods to generate a structural representation of the surrogate particle based on the surrogate particle's topological information and force field parameters.

[0134] The atoms in the structural representation of the surrogate particle are replaced with the atoms of the designated particle to generate the structural representation of the designated particle.

[0135] Specifically, after generating a surrogate particle's structural representation, since the surrogate particle and the designated particle have the same structure except for the atoms, the atoms in the surrogate particle's structural representation can be replaced with the atoms of the designated particle, thereby adjusting the surrogate particle's structural representation to that of the designated particle.

[0136] In this embodiment, when the reference particles cannot generate topological information and force field parameters, substitute particles are selected and processed through the substitute particles to generate a structural representation of the designated particles.

[0137] In one embodiment, the above mentioned processing of substitute particles to generate topological information and force field parameters of designated particles. The following specifically describes how to determine substitute particles. The charged atoms in the designated particles are replaced with neutral atoms from adjacent families to obtain substitute particles. For example, carbon or silicon atoms are used to replace boron anions that form four bonds. The topological structures of the substitute particles and the designated particles are ensured to be consistent, for example, sulfur is used to replace oxygen. The sizes of the atoms of the substitute particles and the designated particles and the bonding distances with adjacent atoms are ensured to be similar, and the bond orders are consistent.

[0138] In one embodiment, generating the structural representation of the surrogate particle according to the topological information and force field parameters of the surrogate particle includes:

[0139] Obtain a lattice description file for the surrogate particle and construct a lattice structure representation of the surrogate particle based on the lattice description file. Construct an object structure representation of the surrogate particle based on the topological information and force field parameters of the surrogate particle. Combine the object structure representation and the lattice structure representation of the surrogate particle to generate a structural representation of the surrogate particle.

[0140] Specifically, the lattice description file for the stand-in particle is obtained, converted into a Python surface data object, and the lattice structure representation of the stand-in particle is constructed. In addition, the Lennard-Jones and partial charge force field information (which only contains coarse atomic pair interactions) for the stand-in particle can be obtained. The Lennard-Jones model is used to describe the potential energy of intermolecular interactions. Based on the Lennard-Jones, partial charge force field information, and lattice description file, the lattice structure representation of the stand-in particle is constructed. Based on the topological information and force field parameters of the stand-in particle, a Python molecular data object for the stand-in particle is constructed. The object structure representation of the stand-in particle and the lattice structure representation are then combined to generate the structural representation of the stand-in particle.

[0141] In some exemplary embodiments, Figure 8As shown, when the surrogate particle is a molecule, the structure file can be in .xyz format. The surrogate particle .xyz file can be converted to a .mol2 file. A .mol2 file typically contains important parameters such as the molecular topology, atom types, and charge distribution. This information is essential for molecular simulations and calculations. By converting the .xyz file to a .mol2 file, the molecular structure and parameters can be imported into molecular force field calculation software (such as GROMACS and AMBER) or quantum chemistry calculation software (such as Gaussian and GAMESS) for molecular simulations and calculations, such as molecular dynamics simulations, energy optimization, and conformational searches. The .mol2 file can then be input into SwissParam, which then outputs the surrogate particle's topological information and force field parameters. The topological information and force field parameters are then converted to the GROMACS .gro format and then to the LAMMPS .dat structure file format. The .dat structure file format is easier to read and parse. Based on the information in the .dat structure file format, a Python molecular data object for the surrogate particle is constructed, containing information such as atomic elements, coordinates, rotatable bonds, and force field parameters. Lennard-Jones and partial charge force field information (containing only rough atomic pair interactions) and a surface structure file (the surface structure is recorded as a POSCAR file in VASP format, containing atomic coordinates and lattice periodicity) are obtained for the surrogate particle. Based on this information, a Python surface data object for the surrogate molecule is generated, containing atomic elements, coordinates, periodic lattice, and force field information. The Python surface data object and Python molecular data object are then combined into a PyTorch model to obtain the structural representation of the surrogate particle.

[0142] In this embodiment, in order to accurately construct a structural representation of the substitute particles, a lattice description file can be used to construct a crystal core structure representation. The use of the lattice structure representation can better simulate the arrangement and interaction of molecules in the lattice, thereby ensuring the reliability and stability of the generated substitute particle structure.

