Chemical bond stress visualisation method

Abstract

The present disclosure provides a chemical bond stress visualization method, which can be applied to the technical field of cheminformatics. The chemical bond stress visualization method comprises: obtaining an input file corresponding to a target molecule, wherein the input file contains coordinate file identification information corresponding to the target molecule; reading a coordinate file from a target folder according to the coordinate file identification information, wherein the coordinate file comprises atomic coordinates of each atom in the target molecule; determining an atomic distance between each two atoms according to the atomic coordinates to obtain an atomic distance table, wherein the atomic distance is used to represent the chemical bond stress between the two atoms; and drawing a molecular model corresponding to the target molecule according to the atomic coordinates and the atomic distance in the atomic distance table, wherein different chemical bond stresses in the molecular model are represented by different colors. The present disclosure also provides a chemical bond stress visualization device.

Description

Technical Field

[0001] This disclosure relates to the field of cheminformatics, and more specifically to a method for visualizing chemical bond stress. Background Technology

[0002] With the continuous improvement of computing power, first-principles calculations have become an important tool in chemistry and materials engineering for studying material properties. However, first-principles calculation software usually requires dedicated computers and systems, and often cannot directly display the calculated molecular model. Therefore, it is necessary to process the coordinate files output by calculation before displaying the molecular model. However, existing molecular models are not convenient for quickly understanding the symmetry and relaxation state of molecular structure. Summary of the Invention

[0003] In view of the above problems, this disclosure provides a method and apparatus for visualizing chemical bond stress.

[0004] According to one aspect of this disclosure, a method for visualizing chemical bond stress is provided, comprising:

[0005] Obtain the input file corresponding to the target molecule, wherein the input file contains coordinate file identification information corresponding to the target molecule;

[0006] Based on the coordinate file identification information mentioned above, the coordinate file is read from the target folder, wherein the coordinate file includes the atomic coordinates of each atom in the target molecule;

[0007] Based on the atomic coordinates described above, the interatomic spacing between every two atoms is determined, resulting in an atomic spacing table. These interatomic spacings characterize the chemical bond stress between the two atoms.

[0008] Based on the atomic coordinates and the atomic spacings in the above atomic spacing table, a molecular model corresponding to the target molecule is drawn, wherein different chemical bond stresses in the molecular model are represented by different colors.

[0009] According to embodiments of this disclosure, the above-described method for visualizing chemical bond stress further includes:

[0010] Before determining the atomic spacing between every two atoms based on the atomic coordinates mentioned above and obtaining the atomic spacing table, the atomic coordinates mentioned above are read from the coordinate file.

[0011] The atomic coordinates are stored in a linked list according to the reading order to obtain the atomic coordinate linked list.

[0012] According to embodiments of this disclosure, the above-described method for visualizing chemical bond stress further includes:

[0013] An initial atomic spacing table is constructed based on the aforementioned atomic coordinate linked list, wherein the initial atomic spacing table includes the storage order of each atom in the aforementioned atomic coordinate linked list;

[0014] Initialize the above initial atomic spacing table so that the atomic spacings in the above initial atomic spacing table are all preset values.

[0015] According to embodiments of this disclosure, the determination of the atomic spacing between every two atoms based on the aforementioned atomic coordinates to obtain an atomic spacing table includes:

[0016] For the i-th atom coordinate in the above atomic coordinate chain, determine the i-th target atom coordinate set corresponding to the i-th atom coordinate, wherein the target atom coordinate in the i-th target atom coordinate set is the atom coordinate in the above atomic coordinate chain that is after the i-th atom coordinate, and i is a positive integer greater than or equal to 1.

[0017] For each target atom coordinate in the i-th target atom coordinate set, the atomic spacing between the i-th atom coordinate and the target atom coordinate is determined to obtain the target atomic spacing.

[0018] If the target atomic spacing meets the preset conditions, the target atomic spacing is used to replace the preset value at the corresponding position in the initial atomic spacing table.

[0019] By traversing the above atomic coordinate linked list, the above atomic spacing table is finally obtained.

[0020] According to embodiments of this disclosure, the above-described method for visualizing chemical bond stress further includes:

[0021] Obtain the preset chemical bond stress value between the coordinates of the i-th atom and the target atom from the preset file;

[0022] If the target atomic spacing is determined to be less than or equal to the preset chemical bond stress value, the preset value at the corresponding position in the initial atomic spacing table is replaced with the target atomic spacing.

[0023] According to embodiments of this disclosure, the above-described method for visualizing chemical bond stress further includes:

[0024] If the preset file does not contain the preset chemical bond stress value between the i-th atomic coordinate and the target atomic coordinate, a data supplementation interface is generated using the command line interface to allow the user to input the preset chemical bond stress value between the i-th atomic coordinate and the target atomic coordinate.

[0025] According to embodiments of this disclosure, drawing a molecular model corresponding to the target molecule based on the atomic coordinates and the atomic spacings in the atomic spacing table includes:

[0026] Based on the atomic coordinates described above, label the atoms in the molecular model coordinate system;

[0027] If a chemical bond is determined to exist between two atoms according to the above atomic spacing table, the color corresponding to the chemical bond identifier is determined according to the atomic spacing between the two atoms to obtain the target color;

[0028] The chemical bond is marked between the two atoms using the target color.

[0029] According to embodiments of this disclosure, the determination of the color corresponding to the chemical bond identifier based on the atomic spacing between the two atoms, resulting in the target color, includes:

[0030] Based on the maximum and minimum atomic spacings in the above atomic spacing table, determine the chemical bond stress range;

[0031] The above chemical bond stress range is divided into a predetermined number of stress sub-ranges, wherein each stress sub-range corresponds to a color;

[0032] By determining the stress sub-interval to which the interatomic distance between the two atoms belongs, the target stress sub-interval is obtained;

[0033] The color corresponding to the aforementioned target stress sub-interval is determined as the aforementioned target color.

[0034] According to embodiments of this disclosure, the input file also includes the total number of atoms, the types of atoms, and the quantity of each type of atom corresponding to the target molecule.

[0035] The above methods also include:

[0036] Based on the total number of atoms, the types of atoms, and the quantity of each type of atom, verify the total number of atoms, the types of atoms, and the quantity of each type of atom in the above atomic coordinate chain.

[0037] According to embodiments of this disclosure, the input file also includes a coordinate system type corresponding to the coordinate file, and the coordinate file also includes the basis vector coordinates of the target molecule.

