Species and reaction space information analysis method based on reaction molecular dynamics simulation

Abstract

The present invention provides a method for analyzing species and reaction space information based on reaction molecular dynamics simulation, which relates to the field of data processing technology. The method comprises filtering initial chemical bond order information based on a custom bond order threshold to obtain custom chemical bond information; extracting all atoms in each molecule according to chemical bond connections based on the custom chemical bond information to obtain complete molecular information; comparing chemical bond information of adjacent trajectories based on atomic trajectory information to obtain complete reaction information of the simulation process; utilizing the complete molecular information in combination with the atomic trajectory information to calculate the molecular center of mass coordinates to obtain species spatial position information; utilizing the complete reaction information of the simulation process in combination with the species spatial position information to obtain reaction space range information, thereby completing the analysis of species and reaction space information. The present invention solves the problem of difficulty in extracting species space information and reaction space information in large-scale reaction molecular dynamics simulation.

Description

Technical Field

[0001] This specification relates to the field of data processing technology, and in particular to a method for analyzing species and reaction space information based on reaction molecular dynamics simulation. Background Art

[0002] Molecular dynamics simulations are an important method for studying the physicochemical properties of materials at the microscale. Reactivity force fields, based on bond-level calculations, enable molecular dynamics simulations to identify chemical reactions (bond formation or bond breaking). However, simulation results only contain atomic trajectory information, bond-level information, and species information, rendering them incapable of analyzing reactions. Existing reaction analysis programs, such as VARxMD, ChemTraYzer, and ReacNetGenerator, can analyze reactions and species based on trajectory and / or bond-level information. However, a wide variety of reactive force fields have been developed for different materials and simulation environments, with significant variations in the types of elements involved and force field parameters. Existing reaction analysis programs are not applicable to all reaction models, have limited applicability to large-scale data, often lack customizable bond-level thresholds, and lack integration with visualization and chemical information tools. More critically, they are unable to extract spatial information about reactions and species, hindering localized reactions or species tracking in large-scale systems. Consequently, they struggle to elucidate the local initiation mechanisms of complex reactions. Summary of the Invention

[0003] In response to the above-mentioned deficiencies in the prior art, the present invention provides a species and reaction space information analysis method based on reaction molecular dynamics simulation, which solves the problem that species space information and reaction space information are difficult to extract on a large scale.

[0004] In order to achieve the above-mentioned purpose, the technical solution adopted by the present invention is: a species and reaction space information analysis method based on reaction molecular dynamics simulation, comprising:

[0005] S1: Based on the custom bond level threshold, filter the initial chemical bond level information to obtain the custom chemical bond information;

[0006] S2: Based on the custom chemical bond information, all atoms in each molecule are extracted according to chemical bond connections to obtain complete molecular information;

[0007] S3: Based on the atomic trajectory information, the chemical bond information of adjacent trajectories is compared to obtain the bond formation and bond breaking information, and the reactants and products in all chemical reactions are extracted to obtain the complete reaction information of the simulation process;

[0008] S4: using the complete molecular information and combining it with the atomic trajectory information to obtain molecular structure information, and obtaining species spatial position information by calculating the molecular center of mass coordinates; using the complete reaction information of the simulation process and combining it with the species spatial position information to obtain reaction space range information;

[0009] S5: Convert the species spatial position information and the reaction spatial range information into one-dimensional list data to complete the analysis of species and reaction spatial information.

[0010] Furthermore, the S1 includes:

[0011] Based on the custom bond level threshold, the bond level values ​​of the chemical bonds in the bond level information are compared, and the initial chemical bond level information is filtered to obtain the custom chemical bond information.

[0012] Furthermore, the S2 includes:

[0013] Based on the custom chemical bond information, all chemical bonds with repeated atoms are merged to establish chemical bond set information of each molecule;

[0014] The chemical bond sets of each molecule are converted into atomic sets, and duplicate atoms are removed to obtain complete molecular information.