[0143] In one embodiment, replacing atoms in the structural representation of the surrogate particle with atoms of the designated particle to generate the structural representation of the designated particle includes:

[0144] Determining a correspondence between each atom in the surrogate particle and each atom in the designated particle based on the topological structure of the surrogate particle and the topological structure of the designated particle;

[0145] According to the corresponding relationship, the atoms in the structural representation of the substitute particle are replaced with the atoms of the designated particle to generate the structural representation of the designated particle.

[0146] Specifically, since the substitute particle and the designated particle have the same structure, except that at least some of the atoms are of different types, it is necessary to replace the types of atoms in the substitute particle with the types of atoms in the designated particle. Since the structural representation of the substitute particle may contain multiple types of atoms, and the positions of each atom are different, for example, there are atoms A, B, and C in the substitute particle, and atoms D, E, and F in the designated particle. The correspondence between atoms A, B, and C, and atoms D, E, and F, needs to be determined before the replacement can be performed. Since the substitute particle and the designated particle have the same structure, the correspondence between each atom in the substitute particle and each atom in the designated particle can be determined based on the topological structure of the substitute particle and the topological structure of the designated particle. Then, according to the correspondence, the atoms in the structural representation of the substitute particle are replaced with the atoms of the designated particle, thereby generating a structural representation of the designated particle.

[0147] In some exemplary embodiments, Figure 9 As shown, the surrogate particle contains three A atoms, three S atoms, two M atoms, and two N atoms, while the designated particle contains three A1 atoms, three X atoms, two Q atoms, and two Z atoms. The number of A atoms, S atoms in the surrogate particle, and A1 and X atoms in the designated particle are all three, while the number of M atoms, N atoms in the surrogate particle, and Q and Z atoms in the designated particle are all two. Because these numbers are identical, it's unclear which atoms will have a corresponding relationship. The A atom actually replaces the A1 atom. Replacing the A atom with an X atom could result in an incorrect representation of the designated particle's structure. Therefore, the correspondence between the atoms in the designated particle and the surrogate particle can be determined based on the topological information of the designated particle and the surrogate particle. Generally, atoms with the same topological information will have a corresponding relationship. For example, if the bond angle of the A atom is 120° and the bond angle of the A1 atom is also 120°, it can be assumed that the A and A1 atoms have a corresponding relationship. As shown in the above example, the determined correspondence can include: A1-A, SX, MQ, NZ, replacing the A1 atom of the substitute particle with the A atom, replacing the S atom of the substitute particle with the X atom, replacing the M atom of the substitute particle with the Q atom, and replacing the N atom of the substitute particle with the Z atom, thereby obtaining the structural representation of the specified particle.

[0148] In this embodiment, the correspondence between each atom is determined by using the topological structure of the substitute particle and the topological structure of the designated particle, and the replacement is performed using the correspondence, thereby ensuring the accuracy of the structural representation of the designated particle obtained after the replacement.

[0149] In one embodiment, the structural representation of the specified particle obtained above is only a relatively coarse-grained structure. In order to obtain a more accurate structural representation of the specified particle, the structural representation of the specified particle can also be optimized using a DFT algorithm. After generating the structural representation of the specified particle, the method further includes:

[0150] An energy of the specified particle is calculated based on an electron distribution in a structural representation of the specified particle.

[0151] Electron distribution refers to the spatial distribution of electrons around an atomic nucleus. According to quantum mechanics, electrons do not move along classical orbits but rather exist in specific energy levels with a certain probability distribution. Electron distribution can be described by the electron cloud density, which describes the probability of finding an electron near a certain point.

[0152] Specifically, the number of electrons and the arrangement of electron orbitals of a specified particle are determined based on the number of atoms and the number of charges in the structure representation of the specified particle. For example, for a hydrogen atom ( ), which consists of a proton and an electron, with the electron distributed in the 1s orbital. Based on this distribution, a wave function is used to describe the electron's motion. The wave function can be represented by a mathematical equation that contains information about the probability distribution of the electron in different orbitals. The Schrödinger equation is used to describe the motion and energy of particles. The Schrödinger equation is a fundamental equation in quantum mechanics that can be used to determine the wave function and energy of a particle. After solving the Schrödinger equation to obtain the particle's wave function, the wave function can be used to calculate the particle's energy. Energy can be expressed as the expectation value of an operator, where the operator corresponds to the particle's energy.

[0153] The force on each atom is calculated based on the energy of the specified particle and the coordinates of each atom in the structure representation.

