JPS62163141A - Calculating device for surface area and volume of compound - Google Patents

Abstract

PURPOSE:To calculate the surface area or volume of a compound and an overlapping area of the surface area or volume of between atoms forming the compound, by using the spot positions obtained by using random numbers as the coordinate points of the surface or the inside of the compound. CONSTITUTION:A data base 7 is formed with the constitution attribute of a compound consisting of plural atoms and a converting means 8 converts a set of random numbers obtained from a random number generator 4 into a coordinate point between atoms extracted out of a compound having a prescribed atom constitution. A counting means 6 counts the coordinate points for each atom whose overlapping area of atoms is excluded by a deciding means 5 and calculates a ratio against all sets of generated random numbers. Then this calculated ratio is multiplied by the value serving as a prescribed unit system. N pieces of spots are produced on the surface or within the volume of an optional compound by means of random numbers. Then it is decided whether the positions of those spots should be checked and counted or not and the areas or volumes of the counted numbers are totalized. Thus the surface area or the volume of a compound is obtained uniformly. This shortens the calculating time and furthermore the area and the volume can also be calculated for an overlapping area between two different atoms.

Description

Detailed Description of the Invention [Summary] By using point positions generated using random numbers as each coordinate point on the surface or inside of a compound, it is possible to calculate the surface area or volume of the compound, as well as the distance between atoms constituting the compound. Calculate the surface area or volume of the overlapping portion.

[Industrial application field]

The present invention relates to the development of a device for calculating the surface area and volume of any compound.

Provided is a calculation device that can calculate the surface area, volume, etc. of a compound regardless of its shape.

[Conventional technology]

In conventional methods, the surface area, volume, etc. of each atom constituting a compound are calculated by, for example, cutting the atom along a plurality of planes perpendicular to the Y-axis and spaced at regular intervals δ.

To find the volume, find the area of the circle that appears on each cut plane,
Multiply this area by the above-mentioned δ to find the volume, perform this operation for each cut plane, and integrate to obtain the volume of the atom.

In the case of surface area, similarly find the circumference (arc) of the circle that appears on each cut plane, multiply this arc by a certain number to find the area,
By performing this operation on each cut plane and integrating them, the surface area of the atom can be determined.

[Problem that the invention seeks to solve]

With the conventional methods described above, it was possible to calculate the surface area, volume, etc. of each atom constituting some compounds individually, but the volume and surface area could not be calculated by the same calculation means, and their It has been impossible to calculate the surface area, volume, etc. when the shape is complex.

An object of the present invention is to provide a calculation device that can calculate the surface area, volume, etc. of a compound regardless of its shape.

[Failure to solve the problem]

As shown in FIG. 1, the above problem is solved by a random number generator 4, a conversion means 8 for positioning a coordinate point using a set of generated random numbers, a determining means 5 for determining a coordinate point, and a set of random numbers that satisfy the above-mentioned determination conditions. A device comprising a counting means 6 for counting a predetermined number of random numbers, and a means 2 for instructing the generation of a predetermined number of random numbers and calculating the ratio of the number of sets counted by the counting means 6 to the total number of sets of generated random numbers. , comprising a database 7 constructed from the constituent attributes of compounds composed of a plurality of atoms, and means for converting a set of random numbers from the random number generator 4 into coordinate points between each atom extracted from a compound having a predetermined atomic composition. 8, and the overlapping portion between each atom is eliminated by the determining means 5. The counting means 6 counts the number of coordinate points for each atom, and calculates the ratio of the generated random numbers to the total number of generated pairs. It is solved by multiplying by values that are in a predetermined unit system.

Further, the coordinate points are surface positions on a three-dimensional surface, and the unit system is area.

Further, the coordinate point is a volume position on a three-dimensional surface, and the unit system is a volume, which solves the problem.

