Method and apparatus for key charge parameter correction, method and apparatus for electrostatic potential calculation based on atomic charge, device and medium

Abstract

The application discloses a method and device for bond charge parameter correction, a method and device for electrostatic potential calculation based on atomic charge, equipment and a medium. The method comprises the following steps: determining the parameter type of the bond charge parameter according to the topological structure of a to-be-corrected molecule; calculating the charge information of the to-be-corrected molecule; calculating the electrostatic potential of the to-be-corrected molecule according to the charge information of the to-be-corrected molecule, the parameter type of the bond charge parameter of the to-be-corrected molecule and the initial bond charge parameter value of the to-be-corrected molecule; calculating the electrostatic potential difference between the to-be-corrected electrostatic potential and the to-be-corrected reference electrostatic potential; and constructing a target function according to the electrostatic potential difference and minimizing the target function to obtain the bond charge parameter value of the to-be-corrected molecule, so as to improve the accuracy of the corrected bond charge parameter, thereby improving the accuracy of the molecular electrostatic potential, and the required calculation amount is low, so that high-throughput calculation and screening can be realized at low cost.

Description

Technical Field

[0001] This application relates to the field of molecular simulation technology, specifically to a method and apparatus for correcting bond charge parameters, a method and apparatus for calculating electrostatic potential based on atomic charge, electronic equipment, and computer-readable storage medium. Background Technology

[0002] Molecular dynamics simulations are methods based on Newtonian mechanics principles to simulate the physical trajectories and states of atoms and molecules. For more complex biomolecular systems, the trajectories of particles within the system are typically determined through numerical analysis of Newton's equations of motion for interacting particles, while the forces and potential energy between particles are determined using molecular mechanical force fields. Atomic charge is one of the most commonly used models to describe the charge distribution in chemical systems. The net charge of each atom is described by a point charge located in the atomic nucleus. Atomic charge models are a class of methods for describing the charge distribution in chemical systems. The idea behind this model is to treat each atom as a single point charge, ignoring the atomic radius. Atomic charge is simple and intuitive, helping scientists understand and study the states and properties of atoms. The study of atomic charge is beneficial for studying the states and properties of molecules and can be practically applied in many technological fields, such as drug development, drug design, materials research, and new materials design.

[0003] Restricted Electrostatic Potential (RESP) charge is a commonly used method for calculating atomic charges, as it can accurately reproduce molecular electrostatic potentials based on quantization calculations. However, significant time is required for quantization calculations before fitting the RESP charge, a computational burden particularly pronounced in high-throughput screening tasks. AM1-BCC charge is another commonly used method for calculating atomic charges. This method utilizes a set of parameters based on chemical bond topology, simultaneously performing semi-empirical (AM1) quantization calculations to obtain the AM1 charge of the atom. It then combines the AM1 charge of the atom with all bond charge correction (BCC) parameters obtained from the bond topology around the atom to arrive at the final charge value. The AM1-BCC charge model outperforms RESP charge in terms of computational time and cost, but its accuracy is lower.

[0004] Therefore, there is an urgent need for a method for calculating atomic charges that balances computation time and accuracy. Summary of the Invention

[0005] To address the aforementioned technical problems, this application is proposed. Embodiments of this application provide a method and apparatus for correcting bond charge parameters, a method and apparatus for calculating electrostatic potential based on atomic charge, an electronic device, and a computer-readable storage medium, thereby solving the aforementioned technical problems.

[0006] According to one aspect of this application, a method for correcting bond charge parameters is provided, comprising: determining the parameter type of the bond charge parameters based on the topological structure of the molecule to be corrected; calculating charge information of the molecule to be corrected; wherein the charge information is calculated by the AM1 method; calculating the electrostatic potential of the molecule to be corrected based on the charge information of the molecule to be corrected, the parameter type of the bond charge parameters of the molecule to be corrected, and the initial bond charge parameter value of the molecule to be corrected; calculating the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected; and constructing an objective function based on the electrostatic potential difference, and minimizing the objective function to obtain the bond charge parameter value of the molecule to be corrected.

[0007] In one embodiment, calculating the electrostatic potential of the molecule to be corrected based on its charge information, the parameter type of its bond charge parameter, and its initial bond charge parameter value includes: calculating the electrostatic potential of the molecule to be corrected based on its charge value, the current parameter value corresponding to the parameter type of its bond charge parameter, and the position information of the grid points surrounding the molecule and the molecule itself.

[0008] In one embodiment, calculating the electrostatic potential of the molecule to be corrected based on the charge value of the molecule to be corrected, the current parameter value corresponding to the parameter type of the bond charge parameter of the molecule to be corrected, and the position information of the lattice points around the molecule to be corrected and the molecule to be corrected includes:

[0009]

[0010] Among them, V l calc It is the electrostatic potential of the molecule to be corrected at the l-th lattice point. It is the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point. r is the AM1 charge value of the j-th atom of the molecule to be corrected. lj T is the distance between the j-th atom and the l-th lattice point. jα Let p be the matrix of bond relationships of the j-th atom. α γ is the bond charge correction value for parameter type α, N is the total number of atoms in the molecule to be corrected, and γ is the total number of parameter types.