[0154] Specifically, the force acting on each atom can be calculated using molecular force fields or quantum force fields, based on the coordinates of each atom in the power and structural representation of the specified particle. The molecular force field method is an approximation of the classical force field, which describes the interactions between atoms in a specified particle by defining the bond, angle, and dihedral parameters between atoms. By calculating the gradients of these interactions, the force acting on each atom in the specified particle can be obtained. The quantum force field method combines the advantages of quantum mechanics and classical force fields to more accurately describe the interactions between atoms in a specified particle. By calculating the potential energy surface of the specified particle and calculating its gradient, the force acting on each atom of the specified particle can be obtained. In general, the force acting on each atom can be calculated by taking the derivative of the energy of the specified particle with respect to the coordinates of each atom.

[0155] According to the force acting on each atom and the energy of the designated particle, the structural representation of the designated particle is iterated until the difference between the particle energy of the structural representation obtained in the current iteration and the particle energy of the structural representation obtained in the previous iteration is less than a first difference threshold, and the difference between the force acting on each atom in the structural representation obtained in the current iteration and the force acting on each atom in the structural representation obtained in the previous iteration is less than a second difference threshold.

[0156] A target structural representation of the designated particle is determined according to the structural representation of the designated particle obtained in the current iteration.

[0157] Among them, the target structure representation is a more accurate and detailed structure compared to the structure representation of the specified particles.

[0158] Specifically, the force exerted on each atom and the energy of the specified particle can be used to adjust the structural representation of the specified particle. Then continue to calculate the particle energy of the adjusted structural representation. Compare the particle energy of the adjusted structural representation with the particle energy of the structural representation before adjustment, and calculate the difference in particle energy. At the same time, calculate the difference between the force exerted on each atom in the adjusted structural representation and the force exerted on each atom in the structural representation before adjustment. When the difference in particle energy is less than the first difference threshold, and the difference between the forces exerted on each atom is less than the second difference threshold, it can be determined that the current adjusted structural representation meets the requirements, and no adjustment iteration is required. Based on the structural representation of the specified particle that meets the requirements obtained in the current iteration, determine the target structural representation of the specified particle.

[0159] In some exemplary embodiments, for example, the energy of a specified particle represented by the structure of a specified particle is A, and the force exerted on each atom (here, a single atom is used as an example, and the force exerted on the atom is also represented in the following text) is F. After the first iteration, the energy of the particle represented by the structure is A11, and the force exerted on the atom is F11. At this time, the difference in particle energy A-A11 and the difference in force exerted on the atom F-F11 are calculated. If the value of A-A11 is less than the first difference threshold, but the value of F-F11 is not less than the second difference threshold, a second iteration is required. After the second iteration, the energy of the particle represented by the structure is A12, and the force exerted on the atom is F12. At this time, the difference in particle energy is calculated as A11-A12, and the difference in force exerted on the atom is F11-F12. If the value of A11-A12 is greater than the first difference threshold, a third iteration is required. After the third iteration, the energy of the particle represented by the structure is A13, and the force exerted on the atom is F13. At this time, the difference in particle energy is A12-A13. If the value of A12-A13 is less than the first difference threshold, the difference in the force exerted on the atoms is F12-F13. If F12-F13 is less than the second difference threshold, the structural representation obtained by the third iterative adjustment can be determined as the target structural representation of the specified particle.

[0160] In this embodiment, by iterating the structural representation of the designated particle, a target structural representation of the designated particle with high precision and accuracy can be obtained.

[0161] In one embodiment, the present disclosure also provides another method for generating a particle structure, such as Figure 10 As shown, it includes: first, the application scenario involved in the present disclosure is explained. The method of the present disclosure can be adapted to the structure generation that can be used for DFT calculation in the Tiered tensor transform (3T) algorithm.

