Method, apparatus, design method and electronic device for determining neighboring molecules

Abstract

The application relates to a method and device for determining adjacent molecules, a design method and electronic equipment. The method comprises the following steps: determining a first distance between each two molecular models in M molecular models; and if the first distance between each two molecular models in N molecular models is greater than a first distance threshold, determining adjacent molecules from Q target molecules in the M molecules except the N molecules, wherein M, N and Q are integers greater than zero, and M is greater than or equal to N. The scheme provided by the application can reduce the computing resources consumed for determining adjacent molecules and improve the response speed.

Description

TECHNICAL FIELD

[0001] The present application relates to the technical field of computer simulation, and in particular, to a method and device for determining adjacent molecules, a design method and an electronic device. BACKGROUND

[0002] With the rapid development of computer technology and basic discipline theory, the computing efficiency and accuracy of molecular simulation have been greatly improved, making molecular simulation widely used in various disciplines. Among them, determining adjacent molecules is an important part of molecular simulation.

[0003] In related technologies, in order to determine whether each molecule is adjacent, the distance between all atoms of each molecule is calculated, and whether each molecule is adjacent is determined according to the distance between all atoms. However, in the simulation of a molecular system, there may be tens of thousands or more molecules, resulting in a large amount of computing resources being consumed. SUMMARY

[0004] To solve or partially solve the problems in related technologies, the present application provides a method and device for determining adjacent molecules, a design method and an electronic device, which can reduce the computing resources consumed in determining adjacent molecules and improve response speed.

[0005] A first aspect of the present application provides a method for determining adjacent molecules, the method comprising: determining a first distance between each pair of molecular models in M molecular models; and if the first distance between each pair of molecular models in N molecular models is greater than a first distance threshold, determining adjacent molecules from Q target molecules in the M molecules excluding the N molecules, wherein M, N and Q are integers greater than zero, and M is greater than or equal to N.

[0006] A second aspect of the present application provides a design method, comprising: determining adjacent molecules according to the method described above; and performing drug design or material design based on the adjacent molecules.

[0007] A third aspect of the present application provides a device for determining adjacent molecules, comprising: a first distance determination module and a first adjacent molecule determination module. The first distance determination module is configured to determine a first distance between each pair of molecular models in M molecular models. The first adjacent molecule determination module is configured to determine adjacent molecules from Q target molecules in the M molecules excluding N molecules if the first distance between each pair of molecular models in N molecular models is greater than a first distance threshold, wherein M, N and Q are integers greater than zero, and M is greater than or equal to N.

[0008] The fourth aspect of the present application provides an electronic device, comprising: a processor; a memory having executable code stored thereon, which, when executed by the processor, causes the processor to perform the above method.

[0009] The fifth aspect of the present application further provides a computer-readable storage medium having executable code stored thereon, which, when executed by a processor of an electronic device, causes the processor to perform the above method.

[0010] The sixth aspect of the present application further provides a computer program product comprising executable code, which, when executed by a processor, implements the above method.

[0011] The method, device, design method and electronic device provided by the present application first determine the first distance between the molecular model of each pair of molecules in the plurality of molecules, which facilitates the rapid determination of molecules that are obviously not adjacent in space through the first distance, so that it is not necessary to calculate the distance between the atomic coordinates of each atom in these obviously not adjacent molecules. The technical solution of the present application effectively reduces the problem of consuming a large amount of computing resources caused by the need to calculate the distance between the atomic coordinates of all atoms of each molecule in the related art, effectively improves the utilization rate of computing resources and response speed, and reduces energy consumption.

[0012] It should be understood that the above general description and the following detailed description are only exemplary and explanatory, and cannot limit the present application. BRIEF DESCRIPTION OF DRAWINGS

[0013] The above and other objects, features and advantages of the present application will become more apparent from the following detailed description when taken in conjunction with the accompanying drawings, in which like reference characters refer to like parts throughout the several views, and in which:

[0014] Figure 1 A process schematic diagram for determining adjacent molecules in the related art is schematically shown;

[0015] Figure 2 A process schematic diagram for determining adjacent molecules according to an embodiment of the present application is schematically shown;

[0016] Figure 3 A flowchart of a method for determining adjacent molecules according to an embodiment of the present application is schematically shown;

[0017] Figures 4A to 4C A schematic diagram of a molecular model according to an embodiment of the present application is schematically shown;

[0018] Figure 5 A schematic diagram of a spherical molecular model according to an embodiment of the present application is schematically shown;

[0019] Figure 6 A schematic diagram of a first distance according to embodiments of the application is shown schematically;

[0020] Figure 7 A schematic diagram of a first distance according to embodiments of the application is shown schematically;

[0021] Figure 8 A schematic diagram of a second distance according to embodiments of the application is shown schematically;

[0022] Figure 9 A schematic diagram of a third distance according to embodiments of the application is shown schematically;

[0023] Figure 10 A flow chart of a design method according to embodiments of the application is shown schematically;

[0024] Figure 11 A block diagram of an apparatus for determining neighboring molecules according to embodiments of the application is shown schematically;

[0025] Figure 12 A block diagram of an apparatus for designing according to embodiments of the application is shown schematically;

[0026] Figure 13 A block diagram of an electronic device for implementing a method for determining neighboring molecules according to embodiments of the application is shown schematically. DETAILED DESCRIPTION

[0027] Embodiments of the application will be described in more detail with reference to the drawings. While the embodiments of the application are shown in the drawings, it is understood that the application can be embodied in various forms and should not be limited by the embodiments set forth herein. Rather, these embodiments are provided so that this application will be thorough and complete, and fully convey the scope of the application to those skilled in the art.

[0028] The terminology used in the present application is for the purpose of describing particular embodiments only and is not intended to be limiting of the present application. As used herein, the terms "comprises", "comprising", "includes", "including" and the like are specifically intended to be open-ended and to mean that other features, steps, operations, and / or components can be added.

[0029] All terms used herein (including technical and scientific terms) have meanings that are commonly understood by one of ordinary skill in the art unless otherwise defined. It should be further understood that terms used herein should be interpreted as having a meaning that is consistent with the context of this specification, and not be interpreted in an overly legal or overly formal sense unless expressly so defined.