[0011] In one embodiment, calculating the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected includes:

[0012]

[0013] Among them, V l diff V is the difference between the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point and the reference electrostatic potential. l QM It is the reference electrostatic potential of the molecule to be corrected at the l-th lattice point obtained by DFT calculation. It is the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point. r is the AM1 charge value of the j-th atom. lj It is the distance between the j-th atom and the l-th lattice point.

[0014] In one embodiment, constructing an objective function based on the electrostatic potential difference value and minimizing the objective function to obtain the bond charge parameter value of the molecule to be corrected includes:

[0015] Construct the objective function; wherein the objective function is the sum of squares of the electrostatic potential differences at each preset lattice point of the molecule to be corrected; and

[0016] The objective function is minimized using the minimum gradient method to obtain the bond charge parameter values ​​of the molecule to be corrected.

[0017] In one embodiment, minimizing the objective function using the minimum gradient method to obtain the bond charge parameter values ​​of the molecule to be corrected includes:

[0018]

[0019] Where, χ 2 The objective function to be minimized is... T is the derivative of the objective function. jα T βk The matrices representing the bond relationships between atoms j and k are p. α It is the bond charge correction value for parameter type α, r kl r lj These are the distances between the k-th and j-th atoms and the l-th lattice point, respectively, V. l diff γ is the difference between the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point and the reference electrostatic potential of the molecule to be corrected, M is the total number of lattice points around the molecule to be corrected, N is the total number of atoms of the molecule to be corrected, and γ is the total number of parameter types.

[0020] In one embodiment, the parameter type for determining the bond charge parameter of the molecule to be corrected based on its topological structure includes:

[0021] Based on the type of each chemical bond in the molecule to be corrected and the type of atoms at both ends of each chemical bond, the parameter type of each bond charge parameter in the molecule to be corrected is determined.

[0022] According to another aspect of this application, a method for calculating electrostatic potential based on atomic charge is provided, comprising: calculating the charge information of a target atom to obtain the charge information of each atom in a target molecule; wherein the target atom is connected to other atoms through chemical bonds to form a target molecule; calculating the electrostatic potential of the target molecule based on the charge information of each atom in the target molecule, the bond charge parameters of the target molecule, and the electrostatic potential lattice information of the target molecule; wherein the bond charge parameters of the target molecule are obtained using the correction method described in any of the preceding claims.

[0023] According to another aspect of this application, an apparatus for correcting bond charge parameters is provided, comprising:

[0024] The type determination module is used to determine the parameter type of the bond charge parameter of the molecule to be corrected based on the topological structure of the molecule to be corrected.

[0025] The first calculation module is used to calculate the charge information of the molecule to be corrected; wherein the charge information is calculated by the AM1 method;

[0026] The second calculation module is used to calculate the electrostatic potential of the molecule to be corrected based on the charge information of the molecule to be corrected, the parameter type of the bond charge parameter of the molecule to be corrected, and the initial bond charge parameter value of the molecule to be corrected.

[0027] The difference calculation module is used to calculate the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected; and

[0028] The parameter determination module is used to construct an objective function based on the electrostatic potential difference value, and to minimize the objective function to obtain the bond charge parameter value of the molecule to be corrected.

[0029] According to another aspect of this application, an electrostatic potential calculation device based on atomic charge is provided, comprising: a third calculation module for calculating the charge information of a target atom to obtain the charge information of each atom in a target molecule; wherein the target atom is connected to other atoms through chemical bonds to form a target molecule; and an electrostatic potential calculation module for calculating the electrostatic potential of the target molecule based on the charge information of each atom in the target molecule, the bond charge parameters of the target molecule, and the electrostatic potential grid information of the target molecule; wherein the bond charge parameters of the target molecule are obtained using the correction method described in any of the preceding claims.

[0030] According to another aspect of this application, a computer-readable storage medium is provided, the storage medium storing a computer program for performing any of the above-described methods for correcting bond charge parameters, and / or performing the above-described methods for calculating electrostatic potential based on atomic charges.

[0031] According to another aspect of this application, an electronic device is provided, comprising: a processor; a memory for storing processor-executable instructions; the processor for performing any of the above-described methods for correcting bond charge parameters, and / or performing the above-described method for calculating electrostatic potential based on atomic charge.