[0038] The above methods also include:

[0039] If it is determined that the above coordinate system type is not the preset coordinate system type, the atomic coordinates of each atom in the above target molecule are transformed using a preset formula based on the basis vector coordinates of the above target molecule to obtain a transformed coordinate file, wherein the coordinate system type corresponding to the above transformed coordinate file is the above preset coordinate system type.

[0040] The atomic spacing table, obtained by determining the atomic spacing between every two atomic coordinates based on the aforementioned atomic coordinates, includes:

[0041] Based on the converted atomic coordinates contained in the above-mentioned converted coordinate file, the atomic spacing between every two atoms is determined, resulting in an atomic spacing table.

[0042] According to another aspect of this disclosure, a chemical bond stress visualization device is provided, comprising:

[0043] The acquisition module is used to acquire the input file corresponding to the target molecule, wherein the input file contains coordinate file identification information corresponding to the target molecule;

[0044] The reading module is used to read the coordinate file from the target folder according to the coordinate file identification information mentioned above, wherein the coordinate file includes the atomic coordinates of each atom in the target molecule;

[0045] The determination module is used to determine the interatomic spacing between every two atoms based on the aforementioned atomic coordinates, thereby obtaining an interatomic spacing table, wherein the aforementioned interatomic spacing is used to characterize the chemical bond stress between the two atoms; and

[0046] The drawing module is used to draw a molecular model corresponding to the target molecule based on the atomic coordinates and the atomic spacings in the atomic spacing table. Different chemical bond stresses in the molecular model are represented by different colors.

[0047] According to the embodiments of this disclosure, because the technical means of reading the coordinate file based on the coordinate file identifier information in the acquired input file; then determining the atomic spacing between every two atoms based on the atomic coordinates in the coordinate file, and using the atomic spacing to characterize the chemical bond stress between two atoms; and then drawing a molecular model corresponding to the target molecule based on the atomic coordinates and atomic spacing, and using different colors to represent different chemical bond stresses, at least partially overcomes the technical problem of the inconvenience of quickly verifying the symmetry of molecular structure, thereby achieving the technical effect of being able to intuitively display the symmetry of molecular structure, facilitating the determination of whether to use symmetry in first-principles calculations, and which symmetry is more appropriate to use. At the same time, the embodiments of this disclosure simultaneously establish the molecular model and display the chemical bond stress, saving data processing time and improving data processing speed. Attached Figure Description

[0048] The foregoing contents, as well as other objects, features, and advantages of this disclosure, will become clearer from the following description of embodiments with reference to the accompanying drawings, in which:

[0049] Figure 1 A flowchart illustrating a method for visualizing chemical bond stress according to an embodiment of the present disclosure is shown schematically.

[0050] Figure 2 A flowchart illustrating a method for visualizing chemical bond stress according to another embodiment of this disclosure is shown schematically;

[0051] Figure 3 A flowchart illustrating a method for drawing molecular models according to an embodiment of the present disclosure is shown schematically.

[0052] Figure 4 A schematic diagram illustrating the structure of a chemical bond stress visualization device according to an embodiment of the present disclosure is shown; and

[0053] Figure 5 A block diagram schematically illustrates an electronic device suitable for implementing a method for visualizing chemical bond stress according to an embodiment of the present disclosure. Detailed Implementation

[0054] The embodiments of the present disclosure will now be described with reference to the accompanying drawings. However, it should be understood that these descriptions are exemplary only and are not intended to limit the scope of the disclosure. In the following detailed description, numerous specific details are set forth to provide a thorough understanding of the embodiments of the present disclosure for ease of explanation. However, it will be apparent that one or more embodiments may be practiced without these specific details. Furthermore, descriptions of well-known structures and techniques are omitted in the following description to avoid unnecessarily obscuring the concepts of the present disclosure.

[0055] The terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit this disclosure. The terms “comprising,” “including,” etc., as used herein indicate the presence of the above-described features, steps, operations, and / or components, but do not exclude the presence or addition of one or more other features, steps, operations, or components.

[0056] All terms used herein (including technical and scientific terms) have the meanings commonly understood by those skilled in the art, unless otherwise defined. It should be noted that the terms used herein are to be interpreted in a manner consistent with the context of this specification, and not in an idealized or overly rigid way.

[0057] When using expressions such as "at least one of A, B, and C", they should generally be interpreted in accordance with the meaning that is commonly understood by a person skilled in the art (e.g., "a system having at least one of A, B, and C" should include, but is not limited to, a system having A alone, a system having B alone, a system having C alone, a system having A and B, a system having A and C, a system having B and C, and / or a system having A, B, and C, etc.).

[0058] In recent years, with the continuous improvement of computing power, first-principles calculations have become an important tool for studying material properties in chemistry and materials engineering. However, first-principles calculation software usually requires dedicated computers and systems, and often cannot directly display the calculated molecular model. Therefore, it is necessary to process the coordinate files output by the calculation before displaying the molecular model. Existing molecular model visualization software and first-principles calculation data processing software often cannot clearly represent the stress magnitude of each chemical bond, making it difficult to quickly understand the symmetry and relaxation state of the molecular structure.

[0059] In view of this, this disclosure addresses the above-mentioned technical problems by determining the interatomic spacing between every two atoms based on a coordinate file, and using the interatomic spacing to characterize the chemical bond stress between atoms. Then, during the process of drawing the molecular model, different chemical bond stresses are represented by different colors, realizing the visualization of chemical bond stress. This facilitates intuitive examination of the molecular structure, quick understanding of the symmetry and relaxation state of the molecular structure, and also facilitates determining whether to use symmetry in first-principles calculations, and which symmetry is more reasonable. At the same time, the establishment of the molecular model and the display of chemical stress are carried out simultaneously, saving data processing time and improving data processing speed.

[0060] Specifically, embodiments of this disclosure provide a method for visualizing chemical bond stress, comprising: acquiring an input file corresponding to a target molecule, wherein the input file contains coordinate file identification information corresponding to the target molecule; reading a coordinate file from a target folder according to the coordinate file identification information, wherein the coordinate file includes atomic coordinates of each atom in the target molecule; determining the atomic spacing between every two atoms according to the atomic coordinates to obtain an atomic spacing table, wherein the atomic spacing is used to characterize the chemical bond stress between the two atoms; and drawing a molecular model corresponding to the target molecule according to the atomic coordinates and the atomic spacing in the atomic spacing table, wherein different chemical bond stresses in the molecular model are represented by different colors.