[0030] It should be understood that although the terms "first", "second", "third", etc. can be used herein to describe various information, these information should not be limited to these terms. These terms are only used to distinguish the same type of information from each other. For example, the first information can also be referred to as the second information, and similarly, the second information can also be referred to as the first information without departing from the scope of the present application. Therefore, the features defined as "first", "second" can explicitly or implicitly include one or more of the features. In the description of the present application, the meaning of "a plurality of" is two or more, unless otherwise specifically limited.

[0031] Before describing the technical solutions of the present application, some technical terms related to the field of the present application are explained.

[0032] Molecular simulation refers to using theoretical methods and computer technology to simulate the structure and physical and chemical properties of molecules or molecular systems.

[0033] Adjacent molecules refer to when at least part of the atoms in a first molecule and at least part of the atoms in a second molecule meet the adjacent distance threshold, the first molecule and the second molecule can be called adjacent molecules.

[0034] Frame is a reference for describing the position and attitude of an object, so it is also called reference system or reference frame. For example, the frame can be a coordinate system created when performing simulation, such as Cartesian coordinates.

[0035] Coordinates are used to represent the absolute position of an object in a specific coordinate system. In mathematics, the essence of coordinates is ordered pairs.

[0036] In the simulation process of a molecular system, the adjacent molecules of a molecule can be calculated, involving the calculation and judgment process of whether each two molecules in the molecular system are adjacent molecules. In related technologies, in order to determine adjacent molecules, the distance between all atoms of each two molecules can be calculated to determine whether the two molecules are adjacent molecules by determining whether the distance between all atoms of each two molecules meets the distance threshold of adjacent molecules.

[0037] Specifically, in the process of determining adjacent molecules in related technologies, the atomic distance between all atoms of each two molecules in the molecular system needs to be calculated. Then, the atomic distance is compared with the distance threshold of adjacent molecules to determine whether two molecules are adjacent. The calculation method involved in the above method is simple, but the calculation amount is large and the efficiency is low, which leads to waste of a large amount of computing resources.

[0038] Applicant has made a large number of researches and analyses on the above problems and found that the related art has the following problems: in a molecular system, when it is assumed that the positions of two molecules in a specified coordinate system are far apart and obviously not adjacent molecules, the related art still needs to calculate the distances between all atoms in the two molecules two by two and compare the distances with a distance threshold value respectively. This calculation process not only has a large amount of calculation and high calculation cost, but also belongs to useless calculation, which greatly wastes the computing resources.

[0039] Figure 1 The process of determining adjacent molecules in the related art is schematically shown.

[0040] As shown in Figure 1 , two molecules 10 are shown, in order to facilitate the description of the process of determining adjacent molecules in the related art, the molecule on the left in Figure 1 is denoted as a first molecule, and the molecule on the right in Figure 1 is denoted as a second molecule. Among them, in order to be simple and intuitive, atoms 11 and molecules 10 are represented by round balls.

[0041] In the related art, no matter how far apart the first molecule and the second molecule are, when determining adjacent molecules, the distances between any two atoms in the two molecules need to be calculated to determine whether the first molecule and the second molecule are adjacent (i.e., they are adjacent molecules to each other). Figure 1 In , only the distance i1, i2 calculation process between two atoms (indicated by bold circles) in the first molecule and each atom in the second molecule is shown. In the related art, the distance between each atom in the first molecule and each atom in the second molecule needs to be calculated respectively, and if the distance between any one atom in the first molecule and any one atom in the second molecule is less than a distance threshold value, it is determined that the first molecule and the second molecule are adjacent molecules, and if the distance between any one atom in the first molecule and any one atom in the second molecule is greater than the distance threshold value, it is determined that the first molecule and the second molecule are non-adjacent molecules.

[0042] In the simulation process of a molecular system, tens of thousands of molecules 10, even hundreds of thousands of molecules 10 or more molecules 10 may be involved, and each molecule 10 is composed of multiple atoms 11. However, most of the molecules 10 are far apart in space, and calculating the distances between the atoms 11 of these far-apart molecules 10 is useless calculation, which leads to a large waste of computing resources.

[0043] In view of the above problems, it is urgent to develop a technical solution that can quickly determine adjacent molecules and reduce the amount of calculation, improve the calculation efficiency and the effective utilization rate of computing resources. The technical solution of the embodiments of the present application can effectively save computing resources and speed up the simulation and simulation process of the molecular system.

[0044] Figure 2 A schematic diagram of a process of determining adjacent molecules according to an embodiment of the present application is shown.

[0045] As shown in Figure 2 the present embodiment, in the process of determining adjacent molecules, the distance i3 between each molecule 10 is first determined. Specifically, the geometric center coordinates of each molecule 10, such as the center or the center of gravity, etc., can be determined first, and then the approximate distance between each molecule 10 can be determined based on the distance between the geometric center coordinates of each molecule and the size of each molecule model. After determining the approximate distance between each molecule 10, the process of calculating / determining adjacent molecules for molecules 10 that are far apart can be excluded, which can effectively save computing resources and speed up the determination efficiency of adjacent molecules in a molecular system containing multiple molecules.

[0046] Specifically, before calculating the distance between all atoms 11 of two molecules 10, the distance i3 between the two molecules 10 is first calculated, and if the distance i3 is greater than the distance threshold, it can be determined that the two molecules 10 cannot be adjacent, and there is no need to continue to calculate the distance between all atoms of the two molecules 10. In this way, the number of times of calculating the distance between atoms is greatly reduced, and the computing resources are effectively saved.

[0047] A method for determining adjacent molecules, a device and a design method according to an embodiment of the present application will be described in detail below. Figures 3 to 11 A method for determining adjacent molecules, a device and a design method according to an embodiment of the present application will be described in detail below.

[0048] Figure 3 A flowchart of a method for determining adjacent molecules according to an embodiment of the present application is shown.

[0049] As shown in Figure 3 the present embodiment, a method for determining adjacent molecules is provided, which includes operations S310-S320, and specifically as follows:

[0050] In operation S310, the first distance between each two molecule models in the molecular model of M molecules is determined.

[0051] Wherein, M can be the number set by the user when performing molecular system simulation, such as M can be an integer greater than zero, and the unit of M can be one, ten, one hundred, one thousand, ten thousand, one million or other counting units, etc.

[0052] The molecule can be an inorganic molecule or an organic molecule, and each molecule is composed of at least two atoms, which is not limited here. For example, the molecule can be a molecule of a pharmaceutical ingredient, the molecule can also be a molecule of a building material, the molecule can also be a molecule of an aerospace material, etc.