[0015] Furthermore, the S3 includes:

[0016] Based on the atomic trajectory information, the chemical bonds of every two adjacent trajectories are compared to obtain the set of bonding atoms and the set of bond-breaking atoms of the latter trajectory:

[0017] B b =P(B i-1 \B i );

[0018] B c =P(B i \B i-1 );

[0019] Among them, B i Indicates the custom chemical bond information of trajectory i, B i-1 represents the custom chemical bond information of trajectory i-1, P represents the exponentiation of two sets, B b represents the set of broken bonds, that is, the set of broken chemical bonds in the current trajectory, B c Represents the set of bonding atoms, that is, the set of chemical bonds generated in the current trajectory;

[0020] Based on the information of any bonding atom set and bond-breaking atom set with the atomic set of all molecules in the previous trajectory, the reactant set of all chemical reactions in the current trajectory is obtained by intersecting them; based on the information of any bonding atom set and bond-breaking atom set with the atomic set of all molecules in the current trajectory, the product set of all chemical reactions in the current trajectory is obtained by intersecting them:

[0021] S r =(B b ∪Bc )∩M i-1 ;

[0022] S p =(B b ∪B c )∩M i ;

[0023] Among them, S r Represents the reactant set of all chemical reactions in the current trajectory, B b represents the set of chemical bonds broken in the current trajectory, B c represents the set of chemical bonds generated in the current trajectory, M i-1 represents the union of the atomic sets of all molecules in trajectory i-1, S p Represents the product set of all chemical reactions in the current trajectory, M i represents the union of the atomic sets of all molecules in trajectory i;

[0024] Based on the reactant set of all chemical reactions in the current trajectory and the product set of all chemical reactions in the current trajectory, each reaction subset of the current trajectory is established by extracting the intersection, and all subsets are summarized to obtain the complete reaction information of the simulation process:

[0025]

[0026] Among them, R1 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory one, R2 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory two, and R3 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory three. n represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory n, R j represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory j, R k represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory k, Represents the complete reaction information of the simulation process, represents the set of atom IDs of reactants in reaction i1, represents the set of atom IDs of the products in reaction i1; where j, k∈{1, 2, ..., n}, j≠k, i1∈{1, 2, ..., n}, and n represents the number of reactions occurring in the current trajectory.

[0027] Furthermore, the S4 includes:

[0028] S410: Based on the complete molecular information, the maximum distance between the bonding atoms of each molecule in the periodic direction of the model is calculated, and compared with the length of the simulated box in the direction to determine whether each molecule is divided into multiple clusters by the box boundary; when each molecule is divided into multiple clusters by the box boundary, a divided molecule is obtained, and the process proceeds to S420; when each molecule is not divided into multiple clusters by the box boundary, a complete spatial structure molecule is obtained, and the process proceeds to S430;

[0029] S420: Aggregating the segmented molecules through coordinate transformation to obtain molecules with a complete spatial structure;

[0030] S430: Calculate the center of mass coordinates of the complete molecule to obtain the spatial position information of the species;

[0031] S440: Based on the complete reaction information of the simulation process, the coordinate ranges of all atoms in all reactants and products are extracted to obtain the reaction space information. Combined with the species spatial position information, a preliminary judgment is made on the reaction type to obtain the reaction space range information.

[0032] Furthermore, the center of mass coordinate expression of the complete spatial structure molecule is:

[0033]

[0034] Among them, x represents the x-axis coordinate of the center of mass, represents the atomic weight of the i2th atom, represents the x-axis coordinate of atom i2, n1 represents the total number of atoms in the molecule, and y represents the y-axis coordinate of the center of mass. represents the y-axis coordinate of atom i2, z represents the z-axis coordinate of the center of mass, represents the z-axis coordinate of atom i2.