[0032] This application provides a method and apparatus for correcting bond charge parameters, a method and apparatus for calculating electrostatic potential based on atomic charge, an electronic device, and a computer-readable storage medium. The method and apparatus determine the parameter type of the bond charge parameters based on the topological structure of the molecule to be corrected; calculate the charge information of the molecule to be corrected, wherein the charge information is obtained by the AM1 method; calculate the electrostatic potential information of the molecule to be corrected based on the charge information, the parameter type of the bond charge parameters, and the initial bond charge parameter values; calculate the electrostatic potential difference between the electrostatic potential information to be corrected and the reference electrostatic potential to be corrected; and construct a target electrostatic potential based on the electrostatic potential difference. The method involves defining and minimizing a target function to obtain the bond charge parameter values ​​of the molecule to be corrected. Specifically, it determines the type of bond charge parameters based on the molecule's topology, calculates the electrostatic potential of the molecule based on its charge information, the type of bond charge parameters, and the initial bond charge parameter values, constructs an objective function using the difference from the reference electrostatic potential, and minimizes this objective function to obtain the current bond charge parameter values. This improves the accuracy of correcting the bond charge parameters, thereby simultaneously improving the accuracy of the molecular electrostatic potential. Furthermore, this method requires relatively low computational resources, enabling high-throughput computation and screening at low cost. Attached Figure Description

[0033] The above and other objects, features, and advantages of this application will become more apparent from the more detailed description of the embodiments of this application in conjunction with the accompanying drawings. The drawings are provided to further illustrate the embodiments of this application and form part of the specification. They are used together with the embodiments of this application to explain this application and do not constitute a limitation thereof. In the drawings, the same reference numerals generally represent the same components or steps.

[0034] Figure 1 This is a flowchart illustrating a method for correcting bond charge parameters provided in an exemplary embodiment of this application.

[0035] Figure 2 This is a flowchart illustrating a method for correcting bond charge parameters provided in another exemplary embodiment of this application.

[0036] Figure 3 This is a flowchart illustrating an exemplary embodiment of the electrostatic potential calculation method based on atomic charge provided in this application.

[0037] Figure 4 This is a schematic diagram of the structure of a device for correcting bond charge parameters provided in an exemplary embodiment of this application.

[0038] Figure 5 This is a schematic diagram of the structure of an electrostatic potential calculation device based on atomic charge provided in an exemplary embodiment of this application.

[0039] Figure 6 This is a structural diagram of an electronic device provided in an exemplary embodiment of this application. Detailed Implementation

[0040] Hereinafter, exemplary embodiments according to this application will be described in detail with reference to the accompanying drawings. Obviously, the described embodiments are merely some embodiments of this application, and not all embodiments of this application. It should be understood that this application is not limited to the exemplary embodiments described herein.

[0041] Figure 1 This is a flowchart illustrating a method for correcting bond charge parameters provided in an exemplary embodiment of this application. Figure 1 As shown, the method for correcting bond charge parameters includes the following steps:

[0042] Step 110: Determine the parameter type of the bond charge parameter based on the topological structure of the molecule to be corrected.

[0043] In one embodiment, step 110 can be implemented by determining the parameter type of the bond charge parameter of each chemical bond in the molecule to be corrected, based on the type of each chemical bond in the molecule to be corrected and the corresponding atom types at both ends of each chemical bond.

[0044] Specifically, by obtaining the topological structure of the molecule to be corrected, the parameter type of the bond charge parameter is determined based on the topological structure. The parameter type specifically includes the type of bond and the types of atoms on both sides involved in the bond formation. The atom type includes the element type, coordination number, and chemical environment of the central atom. The chemical environment includes the bonded atoms around the central atom (the types of these bonds include single bonds, double bonds, triple bonds, and aromatic bonds), whether the atoms carry formal charges, whether the atoms are on a ring, etc.

[0045] Step 120: Calculate the charge information of the molecule to be corrected.

[0046] The charge information is calculated using the AM1 method. That is, the AM1 charge value of each atom in the molecule to be corrected is calculated using existing semi-empirical methods, which is the charge information of the molecule to be corrected.

[0047] Step 130: Calculate the electrostatic potential of the molecule to be corrected based on its charge information, the parameter type of its bond charge parameters, and the initial bond charge parameter values.

[0048] The initial bond charge parameters of the molecule to be corrected can be set as needed. Empirically, they can be initially set to 0. If the bond charge parameter values ​​obtained after the first calculation are not ideal, a second calculation can be performed. In this second calculation, the initial bond charge parameter values ​​of the molecule to be corrected can be the same as those obtained after the first calculation. After obtaining the AM1 charge value of the molecule to be corrected, the electrostatic potential of the molecule to be corrected is calculated by combining the parameter types of the bond charge parameters and the initial bond charge correction parameter values. This is the electrostatic potential value of the molecule to be corrected calculated using the current bond charge parameter values.

[0049] Step 140: Calculate the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected.

[0050] The molecule to be corrected includes at least one conformation. Specifically, the number of conformations contained in the molecule to be corrected can be selected as needed. In organic compound molecules, the specific shape in which atoms or groups are arranged in space by the rotation of rotatable single bonds is called a conformation. That is, a conformation specifically refers to the specific spatial arrangement of atoms around single bonds in a molecule.

