A method, apparatus, device and medium for calculating interatomic forces

Abstract

The application discloses a kind of interatomic force calculation method, device, equipment and storage medium.It includes: obtaining all atoms of intramolecular constituent acceptor and ligand, and all atoms are grouped to construct atom group, wherein each atom group includes a specified number of atoms respectively;Determine the temporary type value sequence corresponding to each atom group, and obtain the attribute parameters of each atom in the atom group according to the temporary type value sequence;According to the attribute parameters of each atom, the atomic forces of each atom in the atom group are calculated in parallel;According to the atomic force corresponding in each atom group, the interatomic force of intramolecular acceptor and ligand is obtained.The computing power of the equipment is used to group the atoms in the molecule to obtain multiple atom groups, and the atomic forces of each atom in the atom group are calculated in parallel, thereby improving the resource utilization of the computing device, to accurately and efficiently obtain the interatomic force of ligand and acceptor in the molecule.

Description

Technical Field

[0001] This invention relates to the field of communication technology, and in particular to a method, apparatus, device, and medium for calculating interatomic forces. Background Technology

[0002] Molecular docking simulations are commonly used in molecular modeling to guide the stable binding sites of one molecule to another. These simulations are primarily used to predict the binding sites of candidate drugs to specific proteins through computer simulations of biochemical experiments.

[0003] Molecular docking simulations typically involve calculating intramolecular atomic forces. However, current methods for calculating atomic forces usually employ a serial calculation process, which significantly reduces the utilization rate of computing devices when their resources are limited. Summary of the Invention

[0004] This invention provides a method, apparatus, device, and storage medium for calculating interatomic forces, so as to accurately and efficiently obtain intramolecular interatomic forces.

[0005] According to one aspect of the present invention, a method for calculating interatomic forces is provided, comprising: obtaining all atoms constituting acceptors and ligands within a molecule, and grouping the all atoms into atomic groups, wherein each atomic group includes a specified number of atoms;

[0006] Determine the temporary type value sequence corresponding to each of the atomic groups, and obtain the attribute parameters of each atom in the atomic group according to the temporary type value sequence;

[0007] The atomic forces of each atom within the atom group are calculated in parallel based on the property parameters of each atom.

[0008] The interatomic forces between the intramolecular receptor and ligand are obtained based on the corresponding atomic forces within each atomic group.

[0009] According to another aspect of the present invention, a device for calculating interatomic forces is provided, comprising:

[0010] An atom group construction module is used to obtain all the atoms that constitute the receptor and ligand within the molecule, and to group all the atoms into atom groups, wherein each atom group includes a specified number of atoms;

[0011] The atom attribute parameter acquisition module is used to determine the temporary type value sequence corresponding to each of the atom groups, and to acquire the attribute parameters of each atom in the atom group according to the temporary type value sequence;

[0012] The module for calculating the interaction forces of each atom is used to calculate the interaction forces of each atom in the group of atoms in parallel based on the property parameters of each atom.

[0013] The module for obtaining the interatomic interaction force between the receptor and ligand is used to obtain the interatomic interaction force between the intramolecular receptor and ligand based on the corresponding atomic interaction force within each atomic group.

[0014] According to another aspect of the present invention, a computer device is provided, the computer device comprising:

[0015] At least one processor; and

[0016] A memory communicatively connected to the at least one processor; wherein,

[0017] The memory stores a computer program that can be executed by the at least one processor, which is then executed by the at least one processor to enable the at least one processor to perform a crane operation alarm method according to any embodiment of the present invention.

[0018] According to another aspect of the present invention, a computer-readable storage medium is provided, the computer-readable storage medium storing computer instructions, the computer instructions being configured to cause a processor to execute and implement a crane operation alarm method according to any embodiment of the present invention.

[0019] The technical solution of this invention improves the resource utilization of the computing device by grouping the atoms in the molecule into multiple atomic groups through the computing power of the device, and calculating the atomic interaction forces of each atom in the atomic group in parallel, thereby achieving accurate and efficient acquisition of the interaction forces between ligand and acceptor atoms in the molecule.