[0053] In some embodiments, the method can further comprise, before determining the first distance between each pair of the molecular models of the M molecules, determining a molecular center coordinate of each of the M molecular models, and determining the first distance between each pair of the molecular models of the M molecules based on the M molecular center coordinates.

[0054] For example, for each molecular system, the molecular model can contain M molecules. Specifically, a molecular model can be constructed with a geometric center coordinate as a molecular center coordinate and with a specified size. The molecule includes P atoms, the geometric center coordinate is a weighted average geometric coordinate of atomic coordinates of at least some of the P atoms in a specified coordinate system, and P is an integer greater than zero.

[0055] It should be noted that the construction process of the molecular model is not an operation that needs to be performed every time the adjacent molecules are determined. For example, the molecular model constructed in a historical period can be used. For example, the molecular model can be directly inputted, which is not limited herein.

[0056] The specified coordinate system can be a Cartesian coordinate system, a polar coordinate system, etc. Each molecule can include a plurality of atoms, and each atom has an atomic coordinate in the specified coordinate system to represent the spatial position of each atom. It should be noted that the coordinates in different coordinate systems can be converted. For example, it is easier to express the coordinates of a spatial point within a certain angle range in a polar coordinate system. When an object within a certain angle range needs to be processed, it can be converted to a polar coordinate system for processing first, and then converted to a Cartesian coordinate system for subsequent processing. In addition, the same coordinate system, especially the spatial coordinate system, can be used in the process of determining the adjacent molecules. For example, part or all of the molecular center coordinates, atomic coordinates, geometric center coordinates, and spherical center coordinates are in the same coordinate system. It should be understood that part or all of the molecular center coordinates, atomic coordinates, geometric center coordinates, and spherical center coordinates can also be in different coordinate systems, but the coordinates in each coordinate system can be converted to each other.

[0057] In the process of determining the geometric center coordinate, the weights of the atoms in a molecule can be the same or different. For example, the weights of the atoms in each region of the molecule are the same, or the weights of the atoms in the dense region are larger, or the weights of the atoms in the dense region are smaller, or the weights of the atoms with larger atomic mass are larger.

[0058] For example, the molecular center coordinate can be the average coordinate (i.e., the center coordinate of all atoms) of all atoms of the molecule in the specified coordinate system as the molecular center coordinate of the molecule.

[0059] For example, the molecular center coordinates can be the average coordinates of the two farthest atoms in the molecule in the specified coordinate system (i.e., the center coordinates between the two farthest atoms).

[0060] For example, the molecular center coordinates can be the average coordinates of the two farthest atoms in the molecule in the specified coordinate system (i.e., the center coordinates between the two farthest atoms).

[0061] In some embodiments, the method further comprises, before determining the first distances between each pair of molecular models of the M molecules, determining sizes of the M molecular models, to determine the first distances between each pair of molecular models of the M molecules based on the M molecular center coordinates and the M sizes, wherein the size comprises a distance between an atomic coordinate of a specified atom in the P atoms and the molecular center coordinates, and the specified atom comprises at least one of a specified number of atoms farthest from the molecular center coordinates within a preset angle range and an atom farthest from the molecular center coordinates.

[0062] For example, the size of a molecular model can be used to indicate a size of a space occupied by the molecular model in the specified coordinate system. Specifically, in order to enable the molecular model to include as many atomic models as possible, the size can be determined according to a distance between the farthest atomic models in the molecular model. The distance can be a maximum size of the molecular model in a certain direction, for example, a side length, a diameter, etc. In this way, it is convenient to determine the first distance between the boundaries of two molecular models based on the molecular center coordinates and the size.

[0063] In some embodiments, determining the first distances between each pair of molecular models of the M molecules can comprise any one of the following operations.

[0064] For example, determining a distance between the outer contours of the molecular models corresponding to any two molecules.

[0065] For example, determining a distance between the molecular center coordinates of the molecular models corresponding to any two molecules.

[0066] For example, determining a distance between the outer contour of the molecular model corresponding to one of any two molecules and the molecular center coordinates of the molecular model corresponding to the other molecule.

[0067] In this embodiment, the distance between two molecules can be calculated based on the molecular center coordinates of the two molecules. For example, the molecular center coordinate 1 is (x1, y1), the molecular center coordinate 2 is (x2, y2), and the distance D can be calculated as shown in equation (1).

[0068] D = [(x2 - x1) 2 + (y2 - y1) 2 ] 1 / 2 Equation (1)

[0069] It should be noted that when calculating the distance between atomic coordinates or calculating the distance between atomic coordinates and molecular center coordinates, the formula of equation (1) can also be used for calculation.

[0070] In addition, in order to reduce the influence of the size difference of each molecule on the accuracy of the determined adjacent molecules, the size factor of the molecule can be removed from the distance. For example, after determining the distance between the centers of two molecules based on the molecular center coordinates of the two molecules, the first distance can be subtracted from the distance occupied by each of the two molecules.

[0071] When a spherical model is used to represent a molecule, the radius of one or two spherical models can be subtracted from the distance D. When a cubic model is used to represent a molecule, half the edge length of one or two cubic models can be subtracted from the distance D.

[0072] In operation S320, if it is determined that the first distance between each two molecular models in the molecular models of the N molecules is greater than the first distance threshold, the adjacent molecules are determined from the Q target molecules in the M molecules excluding the N molecules, wherein M, N and Q are integers greater than zero, and M is greater than or equal to N.

[0073] In this embodiment, if the first distance between two molecules is greater than the preset first distance threshold, it can be determined that the two molecules are not adjacent, and there is no need to calculate the distance between the atoms in the two molecules. The first distance threshold can be obtained according to expert experience or simulation.

[0074] It should be noted that on the basis of excluding molecules that are not likely to be adjacent, various ways can be used to determine adjacent molecules from the remaining molecules.

[0075] In some embodiments, for each of the Q target molecules, determining adjacent molecules from the Q target molecules in the M molecules excluding the N molecules can include the following operations.

[0076] First, a fourth distance between each atom coordinate of at least part of atoms in the current target molecule and each atom coordinate of at least part of atoms in a non-current target molecule is determined, wherein the non-current target molecule is a molecule other than the current target molecule in the Q target molecules.

[0077] Then, if any of the fourth distances is less than a fourth distance threshold, it can be determined that the current target molecule and the non-current target molecule are adjacent.

