JPH09138819A - Storage medium for molecule structure figure generation - Google Patents

Abstract

PROBLEM TO BE SOLVED: To easily grasp structure and to generate a molecule structure figure superior in beauty at high speed by classifying the constitution atoms of a compound into a ring part and a chain part based on bonded atom pair data and individually obtaining the two-dimensional coordinates of the respective atoms. SOLUTION: A main routine 11 calls an atom pair data extraction routine 12, extracts bonded atom pair data and classifies plural pieces of bonded atom pair data extracted by a classification routine 13 into bonded atom pair data constituting the ring part and bonded atom pair data constituting the chain part. A ring part coordinate operation routine 14a and a chain part coordinate operation routine 14b calculate the two-dimensional coordinates of the respective atoms based on bonded atom pair data constituting the ring part and the chain part, and writes obtained two-dimensional coordinate data of the respective atoms into the columns of an X-coordinate and a Y-coordinate on a connection list generated in a main storage device. A molecule structure figure generation routine 15 generates picture data showing molecule structure based on written two-dimensional coordinate data on the respective atoms.

Description

Detailed Description of the Invention

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a storage medium for creating a molecular structure diagram in which a program for creating a molecular structure diagram which automatically creates an aesthetically superior molecular structure diagram at high speed by calculation is stored.

[0002]

2. Description of the Related Art Conventionally, in order to display a molecular structure diagram of a compound on a display or output it from a printer, it has been general to use the molecular structure diagram handwritten by a human with a mouse or the like. Further, for a simple molecular structure diagram, it was possible to perform an operation based on the bond information of each atom and automatically create a molecular structure diagram. A minimization method has been devised as a method for creating this. The minimization method is suitable for preparing a molecular structure diagram of a compound having a monocyclic structure having a small number of ring members.

The minimization method will be described below. For example, when the compound is a monocyclic 6-membered ring, the molecular structure is hexagonal. Each side of this hexagon is r1 to r6, and each apex angle is θ1 to θ6. Is calculated to be a minimum value, and each value (r1 to r6, θ1
~ Θ6) is obtained. Here, r ₀ and θ ₀ are, for example, r ₀
= 1.5, θ ₀ = 120 degrees, and other standard values. Note that k _r and k are weights and are positive constants.

By this calculation, r1 = r2 = ... = r6 =
r ₀ , θ1 = θ2 = ... = θ6 = θ ₀ . That is,
In the minimization method, an approximately regular hexagon is created as a molecular structure diagram of a 6-membered ring.

[0005]

However, none of the above-mentioned conventional methods is suitable for preparing a complicated molecular structure diagram such as a single ring or a condensed ring having a large number of ring members.

That is, when a complicated molecular structure diagram is created by handwriting, the shape is often distorted.
Moreover, when a complicated molecular structure diagram is created by the minimization method, it takes a lot of processing time, which is a problem.

The present invention solves such a problem, makes it easy to visually grasp the structure, and stores a molecular structure diagram creation program for automatically creating an aesthetically superior molecular structure diagram at high speed. The purpose is to provide a storage medium for creation.

[0008]

In order to solve the above-mentioned problems, a storage medium for creating a molecular structure diagram of the present invention is a storage medium having a program area for storing a program,
In the program area, a compound is constructed based on the atom pair data extraction routine that extracts the bond atom pair data that shows the bond relationship of each atom that composes the compound, and the bond atom pair data that is extracted by the atom pair data extraction routine. A classification routine for classifying whether each atom belongs to a ring portion or a chain portion, and a two-dimensional coordinate calculation routine for obtaining two-dimensional coordinates of each atom classified into the ring portion and / or the chain portion by the classification routine And a molecular structure diagram creation routine for creating a molecular structure diagram from the two-dimensional coordinates of each atom obtained by the two-dimensional coordinate calculation routine.