[0020] It should be understood that the description in this section is not intended to identify key or essential features of the embodiments of the present invention, nor is it intended to limit the scope of the invention. Other features of the invention will become readily apparent from the following description. Attached Figure Description

[0021] To more clearly illustrate the technical solutions in the embodiments of the present invention, the accompanying drawings used in the description of the embodiments will be briefly introduced below. Obviously, the accompanying drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0022] Figure 1 This is a flowchart of a method for calculating interatomic forces according to Embodiment 1 of the present invention;

[0023] Figure 2This is a flowchart of a method for calculating interatomic forces according to Embodiment 2 of the present invention;

[0024] Figure 3 This is a schematic diagram of the structure of a calculation device for interatomic forces provided in Embodiment 3 of the present invention;

[0025] Figure 4 This is a schematic diagram of the structure of an electronic device provided in Embodiment 4 of the present invention. Detailed Implementation

[0026] To enable those skilled in the art to better understand the present invention, the technical solutions of the present invention will be clearly and completely described below with reference to the accompanying drawings of the embodiments of the present invention. Obviously, the described embodiments are only some embodiments of the present invention, and not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort should fall within the scope of protection of the present invention.

[0027] It should be noted that the terms "first," "second," etc., in the specification, claims, and accompanying drawings of this invention are used to distinguish similar objects and are not necessarily used to describe a specific order or sequence. It should be understood that such data can be interchanged where appropriate so that the embodiments of the invention described herein can be implemented in orders other than those illustrated or described herein. Furthermore, "comprising" and "having," and any variations thereof, are intended to cover non-exclusive inclusion; for example, a process, method, apparatus, product, or device that includes a series of steps or units is not necessarily limited to those steps or units explicitly listed, but may include other steps or units not explicitly listed or inherent to such processes, methods, products, or devices.

[0028] Example 1

[0029] Figure 1 This is a flowchart illustrating a method for calculating interatomic forces according to Embodiment 1 of the present invention. This embodiment is applicable to calculating the interatomic forces between acceptors and ligands within a molecule. This method can be executed by an interatomic force calculation device, which can be implemented in hardware and / or software and integrated into an electronic device. Figure 1 As shown, the method includes:

[0030] Step S101: Obtain all atoms that constitute the receptor and ligand within the molecule, and group all atoms to construct an atom group.

[0031] Optionally, all atoms can be grouped to construct atomic groups, including: obtaining the instruction slot width of the current computing device and the data bit width occupied by each atomic operation; determining a specified number based on the instruction slot width and data bit width; and grouping all atoms sequentially according to the specified number to construct atomic groups.

[0032] Specifically, in this embodiment, the receptor used for atomic force calculation includes both receptors and ligands, which are typically composed of a large number of atoms. For example, a receptor may contain 120 atoms, and a ligand may contain 200 atoms, resulting in a total of 320 atoms constituting the receptor and ligand within the molecule. After obtaining all 320 atoms within the molecule, the atoms are grouped into multiple atom groups based on the resource capacity of the computing device. The data width occupied by a single atom operation is a double-precision floating-point number, or 64 bits. In this embodiment, the instruction slot width of the computing device performing the operation is 512 bits. Therefore, in this embodiment, the computing device can perform parallel calculations on 8 atoms simultaneously in one operation. Thus, the 320 atoms identified in the molecule can be grouped sequentially into groups of 8 atoms each, resulting in 40 atom groups. Therefore, each atom group includes a specified number of 8 atoms. Of course, this embodiment is merely an example and does not limit the specific number of atoms contained in each atom group. The specific number can be determined based on the specific computing resources of the computing device.

[0033] Step S102: Determine the temporary type value sequence corresponding to each atom group, and obtain the attribute parameters of each atom in the atom group according to the temporary type value sequence.

[0034] Optionally, determining the temporary type value sequence corresponding to each atom group includes: obtaining the original type value of each atom in the atom group, and obtaining the original type value sequence corresponding to the atom group based on the original type value, wherein the original type value is used to indicate the type to which the atom belongs; determining whether the original type value sequence contains a target atom greater than 32, if so, obtaining the qualified type value corresponding to the target atom, and replacing the original type value of the target atom with the qualified type value to obtain the temporary type value sequence; otherwise, directly using the original type value sequence as the temporary type value sequence.

[0035] Optionally, after obtaining the original type values ​​of each atom in the atom group, the method further includes: determining whether the ligand is a macrocyclic compound; if so, modifying the original type values ​​of the specified atom in the atom group according to the qualified values; otherwise, keeping the original type values ​​of each atom in the atom group unchanged.