[0078] For example, the distances between the atoms of different molecules in all Q target molecules are calculated respectively (which can be determined by calculating the atom coordinates), and it is determined whether the molecules to which the atoms belong are adjacent according to the distances between the atom coordinates.

[0079] In addition, the calculation method for determining whether two molecules are adjacent in the related art can also be used, which is not limited here.

[0080] In some embodiments, the above method can further include the operation of at least one of drug design or material design based on the adjacent molecules. Specifically, after the adjacent molecules are determined from a large number of molecules, the structure and physical and chemical properties of the molecules or the molecular system can be simulated based on at least the adjacent molecules, thereby improving the efficiency of the development of new materials or new functions of materials.

[0081] The method for determining adjacent molecules provided in the embodiments of the present application can quickly calculate and filter the molecules far apart in space, greatly reducing the distance calculation process between the atoms of non-adjacent molecules. The embodiments of the present application effectively improve the response speed of determining adjacent molecules and reduce the consumption of computing resources without reducing the accuracy of determining adjacent molecules.

[0082] The construction process of the molecular model is exemplarily described below.

[0083] Determining the distance between the molecular center coordinates of any two molecules in the M molecules can include the following operations: first, a molecular model with a specified size is constructed with the weighted average geometric coordinate as the center, wherein the specified size is related to the distance between the atom coordinates of part of the P atoms and the molecular center coordinates. Then, for any two molecules in the M molecules, the distance between the weighted average geometric coordinates corresponding to the two molecules is determined. The above-mentioned part of the atoms can be the atoms far apart in the molecule. For example, the above-mentioned part of the atoms can be the specified number of atoms farthest apart in the molecule, such as two, three, five, etc., such as the top 5 atoms. In addition, the space can also be divided into multiple subspaces with the molecular center coordinates as the origin, and then the atoms farthest from the origin in each space are obtained.

[0084] In some embodiments, the molecular model comprises any one of a spherical model, a solid geometric model with straight edges, wherein the spherical model has the molecular center coordinate as the center of the sphere and has the size as the radius of the sphere.

[0085] Figures 4A to 4C A schematic diagram of a molecular model according to an embodiment of the present application is shown schematically.

[0086] As shown in Figure 4A , the molecular model can be a sphere. The sphere model is relatively easy to construct, which only needs to determine the coordinates of the center of the sphere and the radius of the sphere. For example, the molecular center coordinate can be taken as the coordinates of the center of the sphere, and the distance between the two atoms farthest apart in the molecule can be taken as the radius or diameter of the sphere.

[0087] In some embodiments, the distance between the outer contours of the molecular models corresponding to any two molecules can comprise: for the spherical model, the distance between the molecular center coordinates of the molecular models corresponding to any two molecules minus the radii of the respective molecular models corresponding to any two molecules, wherein the spherical model has the molecular center coordinate as the center of the sphere and has the size as the radius of the sphere.

[0088] As shown in Figure 4B , the molecular model can be a hexahedron. For example, the center of the hexahedron can be the molecular center coordinate, and at least two vertices of the hexahedron can be the two atoms farthest apart in the molecule. The other vertices of the hexahedron can be the atomic coordinates in the first plane, and the first plane can intersect the line connecting the two atoms farthest apart, such as perpendicular to each other.

[0089] As shown in Figure 4C , the molecular model can be an octahedron. For example, the center of the octahedron can be the molecular center coordinate, and the space can be divided into eight subspaces with the molecular center coordinate as the origin. Then, the atoms farthest apart from the origin in each subspace are determined, and these atoms are taken as the fixed points of the octahedron.

[0090] It should be noted that the above method of constructing a molecular model is only exemplary and is not limited herein. For example, the molecular model can also be a solid model with more faces, such as a football-shaped polyhedron, etc. In addition, the molecular model can also be a solid model constructed by straight edges and curved edges, such as a cylinder, etc.

[0091] In some embodiments, the specified size comprises the distance between the atomic coordinates of the specified atoms in the P atoms and the molecular center coordinate, wherein the specified atoms comprise at least one of the specified number of atoms farthest from the molecular center coordinate within a preset angle range and the atoms farthest from the molecular center coordinate.

[0092] The preset angle range can be an angle range in a polar coordinate system. For example, the angle range can be represented by a first angle range and a second angle range, the first angle range being an angle range in a horizontal plane, and the second angle range being an angle range in a plane perpendicular to the horizontal plane. It should be noted that a space corresponding to the preset angle range in the polar coordinate system can be converted into a coordinate range in a Cartesian coordinate system. The preset angle range can be continuous or discontinuous, for example, the first angle range can include 0°-360°, or 0°-30°, 60°-90°, 120°-150°, 180°-210°, 240°-270°, and 300°-330°.

[0093] The specified number is adjustable, such as 1, 2, 3, 5, 10, or more. There can be long-chain molecules in the molecular system. When the specified number is 1, using the molecular center coordinates to determine adjacent molecules can result in a large number of suspected adjacent molecules (also referred to as candidate adjacent molecules, because the distance between the atom farthest from the molecular center coordinates in the intermolecular distance threshold and the molecular center coordinates is related, the larger the intermolecular distance threshold is set, the more suspected adjacent molecules are obtained). This can cause the need to calculate the distance between too many actual non-adjacent atoms, resulting in a low response speed. In order to improve the response speed, multiple atoms far from the molecular center coordinates can be selected, and the weighted average of the distances between the multiple atoms and the molecular center coordinates can be used to determine the size, such as the radius of the sphere, half the length of the cube edge, etc. In this way, the response speed can be significantly improved without significantly reducing the accuracy of determining adjacent molecules, and the consumption of computing resources can be reduced.

[0094] Figure 5 A schematic diagram of a spherical molecular model according to an embodiment of the present application is schematically shown.

[0095] As Figure 5 illustrated, a spherical model is exemplarily described. The spherical space can include at least part of the atoms, and the center of the spherical model is a point where the molecular center coordinates are located.

[0096] Figure 6 A schematic diagram of a molecular center coordinate according to an embodiment of the present application is schematically shown.

[0097] As Figure 6 illustrated, the coordinate system has an X-axis, a Y-axis, and a Z-axis, and any point in the space can be represented by coordinates (x, y, z). The origin coordinates (0, 0, 0) of the coordinate system, Figure 6The center of the molecule can be represented as ((x1+x2+x3+x4+x5+x6) / 6, (y1+y2+y3+y4+y5+y6) / 6, (z1+z2+z3+z4+z5+z6) / 6) if the molecule has six atoms.