[0061] It's important to note that the magnitude of stress affects molecular symmetry. In first-principles calculations, for molecular structures with high symmetry, most first-principles calculation software can first calculate a portion and then derive the other portion through symmetry, reducing computational load. However, symmetry in first-principles calculations requires user configuration. For unknown molecular structures or calculated molecular structures, the symmetry must be determined manually, impacting data processing speed. Furthermore, since symmetry settings significantly influence calculation results, incorrect symmetry determination can affect the final outcome. Visualizing forces provides a more intuitive representation of molecular symmetry, facilitating the determination of whether and which symmetry is appropriate for first-principles calculations, thereby improving computational efficiency and accuracy.

[0062] Furthermore, stress itself, as a force, is also a factor that needs to be considered in first-principles calculations. The ideal effect of relaxation calculations in first-principles calculations should be to simulate the molecular model under the preset conditions with the final result, in which case stress will also exhibit some of the properties of electrons.

[0063] For example, in an octahedron with oxygen atoms at each vertex and an iron atom at the center, the stress between radial iron and oxygen atoms is greater than the stress between horizontal iron and oxygen atoms. Based on this, it can be concluded that the outer electron orbitals of the iron atom are no longer degenerate, and different electron orbitals have differentiated. Simultaneously, it can be understood that the interaction between horizontal iron and oxygen atoms is stronger, meaning that electronic interactions between horizontal iron and oxygen atoms are more frequent. Therefore, stress not only affects the symmetry of the molecular structure but can also reflect the properties of electrons to a certain extent. This disclosure, by visually demonstrating the chemical stresses of molecules, helps to directly examine the structure or draw other conclusions related to the molecular structure.

[0064] Figure 1 A flowchart illustrating a method for visualizing chemical bond stress according to an embodiment of the present disclosure is shown schematically.

[0065] like Figure 1 As shown, the chemical bond stress visualization method of this embodiment includes operations S110 to S140.

[0066] In operation S110, an input file corresponding to the target molecule is obtained, wherein the input file contains coordinate file identification information corresponding to the target molecule.

[0067] According to embodiments of this disclosure, coordinate file identification information may include coordinate file name, coordinate file number, and other information.

[0068] According to embodiments of this disclosure, the input file can be a text file with a fixed format. The input file is automatically generated when the chemical bond stress visualization device is run for the first time, and the file name can be set to "config.txt". The content of the input file needs to be filled in by the user.

[0069] According to embodiments of this disclosure, the input file may include parameter names, such as coordinate file name, total number of atoms, atom type, coordinate system type, etc. When the chemical bond stress visualization device is running, it first scans the folder for input files. If no input file is found, it automatically creates a text file containing the parameter names in the same folder. The user fills in the parameter content corresponding to the parameter names, and the program runs again after the user has filled it in.

[0070] In operation S120, a coordinate file is read from the target folder according to the coordinate file identification information mentioned above. The coordinate file includes the atomic coordinates of each atom in the target molecule.

[0071] According to embodiments of this disclosure, the coordinate file can be the coordinate file of the target molecule output by first-principles calculation software.

[0072] It should be noted that due to differences in first-principles calculation software, some information in the coordinate file may differ. The coordinate file here only needs to read the atomic coordinates of each atom in the target molecule.

[0073] In operation S130, the atomic spacing between every two atoms is determined based on the aforementioned atomic coordinates, resulting in an atomic spacing table, wherein the aforementioned atomic spacing is used to characterize the chemical bond stress between the aforementioned two atoms.

[0074] According to embodiments of this disclosure, the interatomic distance between two atoms is calculated using an atomic distance formula based on the atomic coordinates of each pair of atoms.

[0075] According to embodiments of this disclosure, the atomic distance formula can be as follows:

[0076]

[0077] Among them, (X) i Y i Z i ), (X j Y j Z j ) represent the coordinates of the two atoms, and r represents the interatomic distance between the two atoms.

[0078] In operation S140, a molecular model corresponding to the target molecule is drawn based on the atomic coordinates and the atomic spacings in the atomic spacing table. Different chemical bond stresses in the molecular model are represented by different colors.

[0079] According to embodiments of this disclosure, in the molecular model, atoms correspond to points, and chemical bonds correspond to lines. Different colors are used to distinguish different atoms, and different colors are used to distinguish different chemical bond stresses. Since the magnitude of chemical bond stress cannot be directly represented in reality, and because the magnitude of chemical bond strain is linearly related to the magnitude of chemical bond stress, as shown in formula... in For stress, Since k is a constant and is a strain, different bond lengths can be distinguished by color to differentiate the magnitude of stress, which can visually demonstrate the symmetry of the molecular structure.

[0080] According to the embodiments of this disclosure, because the technical means of reading the coordinate file based on the coordinate file identifier information in the acquired input file; then determining the atomic spacing between every two atoms based on the atomic coordinates in the coordinate file, and using the atomic spacing to characterize the chemical bond stress between two atoms; and then drawing a molecular model corresponding to the target molecule based on the atomic coordinates and atomic spacing, and using different colors to represent different chemical bond stresses, at least partially overcomes the technical problem of the inconvenience of quickly verifying the symmetry of molecular structure, thereby achieving the technical effect of being able to intuitively display the symmetry of molecular structure, facilitating the determination of whether to use symmetry in first-principles calculations, and which symmetry is more appropriate to use. At the same time, the embodiments of this disclosure simultaneously establish the molecular model and display the chemical bond stress, saving data processing time and improving data processing speed.

[0081] According to embodiments of this disclosure, the input file also includes the total number of atoms, the types of atoms, and the number of atoms of each type corresponding to the target molecule; the method further includes: verifying the total number of atoms, the types of atoms, and the number of atoms of each type in the atomic coordinate chain based on the total number of atoms, the types of atoms, and the number of atoms of each type.

[0082] According to embodiments of this disclosure, since the coordinate files output by different first-principles calculation software contain different information, the calculation accuracy can be improved by inputting the total number of atoms, the types of atoms, and the number of atoms of each type corresponding to the target molecule into the input file, and verifying the total number of atoms, the types of atoms, and the number of atoms of each type in the atomic coordinate chain list based on the content of the input file.

[0083] According to embodiments of this disclosure, the above-described chemical bond stress visualization method further includes: before determining the atomic spacing between every two atoms based on the above-described atomic coordinates to obtain an atomic spacing table, reading the above-described atomic coordinates from the above-described coordinate file; and storing the above-described atomic coordinates into a linked list in the order of reading to obtain an atomic coordinate linked list.