[0036] Specifically, in this embodiment, after obtaining multiple atomic groups through grouping, the atomic forces within each group are calculated in parallel. For example, when two atomic groups are determined, such as atomic group a and atomic group b, and each atomic group contains 8 atoms, this embodiment will use the parallel calculation of atomic forces within atomic group a as an example. For the 8 atoms in atomic group a, the original type value, i.e., the XS type value, of each atom is first obtained. The original type value is used to indicate the type to which the atom belongs, for example, 1 for H atoms, 2 for O atoms, etc. Of course, this embodiment is only an example and does not limit the specific value of the original type value of each atom. In addition, this embodiment also determines whether the ligand is a macrocyclic compound. If the ligand is a macrocyclic compound, the original type values ​​of some atoms need to be modified. For example, 20 / 23 / 26 / 29 is changed to 1, and the original type values ​​21 / 24 / 27 / 30 are changed to 2. The reason for this modification is that atoms numbered 20 / 23 / 26 / 29 and atom numbered 1 have the same characteristics when calculating atomic forces. Therefore, unifying the original type values ​​simplifies the subsequent calculation of atomic forces. When it is determined that the ligand is not a macrocyclic compound, there is no need to modify the original type values ​​of each atom.

[0037] It is worth mentioning that, in this embodiment, after determining the original type values ​​of each atom within atom group a, these original type values ​​can be modified or unmodified. Based on the determined original type values, a sequence of original type values ​​corresponding to atom group a is obtained. For example, the original type value sequence is XS = {122314164833}. Furthermore, after obtaining the original type value sequence, it is determined whether the original type value sequence contains a target atom greater than 32. If it is determined to exist, the qualified type value corresponding to the target atom is obtained, and the qualified type value replaces the original type value of the target atom. For example, the original type value of the 8th atom in the obtained original type value sequence is 33, which is greater than 32. Since the original type values ​​of the other 7 atoms are all different, the qualified type value can be randomly selected from 1 to 7. For example, when the qualified type value is determined to be 4, the obtained temporary type value sequence is XS' = {12231416484}. Of course, this embodiment is only an example and does not limit the specific value of the qualified type value. When there are no atoms greater than 32 in the original type value sequence, for example, when the original type value sequence is XS = {12231416486}, the above original type value sequence is directly used as the temporary type value sequence, that is, XS' = XS = {12231416486}.

[0038] Optionally, the attribute parameters of each atom in the atom group are obtained based on the temporary type value sequence, including: obtaining an attribute parameter grid table, wherein the attribute parameter grid table includes multiple information tables recording the attribute parameters of atoms; for each atom in the atom group, determining the matching type value from the temporary type value sequence, and determining the target information table corresponding to the atom based on the type value; obtaining the grid coordinates of the grid point closest to the atom, determining the target position in the target information table based on the grid coordinates, and using the information recorded at the target position as the attribute parameter of the atom.

[0039] Specifically, in this embodiment, a property parameter grid table is pre-determined using a fitting algorithm before atomic interaction. Since obtaining the property parameter grid table through a fitting algorithm is not the focus of this application, it will not be elaborated upon here. The property parameter grid table includes multiple information tables recording atomic property parameters. Specifically, the property parameter grid table can be a spatial table of N1*N2*8, where N1 represents the number of atom types in the ligand-acceptor pair. For example, if the temporary type value sequence is XS' = {12231416484}, the number of atom types can be determined to be 7. N2 represents the length determined based on the length, width, and height of the docking box. For each atom, its position n1 in N1 is first determined based on the type value matched in the temporary type value sequence XS'. Then, the grid coordinates of the grid point with the smallest distance from its coordinates are found, and its position in N2 is determined based on these grid coordinates.

[0040] For example, if the type value matched by the first atom in the temporary type value sequence XS' is 1, then the information table with the sequence number 1 is found among multiple information tables, and the table with the sequence number 1 is used as the target information table n1. Since atoms have spatial positions, the grid coordinates [x0 y0 z0] of the grid point a closest to the atom are determined according to the previously defined grid space. Then, the target position n2 in the target information table is found based on point a, for example, 2. That is, the information recorded in the second row of the target information table is used as the attribute parameters of the atom. Since each information table contains 8 columns, that is, the attribute parameters specifically contain 8 types of parameters, and the 8 types of parameters are related to the calculation of atomic interaction forces, this embodiment does not limit the specific types of the 8 types of parameters.

[0041] Step S103: Calculate the atomic forces of each atom in the atomic group in parallel based on the property parameters of each atom.

[0042] In this embodiment, after obtaining the attribute parameters of each atom in atom group a, the eight atoms are calculated in parallel according to their respective determined attribute parameters to obtain the atomic forces of each atom in atom group a. However, the atomic forces determined at this time are based on a temporary type value sequence, and some atoms do not generate forces, so there may be virtual forces. When calculating the interatomic forces between the acceptor and ligand later, these virtual forces need to be deleted.

[0043] Step S104: Obtain the interatomic forces of the intramolecular acceptor and ligand based on the corresponding atomic forces within each atomic group.