[0035] The beneficial effects of the present invention are as follows: based on the results of reaction molecular dynamics simulation, the analysis of species space information and reaction space information is completed. (1) In this way, the applicability to all reactive force field molecular simulations can be achieved with high accuracy; (2) key value thresholds can be customized, and the applicability to large-scale simulation systems can be improved; (3) by obtaining species space coordinate information and reaction space range information, the ability to analyze species space distribution and local reactions can be achieved; (4) species space position information and reaction space range information can be customized to be filtered, screened, and output in multiple formats, realizing the docking function with various chemical information analysis programs. BRIEF DESCRIPTION OF THE DRAWINGS

[0036] This specification will be further described in the form of exemplary embodiments, which will be described in detail with reference to the accompanying drawings. These embodiments are not limiting, and in these embodiments, like numbers represent like structures, wherein:

[0037] Figure 1 This is an exemplary flow chart of a method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to some embodiments of this specification. DETAILED DESCRIPTION

[0038] The specific embodiments of the present invention are described below to facilitate understanding of the present invention by those skilled in the art. However, it should be clear that the present invention is not limited to the scope of the specific embodiments. For those skilled in the art, as long as various changes are within the spirit and scope of the present invention as defined and determined by the appended claims, these changes are obvious, and all inventions and creations utilizing the concepts of the present invention are protected.

[0039] Example

[0040] Figure 1 This is an exemplary flow chart of a method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to some embodiments of this specification. Figure 1 As shown, the process includes the following steps. In some embodiments, the process can be executed by a processor.

[0041] S1: Based on the custom bond level threshold, filter the initial chemical bond level information to obtain the custom chemical bond information.

[0042] The bond order threshold is a threshold value for determining whether there is a bond order value between adjacent atoms based on the types of adjacent atomic elements.

[0043] In some embodiments, the default value of the bond level threshold in the reaction molecular dynamics simulation is usually 0.3, which can be customized by experts.

[0044] The bond order value is calculated from the molecular dynamics simulation and is a key indicator for judging the strength of the interaction between adjacent atoms.

[0045] Customized chemical bond information is all chemical bond information derived from bond order information and based on custom bond order thresholds. For example, customized chemical bond information can include track numbers, atom numbers in the bond, element types, atomic weights, and bond order values.

[0046] In some embodiments, the processor may compare the bond level values ​​of the chemical bonds in the bond level information based on a custom bond level threshold, filter the initial chemical bond level information, and obtain the custom chemical bond information.

[0047] Bond order information is information reflecting the chemical bond status of each trajectory. For example, the preliminary cleaned bond order information can include the trajectory number, the atom number in the chemical bond, the element type, the atomic weight, and the bond order value.

[0048] In some embodiments, the processor can compare the custom bond level threshold with the bond level value of each chemical bond in the bond level information based on the bond level information after preliminary cleaning, and judge that the chemical bond exists when the bond level value is not less than the bond level threshold; and judge that the chemical bond does not exist when the bond level value is less than the bond level threshold. All bond level values ​​in the bond level information are analyzed to obtain the chemical bond information of all trajectories.

[0049] In some embodiments, when an unbonded atom appears in a trajectory, the processor can set the bonding atom object number and bond order value of the atom to 0, add it to the chemical bond information, and obtain custom chemical bond information containing all atoms.

[0050] S2: Based on the custom chemical bond information, all atoms in each molecule are extracted according to chemical bond connections to obtain complete molecular information.

[0051] Molecular integrity information is information reflecting the completeness of all molecules in the trajectory. For example, molecular integrity information can include box dimensions, tilt values, periodicity information, atomic coordinates, atomic trajectories, atomic numbers, and center of mass coordinates.

[0052] In some embodiments, the processor can merge all chemical bonds with repeated atoms based on the custom chemical bond information to establish chemical bond set information for each molecule; convert the chemical bond set of each molecule into an atom set, remove repeated atoms, and obtain complete molecular information.

[0053] Atom set information reflects the information of all atoms contained in each molecule in the trajectory. For example, atomic information can include atom numbers, atomic coordinates, and chemical bond conditions.

[0054] In some embodiments, the processor may extract all atoms connected by chemical bonds in the custom chemical bond information to obtain atom set information.