[0084] According to embodiments of this disclosure, in the atomic coordinate linked list, each unit consists of three floating-point numbers and a pointer. The three floating-point numbers represent the x, y, and z coordinates of the atom, and the pointer points to the next unit to access the entire linked list.

[0085] According to embodiments of this disclosure, the above-described chemical bond stress visualization method further includes: constructing an initial atomic spacing table based on the above-described atomic coordinate linked list, wherein the initial atomic spacing table includes the storage order of each atom in the above-described atomic coordinate linked list; and initializing the above-described initial atomic spacing table so that the atomic spacings in the above-described initial atomic spacing table are all preset values.

[0086] According to embodiments of this disclosure, all atomic spacings in the initial atomic spacing table are initialized to preset values. When a chemical bond exists between two atoms, the preset value corresponding to the atomic spacing between the two atoms is modified to the atomic spacing itself. When no chemical bond exists between two atoms, the atomic spacing between the two atoms remains at the preset value. Therefore, during the process of drawing a molecular model, cells with preset values ​​are ignored when accessing the atomic spacing table, reducing the computational load when accessing the atomic spacing table.

[0087] According to embodiments of this disclosure, the preset value may include, for example, any value that characterizes the absence of a chemical bond between two atoms when the interatomic distance is set to that preset value. For example, the preset value may be negative, such as -100, -200, -300, etc.

[0088] According to embodiments of this disclosure, the input file further includes a coordinate system type corresponding to the coordinate file, and the coordinate file further includes the basis vector coordinates of the target molecule; the method further includes: when it is determined that the coordinate system type is not a preset coordinate system type, converting the atomic coordinates of each atom in the target molecule using a preset formula based on the basis vector coordinates of the target molecule to obtain a converted coordinate file, wherein the coordinate system type corresponding to the converted coordinate file is the preset coordinate system type; wherein determining the atomic spacing between every two atomic coordinates based on the atomic coordinates to obtain an atomic spacing table includes: determining the atomic spacing between every two atoms based on the converted atomic coordinates contained in the converted coordinate file to obtain an atomic spacing table.

[0089] According to embodiments of this disclosure, before calculating the atomic spacing, it is determined whether the coordinate system type corresponding to the coordinate file is a preset coordinate system type. If the coordinate system type is a preset coordinate system type, the atomic spacing can be calculated directly. If the coordinate system type is not a preset coordinate system type, the coordinate system type needs to be converted using a preset formula before calculating the atomic spacing.

[0090] According to embodiments of this disclosure, the preset coordinate system type can be a Cartesian coordinate system.

[0091] According to embodiments of this disclosure, the preset formula may include the following formula:

[0092]

[0093] Where (x, y, z) are the atomic coordinate values ​​read from the coordinate file, and (X, Y, Z) are the calculated Cartesian coordinate values. a Y a Z a ), (X b Y b Z b ), (X c Y c Z c ) are the target molecular basis vector coordinates in the coordinate file.

[0094] According to embodiments of this disclosure, determining the atomic spacing between every two atoms based on the atomic coordinates to obtain an atomic spacing table includes: for the i-th atomic coordinate in the atomic coordinate chain, determining the i-th target atomic coordinate set corresponding to the i-th atomic coordinate, wherein the target atomic coordinate in the i-th target atomic coordinate set is the atomic coordinate following the i-th atomic coordinate in the atomic coordinate chain, and i is a positive integer greater than or equal to 1; for each target atomic coordinate in the i-th target atomic coordinate set, determining the atomic spacing between the i-th atomic coordinate and the target atomic coordinate to obtain the target atomic spacing; when the target atomic spacing meets a preset condition, replacing the preset value at the corresponding position in the initial atomic spacing table with the target atomic spacing; traversing the atomic coordinate chain to finally obtain the atomic spacing table.

[0095] According to embodiments of this disclosure, in order to avoid redundant calculations, a double loop can be used when calculating the distance between every two atoms. That is, the outer loop accesses the linked list of atomic coordinates from beginning to end, and the inner loop starts accessing from the last position accessed by the outer loop, and calculates the distance between the atoms accessed by both loops.

[0096] According to embodiments of this disclosure, the above-described chemical bond stress visualization method further includes: obtaining a preset chemical bond stress value between the coordinates of the i-th atom and the coordinates of the target atom from a preset file; and, if it is determined that the target atomic spacing is less than or equal to the preset chemical bond stress value, replacing the preset value at the corresponding position in the initial atomic spacing table with the target atomic spacing.

[0097] According to embodiments of this disclosure, the above-described chemical bond stress visualization method further includes: when the preset file does not contain the preset chemical bond stress value between the i-th atom coordinate and the target atom coordinate, generating a data supplementation interface using a command-line interface to facilitate the user inputting the preset chemical bond stress value between the i-th atom coordinate and the target atom coordinate.

[0098] According to embodiments of this disclosure, the preset chemical bond stress value can be the maximum bond length between two atoms. A chemical bond will only form when the distance between two atoms is less than or equal to the maximum bond length.

[0099] According to embodiments of this disclosure, the preset file can be a database file "distance.info". When calculating the interatomic distance between two atoms, it is necessary to search in the database file "distance.info". If the maximum bond length value corresponding to the two atoms is not found in the database file, the user is asked through the command line interface about the maximum bond length between the two atoms, and the data entered by the user will be directly stored in the database file; if the database file "distance.info" does not exist, it needs to be created so that the user can fill in the corresponding data.

[0100] According to embodiments of this disclosure, for example, the data format of the database file "distance.info" can be "682.2", where "6" represents carbon with atomic number 6, "8" represents oxygen with atomic number 8, and "2.2" represents the maximum bond length between carbon and oxygen. This data occupies one row.

[0101] According to embodiments of this disclosure, a database file is used to record the maximum bond length between atoms, and the maximum bond length between atoms can be modified by modifying the database file.

[0102] Figure 2 A flowchart illustrating a method for visualizing chemical bond stress according to another embodiment of the present disclosure is shown schematically.

[0103] like Figure 2 As shown, the method of this embodiment includes operations S201 to S213.

[0104] In operation S201, an input file corresponding to the target molecule is obtained, wherein the input file contains coordinate file identification information corresponding to the target molecule.

[0105] In operation S202, the coordinate file is read from the target folder according to the coordinate file identification information. The coordinate file includes the atomic coordinates of each atom in the target molecule.

[0106] In operation S203, read the atomic coordinates from the coordinate file.