[0044] Optionally, the interatomic forces between the intramolecular acceptor and ligand are obtained based on the atomic forces corresponding to each atomic group. This includes: determining whether the original type value sequence and the temporary type value sequence corresponding to each atomic group are the same; if so, determining the force sequence based on the atomic forces corresponding to each atomic group; otherwise, determining the target qualified type value in the temporary type value sequence corresponding to each atomic group that is different from the corresponding position in the original type value sequence, determining the target atom corresponding to the target qualified type value, and modifying the atomic force corresponding to the target atom to 0; determining the force sequence based on the modified atomic forces corresponding to each atomic group; and summing the atomic forces in the force sequence to obtain the interatomic forces between the intramolecular acceptor and ligand.

[0045] Specifically, in this embodiment, after obtaining the atomic forces of each atom within atom group a, due to the existence of virtual forces, it is necessary to identify the virtual forces. Specifically, this involves determining whether the original type value sequence and the temporary type value sequence corresponding to each atom group a are the same. For example, if the original type value sequence of atom group a is determined to be XS = {12231416486} and XS' = {12231416486}, and they are the same, then the force sequence F1 = {34352179} is directly determined based on the forces corresponding to each atom, and this force sequence does not contain virtual forces. However, if the original type value sequence is XS = {12231416486}... 833}, the temporary type value sequence is XS'={12231416484}, from which it can be concluded that the two are different. Since the temporary force sequence F1'={343521716} is determined by calculation based on the above temporary type value sequence, it contains virtual force. Since the type value of the 8th atom in XS' and XS is different, the 8th atom is taken as the target atom. Since the temporary type value sequence and the temporary force sequence are one-to-one, the virtual force corresponding to the target atom in the temporary force sequence, i.e., 16, is modified to 0, thereby obtaining the atomic force sequence F1={34352170}.

[0046] It should be noted that this embodiment uses the acquisition of the force sequence of atomic group a as an example. The method for acquiring the force sequence of atomic group b is roughly the same, and will not be repeated in this embodiment. For example, when the atomic force sequence corresponding to atomic group b is determined to be F2 = {15246381}, and F1 = {34352170}, the forces in the above two sets of force sequences are added together to obtain the interatomic force between the acceptor and ligand within the molecule, F = 55. Of course, this embodiment only uses the grouping of all atoms in the molecule to obtain two atomic groups as an example. When the number of atomic groups is other, the method for obtaining the interatomic forces is roughly the same, and will not be repeated in this embodiment.

[0047] This embodiment utilizes the computing power of the device to group the atoms within the molecule into multiple atomic groups, and calculates the atomic interaction forces of each atom within the atomic group in parallel, thereby improving the resource utilization of the computing device and achieving accurate and efficient acquisition of the interaction forces between ligand and acceptor atoms within the molecule.

[0048] Example 2

[0049] Figure 2This is a flowchart of the method for calculating interatomic forces provided in Embodiment 2 of the present invention. Based on the above embodiments, the method of calculating the atomic forces of each atom in parallel according to the property parameters of each atom is specifically described, such as... Figure 2 As shown, the method includes:

[0050] Step S201: Obtain all atoms that constitute the receptor and ligand within the molecule, and group all atoms to construct an atom group.

[0051] Optionally, all atoms can be grouped to construct atomic groups, including: obtaining the instruction slot width of the current computing device and the data bit width occupied by each atomic operation; determining a specified number based on the instruction slot width and data bit width; and grouping all atoms sequentially according to the specified number to construct atomic groups.

[0052] Step S202: Determine the temporary type value sequence corresponding to each atom group, and obtain the attribute parameters of each atom in the atom group according to the temporary type value sequence.

[0053] Optionally, determining the temporary type value sequence corresponding to each atom group includes: obtaining the original type value of each atom in the atom group, and obtaining the original type value sequence corresponding to the atom group based on the original type value, wherein the original type value is used to indicate the type to which the atom belongs; determining whether the original type value sequence contains a target atom greater than 32, if so, obtaining the qualified type value corresponding to the target atom, and replacing the original type value of the target atom with the qualified type value to obtain the temporary type value sequence; otherwise, directly using the original type value sequence as the temporary type value sequence.

[0054] Optionally, after obtaining the original type values ​​of each atom in the atom group, the method further includes: determining whether the ligand is a macrocyclic compound; if so, modifying the original type values ​​of the specified atom in the atom group according to the qualified values; otherwise, keeping the original type values ​​of each atom in the atom group unchanged.