[0051] Specifically, when the molecule to be corrected contains multiple conformations, the electrostatic potential, reference electrostatic potential, and their difference should be calculated for each conformation. Then, objective functions should be constructed separately, and the objective functions should be minimized to obtain the bond charge parameter values ​​of the molecule to be corrected for the corresponding conformation.

[0052] In one embodiment, the reference electrostatic potentials corresponding to various conformations of the molecule to be corrected are calculated using density functional theory (DFT). The reference electrostatic potentials include the electrostatic potentials at multiple preset lattice points of the molecule. Specifically, the reference electrostatic potential values ​​calculated at the DFT level are calculated for each conformation, and the reference electrostatic potential information (including the preset number of lattice points in the molecule to be corrected, the coordinates of each lattice point, and the corresponding ESP value for each lattice point) can be further output. The electrostatic potential values ​​of the molecule to be corrected obtained through DFT calculation are used to obtain a highly accurate reference electrostatic potential. Then, the difference between the electrostatic potential (calculated using the AM1+BCC method) and the reference electrostatic potential is calculated to determine the accuracy of the bond charge parameters.

[0053] Step 150: Construct an objective function based on the electrostatic potential difference and minimize the objective function to obtain the bond charge parameter values ​​of the molecule to be corrected.

[0054] Based on the electrostatic potential difference, an objective function is constructed and minimized to obtain the current parameter values ​​of the bond charge of the molecule to be corrected, thereby improving the accuracy of the electrostatic potential calculation of the atomic charge in this application. Specifically, the difference between the electrostatic potential information of all conformations of the molecule to be corrected and the corresponding reference electrostatic potential can be used as the electrostatic potential difference value. This can take into account all conformations of the molecule to be corrected, thereby improving the generalization ability, and at the same time, it can reduce the influence of a single conformation on the bond charge parameter, thereby improving the final accuracy of the electrostatic potential calculation.

[0055] This application provides a method for correcting bond charge parameters, which involves: determining the parameter type of the bond charge parameters based on the topological structure of the molecule to be corrected; calculating the charge information of the molecule to be corrected, wherein the charge information is obtained by the AM1 method; calculating the electrostatic potential of the molecule to be corrected based on the charge information, the parameter type of the bond charge parameters, and the initial bond charge parameter values; calculating the electrostatic potential difference between the electrostatic potential to be corrected and the reference electrostatic potential; and constructing and minimizing an objective function based on the electrostatic potential difference to obtain the bond charge parameter values ​​of the molecule to be corrected; that is, determining the bond charge parameters based on the topological structure of the molecule to be corrected. The method determines the parameter type of the molecule to be corrected and calculates the electrostatic potential of the molecule based on its charge information, the parameter type of its bond charge parameters, and the initial bond charge parameter values. It then constructs an objective function by comparing the difference with the reference electrostatic potential and minimizes this objective function to obtain the current bond charge parameter values ​​of the molecule to be corrected. This improves the accuracy of correcting the bond charge parameters, thereby simultaneously improving the accuracy of the molecular electrostatic potential (its error is smaller compared to AM1-BCC charge). Furthermore, it requires less computation, enabling high-throughput calculations and screening at low cost. Additionally, it can calculate elements such as boron and silicon, which were previously uncalculated using AM1-BCC charge.

[0056] In one embodiment, step 130 can be implemented by calculating the electrostatic potential of the molecule to be corrected based on the charge value of the molecule to be corrected, the current parameter value corresponding to the parameter type of the bond charge parameter of the molecule to be corrected, and the position information of the lattice points around the molecule to be corrected and the molecule to be corrected.

[0057] Specifically, the electrostatic potential of the molecule to be corrected is calculated using the following formula:

[0058]

[0059] Among them, V l calcIt is the electrostatic potential of the molecule to be corrected at the l-th lattice point (i.e., the corrected electrostatic potential of the molecule to be corrected at the l-th lattice point). It is the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point. r is the AM1 charge value of the j-th atom in the molecule to be corrected. lj T is the distance between the j-th atom and the l-th lattice point. jα Let p be the matrix of bond relationships of the j-th atom. α γ is the bond charge correction value for parameter type α, N is the total number of atoms in the molecule to be corrected, and γ is the total number of parameter types.

[0060] In one embodiment, step 140 can be implemented by calculating the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected using the following formula:

[0061]

[0062] Among them, V l diff V is the difference between the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point and the reference electrostatic potential. l QM It is the reference electrostatic potential of the molecule to be corrected at the l-th lattice point obtained by DFT calculation. It is the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point. r is the AM1 charge value of the j-th atom. lj It is the distance between the j-th atom and the l-th lattice point.

[0063] Figure 2 This is a flowchart illustrating a method for correcting bond charge parameters provided in another exemplary embodiment of this application. Figure 2 As shown, step 150 above may include:

[0064] Step 151: Construct the objective function.