[0107] In operation S204, the atomic coordinates are stored in the linked list according to the reading order, thus obtaining the atomic coordinate linked list.

[0108] In operation S205, an initial atomic spacing table is constructed based on the storage order of each atom in the atomic coordinate linked list.

[0109] In operation S206, the atomic spacing in the initial atomic spacing table is initialized to the preset value.

[0110] In operation S207, for the i-th atom coordinate in the atomic coordinate chain, determine the i-th target atom coordinate set corresponding to the i-th atom coordinate, where the target atom coordinate in the i-th target atom coordinate set is the atom coordinate that is located after the i-th atom coordinate in the atomic coordinate chain, and i is a positive integer greater than or equal to 1.

[0111] In operation S208, for each target atom coordinate in the i-th target atom coordinate set, the atomic spacing between the i-th atom coordinate and the target atom coordinate is determined, thus obtaining the target atomic spacing.

[0112] In operation S209, determine whether the target atomic spacing is less than or equal to the preset chemical bond stress value. If the target atomic spacing is less than or equal to the preset chemical bond stress value, proceed to operation S210. If the target atomic spacing is greater than the preset chemical bond stress value, proceed to operation S211.

[0113] In operation S210, the preset value at the corresponding position in the initial atomic spacing table is replaced with the target atomic spacing.

[0114] In operation S211, the preset values ​​for the corresponding positions in the initial atomic spacing table remain unchanged.

[0115] In operation S212, the atomic coordinate chain is traversed to finally obtain the atomic spacing table, where the atomic spacing is used to characterize the chemical bond stress between two atoms.

[0116] In operation S213, a molecular model corresponding to the target molecule is drawn based on the atomic coordinates and the atomic spacing in the atomic spacing table. Different chemical bond stresses in the molecular model are represented by different colors.

[0117] According to embodiments of this disclosure, by determining the interatomic spacing between every two atoms based on a coordinate file, and then representing different chemical bond stresses with different colors, the visualization of chemical bond stresses is achieved, facilitating intuitive examination of molecular structures and rapid understanding of the symmetry and relaxation states of molecular structures.

[0118] According to an embodiment of this disclosure, drawing a molecular model corresponding to the target molecule based on the atomic coordinates and the atomic spacing in the atomic spacing table includes: marking atomic symbols in the molecular model coordinate system based on the atomic coordinates; determining a color corresponding to the chemical bond symbol based on the atomic spacing between the two atoms when a chemical bond exists between the two atoms, and obtaining a target color; and marking the chemical bond symbol between the two atoms using the target color.

[0119] According to embodiments of this disclosure, determining the color corresponding to the chemical bond identifier based on the atomic spacing between the two atoms to obtain the target color includes: determining the chemical bond stress range based on the maximum and minimum atomic spacing in the atomic spacing table; dividing the chemical bond stress range into a preset number of stress sub-ranges, wherein each stress sub-range corresponds to a color; determining the stress sub-range to which the atomic spacing between the two atoms belongs to obtain the target stress sub-range; and determining the color corresponding to the target stress sub-range as the target color.

[0120] According to embodiments of this disclosure, atomic markers can be represented by dots, drawn as dots based on the corresponding positions of atomic coordinates in the molecular model coordinate system, and different colors can be used to represent different atoms. Chemical bonds can be represented by line segments, drawn between bonded atoms according to an atomic spacing table. During the drawing of chemical bonds, if the corresponding value of the atomic spacing in the atomic spacing table is a preset value, it indicates that there is no chemical bond between the atoms. If the atomic spacing is not a preset value, it indicates that there is a chemical bond between the atoms.

[0121] According to embodiments of this disclosure, when it is determined that chemical bonds exist between atoms, the color of the line segment used to represent the chemical bonds is determined. A chemical bond stress range is determined based on the maximum and minimum atomic spacings in an atomic spacing table; the chemical bond stress range is divided into a predetermined number of stress sub-ranges, where each stress sub-range corresponds to a different color; then, the color of the line segment representing the chemical bond is determined based on the color of the stress sub-range to which the atomic spacing belongs.

[0122] Specifically, the chemical bond stress range can be divided into six stress sub-ranges, which correspond to "red", "orange", "yellow", "cyan", "green" and "blue" respectively. The two colors are displayed with a gradient. Reference color blocks for the ranges can be marked on one side of the molecular model, and the bond lengths corresponding to each color can be marked with scales.

[0123] According to embodiments of this disclosure, the molecular name can also be labeled above the molecular model.

[0124] Figure 3 A flowchart illustrating a method for drawing molecular models according to an embodiment of the present disclosure is shown schematically.

[0125] like Figure 3 As shown, the method of this embodiment includes operations S301 to S307.

[0126] In operation S301, atomic labels are marked in the molecular model coordinate system according to the atomic coordinates.

[0127] In operation S302, determine whether a chemical bond exists between the two atoms currently being drawn based on the interatomic spacing table. If a chemical bond exists between the two atoms, proceed to operations S303-S306; if no chemical bond exists between the two atoms, proceed to operation S307.

[0128] When operating S303, the chemical bond stress range is determined based on the maximum and minimum atomic spacings in the atomic spacing table.

[0129] In operation S304, the chemical bond stress range is divided into a preset number of stress sub-ranges, where each stress sub-range corresponds to a color.

[0130] In operation S305, the color corresponding to the chemical bond between the two atoms is determined based on the stress sub-interval to which the interatomic distance between the two atoms currently being drawn belongs, thus obtaining the target color.

[0131] In operation S306, chemical bonds are marked between the two atoms currently being drawn using the target color chemical bond markers.

[0132] When working with S307, there is no need to label the chemical bonds between the two atoms currently being drawn.

[0133] The following specific examples further illustrate this public method for visualizing chemical bond stress.

[0134] Example

[0135] This embodiment uses indium phosphide molecules as an example to construct an indium phosphide molecule model.

[0136] The method for visualizing the chemical bond stress of indium phosphide molecules using embodiments of this public method includes:

[0137] The user inputs the relevant data of indium phosphide into the file "config.txt". The relevant data includes: the total number of atoms is "158", the atom types are "In" and "P", the number of each type of atom is "7979", the coordinate system type is "D", the project name is "QDs ofInp", and the coordinate file name is "atom.config".

[0138] Based on the coordinate file name "atom.config" in the input file "config.txt", read the basis vector coordinates of the molecular model and the position coordinates of 158 atoms in the coordinate file "atom.config". The basis vector coordinates of the molecular model are "(59.6212, 0, 0)", "(0, 59.6212, 0)", and "(0, 0, 59.6212)".