[0055] Optionally, the attribute parameters of each atom in the atom group are obtained based on the temporary type value sequence, including: obtaining an attribute parameter grid table, wherein the attribute parameter grid table includes multiple information tables recording the attribute parameters of atoms; for each atom in the atom group, determining the matching type value from the temporary type value sequence, and determining the target information table corresponding to the atom based on the type value; obtaining the grid coordinates of the grid point closest to the atom, determining the target position in the target information table based on the grid coordinates, and using the information recorded at the target position as the attribute parameter of the atom.

[0056] Step S203: Obtain the intermediate results corresponding to each atom by parallel calculation based on the property parameters of each atom.

[0057] Specifically, in this embodiment, after obtaining the attribute parameters of each atom, a comparison and selection instruction is used to calculate the atomic force of each atom. Therefore, the calculation of the atomic force of each atom is performed step by step in the process of calculating based on the attribute parameters. There will inevitably be intermediate results before the final force is obtained. For example, atom m obtains the intermediate result W after calculation.

[0058] Step S204: Determine whether the intermediate results of each atom meet the specified requirements. If yes, proceed to step S205; otherwise, proceed to step S206.

[0059] When different atoms have the same intermediate result, the intermediate result W will be compared with a specified value, such as to determine whether W is less than 0. Based on the comparison result, different calculation methods will be used for subsequent calculations.

[0060] Step S205: Calculate and obtain atomic interaction forces based on intermediate results and the first type of calculation operation.

[0061] When W is less than 0, the first type of calculation operation will continue. For example, the first type of calculation operation is an addition operation, which is to add the intermediate result W with the next attribute parameter to obtain the atomic force.

[0062] Step S206: Calculate and obtain atomic interaction forces based on intermediate results and the second type of calculation operation.

[0063] When W is greater than 0, a second type of calculation operation will be performed. This second type of operation differs from the first; for example, it might be a subtraction operation, subtracting the intermediate result W from the next attribute parameter to obtain the atomic force. This embodiment uses two types of calculation operations as an example. In practical applications, multiple operation types may exist. For instance, the intermediate result sequence might be subjected to operations A, B, or C, resulting in three result sequences named a, b, and c. Two comparison selection instructions are then performed: if W is greater than 0, select b; otherwise, select a; if W is greater than 10, select c; otherwise, leave it unchanged. This ensures that the calculation logic for all atoms remains consistent during the force calculation. This embodiment is merely illustrative and does not limit the specific calculation operation corresponding to the comparison selection instructions.

[0064] Step S207: Obtain the interatomic forces of the intramolecular acceptor and ligand based on the corresponding atomic forces within each atomic group.

[0065] Optionally, the interatomic forces between the intramolecular acceptor and ligand are obtained based on the atomic forces corresponding to each atomic group. This includes: determining whether the original type value sequence and the temporary type value sequence corresponding to each atomic group are the same; if so, determining the force sequence based on the atomic forces corresponding to each atomic group; otherwise, determining the target qualified type value in the temporary type value sequence corresponding to each atomic group that is different from the corresponding position in the original type value sequence, determining the target atom corresponding to the target qualified type value, and modifying the atomic force corresponding to the target atom to 0; determining the force sequence based on the modified atomic forces corresponding to each atomic group; and summing the atomic forces in the force sequence to obtain the interatomic forces between the intramolecular acceptor and ligand.

[0066] This embodiment utilizes the computing power of the device to group the atoms within the molecule into multiple atomic groups, and calculates the atomic interaction forces of each atom within the atomic group in parallel, thereby improving the resource utilization of the computing device and achieving accurate and efficient acquisition of the interaction forces between ligand and acceptor atoms within the molecule.

[0067] Example 3

[0068] Figure 3 This is a schematic diagram of the structure of a calculation device for interatomic forces provided in Embodiment 3 of the present invention. Figure 3 As shown, the device includes: an atom assembly construction module 310, an atom property parameter acquisition module 320, an atom interaction force calculation module 330, and an acceptor-ligand interatomic interaction force acquisition module 340.

[0069] The atom group construction module 310 is used to obtain all the atoms that constitute the acceptor and ligand within the molecule, and to group all the atoms to construct atom groups, wherein each atom group includes a specified number of atoms;

[0070] The atom attribute parameter acquisition module 320 is used to determine the temporary type value sequence corresponding to each atom group, and to obtain the attribute parameters of each atom in the atom group according to the temporary type value sequence;

[0071] The atomic force calculation module 330 is used to calculate the atomic forces of each atom in the atomic group in parallel based on the property parameters of each atom.

[0072] The interatomic interaction force acquisition module 340 for receptors and ligands is used to acquire the interatomic interaction forces between receptors and ligands within the molecule based on the corresponding atomic interaction forces within each atomic group.