[0055] In some embodiments, the processor may utilize a traversal method to match atom pairs in the custom chemical bond information one by one, merge atom pairs containing the same atoms, merge duplicate atoms, and obtain complete information of all molecules in the small-scale trajectory data.

[0056] In some embodiments, the processor can cluster atom pairs using a union approach to obtain complete molecular information for large-scale trajectory data. For example, the atom numbers in the custom chemical bond information can be used to combine all intersecting chemical bonds into a union. After merging duplicate atoms, complete information for all molecules in the large-scale trajectory data can be obtained.

[0057] S3: Based on the atomic trajectory information, the chemical bond information of adjacent trajectories is compared to obtain the bonding information and bond breaking information, and the reactants and products in all chemical reactions are extracted to obtain the complete reaction information of the simulation process.

[0058] Atomic trajectory information is information reflecting the trajectory of atomic motion.

[0059] The bonding information is the number of chemical bonds that are added in the current trajectory compared to the previous trajectory.

[0060] The bond breaking information is the number of chemical bonds that are reduced in the current trajectory compared to the previous trajectory.

[0061] Reactants are molecules that take part in a chemical reaction.

[0062] Products are molecules obtained after a chemical reaction.

[0063] The complete reaction information of the simulation process refers to all chemical reaction information extracted from each trajectory, that is, it reflects all chemical reaction information occurring in the entire simulation process.

[0064] In some embodiments, the processor can obtain the reactant set of all chemical reactions in the current trajectory by finding the intersection based on the atomic set information of any bonding atom set and bond-breaking atom set with all molecules in the previous trajectory; obtain the product set of all chemical reactions in the current trajectory by finding the intersection based on the atomic set information of any bonding atom set and bond-breaking atom set with all molecules in the current trajectory; establish each reaction subset of the current trajectory by extracting the intersection based on the reactant set of all chemical reactions in the current trajectory and the product set of all chemical reactions in the current trajectory, and summarize all subsets to obtain complete reaction information of the simulation process.

[0065] The bonding atom set is the set of chemical bonds that do not exist in the previous trajectory but exist in the current trajectory.

[0066] The bond-breaking atom set is the set of chemical bonds that existed in the previous trajectory but do not exist in the current trajectory.

[0067] The reactant set is the set of all molecules participating in the chemical reactions in the current trajectory.

[0068] The product set is the set of molecules generated by all chemical reactions in the current trajectory.

[0069] In some embodiments, the changes in chemical bonds in adjacent trajectories can be analyzed to determine the set of bonding atoms and the set of bond-breaking atoms in the subsequent trajectory, thereby obtaining customized chemical bond information:

[0070] B b =P(B i-1 \B i );

[0071] B c =P(B i \B i-1 );

[0072] Among them, B i Indicates the custom chemical bond information of trajectory i, B i-1 represents the custom chemical bond information of trajectory i-1, P represents the exponentiation of two sets, B b represents the set of broken bonds, that is, the set of broken chemical bonds in the current trajectory, B c Represents the set of bonding atoms, that is, the set of chemical bonds generated in the current trajectory.

[0073] In some embodiments, the reactant set of all chemical reactions in the current trajectory can be obtained by intersecting the bond-forming and bond-breaking atom sets with the complete molecular information of the previous trajectory; the product set of all chemical reactions in the current trajectory can be obtained by intersecting the bond-forming and bond-breaking atom sets with the complete molecular information of the current trajectory:

[0074] S r =(B b ∪B c )∩M i-1 ;

[0075] S p =(B b ∪B c )∩M i ;

[0076] Among them, S r Represents the reactant set of all chemical reactions in the current trajectory, B b represents the set of chemical bonds broken in the current trajectory, B c represents the set of chemical bonds generated in the current trajectory, M i-1 represents the union of the atomic sets of all molecules in trajectory i-1, S p Represents the product set of all chemical reactions in the current trajectory, M i represents the union of the atomic sets of all molecules in trajectory i.