[0098] Figure 7 A diagram illustrating a first distance according to an embodiment of the present application is shown.

[0099] As shown in FIG. 1, a first molecule 100 and a second molecule 200 are shown. The first molecule 100 has a first center of the molecule O1 and a first outer contour 110. The second molecule 200 has a second center of the molecule O2 and a second outer contour 210. The first molecule 100 and the second molecule 200 are adjacent to each other. Figure 7 As shown in FIG. 2, a diagram illustrating a principle of calculating a distance between two spherical models is shown. After the center of the molecule O1 of the first molecule and the center of the molecule O2 of the second molecule are determined, the distance D between O1 and O2 can be calculated using equation (1). Then the distance D can be subtracted by the radius of the spherical model of the first molecule and the radius of the spherical model of the second molecule to obtain the distance I1 between the two spherical models.

[0100] The process of determining adjacent molecules is exemplarily described as follows.

[0101] In some embodiments, determining adjacent molecules from the Q target molecules other than the N molecules for each current target molecule can include the following operations.

[0102] The following operations are repeated until all non-current target molecules are traversed, wherein the non-current target molecule is a molecule other than the current target molecule in the Q target molecules: first, determining a second distance between the atomic coordinates of at least part of the atoms in the current target molecule and the outer contour of the molecule model of the non-current target molecule. Then, if any of the second distances is less than a second distance threshold, determining that the non-current target molecule is a candidate adjacent molecule of the current target molecule.

[0103] In the present embodiment, before calculating the atomic distances between all atoms of different molecules in the above-mentioned Q target molecules, the distances between the atoms in the current target molecule and the outer contour of the non-current target molecule are also calculated, which helps to further reduce the atomic-atomic distances that need to be calculated.

[0104] In some embodiments, the above-mentioned method can further include the following operation: if it is determined that all the second distances for the current target molecule are greater than or equal to the second distance threshold, determining that the current target molecule and all the non-current target molecules are not adjacent.

[0105] For example, if the distances between all the atoms in the current target molecule and the outer contour of the non-current target molecule are greater than the second distance threshold, it indicates that the current target molecule and the non-current target molecule are unlikely to be adjacent, and there is no need to calculate the distances between the atoms in the two molecules.

[0106] It should be noted that the first distance threshold and the second distance threshold can be the same or different.

[0107] Figure 8 A schematic diagram of a second distance according to an embodiment of this application is shown.

[0108] like Figure 8 As shown, a spherical model is used as an example for illustration. The current target molecule includes multiple atoms, and the distance I2 between each atom and the outer contour of the non-current target molecule can be calculated separately. Specifically, the distance between the coordinates of the current atom and the geometric center coordinates of the non-current target molecule can be calculated. Then, the radius of the sphere of the spherical model of the non-current target molecule is subtracted from this distance to obtain the distance I2.

[0109] In some embodiments, for each candidate neighboring molecule of the current target molecule, the above method may further include the following operations.

[0110] First, a third distance is determined between the atomic coordinates of at least a portion of the atoms in the current target molecule and the atomic coordinates of at least a portion of the atoms in the candidate neighboring molecules. Specifically, at least a portion of the atoms in the current target molecule can be atoms whose second distance from the outer contour of a molecular model of a non-target molecule is less than a second distance threshold. Furthermore, at least a portion of the atoms in the current target molecule can also be molecules that are relatively far from the molecular center coordinates of the current target molecule.

[0111] Then, if any third distance is less than the third distance threshold, the candidate neighboring molecule and the current target molecule are determined to be adjacent.

[0112] In some embodiments, the method may further include: if all third distances are greater than or equal to a third distance threshold, then determining that the current target molecule and candidate neighboring molecules are not adjacent. The third distance threshold may be the same as or different from the first distance threshold and the second distance threshold, and is not limited thereto.

[0113] Figure 9 A schematic diagram illustrating a third distance according to an embodiment of this application is shown.

[0114] like Figure 9 As shown, the distance between atoms in the current target molecule and atoms in non-target molecules can be calculated using their respective coordinates. For example, in a specified coordinate system, equation (1) can be used to calculate the distance between the atomic coordinates corresponding to atoms in the current target molecule and the atomic coordinates corresponding to atoms in non-target molecules.

[0115] It should be noted that the calculation method of the third distance can be the same as the calculation method of the fourth distance, and the specific calculation process of the fourth distance will not be described here. The fourth distance threshold can be the same as or different from the first distance threshold, the second distance threshold, and the third distance threshold.

[0116] In one specific embodiment, the determination of adjacent molecules can be achieved by substantially the following four steps.

[0117] First, the molecular center coordinates are calculated. Specifically, the average coordinates of all atoms of a molecule in a specified coordinate system are calculated as the molecular center coordinates of the molecule according to the atom coordinates of each atom of the molecule in the specified coordinate system; and the molecular center coordinates of all molecules in the simulation system are calculated.

[0118] Then, the maximum distance between the center and the atoms in the molecule is calculated. It should be noted that the previous two steps are not necessary steps, for example, the molecular center coordinates and the maximum distance between the molecular center coordinates and the atom coordinates in the molecule can be input by the user, and are not limited here.

[0119] Specifically, the distance between all atom coordinates in a molecule and the molecular center coordinates of the molecule can be calculated to obtain the maximum distance between the molecular center and all atoms. Repeating the above operation can calculate the maximum distance between the molecular center and the atoms in the molecular simulation system.

[0120] Next, a molecular model and an atomic model can be constructed, such as constructing a spherical model for each molecule. For example, a spherical model is constructed with the molecular center coordinates of each molecule in a specified coordinate system as the center of the sphere, and the maximum distance between the atom coordinates and the molecular center coordinates as the radius of the sphere.

[0121] Then, the adjacent molecules of each molecule can be calculated.

[0122] Specifically, the following takes molecules A and B as examples of spherical models. When calculating whether molecules A and B are adjacent, it can be determined whether the distance between the spherical models corresponding to the two molecules satisfies the distance threshold of adjacent molecules. For example, it can be determined whether the distance between the molecular center coordinates of the two molecules minus the sum of the radii of the two molecules is less than the distance threshold of adjacent molecules.