[0073] Optional, the atom group building module is used to group all atoms to build atom groups, including:

[0074] Obtain the instruction slot width of the current computing device and the data bit width occupied by each atomic operation;

[0075] The specified quantity is determined based on the instruction slot width and data bit width;

[0076] All atoms are grouped sequentially according to a specified number to construct an atom group.

[0077] Optionally, the atom attribute parameter acquisition module includes a temporary type value sequence determination unit, which is used to acquire the original type value of each atom in the atom group, and acquire the original type value sequence corresponding to the atom group based on the original type value, wherein the original type value is used to indicate the type to which the atom belongs;

[0078] Determine whether the original type value sequence contains a target atom greater than 32. If so, obtain the qualified type value corresponding to the target atom and replace the original type value of the target atom with the qualified type value to obtain a temporary type value sequence.

[0079] Otherwise, the original type value sequence is directly used as the temporary type value sequence.

[0080] Optionally, the apparatus further includes an original type value determination unit, used to determine whether the ligand is a macrocyclic compound; if so, the original type value of a specified atom within the atom group is modified according to the qualified value.

[0081] Otherwise, keep the original type values ​​of each atom in the atom group unchanged.

[0082] Optionally, the atom attribute parameter acquisition module includes an attribute parameter acquisition unit for acquiring an attribute parameter grid table, wherein the attribute parameter grid table includes multiple information tables that record the atom attribute parameters;

[0083] For each atom within an atom group, the matching type value is determined from the temporary type value sequence, and the target information table corresponding to the atom is determined based on the type value;

[0084] Obtain the grid coordinates of the grid point closest to the atom, determine the target location in the target information table based on the grid coordinates, and use the information recorded at the target location as the atom's attribute parameters.

[0085] Optionally, a module for calculating the interaction forces of each atom is provided to obtain intermediate results for each atom in parallel based on the property parameters of each atom.

[0086] Determine whether the intermediate results for each atom meet the specified requirements. If so, calculate and obtain the atomic forces based on the intermediate results and the first type of calculation operation.

[0087] Otherwise, atomic forces are calculated based on intermediate results and the second type of computational operation, where the first type of computational operation and the second type of computational operation are different.

[0088] Optionally, an interatomic interaction force acquisition module for receptors and ligands is used to determine whether the original type value sequence and the temporary type value sequence corresponding to each atomic group are the same. If so, the interaction force sequence is determined based on the atomic interaction forces corresponding to each atomic group.

[0089] Otherwise, determine the target qualified type value in the temporary type value sequence corresponding to each atom group that is different from the corresponding position in the original type value sequence, determine the target atom corresponding to the target qualified type value, modify the atomic force corresponding to the target atom to 0, and determine the force sequence according to the modified atomic force in each atom group;

[0090] The interatomic forces of the receptors and ligands within the molecule are obtained by summing the forces of each atom in the force sequence.

[0091] The interatomic force calculation device provided in the embodiments of the present invention can execute the interatomic force calculation method provided in any embodiment of the present invention, and has the corresponding functional modules and beneficial effects of the method execution.

[0092] Example 4

[0093] Figure 4 A schematic diagram of an electronic device 10, which can be used to implement embodiments of the present invention, is shown. The electronic device is intended to represent various forms of digital computers, such as laptop computers, desktop computers, workstations, personal digital assistants, servers, blade servers, mainframe computers, and other suitable computers. The electronic device can also represent various forms of mobile devices. The components shown herein, their connections and relationships, and their functions are merely illustrative and are not intended to limit the implementation of the invention described and / or claimed herein.

[0094] The components shown herein, their connections and relationships, and their functions are merely examples and are not intended to limit the implementation of the invention described and / or claimed herein.

[0095] like Figure 4As shown, the electronic device 10 includes at least one processor 11 and a memory, such as a read-only memory (ROM) 12 or a random access memory (RAM) 13, communicatively connected to the at least one processor 11. The memory stores computer programs executable by the at least one processor. The processor 11 can perform various appropriate actions and processes based on the computer program stored in the ROM 12 or loaded from storage unit 18 into the RAM 13. The RAM 13 may also store various programs and data required for the operation of the electronic device 10. The processor 11, ROM 12, and RAM 13 are interconnected via a bus 14. An input / output (I / O) interface 15 is also connected to the bus 14.

[0096] Multiple components in electronic device 10 are connected to I / O interface 15, including: input unit 16, such as keyboard, mouse, etc.; output unit 17, such as various types of displays, speakers, etc.; storage unit 18, such as disk, optical disk, etc.; and communication unit 19, such as network card, modem, wireless transceiver, etc. Communication unit 19 allows electronic device 10 to exchange information / data with other devices through computer networks such as the Internet and / or various telecommunications networks.

