Molecular modeling method and system
First Claim
1. A method for generating a three-dimensional model of a molecule, comprising the steps of:
- establishing X, Y, and Z coordinate axes for the molecule to be modeled such that a rectangular region is established with sides parallel to the coordinate axes;
establishing a grid of coordinates on the X, Y, and Z coordinate axes with a grid mesh size of sufficient resolution to identify atom points of the molecule and solvent points;
identifying for each point in the rectangular grid an identity as an atom point, a solvent point, or an empty space point, labeling each point with a representative identifier, and storing the representative identifiers in a three-dimensional character array;
identifying an important component of a solvent region at a grid point within said solvent region and combining said grid point with all grid points that can be connected to it with a chain of adjacent solvent grid points;
identifying surface points which form a trace in one dimension in each Z cross-section;
generating milling instructions for each Z cross-section by tracing along the surface points in the trace in each Z cross-section and writing the X, Y coordinates to instructions for controlling a computer controlled milling machine;
storing the tracing steps for each Z cross-section and correlated machine instructions;
labeling surface points on sheets with representative identifiers at points corresponding to the identified points in the rectangular grid;
retrieving the stored machine instructions and cutting the sheets representative of each Z cross-section with the milling instructions and the computer controlled milling machine; and
assembling the sheets, including aligning exposed representative identifiers, into labeled three-dimensional models representative of the molecule.
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Accused Products
Abstract
A method, performed on a computer (10), for generating representations of a molecule, both two- and three-dimensional, is provided. The method includes establishing X, Y, and Z coordinate axes for the molecule to be modeled such that a rectangular region is established with sides parallel to the coordinate axes. The method also includes establishing a grid of coordinates on the X, Y, and Z coordinates axes with a grid mesh size of sufficient resolution to identify atom points of the molecule and solvent points. Next, the method includes identifying surface points which form a trace in one dimension in each Z cross-section, and generating tracing instructions for each Z cross-section by tracing along the surface points in the trace in each Z cross-section and writing the X, Y coordinates to instructions for controlling a computer display or for controlling a computer controlled milling machine. The method also includes generating on a computer display a two-dimensional grid and surface geometry for the molecule including atom identifications using the tracing steps for each Z cross-section. Additionally, the method includes cutting sheets representative of each Z cross-section with the milling instructions and assembling the sheets into three-dimensional models representative of the molecule.
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Citations
18 Claims
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1. A method for generating a three-dimensional model of a molecule, comprising the steps of:
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establishing X, Y, and Z coordinate axes for the molecule to be modeled such that a rectangular region is established with sides parallel to the coordinate axes; establishing a grid of coordinates on the X, Y, and Z coordinate axes with a grid mesh size of sufficient resolution to identify atom points of the molecule and solvent points; identifying for each point in the rectangular grid an identity as an atom point, a solvent point, or an empty space point, labeling each point with a representative identifier, and storing the representative identifiers in a three-dimensional character array; identifying an important component of a solvent region at a grid point within said solvent region and combining said grid point with all grid points that can be connected to it with a chain of adjacent solvent grid points; identifying surface points which form a trace in one dimension in each Z cross-section; generating milling instructions for each Z cross-section by tracing along the surface points in the trace in each Z cross-section and writing the X, Y coordinates to instructions for controlling a computer controlled milling machine; storing the tracing steps for each Z cross-section and correlated machine instructions; labeling surface points on sheets with representative identifiers at points corresponding to the identified points in the rectangular grid; retrieving the stored machine instructions and cutting the sheets representative of each Z cross-section with the milling instructions and the computer controlled milling machine; and assembling the sheets, including aligning exposed representative identifiers, into labeled three-dimensional models representative of the molecule. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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10. A method for generating a two-dimensional representation of the surface of a molecule, comprising the steps of:
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establishing X, Y, and Z coordinate axes for the molecule to be modeled such that a rectangular region is established with side parallel to the coordinate axes; establishing a grid of coordinates on the X, Y, and Z coordinates axes with a grid mesh size of sufficient resolution to identify atom points of the molecule and solvent points; identifying for each point in the rectangular grid an identity as an atom point, a solvent point, or an empty space point, labeling each point with a representative identifier; identifying an important component of a solvent region at a grid point within said solvent region and combining said grid point with all grid points that can be connected to it with a chain of adjacent solvent grid points; identifying surface points which form a trace in one dimension in each Z cross-section; generating tracing instructions for each Z cross-section by tracing along the surface points in the trace in each Z cross-section and writing the X, Y coordinates to instructions for controlling a computer display; and generating on a computer display a two-dimensional grid and surface geometry for the molecule including representative identifiers using the tracing steps for each Z cross-section. - View Dependent Claims (11, 12, 13, 14)
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15. A system for generating a model of a molecule, comprising:
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circuitry operable to establish a X, Y, and Z coordinate axes for the molecule to be modeled such that a rectangular region is established with sides parallel to the coordinate axes; circuitry operable to establish a grid of coordinates on the X, Y, and Z coordinate axes with a grid mesh size of sufficient resolution to identify atom points of the molecule and solvent points; memory operable to store the X, Y, and Z coordinate axes, cross-sections, and grid; a processor operable to retrieve from memory the X, Y, and Z coordinate axes, correlated Z cross-sections, and grid and identify for each Z cross-section atom points, solvent points and empty space points in the grid, to identify an important component of a solvent region at a grid point within said solvent region and combining said grid point with all grid points that can be connected to it with a chain of adjacent solvent grid points, to label the atom and solvent points with representative identifiers, and store in said memory in a three-dimensional character array the representative identifiers; wherein said processor is operable to identify surface points which form a trace in one dimension in each Z cross-section; and a computer display to display a two-dimensional grid and surface geometry for the molecule including representative identifiers using the tracing steps for each Z cross-section. - View Dependent Claims (16, 17, 18)
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Specification