[0162] In order to increase the support of the 3T algorithm for common molecules or ions, additional workflows are set up using LigParGen. LigParGen can generate topological information and OPLS-AA force field parameters for general organic small molecules or ions, and is compatible with the CHARMM force field. The SMILES file of the reference particle can be input into LigParGen to generate the topological information and force field parameters of the reference particle. The generated topological information and force field parameters can be recorded in files of various formats. Here, the .lmp format is used to store this information. Since this file format is usually associated with LAMMPS (Large-scale Atomic / Molecular Massively Parallel Simulator) software, which is a widely used molecular dynamics simulation software, it facilitates subsequent processing. The .lmp file usually contains the initial configuration information of the simulation system, including the position, velocity, type, bonds between atoms, angles, dihedrals and other topological information and their force field parameters. The information stored in the .lmp file can be parsed to construct the Python molecular data object of the reference particle. However, LigParGen still has limitations. It can only handle common forms of molecular or ionic structures, and the maximum charge is In order to expand the support of this process to specific particles, a modifier module can be set up. This modifier supports automatically deleting the topological information and force field parameters (including atoms, bonds, bond angles, dihedral angles, Imperfect and other topological relationships and their parameters) corresponding to the deleted atoms when deleting some of them. Figure 11As shown, a .lmp file can be input into the modifier. The modifier reads the topological information and force field parameters in the .lmp file. Based on the differences between the reference particle and the specified particle, it marks the atoms with discrepancies and automatically deletes the topological information and force field parameters of the marked atoms. Because some information has been deleted, the topological information and force field parameters of the reference particle obtained after deletion must be consistent. The topological information and force field parameters of the reference particle obtained after deletion can also be adjusted to meet the requirements of the specified particle. For example, the topological information of the reference particle obtained after deletion can be adjusted using the correct structure. The .lmp modifier module expands the range of molecules or ions supported by the 3T pipeline. The LigParGen pipeline can be used to obtain the topological information and force field parameters of a modifiable reference particle through homologous / similar element substitution. The modifier can then be used to adjust the topological information and force field parameters to match the specified particle's topological information and force field parameters. Once the corrected .lmp file is obtained, the data can be directly passed to the 3T algorithm using the .lmp file parsing process. The 3T algorithm can then be used to generate the structure of the specified particle.

[0163] The methods mentioned above are already quite effective in generating topological information and force field parameters for a given particle. However, there are still some special cases where it is impossible to generate topological information and force field parameters for a reference particle. In such cases, surrogate particles can be used to solve this problem. Alternatively, surrogate particles can be used directly without using reference particles.

[0164] The primary purpose of the FF module in the 3T algorithm is to utilize force fields to optimize the system to a relatively low-energy state while avoiding atomic stacking during PackMol, thereby reducing the overhead required for subsequent, higher-precision DFT optimization. This process does not place high demands on the accuracy of topological information and force field parameters. Therefore, the fundamental logic for the use of surrogate particles is to ensure that the system calculated using DFT-level methods in the 3T VASP stage corresponds to the structure of the specified particle. Any structural adjustments can be made prior to this step (without prioritizing topological information and force field parameter accuracy). To expand the workflow to support a wider range of molecules, ions, and even free radicals, surrogate particles can be used to generate a relatively reasonable structure in the initial step, and then perform final structural corrections before submitting it to the 3T VASP stage (for DFT calculations).

[0165] To ensure the smooth operation of the method using substitute particles, the following key configurations need to be guaranteed: in addition to the same family / similar replacement of key atoms, the designated particle and the substitute particle should have the same number of atoms, topological structure, relative arrangement order of atoms, and as similar a bond order as possible. In order to ensure that the substitute particle is as similar as possible to the designated particle and to ensure the correctness of subsequent structural replacement. Figure 12As shown, various information related to the specified particle is set in the configuration file, such as the name and storage location of the surface structure file of the specified particle. Various information about the substitute particle is also set in the configuration file, such as the name and storage location of the structure file of the substitute particle. Various parameters of the 3T algorithm can also be set in the configuration file, such as the number of steps of executing the 3T algorithm in each stage, the name of each stage, and other parameter information. Run the configuration file and obtain the surface structure file based on the name and storage location of the surface structure file of the specified particle. Obtain the structure file of the substitute particle based on the name and storage location of the structure file of the substitute particle. Generate the structure of the substitute particle based on the parameters of the 3T algorithm and the structure file of the substitute particle in the configuration file. Before finally submitting it to the DFT calculation, the atoms in the structure of the substitute particle are replaced with the atoms in the specified particle to obtain the structure of the specified particle, and then use DFT to complete the final structure correction to generate the final structure of the specified particle.

[0166] This application also provides several application scenarios in which the above-mentioned particle structure generation method is applied. Specifically, the particle structure generation method can also be applied in material simulation scenarios, where it can be used to simulate the structure of a material and thereby predict its crystal structure, electronic structure, magnetic properties, and optical properties. It can also be used in molecular structure optimization, reaction kinetics simulation, and intermolecular interaction scenarios.

