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

Abstract

The invention provides a species and reaction space information analysis method based on reaction molecular dynamics simulation, and relates to the technical field of data processing.The method comprises the steps that initial chemical bond level information is filtered based on a user-defined key level threshold value, and user-defined chemical bond information is obtained; based on the custom chemical bond information, extracting all atoms in each molecule according to chemical bond connection to obtain complete molecule information; based on the atomic trajectory information, comparing adjacent trajectory chemical bond information to obtain simulation process complete reaction information; by using the complete molecule information and combining with the atom trajectory information, calculating the coordinates of the center of mass of the molecules to obtain the spatial position information of the species; reaction space range information is obtained by utilizing complete reaction information in the simulation process and combining the space position information of the species, and analysis of the species and the reaction space information is completed. The problem that species space information and reaction space information are difficult to extract in large-scale reaction molecular dynamics simulation is solved.

Description

Technical Field

[0001] The present invention 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 simulation is an important method to study the physical and chemical properties of materials at a microscopic scale. Reactive force fields give molecular dynamics simulation the ability to identify chemical reactions (bonding or breaking) based on bond-level calculations, but the simulation results only contain atomic trajectory information, chemical bond level information, and species information, and cannot analyze reactions. Existing reaction analysis programs such as VARxMD, ChemTraYzer, and ReacNetGenerator can analyze reactions and species information based on trajectory information and (or) bond-level information, but there are many types of reactive force fields developed for different materials and different simulation environments, and there are large differences in the types of elements involved and force field parameters. Existing reaction analysis programs cannot be applied to all reaction models, have poor applicability to large-scale data, and often cannot customize bond-level thresholds. At the same time, they lack docking functions with visualization tools, chemical information tools, etc. More importantly, it is impossible to extract reaction and species spatial information, and it is impossible to achieve local reactions or species tracking in large-scale systems, so it is difficult to explain the local initiation mechanism of complex reactions. Summary of the invention

[0003] In view of the above-mentioned deficiencies in the prior art, the species and reaction space information analysis method based on reaction molecular dynamics simulation provided by the present invention 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 invention object, 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, compare the chemical bond information of adjacent trajectories, obtain the bonding information and bond breaking information, extract the reactants and products in all chemical reactions, and obtain the complete reaction information of the simulation process;

[0008] S4: using the complete molecular information and combining it with the atomic trajectory information, obtaining the molecular structure information, and obtaining the 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, obtaining the 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] Further, 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] Further, the S2 includes:

[0013] Based on the user-defined 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] Further, the S3 includes:

[0016] Based on the atomic trajectory information, compare the chemical bonds of every two adjacent trajectories 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 chemical bonds that are broken in the current trajectory, B c Represents the set of bonded 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 atom set of all molecules in the previous trajectory, the reactant set of all chemical reactions in the current trajectory is obtained by finding the intersection; based on the information of any bonding atom set and bond-breaking atom set with the atom set of all molecules in the current trajectory, the product set of all chemical reactions in the current trajectory is obtained by finding the intersection:

[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 set of reactants 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 1, R2 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 2, and R3 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 3. 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] Further, 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: Aggregate the segmented molecules through coordinate transformation to obtain molecules with a complete spatial structure;

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

[0031] S440: Based on the complete reaction information of the simulation process, extract the coordinate ranges of all atoms in all reactants and products to obtain the reaction space information. Combined with the species spatial position information, make a preliminary judgment 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 the molecular dynamics simulation of the reaction, the analysis of the species space information and the 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) the key value threshold can be customized and the applicability to large-scale simulation systems can be improved; (3) by obtaining the species space coordinate information and the reaction space range information, the species space distribution and local reaction analysis capabilities can be obtained; (4) the species space position information and the reaction space range information can be customized to be filtered, screened, and output in multiple formats, realizing the docking function with a variety of 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 by the accompanying drawings. These embodiments are not restrictive, and in these embodiments, the same number represents the same structure, wherein:

[0037] Figure 1 It is an exemplary flow chart of the species and reaction space information analysis method based on reaction molecular dynamics simulation shown in some embodiments of this specification. DETAILED DESCRIPTION

[0038] The specific implementation modes of the present invention are described below so that those skilled in the art can understand the present invention. However, it should be clear that the present invention is not limited to the scope of the specific implementation modes. For those of ordinary skill in the art, as long as various changes are within the spirit and scope of the present invention as defined and determined by the attached claims, these changes are obvious, and all inventions and creations utilizing the concept of the present invention are protected.

[0039] Example

[0040] Figure 1 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 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 order 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 of the reaction and is a key indicator for judging the strength of the interaction between adjacent atoms.

[0045] The custom chemical bond information is all the chemical bond information obtained based on the bond level information and according to the custom bond level threshold. For example, the custom chemical bond information may include the track number, the atom number in the chemical bond, the element type, the atomic weight and the bond level value.

[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] The bond order information is information reflecting the chemical bond conditions in each track. For example, the preliminary cleaned bond order information may include track number, atom number in the chemical bond, element type, atomic weight and bond order value, etc.