[0123] If the distance between the two spherical models is greater than or equal to the distance threshold of adjacent molecules, it can be determined that the two molecules are not adjacent. Therefore, it is not necessary to calculate the distance between all atoms of molecules A and B. In this embodiment, molecules that are relatively far apart and obviously not adjacent in space can be quickly determined, effectively improving the speed of determining adjacent molecules and improving the utilization of computing resources.

[0124] Further, if the distance between the spherical model corresponding to molecule A and molecule B is less than the distance threshold of adjacent molecules, it can be further determined whether the distance between each atom in molecule A and molecule B satisfies the distance threshold of adjacent molecules. For example, it is determined whether the distance between the atomic coordinates of each atom of molecule A and the outer contour of molecule B is less than the distance threshold of adjacent molecules. Wherein, the distance between the atomic coordinates of each atom of molecule A and the outer contour of molecule B can be determined by calculating the distance between the atomic coordinates of each atom of molecule A and the molecular center coordinates of molecule B, and subtracting the spherical radius of the spherical model of molecule B.

[0125] If the distance between the atomic coordinates of each atom of molecule A and the outer contour of molecule B is greater than or equal to the distance threshold of adjacent molecules, it can be determined that molecule A and molecule B are not adjacent.

[0126] If there is at least one atom in molecule A whose distance to the outer contour of the spherical model of molecule B is less than the distance threshold of adjacent molecules, it can be calculated whether the distance between the at least one atom and at least one atom in molecule B is less than the distance threshold of adjacent molecules, so as to accurately determine whether molecule A and molecule B are adjacent.

[0127] For example, if there is at least one atom in molecule B whose distance to at least one atom in molecule A is less than the distance threshold of adjacent molecules, it can be determined that molecule A and molecule B are adjacent.

[0128] For example, if there are multiple atoms in molecule A whose distances to the spherical model of molecule B are all less than the distance threshold of adjacent molecules, the distances between each of the multiple atoms in molecule A and each atom in molecule B can be traversed. Specifically, the distances between one atom in molecule A and each atom in molecule B can be calculated first. If the multiple distances are all greater than or equal to the distance threshold of adjacent molecules, the distance between the next atom of the multiple atoms in molecule A and each atom in molecule B can be calculated according to the above method. If the distances between the multiple atoms in molecule A and all atoms in molecule B are all greater than or equal to the distance threshold, it can be determined that molecule A and molecule B are not adjacent.

[0129] In the embodiment, each molecule in the molecular simulation system is constructed as a spherical model. By judging the distance between two spherical models, two molecules that are obviously not adjacent molecules in space can be quickly determined. In addition, by calculating the distance between each atom of molecule A and the outer contour of molecule B, the atoms in molecule A that are relatively far away from molecule B in space can be quickly determined and filtered. This process can avoid directly calculating the atomic distance between all atoms of molecule A and molecule B. The above method can greatly reduce the calculation amount of adjacent molecules in the molecular simulation process, effectively reduce the calculation resources, improve the calculation efficiency, and reduce the calculation cost. When the above method is applied to drug design and new material development, the speed of drug design and new material development can be effectively improved.

[0130] By determining whether two molecules are adjacent through the above method, direct calculation of the distance between all atoms of two molecules is avoided. Through this method, whether all molecules in the molecular simulation system are adjacent to each other can be quickly calculated, and less computing resources are consumed.

[0131] Another aspect of the present application also provides a design method.

[0132] Figure 10 A flowchart of a design method according to an embodiment of the present application is schematically shown.

[0133] As shown in Figure 10 , the design method includes operation S1010 to operation S1020.

[0134] In operation S1010, adjacent molecules are determined.

[0135] In operation S1020, drug design or material design is performed based on the adjacent molecules.

[0136] It should be noted that the process of determining adjacent molecules can refer to the related content as shown above, which will not be described in detail here.

[0137] Another aspect of the present application also provides a device for determining adjacent molecules.

[0138] Figure 11 A structural block diagram of a device for determining adjacent molecules according to an embodiment of the present application is schematically shown.

[0139] As shown in Figure 11 , the device 1100 for determining adjacent molecules can include a first distance determination module 1110 and a first adjacent molecule determination module 1120.

[0140] The first distance determination module 1110 is configured to determine the first distance between two molecule models in the M molecule models.

[0141] The first adjacent molecule determination module 1120 is configured to determine, from the Q target molecules other than the N molecules, the adjacent molecules if it is determined that the first distance between any two of the N molecular models is greater than the first distance threshold, where M, N and Q are integers greater than zero, and M is greater than or equal to N.

[0142] In some embodiments, the apparatus 1100 further includes a molecule center coordinate determination module configured to determine the molecule center coordinates of the M molecular models before determining the first distances between any two of the M molecular models based on the M molecule center coordinates. The molecule includes P atoms, and the geometric center coordinate is a weighted average geometric coordinate of the atomic coordinates of at least some of the P atoms in a specified coordinate system, where P is an integer greater than zero.

[0143] In some embodiments, the apparatus 1100 further includes a size determination module configured to determine the sizes of the M molecular models before determining the first distances between any two of the M molecular models based on the M molecule center coordinates and the M sizes. The size includes the distance between the atomic coordinates of a specified atom of the P atoms and the molecule center coordinate, where the specified atom includes at least one of a specified number of atoms farthest from the molecule center coordinate within a preset angle range and the atom farthest from the molecule center coordinate.

[0144] In some embodiments, the first distance determination module 1110 includes any one of a first molecular distance determination unit, a second molecular distance determination unit or a third molecular distance determination unit. The first molecular distance determination unit is configured to determine, for any two molecules of the M molecules, the distance between the outer contours of the molecular models corresponding to the any two molecules. The second molecular distance determination unit is configured to determine, for any two molecules of the M molecules, the distance between the molecule center coordinates of the molecular models corresponding to the any two molecules. The third molecular distance determination unit is configured to determine, for any two molecules of the M molecules, the distance between the outer contour of the molecular model corresponding to one of the any two molecules and the molecule center coordinate of the molecular model corresponding to the other molecule.

[0145] In some embodiments, the molecular model comprises any one of a spherical model, a solid geometric model with straight edges. The distance between the outer contours of the molecular models corresponding to any two molecules comprises: for the spherical model, the distance between the coordinates of the geometric centers of the molecular models corresponding to any two molecules minus the radii of the respective molecular models corresponding to any two molecules, wherein the spherical model takes the coordinates of the centers of the molecules as the coordinates of the centers of the spheres and the sizes as the radii.