[0167] It should be understood that, although the various steps in the flowcharts involved in the various embodiments described above are displayed in sequence according to the instructions of the arrows, these steps are not necessarily executed in sequence in the order indicated by the arrows. Unless otherwise specified herein, there is no strict order restriction on the execution of these steps, and these steps can be executed in other orders. Moreover, at least a portion of the steps in the flowcharts involved in the various embodiments described above can include multiple steps or multiple stages, and these steps or stages are not necessarily executed and completed at the same time, but can be executed at different times, and the execution order of these steps or stages is not necessarily to be carried out in sequence, but can be executed in turn or alternately with other steps or at least a portion of steps or stages in other steps.

[0168] Based on the same inventive concept, the presently disclosed embodiments further provide a particle structure generation device for implementing the aforementioned particle structure generation method. The solution provided by this device is similar to the solution described in the aforementioned method. Therefore, the specific limitations of one or more of the particle structure generation device embodiments provided below can be found in the aforementioned limitations of the particle structure generation method and will not be further elaborated here.

[0169] In one embodiment, Figure 13As shown, a particle structure generation device 200 is provided, comprising: an information acquisition module 202, a data generation module 204, a first data adjustment module 206, a second data adjustment module 208 and a structure generation module 210, wherein:

[0170] The information acquisition module 202 is used to obtain a particle structure description file of a reference particle, where the reference particle includes at least a portion of the structure of a designated particle.

[0171] The data generation module 204 is used to generate the topological information and force field parameters of the reference particles based on the particle structure description file.

[0172] The first data adjustment module 206 is used to determine a first structural difference between the designated particle and the reference particle, and adjust the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle.

[0173] The second data adjustment module 208 is used to obtain the preset structural information of the specified particle, determine the second structural difference between the particle structure represented by the adjusted topological information of the specified particle and the structure represented by the preset structural information; and correct the topological information of the specified particle according to the second structural difference.

[0174] The structure generation module 210 is configured to generate a structural representation of the designated particle based on the corrected topological information of the designated particle and the force field parameters of the designated particle.

[0175] In one embodiment of the apparatus, when the first structural difference includes atoms to be deleted from the reference particle, the first data adjustment module 206 is further configured to determine topological information and force field parameters of the atoms to be deleted from the reference particle; delete the topological information of the atoms to be deleted from the topological information of the reference particle, and delete the force field parameters of the atoms to be deleted from the force field parameters of the reference particle, to obtain the topological information and force field parameters of the designated particle.

[0176] In one embodiment of the device, when the first structural difference includes: the replaced atom and the replaced atom in the reference particle, the first data adjustment module 206 is further configured to determine the topological information and force field parameters of the replaced atom in the reference particle, as well as the topological information and force field parameters of the replaced atom; adjust the topological information of the replaced atom to the topological information of the replaced atom, and adjust the force field parameters of the replaced atom to the force field parameters of the replaced atom, to obtain the topological information and force field parameters of the designated particle.

[0177] In one embodiment of the device, when the first structural difference includes: atoms that need to be deleted in the reference particle, replaced atoms, and replaced atoms in the reference particle. The first data adjustment module 206 is further used to determine the topological information and force field parameters of the atoms that need to be deleted in the reference particle, the topological information and force field parameters of the replaced atoms, and the topological information and force field parameters of the replaced atoms; delete the topological information of the atoms that need to be deleted from the topological information of the reference particle, and adjust the topological information of the replaced atoms to the topological information of the replaced atoms to obtain the topological information of the designated particle; delete the reference information of the atoms that need to be deleted from the force field parameters of the reference particle, and adjust the force field parameters of the replaced atoms to the force field parameters of the replaced atoms to obtain the force field parameters of the designated particle.

[0178] In one embodiment of the device, when the preset structural information includes preset atomic order information, the second data adjustment module 208 is further configured to determine the particle structure represented by the adjusted topological information of the designated particle; determine atoms having different order information based on the order information of atoms in the particle structure and the preset atomic order information; and determine, based on the atoms having different order information, a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information.

[0179] In one embodiment of the device, when the preset structural information includes preset spatial coordinate information of atoms, the second data adjustment module 208 is further used to determine the particle structure represented by the adjusted topological information of the designated particle; calculate the coordinate difference information of each atom according to the spatial coordinate information of each atom in the particle structure and the preset spatial coordinate information of the atom; determine the second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information according to the coordinate difference information of each atom;

[0180] In one embodiment of the apparatus, the structure generation module 210 includes:

[0181] The lattice structure representation generating module is used to obtain the lattice description file of the specified particle and construct the lattice structure representation of the specified particle according to the lattice description file of the specified particle.