By storing the above-mentioned storage medium for creating a molecular structure diagram of the present invention in a predetermined information processing apparatus and reading the program for creating a molecular structure diagram stored in the program area, the program for creating a molecular structure diagram is informed. It can be executed by the processing device. That is, first, the atom pair data extraction routine is executed to extract the bond atom pair data indicating the bond relation of each atom constituting the compound. Next, a classification routine is executed to classify each atom into either a ring portion or a chain portion. This classification is performed based on the bonded atom pair data extracted by the atom pair data extraction routine.

Further, the two-dimensional coordinate calculation routine is executed to obtain the two-dimensional coordinates of each atom classified into the annular portion. In addition, the two-dimensional coordinates of each atom classified into the chain portion can be obtained. Then, a molecular structure diagram creation routine is executed to create a molecular structure diagram based on the thus obtained two-dimensional coordinates of each atom.

Here, the two-dimensional coordinate calculation routine has a first step of dividing the condensed ring into a plurality of single rings when the ring composed of each atom classified into the ring portion is a condensed ring, A predetermined monocycle is selected from among the monocycles divided in the first step, and when this monocycle is an m-membered ring (m is a natural number of 3 or more), it is regarded as a regular m-gon and the two From the second step of obtaining the two-dimensional coordinates and each of the single rings divided in the first step, select the single ring that is condensed to the specific single ring for which the two-dimensional coordinates of the atom have already been obtained. When the ring is an n-membered ring (n is a natural number of 3 or more), the two-dimensional coordinates of each atom are obtained as an n-gon that shares k (k is a natural number) sides with a specific monocycle. And the third step until all two-dimensional coordinates of each single ring divided in the first step are obtained. May and a fourth step of repeating.

Further, in the second step, a predetermined monocycle may be selected in accordance with the priority order defined corresponding to the number of members of each monocycle divided in the first step.

Further, in the third step, among the sides of the n-sided polygon, k sides shared with a specific monocycle are shared sides,
Let each other side be a non-shared side, and let the length of the auxiliary straight line connecting both ends of the line segment consisting of all shared sides be L (L is a known value)
In addition, the length of each side other than the shared side is set to r (r is a predetermined value), and the auxiliary straight line among the interior angles of the (n−k + 1) polygon that is composed of the auxiliary straight line and all non-shared sides The inner angle between the non-shared edge is α (radian) and the inner angle between the unshared edges is β (radian), and r · cos {((n−k−1)
[beta]-(n-k) [beta]) / 2} = L.cos ([beta] / 2) is calculated, and [alpha] = (n-k-1) ([pi]-
It is recommended that β) / 2 be calculated (π is the circular constant) and the two-dimensional coordinates of each atom be obtained from these calculated values.

Furthermore, the two-dimensional coordinate calculation routine is
From each atom classified as a chain, all the terminal atoms that are the ends of the chain structure are extracted, and from the extracted pair of terminal atoms, the terminal with the largest number of bonds contained between them. The fifth step of selecting an atom pair, the sixth step of finding the two-dimensional coordinates of each atom between the pair of terminal atoms selected in the fifth step, and the step of finding the terminal atom for which the two-dimensional coordinates have not yet been found. The 7th step of selecting the terminal atom having the largest number of bonds contained between the atom and the atom whose 2D coordinate has already been obtained, the terminal atom selected in the 7th step, and the 2D coordinate And an eighth step of obtaining two-dimensional coordinates of each atom between the obtained atom and the obtained atom.

Furthermore, in the sixth step and the eighth step, while keeping the inter-atom length constant and changing the bond angle in accordance with the number of atoms bonded to each atom,
It is recommended to obtain the two-dimensional coordinates of each atom in order from one end.

Further, in the atom pair data extraction routine, it is preferable that a pointing device is used to draw a molecular structure diagram of the compound on the display to extract the bond atom pair data based on the molecular structure diagram.

Furthermore, in the atom pair data extraction routine, the bond atom pair data may be extracted by reading out predetermined bond atom pair data from a bond table file in which a list of bond atom pair data is recorded.