[0139] Since the coordinate file uses a fractional coordinate system, a conversion from fractional to Cartesian coordinates is required. Taking the coordinates of atom 1 "In" as an example (0.4028, 0.4507, 0.4504), the conversion is as follows: After the transformation, the corresponding Cartesian coordinates of this atom are "(24.0154, 26.8713, 26.8534)". Thus, the coordinates of the 158 atoms are transformed and stored sequentially in the linked list of atomic coordinates, `point`.

[0140] Calculate the distance between two atoms based on their atomic coordinates in the atomic coordinate chain. Taking atom 1 "In" and atom 84 "P" as an example, their fractional coordinates are "(0.4028, 0.4507, 0.4504)" and "(0.3798, 0.4253, 0.42538)" respectively. Their transformed Cartesian coordinates are "(24.0154, 26.8713, 26.8534)" and "(22.6186, 25.3550, 25.3572)" respectively. The distance can be calculated using the following formula... The distance between the two atoms is calculated as follows:

[0141] The distance between atoms is compared with the given maximum bond length. If the distance between atoms is greater than the maximum bond length, the data in the atomic distance table link[i,j] remains at -100. If the distance between atoms is less than or equal to the maximum bond length, the data in the atomic distance table link[i,j] is modified to 2.5460. Taking atom 1 "In" and atom 84 "P" as an example, since the database file "distance.info" does not contain the maximum bond lengths between "In" and "P", "P" and "P", and "In" and "In", a data supplementation interface is generated using the command-line interface. The user enters the values ​​2.55, 2.48, and 3.41 on the data supplementation page as the maximum bond lengths between "In" and "P", "P" and "P", and "In" and "In", respectively. The distance between "In" and "P" is... Less than the maximum bond length between "In" and "P" If bonding is determined, the values ​​of the cells i=1 and j=84 in the interatomic spacing table link[i,j] are modified to 2.55.

[0142] A molecular model is constructed using the atomic coordinate linked list `point` and the interatomic spacing table `link[i,j]`. The maximum and minimum interatomic spacing values ​​in `link[i,j]` are found to be 2.5452 and 2.4890, respectively, yielding the chemical bond stress intervals. These intervals are further divided into seven sub-intervals: [2.4890, 2.49), [2.49, 2.50), [2.50, 2.51), [2.51, 2.52), [2.52, 2.53), [2.53, 2.54), and [2.54, 2.5452]. Each sub-interval corresponds to a different color, and the color of the chemical bond is determined based on the sub-interval to which the interatomic spacing belongs.

[0143] It should be noted that reference color blocks can be set on one side of the molecular model to represent the colors corresponding to stress sub-regions. For example, the stress sub-region [2.4890, 2.49) corresponds to blue, and the stress sub-region [2.49, 2.50) corresponds to green, etc., which makes it easier for users to intuitively determine the relative magnitude of chemical bond stresses. For example, if a phosphorus molecule is connected to two chemical bonds, namely chemical bond A and chemical bond B, and the color of chemical bond A is blue and the color of chemical bond B is green, then the length of chemical bond A is less than the length of chemical bond B.

[0144] Based on the entered project name "QDs of InP", the project name "QDs of InP" will be labeled above the molecular model. Additionally, this molecular model is a 3D model that can be rotated freely, and a save button is provided on the molecular model window; clicking it will save the image as a PNG file.

[0145] It should be noted that, unless it is explicitly stated that there is a sequential order of execution between different operations, or that there is a sequential order of execution between different operations in terms of technical implementation, the execution order between multiple operations may not be significant, and multiple operations may be executed simultaneously.

[0146] Based on the above-mentioned method for visualizing chemical bond stress, this disclosure also provides a device for visualizing chemical bond stress. The following will be combined with... Figure 4 The device is described in detail.

[0147] Figure 4 A schematic block diagram of a chemical bond stress visualization device according to an embodiment of the present disclosure is shown.

[0148] like Figure 4 As shown, the chemical bond stress visualization device 400 of this embodiment includes an acquisition module 410, a reading module 420, a determination module 430, and a drawing module 440.

[0149] The acquisition module 410 is used to acquire an input file corresponding to the target molecule, wherein the input file contains coordinate file identification information corresponding to the target molecule. In one embodiment, the acquisition module 410 can be used to perform the operation S110 described above, which will not be repeated here.

[0150] The reading module 420 is used to read a coordinate file from the target folder according to the coordinate file identification information mentioned above, wherein the coordinate file includes the atomic coordinates of each atom in the target molecule. In one embodiment, the reading module 420 can be used to perform the operation S120 described above, which will not be repeated here.

[0151] The determining module 430 is used to determine the interatomic spacing between every two atoms based on the aforementioned atomic coordinates, thereby obtaining an interatomic spacing table, wherein the aforementioned interatomic spacing is used to characterize the chemical bond stress between the two atoms. In one embodiment, the determining module 430 may be used to perform the operation S130 described above, which will not be repeated here.

[0152] The drawing module 440 is used to draw a molecular model corresponding to the target molecule based on the atomic coordinates and the atomic spacings in the atomic spacing table. Different chemical bond stresses in the molecular model are represented by different colors. In one embodiment, the drawing module 440 can be used to perform the operation S140 described above, which will not be repeated here.

[0153] Any one or more of the modules, submodules, units, and subunits according to embodiments of the present disclosure, or at least part of the functions of any one or more of them, can be implemented in one module. Any one or more of the modules, submodules, units, and subunits according to embodiments of the present disclosure can be implemented by dividing them into multiple modules. Any one or more of the modules, submodules, units, and subunits according to embodiments of the present disclosure can be at least partially implemented as hardware circuitry, such as Field Programmable Gate Arrays (FPGAs), Programmable Logic Arrays (PLAs), Systems-on-Chip, Systems-on-Substrate, Systems-on-Package, Application-Specific Integrated Circuits (ASICs), or implemented in hardware or firmware by any other reasonable means of integrating or packaging circuitry, or implemented in software, hardware, or firmware, or in any suitable combination of any of these three implementation methods. Alternatively, one or more of the modules, submodules, units, and subunits according to embodiments of the present disclosure can be at least partially implemented as computer program modules, which, when run, can perform corresponding functions.

