Permutation Matrix Completion for Accurate Conformer Classification
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current conformer search software fails to accurately sort molecular structures based on their internal coordinates, leading to incomplete and flawed assignments of conformers and rotamers, which compromises the accuracy of spectroscopic predictions and analyses.
Innovation Solution
An apparatus and method utilizing graph theory to classify molecular structures into equivalent and non-equivalent sets by generating permutation matrices and comparing them for identity, and classifying graphs based on structural parameters like bond lengths and dihedrals, ensuring accurate identification and sorting of rotamers and conformers.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current conformer search software is used to sort molecular structures, then the process is simple and fast, but the accuracy of conformer and rotamer assignments is incomplete and flawed
Solution Approach 1:
The classification process is divided into distinct segments: generating permutation matrices from molecular structures, comparing matrices using graph theory, and classifying into conformers or rotamers based on equivalence. This segmentation allows each step to be optimized independently, improving accuracy without overwhelming complexity
Solution Approach 2:
Permutation matrices serve as an intermediary representation between raw molecular structures and final classifications. These matrices enable systematic comparison using graph theory, bridging the gap between structural data and accurate conformer/rotamer identification
2Reliability
If a simple classification method is used, then the computational process is fast, but the reliability of spectroscopic predictions is compromised
Solution Approach 1:
The method performs preliminary classification of molecular structures into conformers and rotamers before spectroscopic prediction. By pre-organizing structures using permutation matrices and graph theory equivalence checks, the reliability of subsequent spectroscopic calculations is enhanced without requiring complex post-processing
Solution Approach 2:
The patent replaces traditional mechanical comparison methods with graph theory-based equivalence checking. This substitution provides a more rigorous mathematical foundation for determining structural equivalence, improving reliability while maintaining computational efficiency
3Measurement precision
If manual verification of molecular structure assignments is performed, then accuracy improves, but productivity and time consumption decrease
Solution Approach 1:
The classification system performs self-verification through automated permutation matrix comparison and graph theory equivalence checks. The method autonomously identifies conformers and rotamers without requiring manual intervention, maintaining high accuracy while preserving computational speed and productivity
Data Source
Figure 1
Figure 2
Figure 3
AI summary
The present invention relates to an apparatus (10) for completing an incomplete set of permutations (31) representing a plurality of equivalent sets (30) of molecular structures, for example for simulating NMR spectra (40) and/or thermodynamic properties and/or chemical reactions, comprising: an interface (60) for receiving input data (70) relating to the incomplete set of permutations (31), a processing unit (80) for (a) converting the incomplete set of permutations (31) into a plurality of permutation matrices (32), wherein each permutation matrix preferably represents one individual molecular structure, (b) generating a new permutation matrix (34) by multiplying (33) one individual permutation matrix of the plurality of permutation matrices (32) with another individual permutation matrix of the plurality of permutation matrices (32) or with itself, (c) comparing (35) the new permutation matrix (34) with the plurality of permutation matrices (32) for determining if the new permutation matrix (34) is identical or not identical to any other individual permutation matrix of the plurality of permutation matrices (32), (d) including (36) the new permutation matrix (34) into the plurality of permutation matrices (32), if the new permutation matrix (34) is not identical to any other individual permutation matrix of the plurality of permutation matrices (32), (e) repeating (b) to (d), at least until all possible different multiplications (33) within the plurality of permutation matrices (32), including the multiplications of individual permutation matrices with themselves, have been performed. The present invention further relates to a method for completing an incomplete set of permutations (31), a computer program, a data carrier signal and a computer-readable medium.