[0097] Processor 11 can be a variety of general-purpose and / or special-purpose processing components with processing and computing capabilities. Some examples of processor 11 include, but are not limited to, a central processing unit (CPU), a graphics processing unit (GPU), various special-purpose artificial intelligence (AI) computing chips, various processors running machine learning model algorithms, digital signal processors (DSPs), and any suitable processor, controller, microcontroller, etc. Processor 11 performs the various methods and processes described above, such as methods for calculating interatomic forces.

[0098] In some embodiments, the method for calculating interatomic forces may be implemented as a computer program tangibly contained in a computer-readable storage medium, such as storage unit 18. In some embodiments, part or all of the computer program may be loaded and / or installed on device 10 via ROM 12 and / or communication unit 19. When the computer program is loaded into RAM 13 and executed by processor 11, one or more steps of the method for calculating interatomic forces described above may be performed. Alternatively, in other embodiments, processor 11 may be configured to perform the method for calculating interatomic forces by any other suitable means (e.g., by means of firmware).

[0099] Various embodiments of the apparatuses and techniques described above herein can be implemented in digital electronic circuit devices, integrated circuit devices, field-programmable gate arrays (FPGAs), application-specific integrated circuits (ASICs), application-specific standard products (ASSPs), device-on-a-chip (SoC) devices, complex programmable logic devices (CPLDs), computer hardware, firmware, software, and / or combinations thereof. These various embodiments may include implementations in one or more computer programs that can be executed and / or interpreted on a programmable device including at least one programmable processor, which may be a dedicated or general-purpose programmable processor, capable of receiving data and instructions from a storage device, at least one input device, and at least one output device, and transmitting data and instructions to the storage device, the at least one input device, and the at least one output device.

[0100] Computer programs used to implement the methods of the present invention can be written in any combination of one or more programming languages. These computer programs can be provided to a processor of a general-purpose computer, a special-purpose computer, or other programmable overhead crane operation alarm device, such that when executed by the processor, the computer programs cause the functions / operations specified in the flowcharts and / or block diagrams to be implemented. The computer programs can be executed entirely on the machine, partially on the machine, as a standalone software package partially on the machine and partially on a remote machine, or entirely on a remote machine or server.

[0101] In the context of this invention, a computer-readable storage medium can be a tangible medium that may contain or store a computer program for use by or in conjunction with an instruction execution means, apparatus, or device. A computer-readable storage medium may include, but is not limited to, electronic, magnetic, optical, electromagnetic, infrared, or semiconductor devices, apparatus, or devices, or any suitable combination thereof. Alternatively, a computer-readable storage medium may be a machine-readable signal medium. More specific examples of machine-readable storage media include electrical connections based on one or more wires, portable computer 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.

[0102] To provide interaction with a user, the apparatus and techniques described herein can be implemented on a device having: a display device (e.g., a touchscreen) for displaying information to the user; and buttons through which the user can provide input to the device. Other types of apparatus can also be used to provide interaction with the user; for example, feedback provided to the user can be any form of sensory feedback (e.g., visual feedback, auditory feedback, or haptic feedback); and input from the user can be received in any form (including voice input, speech input, or haptic input).

[0103] It should be understood that the various forms of processes shown above can be used, with steps reordered, added, or deleted. For example, the steps described in this invention can be executed in parallel, sequentially, or in different orders, as long as the desired result of the technical solution of this invention can be achieved, and this is not limited herein.

[0104] The specific embodiments described above do not constitute a limitation on the scope of protection of this invention. Those skilled in the art should understand that various modifications, combinations, sub-combinations, and substitutions can be made according to design requirements and other factors. Any modifications, equivalent substitutions, and improvements made within the spirit and principles of this invention should be included within the scope of protection of this invention.

Claims

1. A method of calculating interatomic forces, characterized by, The method comprises the following steps: acquiring all atoms constituting a receptor and a ligand in a molecule, and grouping the atoms to form atom groups, wherein each atom group comprises a specified number of atoms; determining a temporary type value sequence corresponding to each atom group, and acquiring attribute parameters of each atom in the atom group according to the temporary type value sequence; calculating atom interaction forces of each atom in the atom group in parallel according to the attribute parameters of each atom; acquiring atom interaction forces between the receptor and the ligand in the molecule according to the atom interaction forces corresponding to each atom group; the grouping of the atoms to form atom groups comprises the following steps: acquiring an instruction slot width of a current computing device and a data width occupied by each atom operation; determining the specified number according to the instruction slot width and the data width; and grouping the atoms in sequence according to the specified number to form the atom groups; the determination of the temporary type value sequence corresponding to each atom group comprises the following steps: acquiring original type values of each atom in the atom group, and acquiring an original type value sequence corresponding to the atom group according to the original type values, wherein the original type values are used to indicate the types to which the atoms belong; judging whether the original type value sequence contains a target atom greater than 32, if yes, acquiring a qualified type value corresponding to the target atom, and replacing the original type value of the target atom with the qualified type value to acquire the temporary type value sequence; otherwise, directly taking the original type value sequence as the temporary type value sequence.