[0182] The object structure representation generating module is used to construct the object structure representation of the designated particle according to the modified topological information of the designated particle and the force field parameters of the designated particle.

[0183] The structure generation submodule is used to combine the object structure representation and the lattice structure representation of the specified particle to generate the structure representation of the specified particle.

[0184] In one embodiment of the device, when the force field parameters of the reference particle cannot be generated based on the particle structure description file, the device further includes:

[0185] The surrogate particle determination module is configured to determine a surrogate particle having the same topological structure as the designated particle, wherein the atoms contained in the surrogate particle are of a different type from at least a portion of the atoms contained in the designated particle.

[0186] The parameter generation module is used to obtain the structure file of the substitute particle and generate the topological information and force field parameters of the substitute particle according to the structure file.

[0187] The surrogate structure generation module is used to generate a structural representation of the surrogate particle according to the topological information and force field parameters of the surrogate particle.

[0188] The replacement module is used to replace the atoms in the structural representation of the substitute particle with the atoms of the designated particle to generate the structural representation of the designated particle.

[0189] In one embodiment of the device, the substitute structure generation module is further used to obtain the lattice description file of the substitute particle, and construct the lattice structure representation of the substitute particle according to the lattice description file of the substitute particle; construct the object structure representation of the substitute particle based on the topological information and force field parameters of the substitute particle; and combine the object structure representation and the lattice structure representation of the substitute particle to generate the structural representation of the substitute particle.

[0190] In one embodiment of the device, the replacement module is further used to determine the correspondence between each atom in the substitute particle and each atom in the designated particle based on the topological structure of the substitute particle and the topological structure of the designated particle; according to the correspondence, the atoms in the structural representation of the substitute particle are replaced with the atoms of the designated particle to generate the structural representation of the designated particle.

[0191] In one embodiment of the device, the device further includes: a target structure generation module, configured to calculate the energy of the specified particle based on the electron distribution in the structural representation of the specified particle; calculate the force acting on each atom based on the energy of the specified particle and the coordinates of each atom in the structural representation; iterate the structural representation of the specified particle based on the force acting on each atom and the energy of the specified particle, until the difference between the particle energy of the structural representation obtained in the current iteration and the particle energy of the structural representation obtained in the previous iteration is less than a first difference threshold, and the difference between the force acting on each atom in the structural representation obtained in the current iteration and the force acting on each atom in the structural representation obtained in the previous iteration is less than a second difference threshold; and determine the target structural representation of the specified particle based on the structural representation of the specified particle obtained in the current iteration.

[0192] Each module in the particle structure generation device can be implemented in whole or in part through software, hardware, or a combination thereof. Each module can be embedded in or independent of a processor in a computer device in the form of hardware, or can be stored in a memory in the computer device in the form of software, so that the processor can call and execute the corresponding operations of each module.

[0193] In one embodiment, a computer device is provided. The computer device may be a server, and its internal structure diagram may be as follows: Figure 14 As shown. The computer device includes a processor, a memory and a network interface connected via a system bus. The processor of the computer device is used to provide computing and control capabilities. The memory of the computer device includes a non-volatile storage medium and an internal memory. The non-volatile storage medium stores an operating system, a computer program and a database. The internal memory provides an environment for the operation of the operating system and the computer program in the non-volatile storage medium. The database of the computer device is used to store data such as topological information and force field parameters. The network interface of the computer device is used to communicate with an external terminal via a network connection. When the computer program is executed by the processor, a particle structure generation method is implemented.

[0194] Those skilled in the art will understand that Figure 14 The structure shown in the figure is merely a block diagram of a portion of the structure related to the solution of the present disclosure, and does not constitute a limitation on the computer device to which the solution of the present disclosure is applied. The specific computer device may include more or fewer components than shown in the figure, or combine certain components, or have a different component arrangement.

[0195] In one embodiment, a computer device is provided, including a memory and a processor. The memory stores a computer program, and the processor implements the steps of any of the above method embodiments when executing the computer program.

[0196] In one embodiment, a computer-readable storage medium is provided, on which a computer program is stored. When the computer program is executed by a processor, the steps in any of the above method embodiments are implemented.

[0197] In one embodiment, a computer program product is provided, comprising a computer program, which implements the steps of any of the above method embodiments when executed by a processor.