[0154] According to embodiments of this disclosure, any plurality of modules among the acquisition module 410, reading module 420, determining module 430, and drawing module 440 can be combined into one module, or any one of these modules can be split into multiple modules. Alternatively, at least part of the functionality of one or more of these modules can be combined with at least part of the functionality of other modules and implemented in one module. According to embodiments of this disclosure, at least one of the acquisition module 410, reading module 420, determining module 430, and drawing module 440 can be at least partially implemented as hardware circuitry, such as a field-programmable gate array (FPGA), a programmable logic array (PLA), a system-on-a-chip, a system-on-a-substrate, a system-on-package, an application-specific integrated circuit (ASIC), or implemented by any other reasonable means of integrating or packaging circuitry, or implemented in any one of software, hardware, and firmware methods, or in a suitable combination of any of these. Alternatively, at least one of the acquisition module 410, reading module 420, determining module 430, and drawing module 440 can be at least partially implemented as a computer program module, which, when run, can perform corresponding functions.

[0155] It should be noted that the chemical bond stress visualization device part in the embodiments of this disclosure corresponds to the chemical bond stress visualization method part in the embodiments of this disclosure. For a detailed description of the chemical bond stress visualization device part, please refer to the chemical bond stress visualization method part, which will not be repeated here.

[0156] Figure 5 A block diagram schematically illustrates an electronic device suitable for implementing a method for visualizing chemical bond stress according to an embodiment of the present disclosure.

[0157] like Figure 5 As shown, an electronic device 500 according to an embodiment of the present disclosure includes a processor 501, which can perform various appropriate actions and processes according to a program stored in a read-only memory (ROM) 502 or a program loaded from a storage portion 508 into a random access memory (RAM) 503. The processor 501 may include, for example, a general-purpose microprocessor (e.g., a CPU), an instruction set processor and / or an associated chipset and / or a special-purpose microprocessor (e.g., an application-specific integrated circuit (ASIC)), etc. The processor 501 may also include onboard memory for caching purposes. The processor 501 may include a single processing unit or multiple processing units for performing different actions of the method flow according to an embodiment of the present disclosure.

[0158] RAM 503 stores various programs and data required for the operation of electronic device 500. Processor 501, ROM 502, and RAM 503 are interconnected via bus 504. Processor 501 executes various operations of the method flow according to embodiments of the present disclosure by executing programs in ROM 502 and / or RAM 503. It should be noted that the aforementioned programs may also be stored in one or more memories other than ROM 502 and RAM 503. Processor 501 may also execute various operations of the method flow according to embodiments of the present disclosure by executing programs stored in the aforementioned one or more memories.

[0159] According to embodiments of this disclosure, the electronic device 500 may further include an input / output (I / O) interface 505, which is also connected to a bus 504. The electronic device 500 may also include one or more of the following components connected to the I / O interface 505: an input section 506 including a keyboard, mouse, etc.; an output section 507 including a cathode ray tube (CRT), liquid crystal display (LCD), etc., and a speaker, etc.; a storage section 508 including a hard disk, etc.; and a communication section 509 including a network interface card such as a LAN card, modem, etc. The communication section 509 performs communication processing via a network such as the Internet. A drive 510 is also connected to the I / O interface 505 as needed. A removable medium 511, such as a disk, optical disk, magneto-optical disk, semiconductor memory, etc., is installed on the drive 510 as needed so that computer programs read from it can be installed into the storage section 508 as needed.

[0160] This disclosure also provides a computer-readable storage medium, which may be included in the device / apparatus / system described in the above embodiments; or it may exist independently and not assembled into the device / apparatus / system. The computer-readable storage medium carries one or more programs that, when executed, implement the method according to the embodiments of this disclosure.

[0161] According to embodiments of this disclosure, the computer-readable storage medium may be a non-volatile computer-readable storage medium, such as including, but not limited to: portable computer disks, hard disks, random access memory (RAM), read-only memory (ROM), erasable programmable read-only memory (EPROM or flash memory), portable compact disk read-only memory (CD-ROM), optical storage devices, magnetic storage devices, or any suitable combination thereof. In this disclosure, the computer-readable storage medium may be any tangible medium that contains or stores a program that can be used by or in conjunction with an instruction execution system, apparatus, or device. For example, according to embodiments of this disclosure, the computer-readable storage medium may include ROM 502 and / or RAM 503 and / or one or more memories other than ROM 502 and RAM 503 described above.

[0162] Embodiments of this disclosure also include a computer program product comprising a computer program containing program code for performing the methods shown in the flowchart. When the computer program product is run on a computer system, the program code enables the computer system to implement the chemical bond stress visualization method provided in the embodiments of this disclosure.

[0163] When the computer program is executed by the processor 501, it performs the functions defined in the system / apparatus of this disclosure embodiments. According to embodiments of this disclosure, the systems, apparatuses, modules, units, etc., described above can be implemented by computer program modules.

[0164] In one embodiment, the computer program may rely on a tangible storage medium such as an optical storage device or a magnetic storage device. In another embodiment, the computer program may also be transmitted and distributed in the form of signals over a network medium, and may be downloaded and installed via the communication section 509, and / or installed from a removable medium 511. The program code contained in the computer program can be transmitted using any suitable network medium, including but not limited to: wireless, wired, etc., or any suitable combination thereof.

[0165] In such an embodiment, the computer program can be downloaded and installed from a network via communication section 509, and / or installed from removable medium 511. When the computer program is executed by processor 501, it performs the functions defined in the system of this disclosure embodiment. According to embodiments of this disclosure, the systems, devices, apparatuses, modules, units, etc., described above can be implemented by computer program modules.

[0166] According to embodiments of this disclosure, program code for executing the computer programs provided in embodiments of this disclosure can be written in any combination of one or more programming languages. Specifically, these computational programs can be implemented using high-level procedural and / or object-oriented programming languages, and / or assembly / machine languages. Programming languages ​​include, but are not limited to, languages ​​such as Java, C++, Python, "C", or similar programming languages. The program code can execute entirely on the user's computing device, partially on the user's device, partially on a remote computing device, or entirely on a remote computing device or server. In cases involving remote computing devices, the remote computing device can be connected to the user's computing device via any type of network, including a local area network (LAN) or a wide area network (WAN), or it can be connected to an external computing device (e.g., via the Internet using an Internet service provider).