[0077] Based on the reactant set and product set, each reaction subset of the current trajectory is established by extracting the intersection, and all subsets are summarized to obtain the complete reaction information of the simulation process:

[0078]

[0079] Among them, R1 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory one, R2 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory two, and R3 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory three. n represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory n, R jrepresents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory j, R k represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory k, Represents the complete reaction information of the simulation process, represents the set of atom IDs of reactants in reaction i1, represents the set of atom IDs of the products in reaction i1; where j, k∈{1, 2, ..., n}, j≠k, i1∈{1, 2, ..., n}, and n represents the number of reactions occurring in the current trajectory.

[0080] S4: Using the complete molecular information and combining it with the atomic trajectory information, the molecular structure information is obtained, and the species spatial position information is obtained by calculating the molecular center of mass coordinates; using the complete reaction information of the simulation process and combining it with the species spatial position information, the reaction space range information is obtained.

[0081] Species spatial location information is information reflecting the spatial location coordinates of all species contained in different trajectories in the simulation box.

[0082] The reaction space range information is information indicating the spatial position range of all chemical reactions occurring in each trajectory.

[0083] In some embodiments, S4 may be implemented based on the following steps.

[0084] S410: Based on the complete molecular information, the maximum distance between the bonding atoms of each molecule in the periodic direction of the model is calculated, and compared with the length of the simulated box in this direction to determine whether each molecule is divided into multiple clusters by the box boundary; when each molecule is divided into multiple clusters by the box boundary, a divided molecule is obtained and the process proceeds to S420; when each molecule is not divided into multiple clusters by the box boundary, a complete spatial structure molecule is obtained and the process proceeds to S430.

[0085] The model periodic direction refers to the direction in which the simulation box boundary is set to be periodic during simulation.

[0086] Periodicity refers to the simulation settings that map molecular clusters outside the simulation box boundary to the simulation box boundary on the other side in the same direction.

[0087] The bonding atomic distance refers to the distance between atoms in the periodic direction, which is obtained by subtracting the atomic coordinate values ​​in that direction and taking the absolute value.

[0088] S420: Aggregating the divided molecules through coordinate transformation to obtain molecules with a complete spatial structure.

[0089] The simulation box length is the length of the model in each spatial direction during the simulation process.

[0090] In some embodiments, the ratio of the maximum distance between bonding atoms within the molecule in a periodic direction to the length of the simulation box in that direction can be compared with the segmentation factor to determine whether the molecule is segmented by a periodic boundary. The segmented molecules can be aggregated through coordinate transformation to obtain a spatially complete structured molecule.

[0091] The split factor is a custom value between 0 and 1, and 0.9 is generally used.

[0092] S430: Calculate the center of mass coordinates of the molecule with a complete spatial structure to obtain the spatial position information of the species.

[0093] Tilt correction is a method to correct the molecular center of mass coordinates based on the tilt value of the simulation box.

[0094] In some embodiments, during the calculation of the molecular center of mass coordinates, the tilt value of the simulation box is taken into consideration, and the calculation method of the molecular center of mass coordinates is corrected to obtain the corrected molecular center of mass coordinates.

[0095] In some embodiments, the corrected molecular center of mass coordinates can be calculated to obtain complete species information.

[0096] In some embodiments, the triclinic crystal model can be corrected for tilt values ​​during centroid calculation to obtain complete species information.

[0097] In some embodiments, the corrected center of mass coordinate expression may be:

[0098]

[0099] Among them, x represents the x-axis coordinate of the center of mass, represents the atomic weight of the i2th atom, represents the x-axis coordinate of atom i2, n1 represents the total number of atoms in the molecule, and y represents the y-axis coordinate of the center of mass. represents the y-axis coordinate of atom i2, z represents the z-axis coordinate of the center of mass, represents the z-axis coordinate of atom i2.

[0100] S440: Based on the complete reaction information of the simulation process, the coordinate ranges of all atoms in all reactants and products are extracted to obtain the reaction space information. Combined with the species spatial position information, a preliminary judgment is made on the reaction type to obtain the reaction space range information.