2. The method of claim 1, wherein, after the acquisition of the original type values of each atom in the atom group, the method further comprises the following steps: judging whether the ligand is a macrocyclic compound, if yes, modifying the original type values of specified atoms in the atom group according to qualified values, otherwise, keeping the original type values of each atom in the atom group unchanged.

3. The method of claim 1, wherein, the acquisition of the attribute parameters of each atom in the atom group according to the temporary type value sequence comprises the following steps: acquiring an attribute parameter grid point table, wherein the attribute parameter grid point table comprises a plurality of information tables recording atom attribute parameters; for each atom in the atom group, determining a matched type value from the temporary type value sequence, and determining a target information table corresponding to the atom according to the type value; acquiring a grid point coordinate of a grid point closest to the atom, determining a target position in the target information table according to the grid point coordinate, and taking information recorded at the target position as the attribute parameters of the atom.

4. The method of claim 1, wherein, the parallel calculation of the atom interaction forces of each atom in the atom group according to the attribute parameters of each atom comprises the following steps: parallel calculation of intermediate results corresponding to each atom according to the attribute parameters of each atom; judging whether the intermediate results of each atom meet specified requirements, if yes, calculating the atom interaction forces according to the intermediate results and a first type of calculation operation, otherwise, calculating the atom interaction forces according to the intermediate results and a second type of calculation operation, wherein the first type of calculation operation and the second type of calculation operation are different.

5. The method of claim 1, wherein, The atomic interaction force between the receptor and the ligand in the molecule is obtained according to the atomic interaction force corresponding to each atomic group, and the method comprises the following steps: It is determined whether the original type value sequence corresponding to each atomic group and the temporary type value sequence are the same, if yes, the force sequence is determined according to the atomic interaction force corresponding to each atomic group; Otherwise, the target qualified type value which is different from the original type value sequence in the corresponding position of the temporary type value sequence corresponding to each atomic group is determined, the target atom corresponding to the target qualified type value is determined, the atomic interaction force corresponding to the target atom is modified to 0, and the force sequence is determined according to the modified atomic interaction force corresponding to each atomic group; The atomic interaction force between the receptor and the ligand in the molecule is obtained according to the atomic interaction force corresponding to each atomic group, and the method comprises the following steps:

6. An apparatus for calculating interatomic forces, characterized by It comprises: The atomic group construction module is used to obtain all atoms constituting the receptor and the ligand in the molecule, and the all atoms are grouped to construct atomic groups, wherein each atomic group comprises a specified number of atoms; The attribute parameter acquisition module of the atom is used to determine the temporary type value sequence corresponding to each atomic group, and the attribute parameter of each atom in the atomic group is obtained according to the temporary type value sequence; The atomic interaction force between the receptor and the ligand in the molecule is obtained according to the atomic interaction force corresponding to each atomic group, and the method comprises the following steps: The atomic interaction force between the receptor and the ligand in the molecule is obtained according to the atomic interaction force corresponding to each atomic group, and the method comprises the following steps: The atomic group construction module is also used to obtain the instruction slot width of the current computing device and the data width occupied by each atomic operation; the specified number is determined according to the instruction slot width and the data width; the all atoms are sequentially grouped according to the specified number to construct the atomic groups; The attribute parameter acquisition module of the atom is used to obtain the original type value of each atom in the atomic group, and the original type value sequence corresponding to the atomic group is obtained according to the original type value, wherein the original type value is used to indicate the type to which the atom belongs; It is determined whether the original type value sequence contains a target atom greater than 32, if yes, the qualified type value corresponding to the target atom is obtained, and the qualified type value is replaced with the original type value of the target atom to obtain the temporary type value sequence; Otherwise, the original type value sequence is directly taken as the temporary type value sequence.

7. A computer device comprising a memory, a processor, and a computer program stored on the memory and executable on the processor, characterized in that, The processor executes the program to realize the method in any one of claims 1-5.

8. A storage medium of computer executable instructions, on which a computer program is stored, characterized in that, The program is executed by the processor to realize the method in any one of claims 1-5.

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