[0065] The objective function is the sum of squares of the electrostatic potential differences of each preset grid point of the molecule to be corrected. The number and position of the preset grid points can be set as needed. For example, the three-dimensional space structure occupied by the preset grid points can completely contain the grid points of the molecule to be corrected. Specifically, the number of preset grid points corresponding to the molecule to be corrected and the position of each preset grid point can be determined according to the method of calculating the reference electrostatic potential of the molecule to be corrected (such as the DFT method in the prior art).

[0066] Step 152: Minimize the objective function using the minimum gradient method to obtain the bond charge parameter values ​​of the molecule to be corrected.

[0067] In one embodiment, step 152 can be implemented by calculating the bond charge parameter value corresponding to the minimum objective function using the following formula:

[0068]

[0069] Where, χ 2 The objective function to be minimized is... T is the derivative of the objective function. jα T βk The matrices representing the bond relationships between atoms j and k are p. α It is the bond charge correction value for parameter type α, r kl r lj These are the distances between the k-th and j-th atoms and the l-th lattice point, respectively, V. l diff γ is the difference between the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the l-th lattice point and the reference electrostatic potential of the molecule to be corrected. M is the total number of lattice points around the molecule to be corrected, N is the total number of atoms in the molecule to be corrected, and γ is the total number of parameter types.

[0070] Figure 3 This is a flowchart illustrating an exemplary embodiment of the electrostatic potential calculation method based on atomic charge provided in this application. Figure 3 As shown, the method for calculating electrostatic potential based on atomic charge includes the following steps:

[0071] Step 310: Calculate the charge information of the target atom to obtain the charge information of each atom in the target molecule.

[0072] In this process, the target atom is connected to other atoms through chemical bonds to form the target molecule.

[0073] Step 320: Calculate the electrostatic potential of the target molecule based on the charge information of each atom in the target molecule, the bond charge parameters of the target molecule, and the electrostatic potential lattice information of the target molecule.

[0074] The bond charge parameters of the target molecule are obtained using any of the correction methods described above. The bond charge parameters are calculated using the correction methods described in the above embodiments. Based on these calculated bond charge parameters, the electrostatic potential of the target molecule is calculated according to the charge information of each atom in the target molecule, the bond charge parameters of the target molecule, and the electrostatic potential lattice information of the target molecule. This ensures the accuracy of the calculated electrostatic potential of the target molecule while maintaining a low computational load.

[0075] This application provides a method for calculating electrostatic potential based on atomic charge. The method involves: determining the type of bond charge parameters based on the topological structure of the molecule to be corrected; calculating the charge information of the molecule to be corrected, wherein the charge information is obtained by the AM1 method; calculating the electrostatic potential of the molecule to be corrected based on the charge information, the type of bond charge parameters, and the initial bond charge parameter values; calculating the electrostatic potential difference between the electrostatic potential to be corrected and the reference electrostatic potential; and constructing and minimizing an objective function based on the electrostatic potential difference to obtain the bond charge parameter values ​​of the molecule to be corrected. The type of bond charge parameter is determined based on the topological structure of the molecule to be corrected. The electrostatic potential of the molecule to be corrected is calculated based on the charge information, the type of bond charge parameter, and the initial bond charge parameter value. The objective function is constructed by the difference between the objective function and the reference electrostatic potential, and the current bond charge parameter value of the molecule to be corrected is obtained by minimizing the objective function. This improves the accuracy of correcting the bond charge parameter, thereby improving the accuracy of the molecular electrostatic potential (its error is smaller than that of AM1-BCC charge). Furthermore, it requires less computation, thus enabling high-throughput computation and screening at low cost.

[0076] Figure 4 This is a schematic diagram of the structure of a device for correcting bond charge parameters provided in an exemplary embodiment of this application. Figure 4 As shown, the apparatus 40 for correcting bond charge parameters includes: a type determination module 41, used to determine the parameter type of the bond charge parameters of the molecule to be corrected based on the topological structure of the molecule to be corrected; a first calculation module 42, used to calculate the charge information of the molecule to be corrected; wherein the charge information is calculated by the AM1 method; a second calculation module 43, used to calculate the electrostatic potential of the molecule to be corrected based on the charge information of the molecule to be corrected, the parameter type of the bond charge parameters of the molecule to be corrected, and the initial bond charge parameter value of the molecule to be corrected; a difference calculation module 44, used to calculate the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected; and a parameter determination module 45, used to construct an objective function based on the electrostatic potential difference and minimize the objective function to obtain the bond charge parameter value of the molecule to be corrected.