[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 level 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] The complete molecular information is information reflecting the complete status of all molecules in the trajectory. For example, the complete molecular information may include box size, tilt value, periodicity information, atomic coordinates, atomic trajectory, atomic number 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] The atomic set information reflects the information of all atoms contained in each molecule in the trajectory. For example, the atomic information may include the atomic number, atomic coordinates, and chemical bond status.

[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 use 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 the atom pairs in a collection manner to obtain complete molecular information of the large-scale trajectory data. For example, the atom numbers in the custom chemical bond information can be used to combine all chemical bonds with intersections into a union, and after merging repeated atoms, complete information of all molecules in the large-scale trajectory data can be obtained.

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

[0058] Atomic trajectory information is information that reflects 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 the chemical reaction information extracted from each trajectory, that is, it reflects all the chemical reaction information occurring in the entire simulation process.

[0064] In some embodiments, the processor can obtain a reactant set of all chemical reactions in the current trajectory by finding the intersection based on any bonding atom set and bond-breaking atom set with the atom set information of all molecules in the previous trajectory; obtain a product set of all chemical reactions in the current trajectory by finding the intersection based on any bonding atom set and bond-breaking atom set with the atom set information of 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 of adjacent trajectories can be analyzed to determine the set of bonding atoms and the set of breaking bonds atoms of the subsequent trajectory, and obtain custom 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 chemical bonds that are broken 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 finding the intersection of the bond-forming and bond-breaking atom set with the complete molecular information of the previous trajectory; the product set of all chemical reactions in the current trajectory can be obtained by finding the intersection of the bond-forming and bond-breaking atom set 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 sets of atoms 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 1, R2 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 2, and R3 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 3. 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 position information is information reflecting the spatial position 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 simulated box length 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 periodicity 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: Aggregate the segmented 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.

[0090] In some embodiments, the ratio of the maximum distance between bonding atoms inside 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 periodic boundaries, and 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 molecular mass center coordinate calculation process, the tilt value of the simulation box is taken into account, and the molecular mass center coordinate calculation method is corrected to obtain the corrected molecular mass center 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 centroid 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, extract the coordinate ranges of all atoms in all reactants and products to obtain the reaction space information. Combined with the species spatial position information, make a preliminary judgment 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 type of reaction can be determined using the information of the reactants and products of the reaction to obtain the reaction type information. For example, when the molecular formulas of the reactants and products are both single molecules and the molecular formulas are the same, it is an isomerization reaction, and other cases are normal reactions.

[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 species complete information (number of trajectories, atom numbers in molecules, atom numbers corresponding to chemical bonds, molecular formulas, SMILES format molecular formulas, species centroid coordinate information, 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, lists of reactants and products in each reaction, reaction formulas, SMILES format reaction formulas, reaction coordinate ranges and reaction types, 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 the 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 the present specification, the analysis of species space information and reaction space information is completed based on the results of reaction molecular dynamics simulation. (1) In this way, the applicability to all reactive force field molecular simulations can be achieved with high accuracy; (2) the key value threshold 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 obtained; (4) the 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 a variety of chemical information analysis programs.

Claims

1. A method for analyzing species and reaction space information 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, compare the chemical bond information of adjacent trajectories, obtain the bonding information and bond breaking information, extract the reactants and products in all chemical reactions, and obtain the complete reaction information of the simulation process; S4: using the complete molecular information and combining it with the atomic trajectory information, obtaining the molecular structure information, and obtaining the 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, obtaining the 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: The S1 includes: 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 user-defined 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 1, characterized in that: The S3 includes: Based on the atomic trajectory information, compare the chemical bonds of every two adjacent trajectories to obtain the set of bonding atoms and the set of bond-breaking atoms of the latter trajectory: B b =P(B i-1 \B i ); B c =P(B i \B i-1 ); Among them, B i Indicates the custom chemical bond information of track 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 chemical bonds that are broken in the current trajectory, B c Represents the set of bonded 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 atom set of all molecules in the previous trajectory, the reactant set of all chemical reactions in the current trajectory is obtained by finding the intersection; based on the information of any bonding atom set and bond-breaking atom set with the atom set of all molecules in the current trajectory, the product set of all chemical reactions in the current trajectory is obtained by finding the intersection: S r =(B b ∪B c )∩M i-1 ; S p =(B b ∪B c )∩M i ; 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; 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: Among them, R1 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 1, R2 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 2, and R3 represents the reaction atom ID set obtained by taking the union of the atom ID sets of different molecules in trajectory 3. 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.

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: Aggregate the segmented molecules through coordinate transformation to obtain molecules with a complete spatial structure; S430: Calculate the center of mass coordinates of the molecule with complete spatial structure to obtain the spatial position information of the species; S440: Based on the complete reaction information of the simulation process, extract the coordinate ranges of all atoms in all reactants and products to obtain the reaction space information. Combined with the species spatial position information, make a preliminary judgment 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 center of mass coordinate expression of the complete spatial structure molecule is: 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.

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