[0101] In some embodiments, the coordinate range of reactants and the coordinate range of products can be used to determine the spatial coordinate range where the reaction occurs.

[0102] In some embodiments, the reaction type can be determined using information about the reactants and products of the reaction to obtain reaction type information. For example, when both the reactant and product have the same molecular formula, it is an isomerization reaction; otherwise, it is a normal reaction.

[0103] S5: Convert the species spatial position information and the reaction spatial range information into one-dimensional list data to complete the analysis of species and reaction spatial information.

[0104] The statistical list is a one-dimensional list of species spatial position information and reaction space range information based on trajectory time. For example, the statistical list can include a statistical list of complete species information (number of trajectories, atom numbers in the molecule, atom numbers corresponding to chemical bonds, molecular formula, SMILES format molecular formula, species centroid coordinates, etc.) and a statistical list of reaction space range information (number of trajectories, atom numbers participating in the reaction, reactant atom numbers, product atom numbers, bond-breaking atom pair numbers, bonding atom pair numbers, a list of reactants and products in each reaction, reaction formula, SMILES format reaction formula, reaction coordinate range, reaction type, etc.).

[0105] In some embodiments, the data in the species spatial location information statistical list can be filtered and format converted, and connected to a visualization tool for visual presentation of species spatial information and molecular structure.

[0106] In some embodiments, the data in the statistical list of reaction space range information can be filtered and format converted, the SMILES structures of reactant and product molecules can be extracted and converted into molecular structure diagrams, and chemical reaction molecular structure change diagrams can be drawn to achieve visualization of reaction space information and reaction molecular structures.

[0107] In some embodiments of this specification, analysis of species space information and reaction space information is performed based on the results of reaction molecular dynamics simulation. (1) In this way, applicability to all reactive force field molecular simulations can be achieved with high accuracy; (2) key value thresholds can be customized, and applicability to large-scale simulation systems can be improved; (3) by obtaining species space coordinate information and reaction space range information, species space distribution and local reaction analysis capabilities can be obtained; (4) species space position information and reaction space range information can be customized to filter, screen, and output in multiple formats, realizing docking with various chemical information analysis programs.

Claims

1. A species and reaction space information analysis method based on reaction molecular dynamics simulation, characterized in that: include: S1: Based on the custom bond level threshold, filter the initial chemical bond level information to obtain the custom chemical bond information; S2: Based on the custom chemical bond information, all atoms in each molecule are extracted according to chemical bond connections to obtain complete molecular information; S3: Based on the atomic trajectory information, the chemical bond information of adjacent trajectories is compared to obtain the bond formation and bond breaking information, and the reactants and products in all chemical reactions are extracted to obtain the complete reaction information of the simulation process; Based on the atomic trajectory information, the chemical bonds of every two adjacent trajectories are compared to obtain the set of bonding atoms and the set of bond-breaking atoms of the latter trajectory: ； ； in, Represents trajectory Custom chemical bond information, Represents trajectory Custom chemical bond information, represents two sets of power sets, represents the set of broken bonds, that is, the set of broken chemical bonds in the current trajectory. Represents the set of bonding atoms, that is, the set of chemical bonds generated in the current trajectory; Based on the information of any bonding atom set and bond-breaking atom set with the atomic set of all molecules in the previous trajectory, the reactant set of all chemical reactions in the current trajectory is obtained by intersecting them; based on the information of any bonding atom set and bond-breaking atom set with the atomic set of all molecules in the current trajectory, the product set of all chemical reactions in the current trajectory is obtained by intersecting them: ； ； in, Represents the set of reactants for all chemical reactions in the current trajectory, Represents trajectory The union of the sets of atoms of all molecules, Represents the set of products of all chemical reactions in the current trajectory, Represents trajectory The union of the sets of atoms of all molecules; Based on the reactant set of all chemical reactions in the current trajectory and the product set of all chemical reactions in the current trajectory, each reaction subset of the current trajectory is established by extracting the intersection, and all subsets are summarized to obtain the complete reaction information of the simulation process: ； ； in, represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 1, represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 2, represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory three, Represents trajectory The reaction atom ID set is obtained by taking the union of the atom ID sets of different molecules in the reaction atom ID set. Represents trajectory The reaction atom ID set is obtained by taking the union of the atom ID sets of different molecules in the reaction atom ID set. Represents trajectory The reaction atom ID set is obtained by taking the union of the atom ID sets of different molecules in the reaction atom ID set. Represents the complete reaction information of the simulation process, Express reaction The set of atom IDs of the reactants in Express reaction The atom ID set of the generated objects; , , , n Indicates the number of reactions occurring in the current trajectory; S4: using the complete molecular information and combining it with the atomic trajectory information to obtain molecular structure information, and obtaining species spatial position information by calculating the molecular center of mass coordinates; using the complete reaction information of the simulation process and combining it with the species spatial position information to obtain reaction space range information; S5: Convert the species spatial position information and the reaction spatial range information into one-dimensional list data to complete the analysis of species and reaction spatial information.

