Molecular Coordinate Alteration via Vector and Matrix Operations
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Solution Overview
Problem
Existing methods face difficulties in specifying and altering the coordinates of atoms in a target molecule to change bond lengths, bond angles, or rotation angles, making it challenging to generate multiple states and calculate potential energy curves (PEC) effectively for drug or material development.
Innovation Solution
An information processing program and device that allow users to select atoms, designate changes in bond lengths, bond angles, or rotation angles, and alter coordinates based on unit vectors, normal vectors, or rotation matrices within a predetermined coordinate space, facilitating the generation of new states and PEC calculations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If existing methods are used to specify and alter atom coordinates, then the process becomes complex and difficult to operate, but the patent aims to improve ease of operation through a user-friendly interface
Solution Approach 1:
The patent introduces an information processing device as an intermediary between the user and the complex coordinate alteration process. The device provides a user interface that accepts simple designations (atom selections, bond length/angle/rotation specifications) and automatically performs the complex coordinate calculations and alterations, shielding the user from mathematical complexity while achieving precise molecular state generation
Solution Approach 2:
The system enables self-service by allowing users to directly designate atomic selections and geometric parameters through an intuitive interface. The information processing device then autonomously handles all coordinate alteration computations and state generation without requiring users to manually calculate or understand complex coordinate transformation mathematics
2Manufacturing precision
If manual coordinate specification methods are used, then manufacturing precision of molecular states is difficult to achieve, but the patent aims to improve precision through automated calculations
Solution Approach 1:
The patent replaces manual mechanical coordinate specification with automated computational methods. The information processing device uses mathematical calculations based on designated geometric parameters (bond lengths, angles, rotations) to precisely compute atomic coordinates, substituting error-prone manual specification with exact computational determination of molecular states
3Productivity
If multiple molecular states are generated for PEC calculation, then productivity increases, but the complexity of specifying each state increases
Solution Approach 1:
The patent implements dynamic state generation where the system can iteratively create multiple molecular states by sequentially altering coordinates based on different geometric parameter designations. The information processing device maintains flexibility to generate various states (different bond lengths, angles, rotations) from a base structure, enabling efficient PEC calculation across multiple conformations without requiring complex individual specification for each state
Data Source
AI summary
A recording medium stores a program for causing a computer to execute a process including: accepting selection of one or more atoms among a plurality of atoms that form a target molecule that exists in a predetermined coordinate space; and altering coordinates of each atom of the one or more atoms from first coordinates to second coordinates in the coordinate space based on: a unit vector between the coordinates of a first atom and a second atom of which a bond length is to be changed; a normal vector with respect to a plane formed by a first bond axis and a second bond axis of which a bond angle is to be changed; or a rotation matrix of the second atom of which a rotation angle is to be changed; or any combination of the unit vector, the normal vector, or the rotation matrix, in the coordinate space.