[0077] This application provides an apparatus for correcting bond charge parameters. A type determination module 41 determines the parameter type of the bond charge parameters based on the topological structure of the molecule to be corrected; a first calculation module 42 calculates the charge information of the molecule to be corrected, wherein the charge information is obtained by the AM1 method; a second calculation module 43 calculates the electrostatic potential of the molecule to be corrected based on the charge information, the parameter type of the bond charge parameters, and the initial bond charge parameter values; a difference calculation module 44 calculates the electrostatic potential difference between the electrostatic potential to be corrected and the reference electrostatic potential; and a parameter determination module 45 constructs a parameter based on the electrostatic potential difference. The objective function is constructed and minimized to obtain the bond charge parameter values ​​of the molecule to be corrected. Specifically, the parameter type of the bond charge parameter is determined based on the topology of the molecule to be corrected, and the electrostatic potential of the molecule to be corrected is calculated based on the charge information, the parameter type of the bond charge parameter, and the initial bond charge parameter values. The objective function is constructed and minimized by the difference between the objective function and the reference electrostatic potential to obtain the current bond charge parameter values ​​of the molecule to be corrected, thereby improving the accuracy of correcting the bond charge parameters and thus improving the accuracy of the molecular electrostatic potential. Moreover, the computational cost required is low, thus enabling high-throughput computation and screening at low cost.

[0078] In one embodiment, the type determination module 41 may be further configured to determine the parameter type of the bond charge parameter based on the type of chemical bond of the molecule to be corrected and the type of atoms at both ends of the chemical bond.

[0079] In one embodiment, the first calculation module 42 may be further configured to calculate the charge information of the molecule to be corrected, i.e., the AM1 charge value of each atom in the molecule to be corrected, using a semi-empirical method.

[0080] In one embodiment, the second calculation module 43 may be further configured to: calculate the electrostatic potential of the molecule to be corrected based on the charge value of the molecule to be corrected, the current parameter value corresponding to the parameter type of the bond charge parameter of the molecule to be corrected, and the position information of the grid points around the molecule to be corrected and the molecule to be corrected.

[0081] In one embodiment, the parameter determination module 45 may be further configured to: construct an objective function, wherein the objective function is the sum of squares of the electrostatic potential differences of each preset grid point of the molecule to be corrected; and minimize the objective function using the minimum gradient method to obtain the bond charge parameter values ​​of the molecule to be corrected.

[0082] Figure 5 This is a schematic diagram of the structure of an electrostatic potential calculation device based on atomic charge provided in an exemplary embodiment of this application. Figure 5As shown, the electrostatic potential calculation device 50 includes: a third calculation module 51, used to calculate the charge information of the target atom to obtain the charge information of each atom in the target molecule; wherein the target atom is connected to other atoms through chemical bonds to form the target molecule; and an electrostatic potential calculation module 52, used to calculate the electrostatic potential of the target molecule based on the charge information of each atom in the target molecule, the bond charge parameters of the target molecule, and the electrostatic potential grid information of the target molecule; wherein the bond charge parameters of the target molecule are obtained using any of the above correction methods.

[0083] This application provides an electrostatic potential calculation device based on atomic charge. The device determines the parameter type of the bond charge parameters based on the topological structure of the molecule to be corrected; calculates the charge information of the molecule to be corrected, wherein the charge information is obtained by the AM1 method; calculates the electrostatic potential of the molecule to be corrected based on the charge information, the parameter type of the bond charge parameters, and the initial bond charge parameter values; calculates the electrostatic potential difference between the electrostatic potential to be corrected and the reference electrostatic potential; and constructs and minimizes an objective function based on the electrostatic potential difference to obtain the bond charge parameter values ​​of the molecule to be corrected. In other words, the device determines the parameter type of the bond charge parameters based on the topological structure of the molecule to be corrected, calculates the electrostatic potential of the molecule to be corrected based on the charge information, the parameter type of the bond charge parameters, and the initial bond charge parameter values, and constructs and minimizes the objective function based on the difference between the objective and reference electrostatic potentials. The current bond charge parameter values ​​of the molecule to be corrected are obtained to improve the accuracy of correcting the bond charge parameters, thereby improving the accuracy of the atomic electrostatic potential. Furthermore, the computational complexity is low, enabling high-throughput calculation and screening at low cost. The third calculation module 51 calculates the charge information of the target atom, obtaining the charge information of each atom in the target molecule. The target atom is connected to other atoms through chemical bonds to form the target molecule. The electrostatic potential calculation module 52 calculates the electrostatic potential of the target molecule based on the charge information of each atom in the target molecule, the bond charge parameters of the target molecule, and the electrostatic potential grid information of the target molecule. That is, based on the calculated bond charge parameter values, the electrostatic potential of the target molecule is calculated according to the charge information, the bond charge parameters of the target molecule, and the electrostatic potential grid information of the target molecule, thereby improving the accuracy of the molecular electrostatic potential. The computational complexity is low, enabling high-throughput calculation and screening at low cost.

[0084] Below, for reference Figure 6 This application describes an electronic device according to embodiments thereof. The electronic device may be either or both of a first device and a second device, or a standalone device independent of them, which may communicate with the first device and the second device to receive acquired input signals from them.

[0085] Figure 6 A block diagram of an electronic device according to an embodiment of this application is illustrated.