[0198] Those skilled in the art will appreciate that all or part of the processes in the above-described method embodiments can be implemented by instructing the relevant hardware through a computer program. The computer program can be stored in a non-volatile computer-readable storage medium. When executed, the computer program can include the processes of the above-described method embodiments. Any reference to a memory, database, or other medium used in the embodiments provided herein may include at least one of non-volatile and volatile memory. Non-volatile memory may include read-only memory (ROM), magnetic tape, floppy disk, flash memory, optical memory, high-density embedded non-volatile memory, resistive random access memory (ReRAM), magnetic random access memory (MRAM), ferroelectric random access memory (FRAM), phase change memory (PCM), graphene memory, etc. Volatile memory may include random access memory (RAM) or external cache memory, etc. By way of illustration and not limitation, RAM can take various forms, such as static random access memory (SRAM) or dynamic random access memory (DRAM). The databases involved in the various embodiments provided herein may include at least one of a relational database and a non-relational database. Non-relational databases may include, but are not limited to, blockchain-based distributed databases. The processors involved in the various embodiments provided herein may be, but are not limited to, general-purpose processors, central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), programmable logic devices (PLDs), quantum computing-based data processing logic devices, and the like.

[0199] The technical features of the above embodiments can be combined arbitrarily. To make the description concise, not all possible combinations of the technical features in the above embodiments are described. However, as long as there is no contradiction in the combination of these technical features, they should be considered to be within the scope of this specification.

[0200] The above-described embodiments merely represent several implementation methods of the present disclosure. While the descriptions are relatively specific and detailed, they should not be construed as limiting the scope of the present disclosure. It should be noted that a person of ordinary skill in the art may make various modifications and improvements without departing from the spirit of the present disclosure, all of which fall within the scope of protection of the present disclosure. Therefore, the scope of protection of the present disclosure shall be determined by the appended claims.

Claims

1. A particle structure generation method, characterized in that: The method comprises: Obtaining a particle structure description file of a reference particle, wherein the reference particle includes at least a portion of the structure of the designated particle; Based on the particle structure description file, generating topological information and force field parameters of the reference particle; determining a first structural difference between the designated particle and the reference particle, and adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle; Acquiring preset structural information of the designated particle, and determining a second structural difference between a particle structure represented by the adjusted topological information of the designated particle and a structure represented by the preset structural information; Correcting the topological information of the designated particle according to the second structural difference; A structural representation of the designated particle is generated based on the corrected topological information of the designated particle and the force field parameters of the designated particle.

2. The method according to claim 1, characterized in that When the first structural difference includes: atoms to be deleted in the reference particle; adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle; including: Determining the topological information and force field parameters of the atoms to be deleted in the reference particle; The topological information of the atom to be deleted is deleted from the topological information of the reference particle, and the force field parameters of the atom to be deleted are deleted from the force field parameters of the reference particle to obtain the topological information and force field parameters of the designated particle.

3. The method according to claim 1, characterized in that When the first structural difference includes: the replaced atoms and the replaced atoms in the reference particle, adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle includes: Determining topological information and force field parameters of the replaced atom in the reference particle, as well as topological information and force field parameters of the replaced atom; The topological information of the replaced atom is adjusted to the topological information of the replaced atom, and the force field parameters of the replaced atom are adjusted to the force field parameters of the replaced atom, so as to obtain the topological information and force field parameters of the designated particle.

4. The method according to claim 1, wherein When the first structural difference includes: atoms to be deleted in the reference particle, atoms to be replaced, and atoms to be replaced in the reference particle, adjusting the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle includes: Determining the topological information and force field parameters of the atom to be deleted in the reference particle, the topological information and force field parameters of the atom to be replaced, and the topological information and force field parameters of the replaced atom; Deleting the topological information of the atom to be deleted from the topological information of the reference particle, and adjusting the topological information of the replaced atom to the topological information of the replaced atom, to obtain the topological information of the designated particle; The reference information of the atom to be deleted is deleted from the force field parameters of the reference particle, and the force field parameters of the replaced atom are adjusted to the force field parameters of the replaced atom to obtain the force field parameters of the designated particle.

5. The method according to claim 1, wherein When the preset structural information includes preset order information of atoms, determining a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information includes: Determining a particle structure represented by the adjusted topological information of the designated particle; Determining atoms having different sequence information based on the sequence information of the atoms in the particle structure and the preset sequence information of the atoms; According to the atoms having different sequence information, a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information is determined.