2. The method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to claim 1, characterized in that: Said S1 comprises: Based on the custom bond level threshold, the bond level values ​​of the chemical bonds in the bond level information are compared, and the initial chemical bond level information is filtered to obtain the custom chemical bond information.

3. The method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to claim 1, characterized in that: The S2 includes: Based on the custom chemical bond information, all chemical bonds with repeated atoms are merged to establish chemical bond set information of each molecule; The chemical bond sets of each molecule are converted into atomic sets, and duplicate atoms are removed to obtain complete molecular information.

4. The method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to claim 3, characterized in that: The converting of the chemical bond set of each molecule into an atom set and removing duplicate atoms to obtain complete molecular information includes: Using the traversal method, the atom pairs in the custom chemical bond information are matched one by one, the atom pairs containing the same atoms are merged, and the duplicate atoms are merged to obtain the complete information of all molecules in the small-scale trajectory data; Using the atom numbers in the custom chemical bond information, all chemical bonds with intersections are combined into a union. After merging duplicate atoms, the complete information of all molecules in the large-scale trajectory data is obtained. The complete molecular information is obtained by integrating the complete information of all molecules in the small-scale trajectory data and the complete information of all molecules in the large-scale trajectory data.

5. The method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to claim 1, characterized in that: The S4 includes: S410: Based on the complete molecular information, the maximum distance between the bonding atoms of each molecule in the periodic direction of the model is calculated, and compared with the length of the simulated box in the direction to determine whether each molecule is divided into multiple clusters by the box boundary; when each molecule is divided into multiple clusters by the box boundary, a divided molecule is obtained, and the process proceeds to S420; when each molecule is not divided into multiple clusters by the box boundary, a complete spatial structure molecule is obtained, and the process proceeds to S430; S420: Aggregating the segmented molecules through coordinate transformation to obtain molecules with a complete spatial structure; S430: Calculate the center of mass coordinates of the complete molecule to obtain the spatial position information of the species; S440: Based on the complete reaction information of the simulation process, the coordinate ranges of all atoms in all reactants and products are extracted to obtain the reaction space information. Combined with the species spatial position information, a preliminary judgment is made on the reaction type to obtain the reaction space range information.

6. The method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to claim 5, characterized in that: The S420 includes: The maximum distance between bonding atoms in the molecule in the periodic direction is compared with the ratio of the length of the simulation box in this direction and the segmentation factor to determine whether the molecule is divided by the periodic boundary. The divided molecules are aggregated through coordinate transformation to obtain a molecule with a complete spatial structure.

7. The method for analyzing species and reaction space information based on reaction molecular dynamics simulation according to claim 5, characterized in that: The center of mass coordinate expression of the complete spatial structure molecule is: ； ； ； in, Represents the center of mass Axis coordinates, Indicates the The atomic weight of an atom, Represents atoms of Axis coordinates, represents the total number of atoms in the molecule, Represents the center of mass Axis coordinates, Represents atoms of Axis coordinates, Represents the center of mass Axis coordinates, Represents atoms of Axis coordinates.

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