[0167] The flowcharts and block diagrams in the accompanying drawings illustrate the architecture, functionality, and operation of possible implementations of systems, methods, and computer program products according to various embodiments of this disclosure. In this regard, each block in a flowchart or block diagram may represent a module, segment, or portion of code containing one or more executable instructions for implementing a specified logical function. It should also be noted that in some alternative implementations, the functions indicated in the blocks may occur in a different order than those indicated in the drawings. For example, two consecutively indicated blocks may actually be executed substantially in parallel, and they may sometimes be executed in reverse order, depending on the functions involved. It should also be noted that each block in a block diagram or flowchart, and combinations of blocks in a block diagram or flowchart, may be implemented using a dedicated hardware-based system that performs the specified function or operation, or using a combination of dedicated hardware and computer instructions.

[0168] Those skilled in the art will understand that the features described in the various embodiments and / or claims of this disclosure can be combined or combined in various ways, even if such combinations or combinations are not explicitly described in this disclosure. In particular, the features described in the various embodiments and / or claims of this disclosure can be combined or combined in various ways without departing from the spirit and teachings of this disclosure. All such combinations and / or combinations fall within the scope of this disclosure.

[0169] The embodiments of this disclosure have been described above. However, these embodiments are for illustrative purposes only and are not intended to limit the scope of this disclosure. Although various embodiments have been described above, this does not mean that the measures in the various embodiments cannot be used advantageously in combination. The scope of this disclosure is defined by the appended claims and their equivalents. Various substitutions and modifications can be made by those skilled in the art without departing from the scope of this disclosure, and all such substitutions and modifications should fall within the scope of this disclosure.

Claims

1. A method for visualizing chemical bond stress, comprising: obtaining an input file corresponding to a target molecule, wherein the input file comprises coordinate file identification information corresponding to the target molecule; reading a coordinate file from a target folder according to the coordinate file identification information, wherein the coordinate file comprises atomic coordinates of each atom in the target molecule; determining atomic distances between each two atoms according to the atomic coordinates, to obtain an atomic distance table, wherein the atomic distance is used to represent chemical bond stress between the two atoms; and drawing a molecular model corresponding to the target molecule according to the atomic coordinates and the atomic distances in the atomic distance table, wherein different chemical bond stresses in the molecular model are represented by different colors; a line segment color representing a chemical bond in the molecular model is determined by: determining a chemical bond stress interval according to a maximum atomic distance and a minimum atomic distance in the atomic distance table; dividing the chemical bond stress interval into a preset number of stress sub-intervals, wherein each stress sub-interval corresponds to a color; determining the line segment color of the chemical bond according to the color corresponding to the stress sub-interval to which the atomic distance between each two atoms belongs. 2.The method of claim 1, further comprising: before the determining the atomic distances between each two atoms according to the atomic coordinates, to obtain the atomic distance table, reading the atomic coordinates in the coordinate file; and storing the atomic coordinates into a linked list in a reading order, to obtain an atomic coordinate linked list. 3.The method of claim 2, further comprising: constructing an initial atomic distance table according to the atomic coordinate linked list, wherein the initial atomic distance table comprises a storage order of each atom in the atomic coordinate linked list; and initializing the initial atomic distance table, so that the atomic distances in the initial atomic distance table are all preset values.

4. The method of claim 3, wherein, The determining the atomic distances between each two atoms according to the atomic coordinates, to obtain the atomic distance table comprises: for an i-th atomic coordinate in the atomic coordinate linked list, determining an i-th target atomic coordinate set corresponding to the i-th atomic coordinate, wherein a target atomic coordinate in the i-th target atomic coordinate set is an atomic coordinate after the i-th atomic coordinate in the atomic coordinate linked list, and i is a positive integer greater than or equal to 1; for each target atomic coordinate in the i-th target atomic coordinate set, determining an atomic distance between the i-th atomic coordinate and the target atomic coordinate, to obtain a target atomic distance; in a case where the target atomic distance satisfies a preset condition, replacing the preset value in a corresponding position in the initial atomic distance table by the target atomic distance; traversing the atomic coordinate linked list, to finally obtain the atomic distance table. 5.The method of claim 4, further comprising: obtaining a preset chemical bond stress value between the i-th atomic coordinate and the target atomic coordinate from a preset file. In a case where the target atomic distance is determined to be less than or equal to the preset chemical bond stress value, the preset value at a corresponding position in the initial atomic distance table is replaced by the target atomic distance.

6. The method of claim 5, further comprising: In a case where the preset file does not contain the preset chemical bond stress value between the i-th atomic coordinate and the target atomic coordinate, a data supplement interface is generated by using a command line interface to facilitate user input of the preset chemical bond stress value between the i-th atomic coordinate and the target atomic coordinate.

7. The method of claim 1, wherein, The drawing of the molecular model corresponding to the target molecule according to the atomic coordinates and the atomic distances in the atomic distance table comprises: According to the atomic coordinates, atomic identifiers are labeled in a molecular model coordinate system; In a case where it is determined according to the atomic distance table that there is a chemical bond between two atoms, a color corresponding to a chemical bond identifier is determined according to the atomic distance between the two atoms, to obtain a target color; The chemical bond identifier is labeled between the two atoms by using the target color.

8. The method of claim 7, wherein, The determination of the color corresponding to the chemical bond identifier according to the atomic distance between the two atoms to obtain the target color comprises: According to the maximum atomic distance and the minimum atomic distance in the atomic distance table, a chemical bond stress interval is determined; The chemical bond stress interval is divided into a preset number of stress subintervals, wherein each stress subinterval corresponds to a color; The atomic distance between the two atoms belongs to a target stress subinterval is determined, to obtain the target stress subinterval; The color corresponding to the target stress subinterval is determined as the target color.

9. The method of claim 2, wherein, The input file further comprises a total number of atoms, atomic species, and a number of each type of atom corresponding to the target molecule; The method further comprises: According to the total number of atoms, the atomic species, and the number of each type of atom, the total number of atoms, the atomic species, and the number of each type of atom in the atomic coordinate linked list are reviewed.

10. The method of claim 1, wherein, The input file further comprises a coordinate system type corresponding to the coordinate file, and the coordinate file further comprises a basis vector coordinate of the target molecule; The method further comprises: In a case where it is determined that the coordinate system type is not a preset coordinate system type, the atomic coordinates of each atom in the target molecule are converted by using a preset formula according to the basis vector coordinate of the target molecule, to obtain a converted coordinate file, wherein a coordinate system type corresponding to the converted coordinate file is the preset coordinate system type; The determination of the atomic distance between each two atoms according to the converted atomic coordinates in the converted coordinate file to obtain the atomic distance table comprises: The atomic distance between each two atoms is determined according to the converted atomic coordinates contained in the converted coordinate file, to obtain the atomic distance table.

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