[Effect]

According to the present invention, N points are generated on the surface or volume of an arbitrary compound using random numbers, the position of the point is checked, it is determined whether to count, and the area or volume of the counted point is determined. By calculating the total amount, the surface area or volume of the compound can be uniformly determined, which reduces the calculation time and makes it possible to calculate the area and volume of the overlapping part when two different atoms overlap. be.

〔Example〕

FIG. 1 is a diagram showing an embodiment of the present invention.

FIG. 2(a) is a diagram illustrating an example of a compound whose surface area, volume, etc. are calculated according to the present invention.

FIG. 2 (bl is an explanatory diagram of polar coordinates showing individual and mutual coordinates of atoms.

Figure 3 is a diagram showing whether a point on the surface of an atom overlaps with an adjacent atom. It is a diagram.

In the figure, 2 is a processor, 3 is a storage device, 4 is a random number generator, 5 is a determining means, 6 is a counting means, 7 is a database storing the composition of compounds and their attributes, etc., and 8 is a converting means.

Note that the storage device 3 stores an attribute development table for one compound α stored in the database 7.

This compound α is composed of atoms A, B, and C, as shown in FIG. Indicated by the attribute expansion table.

First, to find the surface area of atom A, random numbers are used to find points on the surface of the atom.

In this case, it is convenient to use three-dimensional polar coordinates to represent the position of the point. Since it is three-dimensional, the radius r, the angle θ,
Three elements of angle φ are required, but in this case, since it is a surface area, the radius r is constant. Therefore, the random number generator 4 is a random number for angle θ and angle φ (random number with minimum value 0 and maximum value 1)
is output, and converted into the output value of the random number generator 4 by the conversion means 8.
The second point on the surface is generated by multiplying the value by π as the value of angle θ and angle φ.

The larger the total number of points N8 is, the more accurate it is, and the area of one point generated on the surface of atom A is N3 of the surface area S of atom A.
It is 1/1.

Note that S, , -4πr8', r8 is the radius of the atom A, and a table in the storage device 3 developed from the database 7 is used.

In this case, the determination is that atom A and atom B overlap (the interatomic distance L1b is smaller than r, +rb), so the random number generator 4 is used to generate one point on the surface of the atom. For each point, the determining means 5 checks whether or not the point is in a part overlapping with atom B. If the point does not overlap with atom B, the counting means 6 counts the point and determines whether or not the point is in a part overlapping with atom B. If they overlap, they are not counted.

The determining means 5 calculates the distance Qnb between the point P8 generated on the surface of the atom A [Fig. 3 (a)] and the center of the atom B, and when this distance is smaller than the radius r of the atom B, it is determined that they overlap. Ori,
When the radius of atom B is larger than r, they do not overlap. Furthermore, when they are equal, they are touching.

Such a procedure is repeated N3 times, and the count number 03 at the time of completion is placed in the counting means 6.

The area of one point on the surface of an atom is S, /N, so the surface area of atom A that does not overlap with atom B is S x l
is expressed by the following formula.

S a l = ' n a However, na≦N
Similarly to II, the surface area Sel of the atom C can also be calculated.

In the case of the surface area Sbl of atom B, in order to calculate the overlapping atoms A and C on both sides, point P on the surface of atom B is calculated using a set of random numbers as shown in Figure 3(b). By calculating the distance Qba between this point P and the center of atom A, and the distance Qbc between this point P and the center of atom C, point P on the surface of atom B overlaps with atoms A and C. Determine whether or not the

Therefore, the surface area of the compound shown in FIG. 2(a) is Sa++
It can be easily obtained by calculating Sb+ + Sc+.

A similar calculation method can be used to calculate the volume.

The volume of atom A in the total volume of the compound shown in FIG. 2(a) is calculated as follows.

A random number generator 4 is used to generate points within the volume of the atom A. In this case, it is necessary for the random number generator 4 to prepare three random numbers with a minimum value of 0 and a maximum value of 1. That is, one for radius r, one for angle θ, and one for angle φ.

