Method for identifying molecular structure and constructing reaction network based on atomic coordinates

By identifying molecular structures through minimum mirror convention and depth-first search algorithms, and constructing reaction networks by combining time windows and reaction cancellation, the problems of long construction cycles and low efficiency in existing technologies for reaction network construction are solved, and efficient and widely applicable molecular structure and reaction network construction is achieved.

CN122024911APending Publication Date: 2026-05-12ROCKET FORCE UNIV OF ENG
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Patent Information

Application Number
CN202511722386.1
Authority / Receiving Office
CN · China
Patent Type
Applications(China)
Current Assignee / Owner
Filing Date
2025-11-21
Publication Date
2026-05-12

AI Technical Summary

Technical Problem

Existing technologies cannot efficiently construct reaction networks and are only suitable for single simulation systems, resulting in long reaction network construction cycles and low efficiency, making it difficult to meet the rapid analysis needs of high-throughput materials research and development.

Method used

Atomic coordinates are transformed and meshed using the minimum mirror convention. Molecular structures are identified by combining a depth-first search algorithm. A reaction network is constructed using time windows and reaction cancellation. RDKit is used to generate SMILES descriptors and HTML visualizations of the reaction network.

Benefits of technology

It enables efficient identification of molecular structures and construction of reaction networks, adapts to various simulation systems, significantly improves processing efficiency, and provides quantitative reaction correlation data support.

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Abstract

The invention discloses a method for identifying a molecular structure and constructing a reaction network based on atomic coordinates, and belongs to the technical field of material simulation. According to the method for recognizing the molecular structure based on the atomic coordinates, by obtaining trajectory data, atoms outside a box are converted into atoms inside the box through minimum mirror agreement; grids are divided according to a space truncation radius, potential bonding atoms are accurately screened, and redundancy of distance calculation between every two atoms of the whole system is avoided; atomic clusters are quickly divided in combination with depth-first search, and molecular structure recognition is achieved. The method only depends on basic data such as atomic coordinates and does not depend on a simulation software post-processing module, and the limitation that only a single simulation system is adapted in the prior art is broken through. According to the method for constructing the reaction network, molecular structure description is compared frame by frame, and invalid reactions are offset and filtered through positive and negative reactions to obtain net reactions; counting the net reaction times to determine the reaction probability so as to quantify the tendency of the reaction; and constructing a reaction network by taking the molecular structure as a node and the reaction frequency as an edge weight.
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