[0086] like Figure 6 As shown, the electronic device 10 includes one or more processors 11 and memory 12.

[0087] The processor 11 may be a central processing unit (CPU) or other form of processing unit with data processing capabilities and / or instruction execution capabilities, and may control other components in the electronic device 10 to perform desired functions.

[0088] The memory 12 may include one or more computer program products, which may include various forms of computer-readable storage media, such as volatile memory and / or non-volatile memory. The volatile memory may include, for example, random access memory (RAM) and / or cache memory. The non-volatile memory may include, for example, read-only memory (ROM), hard disk, flash memory, etc. One or more computer program instructions may be stored on the computer-readable storage medium, and the processor 11 may execute the program instructions to implement the methods of the various embodiments of this application described above and / or other desired functions. Various contents such as input signals, signal components, and noise components may also be stored in the computer-readable storage medium.

[0089] In one example, the electronic device 10 may also include an input device 13 and an output device 14, which are interconnected via a bus system and / or other forms of connection mechanism (not shown).

[0090] When the electronic device is a standalone device, the input device 13 can be a communication network connector for receiving the collected input signals from the first device and the second device.

[0091] In addition, the input device 13 may also include, for example, a keyboard, a mouse, etc.

[0092] The output device 14 can output various information to the outside, including determined distance information, direction information, etc. The output device 14 may include, for example, a display, a speaker, a printer, and a communication network and its connected remote output devices, etc.

[0093] Of course, for the sake of simplicity, Figure 6 Only some of the components of the electronic device 10 relevant to this application are shown in this illustration; components such as buses, input / output interfaces, etc., are omitted. In addition, the electronic device 10 may include any other suitable components depending on the specific application.

[0094] The computer program product can be written in any combination of one or more programming languages ​​to perform the operations of the embodiments of this application. The programming languages ​​include object-oriented programming languages ​​such as Java and C++, as well as conventional procedural programming languages ​​such as C or similar languages. The program code can be executed entirely on the user's computing device, partially on the user's computing device, as a standalone software package, partially on the user's computing device and partially on a remote computing device, or entirely on a remote computing device or server.

[0095] The computer-readable storage medium may be any combination of one or more readable media. A readable medium may be a readable signal medium or a readable storage medium. A readable storage medium may, for example, include, but is not limited to, electrical, magnetic, optical, electromagnetic, infrared, or semiconductor systems, apparatuses, or devices, or any combination thereof. More specific examples of readable storage media (a non-exhaustive list) include: electrical connections having one or more wires, portable disks, hard disks, random access memory (RAM), read-only memory (ROM), erasable programmable read-only memory (EPROM or flash memory), optical fibers, portable compact disk read-only memory (CD-ROM), optical storage devices, magnetic storage devices, or any suitable combination thereof.

[0096] The above description has been given for purposes of illustration and description. Furthermore, this description is not intended to limit the embodiments of this application to the forms disclosed herein. Although numerous exemplary aspects and embodiments have been discussed above, those skilled in the art will recognize certain variations, modifications, alterations, additions, and sub-combinations thereof.

Claims

1. A method of correcting a key charge parameter, characterized by, The method comprises the following steps: determining the parameter type of the bond charge parameter of the molecule to be corrected according to the topological structure of the molecule to be corrected; calculating the charge information of the molecule to be corrected; wherein the charge information is calculated by the AM1 method; calculating the electrostatic potential of the molecule to be corrected according to the charge information of the molecule to be corrected, the parameter type of the bond charge parameter of the molecule to be corrected and the initial bond charge parameter value of the molecule to be corrected; calculating the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected; and constructing an objective function according to the electrostatic potential difference, and minimizing the objective function to obtain the bond charge parameter value of the molecule to be corrected; wherein the calculation of the electrostatic potential of the molecule to be corrected according to the charge information of the molecule to be corrected, the parameter type of the bond charge parameter of the molecule to be corrected and the initial bond charge parameter value of the molecule to be corrected comprises: calculating the electrostatic potential of the molecule to be corrected according to the charge value of the molecule to be corrected, the current parameter value corresponding to the parameter type of the bond charge parameter of the molecule to be corrected and the position information of the lattice points around the molecule to be corrected and the molecule to be corrected.

2. The method of claim 1, wherein, The calculation of the electrostatic potential of the molecule to be corrected according to the charge value of the molecule to be corrected, the current parameter value corresponding to the parameter type of the bond charge parameter of the molecule to be corrected and the position information of the lattice points around the molecule to be corrected and the molecule to be corrected comprises: wherein, is the electrostatic potential of the molecule to be corrected at the th grid point, is the electrostatic potential of the molecule to be corrected at the th grid point generated by AM1 charge, is the AM1 charge value of the th atom of the molecule to be corrected, is the distance between the th atom and the th grid point, is the matrix of the bonding relationship of the th atom, is the bond charge correction value of the parameter type , and N is the total number of atoms of the molecule to be corrected, is the total number of parameters.