[0146] In some embodiments, the first neighboring molecule determining module 1120 comprises: a second distance determining unit, a second neighboring molecule determining unit and a traversal unit.

[0147] The second distance determining unit is configured to determine a second distance between the atomic coordinates of at least some atoms in the current target molecule and the outer contour of the molecular model of the non-current target molecule. The non-current target molecule is a molecule other than the current target molecule among the Q target molecules.

[0148] The second neighboring molecule determining unit is configured to determine that the non-current target molecule is a candidate neighboring molecule of the current target molecule if the second distance is less than a second distance threshold.

[0149] The traversal unit is configured to repeatedly execute the second distance determining unit and the candidate neighboring molecule determining unit until all non-current target molecules are traversed.

[0150] In some embodiments, the apparatus 1100 further comprises a second non- neighboring molecule determining module. The second non- neighboring molecule determining module is configured to determine that the current target molecule and all non-current target molecules are non- neighboring if it is determined that all second distances for the current target molecule are greater than or equal to the second distance threshold.

[0151] In some embodiments, the apparatus 1100 further comprises a third distance determining module and a third neighboring molecule determining module. The third distance determining module is configured to determine, for each candidate neighboring molecule of the current target molecule, a third distance between the atomic coordinates of at least some atoms in the current target molecule and the atomic coordinates of at least some atoms in the candidate neighboring molecule.

[0152] The third neighboring molecule determining module is configured to determine that the candidate neighboring molecule and the current target molecule are neighboring if the third distance is less than a third distance threshold.

[0153] In some embodiments, the at least some atoms in the current target molecule are atoms in the current target molecule whose second distance to the outer contour of the molecular model of the non-current target molecule is less than the second distance threshold.

[0154] In some embodiments, the apparatus 1100 further includes a third non-adjacent molecule determining module. The third non-adjacent molecule determining module is configured to determine that the current target molecule and the candidate adjacent molecule are non-adjacent if the third distance is greater than or equal to a third distance threshold.

[0155] In some embodiments, the first adjacent molecule determining module 1120 further includes a fourth distance determining unit and a fourth adjacent molecule determining unit.

[0156] The fourth distance determining unit is configured to determine, for each of the Q target molecules, a fourth distance between the atomic coordinates of the at least some atoms in the current target molecule and the atomic coordinates of the at least some atoms in a non-current target molecule, wherein the non-current target molecule is a molecule other than the current target molecule among the Q target molecules.

[0157] The fourth adjacent molecule determining unit is configured to determine that the current target molecule and the non-current target molecule are adjacent if the fourth distance is less than a fourth distance threshold.

[0158] Another aspect of the present application provides a design apparatus.

[0159] Figure 12 Fig. 12 shows a structural block diagram of a design apparatus according to an embodiment of the present application.

[0160] As shown in Fig. 12, the design apparatus 1200 can include an adjacent molecule determining module 1210 and a design module 1220. Figure 12 The adjacent molecule determining module 1210 is configured to determine the adjacent molecule by using the apparatus 1100 for determining the adjacent molecule as described above.

[0161] The design module 1220 is configured to perform drug design or material design based on the adjacent molecule.

[0162] For the apparatus 1100 for determining the adjacent molecule and the design apparatus 1200 in the above-described embodiments, the specific manners in which the modules and units perform operations have been described in detail in the embodiments of the method, and thus will not be described in detail here.

[0163] Another aspect of the present application provides an electronic device.

[0164]

[0165] Fig. 13 shows a block diagram of an electronic device implementing a method for determining the adjacent molecule according to an embodiment of the present application. Figure 13 As shown in Fig. 13, the electronic device 1300 includes a memory 1310 and a processor 1320.

[0166] Figure 13 As shown in Fig. 13, the electronic device 1300 includes a memory 1310 and a processor 1320.​

[0167] The processor 1320 can be a central processing unit (CPU), and can also be other general-purpose processors, digital signal processors (DSPs), application-specific integrated circuits (ASICs), field-programmable gate arrays (FPGAs), or other programmable logic devices, discrete gates or transistor logic, discrete hardware components, etc. The general-purpose processor can be a microprocessor or the processor can be any conventional processor.

[0168] The memory 1310 can include various types of storage units, such as a system memory, a read-only memory (ROM), and a permanent storage device. Among them, the ROM can store static data or instructions required by the processor 1320 or other modules of the computer. The permanent storage device can be a read-write storage device. The permanent storage device can be a non-volatile storage device that does not lose stored instructions and data even after the computer is powered off. In some embodiments, the permanent storage device uses a mass storage device (such as a magnetic or optical disk, a flash memory) as a permanent storage device. In some other embodiments, the permanent storage device can be a removable storage device (such as a floppy disk, an optical drive). The system memory can be a read-write storage device or a volatile read-write storage device, such as a dynamic random access memory. The system memory can store some or all of the instructions and data required by the processor during runtime. In addition, the memory 1310 can include a combination of any computer-readable storage media, including various types of semiconductor memory chips (such as DRAM, SRAM, SDRAM, flash memory, programmable read-only memory), magnetic disks and / or optical disks. In some embodiments, the memory 1310 can include a read and / or write removable storage device, such as a compact disc (CD), a read-only digital versatile disc (such as DVD-ROM, double-layer DVD-ROM), a read-only Blu-ray disc, an ultra-density optical disc, a flash memory card (such as an SD card, a min SD card, a Micro-SD card, etc.), a magnetic floppy disk, etc. The computer-readable storage medium does not include a carrier wave and a transient electronic signal transmitted through a wireless or wired transmission.

[0169] The memory 1310 stores executable code, which, when processed by the processor 1320, can cause the processor 1320 to perform part or all of the above-mentioned methods.

[0170] Furthermore, the method according to the present application can also be implemented as a computer program or a computer program product, which comprises computer program code instructions for executing some or all of the steps of the above-mentioned method according to the present application.

[0171] Alternatively, the present application can also be implemented as a computer readable storage medium (or a non-transitory machine readable storage medium or a machine readable storage medium) having stored thereon executable codes (or computer programs or computer instruction codes) which, when executed by a processor of an electronic device (or a server, etc.), cause the processor to perform some or all of the steps of the above-mentioned method according to the present application.