The coordinate value for the radius r is the value obtained by multiplying the output value of the random number generator 4 by the radius of the atom A using the value in the table stored in the storage device 3 extracted from the database 7 by the conversion means 8. .

The larger the total number of points N3 is, the more accurate it is, and the volume of one point generated within the volume of the atom A is 1/N8 of the volume of the atom A, ■3. Note that V,=4πr,'/3, and r3 is the radius of the atom A.

In this case, since atoms A and B overlap,
Each time a point is generated within the volume of the atom using a random number, the determining means 5 checks whether or not that point overlaps with atom B, and if it does not overlap with atom B. If so, that point is counted, and if it overlaps with atom B, it is not counted.

Judgment means 5 calculates the distance between a point generated inside atom A and the center of atom B, and when this distance is smaller than radius r of atom B, they overlap, and when it is larger than radius r of atom B, do not overlap. Furthermore, when they are equal, they are touching.

This procedure is repeated N@ times, and the count at the end is set as n8.

Since the volume of one point within the volume of an atom is V@/N8, the volume val of the atom A that does not overlap with the atom B is expressed by the following formula.

ll Using exactly the same method, the volume VCI of atom C that does not overlap with atom B is expressed by the following formula.

■, The volumes of atoms A and C were calculated excluding the parts that overlapped with atom B, so when calculating the volume of atom B, it is sufficient to calculate the total volume without considering the overlapped parts, so ■, -4πrb
It is 3/3.

Therefore, in Figure 2 (the total volume of the compound al is V B 1
+V 1. + VC.

As described above, according to the present invention, the surface area and volume of any compound can be easily calculated using the same calculation means.

〔Effect of the invention〕

As explained in detail above, according to the present invention, not only can the surface area and volume of any compound be easily calculated, but the algorithm is extremely simple and clear, so coding is simple and programs can be created easily. Furthermore, the surface area and volume of the overlapping portions of atoms constituting a compound can be easily determined using the same algorithm, and this has the great effect that if you want to improve accuracy, you only need to increase the number of points.

[Brief explanation of drawings]

FIG. 1 is a diagram showing an embodiment of the present invention. FIG. 2 (al is a diagram for explaining an example of a compound whose surface area, volume, etc. are calculated according to the present invention. FIG. 2 (bl is an explanatory diagram of polar coordinates showing individual and mutual coordinates of atoms. Figure 3 is a diagram showing whether a point on the surface of an atom overlaps with an adjacent atom, (a) shows the relationship between atom A and atom B, and fbl shows the relationship between atom A and atom C with respect to atom B. In the figure, 2 is a processor, 3 is a storage device, 4 is a random number generator, 5 is a determination means, 6 is a counting means, 7 is a data storage storing the composition of the compound and its attributes, etc., and 8 is a conversion device. It is a means.

Claims (1)

[Claims] 1. Random number generator (4), conversion means (8) for positioning coordinate points using a set of generated random numbers, determination means (8) for determining coordinate points (
5), a counting means (6) for counting the sets of random numbers that satisfy the above-mentioned judgment condition; a number of sets counted by the above-mentioned counting means (6) among the total number of sets of random numbers generated while instructing generation of a predetermined number of random numbers; means (2) for calculating the ratio of The set of coordinates for each atom are converted by the conversion means (8) into coordinate points between each atom extracted from a compound having a predetermined atomic configuration, and the overlapping portion between each atom is eliminated by the determination means (5). A surface area of a compound characterized in that the points are counted by the counting means (6), the ratio of the generated random numbers to the total number of generated pairs is calculated, and the ratio is multiplied by a value that becomes a predetermined unit system. Volume calculation device. 2. The device for calculating the surface area and volume of a compound according to claim 1, wherein the coordinate point is a surface position on a three-dimensional surface, and the unit system is area. 3. The device for calculating the surface area and volume of a compound according to claim 1, wherein the coordinate point is a volume position on a three-dimensional surface, and the unit system is volume.