6. The method according to claim 1, wherein When the preset structure information includes preset spatial coordinate information of atoms; The determining of a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information includes: Determining a particle structure represented by the adjusted topological information of the designated particle; Calculating coordinate difference information of each atom according to the spatial coordinate information of each atom in the particle structure and the preset spatial coordinate information of the atom; According to the coordinate difference information of each atom, a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information is determined.

7. The method according to claim 1, characterized in that Generating a structural representation of the designated particle based on the corrected topological information of the designated particle and the force field parameters of the designated particle includes: Obtaining a lattice description file of the designated particle, and constructing a lattice structure representation of the designated particle according to the lattice description file of the designated particle; constructing an object structure representation of the designated particle according to the corrected topological information of the designated particle and the force field parameters of the designated particle; The object structure representation and the lattice structure representation of the specified particle are combined to generate a structure representation of the specified particle.

8. The method according to claim 1, characterized in that When the force field parameters of the reference particle cannot be generated based on the particle structure description file, the method further includes: determining a surrogate particle having the same topological structure as the designated particle, wherein atoms contained in the surrogate particle are of a different type from at least a portion of atoms contained in the designated particle; Obtaining a structure file of a surrogate particle, and generating topological information and force field parameters of the surrogate particle according to the structure file; generating a structural representation of the surrogate particle according to the topological information and force field parameters of the surrogate particle; The atoms in the structural representation of the surrogate particle are replaced with the atoms of the designated particle to generate the structural representation of the designated particle.

9. The method according to claim 8, characterized in that Generating a structural representation of the surrogate particle according to the topological information and force field parameters of the surrogate particle includes: Obtaining a lattice description file of the stand-in particle, and constructing a lattice structure representation of the stand-in particle according to the lattice description file of the stand-in particle; constructing an object structure representation of the surrogate particle based on the topological information and force field parameters of the surrogate particle; The object structure representation and the lattice structure representation of the surrogate particle are combined to generate a structure representation of the surrogate particle.

10. The method according to claim 8, characterized in that The replacing atoms in the structural representation of the substitute particle with atoms of the designated particle to generate the structural representation of the designated particle includes: Determining a correspondence between each atom in the surrogate particle and each atom in the designated particle based on the topological structure of the surrogate particle and the topological structure of the designated particle; According to the corresponding relationship, the atoms in the structural representation of the substitute particle are replaced with the atoms of the designated particle to generate the structural representation of the designated particle.

11. The method according to any one of claims 1 to 10, characterized in that After generating the structural representation of the designated particle, the method further includes: calculating an energy of the specified particle based on an electron distribution in a structural representation of the specified particle; calculating a force on each atom based on the energy of the designated particle and the coordinates of each atom in the structural representation; Iterating the structural representation of the designated particle according to the force acting on each atom and the energy of the designated particle until a difference between the particle energy of the structural representation obtained in a current iteration and the particle energy of the structural representation obtained in a previous iteration is less than a first difference threshold, and a difference between the force acting on each atom in the structural representation obtained in the current iteration and the force acting on each atom in the structural representation obtained in a previous iteration is less than a second difference threshold; A target structural representation of the designated particle is determined according to the structural representation of the designated particle obtained in the current iteration.

12. A particle structure generating device, characterized in that: The device comprises: an information acquisition module, configured to acquire a particle structure description file of a reference particle, wherein the reference particle includes at least a portion of the structure of a designated particle; A data generation module, configured to generate topological information and force field parameters of the reference particle based on the particle structure description file; a first data adjustment module, configured to determine a first structural difference between the designated particle and the reference particle, and adjust the topological information and force field parameters of the reference particle according to the first structural difference to obtain the topological information and force field parameters of the designated particle; a second data adjustment module, configured to obtain preset structural information of the designated particle, determine a second structural difference between the particle structure represented by the adjusted topological information of the designated particle and the structure represented by the preset structural information; and correct the topological information of the designated particle according to the second structural difference; The structure generation module is used to generate a structural representation of the designated particle based on the corrected topological information of the designated particle and the force field parameters of the designated particle.

13. A computer device comprising a memory and a processor, wherein the memory stores a computer program, wherein: When the processor executes the computer program, the steps of the method according to any one of claims 1 to 11 are implemented.

14. A computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the steps of the method according to any one of claims 1 to 11 are implemented.

15. A computer program product comprising a computer program, characterized in that When the computer program is executed by a processor, the steps of the method according to any one of claims 1 to 11 are implemented.

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