[0172] The above has described the embodiments of the present application, the above description is exemplary, not exhaustive, and is not limited to the disclosed embodiments. Many modifications and changes are obvious to those skilled in the art without departing from the scope and spirit of the described embodiments. The selection of the terms used herein is intended to best explain the principles of the embodiments, practical application, or improvement to the technology in the market, or to enable other ordinary skilled in the art to understand the embodiments disclosed herein.

Claims

1. A method for determining adjacent molecules, characterized in that, The method includes: Based on the coordinates of the centers of M molecules, the first distance between each pair of molecular models in the molecular model of the M molecules is determined, wherein the molecule includes P atoms, and the coordinates of the molecular centers are the weighted average geometric coordinates of the atomic coordinates of at least some of the P atoms in a specified coordinate system, where P is an integer greater than zero. If it is determined that the first distance between any two molecular models in the molecular model of N molecules is greater than a first distance threshold, then adjacent molecules are determined from the Q target molecules other than the N molecules in the M molecules, where M, N and Q are integers greater than zero, and M is greater than or equal to N.

2. The method according to claim 1, characterized in that, Also includes: Before determining the first distance between any two molecular models in the molecular model of M molecules, Determine the molecular center coordinates of each of the M molecular models, and determine the first distance between each pair of molecular models in the M molecular models based on the M molecular center coordinates.

3. The method according to claim 2, characterized in that, Also includes: Before determining the first distance between any two molecular models in the molecular model of M molecules, The dimensions of each of the M molecular models are determined, and a first distance between each pair of molecular models is determined based on the coordinates of the M molecular centers and the M dimensions. The dimensions include the distance between the atomic coordinates of a specified atom among the P atoms and the coordinates of the molecular center. The specified atom includes at least one of a specified number of atoms farthest from the molecular center coordinates within a preset angle range and the atom farthest from the molecular center coordinates.

4. The method according to claim 3, characterized in that, The first distance between any two molecular models in the molecular model of M molecules includes: for any two molecules among the M molecules, Determine the distance between the outer contours of the molecular models corresponding to any two molecules; or Determine the distance between the molecular center coordinates of the molecular model corresponding to any two molecules; or Determine the distance between the outer contour of the molecular model corresponding to one of the two molecules and the molecular center coordinates of the molecular model corresponding to the other molecule.

5. The method according to claim 4, characterized in that, The molecular model includes any one of the following: a spherical model or a solid geometric model with straight edges; The distance between the outer contours of the molecular models corresponding to any two molecules includes, for a spherical model, the distance between the geometric center coordinates of the molecular models corresponding to any two molecules minus the radius of each of the molecular models corresponding to any two molecules, wherein the spherical model has the molecular center coordinates as its center coordinates and the size as its radius.

6. The method according to any one of claims 1 to 5, characterized in that, The step of determining neighboring molecules from the Q target molecules (excluding the N molecules) out of the M molecules includes: for each current target molecule among the Q target molecules, Repeat the following operation until all non-current target molecules have been traversed, wherein the non-current target molecules are molecules other than the current target molecule among the Q target molecules: Determine a second distance between the atomic coordinates of at least some atoms in the current target molecule and the outer contour of the molecular model of the non-current target molecule; If the second distance is less than the second distance threshold, then the non-current target molecule is determined to be a candidate neighbor molecule of the current target molecule.

7. The method according to claim 6, characterized in that, The method further includes: If it is determined that all second distances to the current target molecule are greater than or equal to the second distance threshold, then it is determined that the current target molecule and all non-current target molecules are not adjacent.

8. The method according to claim 6, characterized in that, The method further includes: for each candidate neighboring molecule of the current target molecule. Determine a third distance between the atomic coordinates of at least some atoms in the current target molecule and the atomic coordinates of at least some atoms in the candidate adjacent molecules; If the third distance is less than the third distance threshold, then the candidate neighboring molecule and the current target molecule are determined to be adjacent.

9. The method according to claim 8, characterized in that, At least some atoms in the current target molecule are atoms in the current target molecule whose second distance from the outer contour of the molecular model of the non-current target molecule is less than the second distance threshold.

10. The method according to claim 8, characterized in that, The method further includes: If the third distance is greater than or equal to the third distance threshold, then it is determined that the current target molecule and the candidate neighboring molecule are not adjacent.

11. The method according to any one of claims 1 to 5, characterized in that, The step of determining neighboring molecules from the Q target molecules (excluding the N molecules) out of the M molecules includes: for each of the Q target molecules, Determine a fourth distance between the atomic coordinates of at least some atoms in the current target molecule and the atomic coordinates of at least some atoms in the non-current target molecule, wherein the non-current target molecule is a molecule other than the current target molecule among the Q target molecules; If the fourth distance is less than the fourth distance threshold, then the current target molecule and the non-current target molecule are determined to be adjacent.

12. A design method, characterized in that, The method includes: The method according to any one of claims 1 to 11 is used to determine adjacent molecules; Drug or material design can be performed based on the adjacent molecules.

13. An apparatus for determining adjacent molecules, characterized in that, include: The first distance determination module is used to determine the first distance between any two molecular models in the molecular model of the M molecules based on the coordinates of the center of the M molecules, wherein the molecule includes P atoms, and the coordinates of the center of the molecules are the weighted average geometric coordinates of the atomic coordinates of at least some of the P atoms in a specified coordinate system, where P is an integer greater than zero. The first adjacent molecule determination module is used to determine adjacent molecules from Q target molecules other than the N molecules in the M molecules if the first distance between any two molecular models in the molecular models of the N molecules is greater than a first distance threshold, wherein M, N and Q are integers greater than zero, and M is greater than or equal to N.

14. A design device, characterized in that, include: A neighboring molecule determination module, used to determine neighboring molecules using the apparatus for determining neighboring molecules according to claim 13; The design module is used for drug design or material design based on the adjacent molecules.

15. An electronic device, characterized in that, include: processor; as well as A memory having executable code stored thereon, which, when executed by the processor, causes the processor to perform the method as described in any one of claims 1-12.

16. A computer-readable storage medium, characterized in that, It stores executable code that, when executed by a processor of an electronic device, causes the processor to perform the method as described in any one of claims 1-12.

17. A computer program product, characterized in that, Includes executable code, which, when executed by a processor, implements the method according to any one of claims 1-12.

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