Molecular design apparatus and method

Patent metadata

Field	Value
Publication number	US-9514253-B2
Application number	US-201213692546-A
Country	US
Kind code	B2
Filing date	Dec 3, 2012
Priority date	Feb 1, 2012
Publication date	Dec 6, 2016
Grant date	Dec 6, 2016

Abstract

A molecular design apparatus is disclosed. Expansion coefficients applied to basis functions are calculated by expanding molecular orbital functions used to draw molecular orbitals based on the molecular structure design data. First molecular orbital data in which the expansion coefficients are corresponded to the basis functions is stored to the storage part. A coefficient threshold is determined for the expansion coefficients of the basis functions by using a drawing threshold which indicates a constant function value, to draw the molecular orbital functions as an isosurface of the constant function value on a screen of a display device. Second molecular orbital data pertinent to the expansion coefficients is stored based on the coefficient threshold to the storage part.

First claim

What is claimed is:

1. A molecular design apparatus, comprising:
a storage part configured to store molecular structure design data;
a molecular orbital function expansion part configured to calculate expansion coefficients applied to basis functions by expanding a molecular orbital function used to draw molecular orbitals based on the molecular structure design data, and stores to the storage part first molecular orbital data, the expansion coefficients corresponding to the basis functions;
a molecular orbital data reduction part configured to determine a coefficient threshold for the expansion coefficients of the basis functions acquired by the molecular orbital function expansion part by using a drawing threshold which indicates a constant function value to draw the molecular orbital functions as an isosurface of the constant function value on a screen of a display device, and to store to the storage part second molecular orbital data in which the expansion coefficients of the basis functions are reduced based on the coefficient threshold; and
a molecular orbital drawing part configured to draw the molecular orbitals on the screen of the display device by using the second molecular orbital data stored in the storage part,
wherein the molecular orbital data reduction part includes a threshold determination part configured to set a basis threshold indicating function values in a range for ignoring overlaps of a basis function to other basis functions for each of the basis functions in the molecular orbital function, to calculate a coordinate threshold indicating a coordinate value corresponding to the basis threshold, to calculate a maximum value of a number of atoms included in a sphere having a predetermined radius based on the coordinate threshold from a center coordinate of each of the atoms forming a molecule, to calculate a value where a ratio of a total electron number of the molecule to a total number of the basis functions is multiplied to a number of the basis functions for each of the atoms or a basis ratio corresponding to the value, and to determine the coefficient threshold based on the drawing threshold, the basis threshold, the maximum value of the number of the atoms, and the basis ratio.

2. The molecular design apparatus as claimed in claim 1 , wherein the molecular orbital data reduction part includes a data deletion storage part configured to store the second molecular orbital data including the expansion coefficients being greater than or equal to the coefficient threshold determined by the threshold determination part by referring to the first molecular orbital data.

3. The molecular design apparatus as claimed in claim 2 , wherein the second molecular orbital data includes
a coefficient array which stores the expansion coefficients being greater than or equal to the coefficient threshold;
a basis function indication array in which an element number thereof is equal to the element number of the coefficient array and stores pointers to the basis functions; and
a molecular orbital indication array in which the element number thereof is equal to a total number of the basis functions or is one more than the element number of the basis functions, and which stores a pointer to a first expansion coefficient for each of the molecular orbital functions in the expansion coefficient data, and
when the molecular orbital data reduction part stores the second molecular orbital data in the storage part, a reduction flag in the storage part is set to indicate that the expansion coefficients are reduced in which the reduction flag is not set when the first molecular orbital data is stored in the storage part.

4. The molecular design apparatus as claimed in claim 3 ,
wherein the molecular orbital drawing part includes:
a molecular orbital function determination part configured to determine each of approximate orbital functions approximating the molecular orbital functions by using the coefficient array, the basis function indication array, and the molecular orbital indication array in the second molecular orbital data, when the reduction flag indicates that the expansion coefficients are reduced.

5. The molecular design apparatus as claimed in claim 4 , wherein the molecular orbital drawing part draws the molecular orbitals by using the first molecular orbital data when the reduction flag does not indicate that the expansion coefficients are reduced.

6. A molecular design method performed in a computer, the method comprising:
calculating, by the computer, expansion coefficients pertinent to basis functions by expanding molecular orbital functions used to draw molecular orbitals to the basis functions based on molecular structure design data stored in a storage part, and stores first molecular orbital data, the expansion coefficients corresponding to the basis functions, to the storage part;
determining, by the computer, a coefficient threshold with respect to the expansion coefficients of the basis functions acquired in the calculating, by using a drawing threshold which indicates a constant function value to draw the molecular orbital functions as an isosurface of the constant function value on a screen of a display device;
storing, by the computer, second molecular orbital data in which the expansion coefficients of the basis functions are reduced based on the coefficient threshold to the storage part; and
drawing, by the computer, the molecular orbitals on the screen of the display device by using the second molecular orbital data stored in the storage part
wherein the determining of the coefficient threshold includes setting a basis threshold indicating function values in a range for ignoring overlaps of a basis function to other basis functions for each of the basis functions in the molecular orbital function, calculating a coordinate threshold indicating a coordinate value corresponding to the basis threshold, calculating a maximum value of a number of atoms included in a sphere having a predetermined radius based on the coordinate threshold from a center coordinate of each of the atoms forming a molecule, calculating a value where a ratio of a total electron number of the molecule to a total number of the basis functions is multiplied to a number of the basis functions for each of the atoms or a basis ratio corresponding to the value, and determining the coefficient threshold based on the drawing threshold, the basis threshold, the maximum value of the number of the atoms, and the basis ratio.

7. A non-transitory computer-readable recording medium having stored therein a program for causing a computer to execute a molecular design process comprising:
calculating expansion coefficients pertinent to basis functions by expanding molecular orbital functions used to draw molecular orbitals to the basis functions based on molecular structure design data stored in a storage part, and stores first molecular orbital data, the expansion coefficients corresponding to the basis functions, to the storage part;
determining a coefficient threshold with respect to the expansion coefficients of the basis functions acquired in the calculating, by using a drawing threshold which indicates a constant function value to draw the molecular orbital functions as an isosurface of the constant function value on a screen of a display device;
storing second molecular orbital data in which the expansion coefficients of the basis functions are reduced based on the coefficient threshold to the storage part; and
drawing the molecular orbitals on the screen of the display device by using the second molecular orbital data stored in the storage part
wherein the determining of the coefficient threshold includes setting a basis threshold indicating function values in a range for ignoring overla

Assignees

• Fujitsu Ltd

Inventors

• Satou Hiroyuki
• Matsuura Azuma

Classifications

• G16C10/00

  Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like · CPC title

• G09B23/26 Primary

  for molecular structures; for crystallography · CPC title

• G06F30/20

  Design optimisation, verification or simulation (optimisation, verification or simulation of circuit designs G06F30/30) · CPC title

• G16C20/50 Primary

  Molecular design, e.g. of drugs · CPC title

• G06F19/701

  Physics · mapped topic