3. The method of claim 1, wherein, The calculation of the electrostatic potential difference between the electrostatic potential of the molecule to be corrected and the reference electrostatic potential of the molecule to be corrected comprises: wherein, is the difference between the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the th grid point and the reference electrostatic potential, is the reference electrostatic potential of the molecule to be corrected at the th grid point obtained by DFT calculation, is the electrostatic potential generated by the AM1 charge of the molecule to be corrected at the th grid point, is the AM1 charge value of the th atom, is the distance between the th atom and the th grid point.

4. The method of claim 1, wherein, The construction of the objective function according to the electrostatic potential difference, and the minimization of the objective function to obtain the bond charge parameter value of the molecule to be corrected comprises: constructing the objective function; wherein the objective function is the sum of squares of the electrostatic potential difference of each preset lattice point of the molecule to be corrected; and minimizing the objective function by using the minimum gradient method to obtain the bond charge parameter value of the molecule to be corrected.

5. The method of claim 4, wherein, The minimization of the objective function by using the minimum gradient method to obtain the bond charge parameter value of the molecule to be corrected comprises: in, The objective function to be minimized is... Let be the derivative of the objective function. , Atoms ,atom A matrix of bond relationships. It is a parameter type The bond charge correction value, , They are the first The atom and the first The atom and the first The distance between grid points It is in the The difference between the electrostatic potential generated by the AM1 charge of the molecule to be corrected at each lattice point and the reference electrostatic potential of the molecule to be corrected, where M is the total number of lattice points around the molecule to be corrected, and N is the total number of atoms in the molecule to be corrected. It represents the total number of parameter types.

6. The method of claim 1, wherein, The determination of the parameter type of the bond charge parameter of the molecule to be corrected according to the topological structure of the molecule to be corrected comprises: determining the parameter type of each bond charge parameter in the molecule to be corrected according to the type of each chemical bond in the molecule to be corrected and the atomic type at both ends of the chemical bond.

7. A method of calculating electrostatic potential based on atomic charge, characterized by, The method comprises the following steps: calculating the charge information of the target atom to obtain the charge information of all atoms in the target molecule; wherein the target atom and other atoms are connected by chemical bonds to form a target molecule; calculating the electrostatic potential of the target molecule according to the charge information of all atoms in the target molecule, the bond charge parameter of the target molecule and the electrostatic potential lattice point information of the target molecule; wherein the bond charge parameter of the target molecule is obtained by the correction method in any one of the above claims 1-6.

8. An apparatus for correcting key charge parameters, characterized by The method comprises the following steps: The type determination module is configured to determine the parameter type of the bond charge parameter of the molecule to be corrected according to the topological structure of the molecule to be corrected. The first calculation module is configured to calculate charge information of the molecule to be corrected, wherein the charge information is calculated by an AM1 method. The second calculation module is configured to calculate an electrostatic potential of the molecule to be corrected according to the charge information of the molecule to be corrected, a parameter type of the bond charge parameter of the molecule to be corrected, and an initial bond charge parameter value of the molecule to be corrected. The difference calculation module is configured to calculate an electrostatic potential difference between the electrostatic potential of the molecule to be corrected and a reference electrostatic potential of the molecule to be corrected. The parameter determination module is configured to construct an objective function according to the electrostatic potential difference, and minimize the objective function to obtain the bond charge parameter value of the molecule to be corrected. The second calculation module is configured to calculate an electrostatic potential of the molecule to be corrected according to the charge information of the molecule to be corrected, a parameter type of the bond charge parameter of the molecule to be corrected, and an initial bond charge parameter value of the molecule to be corrected. The second calculation module is configured to calculate an electrostatic potential of the molecule to be corrected according to the charge information of the molecule to be corrected, a parameter type of the bond charge parameter of the molecule to be corrected, and an initial bond charge parameter value of the molecule to be corrected.

9. An apparatus for calculating electrostatic potential based on atomic charge, characterized by, The third calculation module is configured to calculate charge information of a target atom to obtain respective charge information of all atoms in a target molecule, wherein the target atom and other atoms are connected by chemical bonds to form the target molecule. The electrostatic potential calculation module is configured to calculate an electrostatic potential of the target molecule according to the respective charge information of all atoms in the target molecule, a bond charge parameter of the target molecule, and electrostatic potential grid information of the target molecule, wherein the bond charge parameter of the target molecule is obtained by the correction method in any one of claims 1-6. The storage medium stores a computer program, and the computer program is configured to execute the method for correcting the bond charge parameter in any one of claims 1-6, and / or execute the method for calculating the electrostatic potential based on the atomic charge in claim 7.

10. A computer-readable storage medium, characterized in that, The processor is configured to execute the method for correcting the bond charge parameter in any one of claims 1-6, and / or execute the method for calculating the electrostatic potential based on the atomic charge in claim 7.

11. An electronic device, comprising: ​ ​ ​ ​

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