[0018]

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT A preferred embodiment of the present invention will be described below with reference to the accompanying drawings. FIG. 1 is a block diagram showing a data structure of a storage medium 1 for creating a molecular structure diagram according to an embodiment of the present invention. The storage medium 1 for creating a molecular structure diagram comprises a program area A for storing programs, and a header area B for storing the number of blocks in the program area A, area management data of the program area A, and the like. Then, in the program area A, a molecular structure diagram creation program 10 that obtains two-dimensional coordinate data of each atom constituting the compound from the bond atom pair data of the compound and creates a molecular structure diagram from these two-dimensional coordinate data It is stored.

This molecular structure diagram creation program 10 constitutes a main routine 11 for supervising the processing, an atom pair data extraction routine 12 for extracting atom pair data showing the bond relation of each atom constituting the compound, and a compound. A classification routine 13 for classifying each atom into a ring portion and a chain portion is provided. Further, the molecular structure diagram creation program 10 includes a two-dimensional coordinate calculation routine 14 for obtaining two-dimensional coordinates of each atom classified into a ring portion and / or a chain portion, and a molecular structure diagram creation routine 15 for creating a molecular structure diagram. And a ring chain determination routine 16 for determining whether each atom pair data belongs to a ring portion or a chain portion. Further, the molecular structure diagram creation program 10 includes a ring portion detection routine 17 for detecting a ring portion and a chain portion detection routine 18 for detecting a chain portion.

Here, the two-dimensional coordinate calculation routine 14 is
It is composed of a ring portion coordinate calculation routine 14a for obtaining the two-dimensional coordinate data of each atom classified into the ring portion and a chain portion coordinate calculation routine 14b for obtaining the two-dimensional coordinate data of each atom classified into the chain portion. ing. Further, as the storage medium 1 for creating the molecular structure diagram, a flexible disk, a CD
Any information medium capable of recording information optically or magnetically such as ROM and MD may be used.

The molecular structure diagram creating program 10 stored in the molecular structure diagram creating storage medium 1 can be executed by a predetermined information processing device. An example of this information processing apparatus is shown in FIG.

FIG. 2 is a block diagram showing the configuration of the information processing device 20. As shown in FIG. 2, the information processing device 20
Is an image memory 30 for storing the image data 30a of the molecular structure diagram, a working memory 31 for temporarily storing the symbol data 31a and the like, and a molecular structure diagram creation program stored in the molecular structure diagram creation storage medium 1. A storage medium reader 40 for reading 10 is provided. In addition, the information processing device 20
Includes a main storage device 50 in which an operating system (OS) 51 is stored, a hard disk device 60 in which a binding table file 61 is stored, and a display 70 for displaying a molecular structure diagram.

Further, the information processing apparatus 20 has a mouse 71 which is a pointing device which receives input of handwritten figures, a keyboard 72 which receives input of symbol data such as chemical formulas, and a printer 73 which outputs a molecular structure diagram.
And a CPU 80 for controlling execution of the molecular structure drawing creation program 10 and the like. In addition to the mouse 71, the pointing device includes a tablet, a digitizer, and a light pen, and any of these devices may be provided instead of the mouse 71.

A plurality of connection tables 62 are registered in the connection table file 61 stored in the hard disk device 60. As shown in FIGS. 3A and 3B, the binding table 6
2 includes an atom table 62a and an atom pair table 62b. The atom table 62a is provided with columns for writing atom numbers, atom two-dimensional coordinates (X coordinates / Y coordinates), element names (generally, element symbols are used), and attributes (FIG. 3). (See (a)), the atom pair table 62b contains bond atom pair data, bond species (for example,
A single bond is 1, a double bond is 2, and a column for writing the structure is provided (see FIG. 3B). Here, the atom number is a number for identifying each atom constituting the compound by a computer. Although numbers are used as atomic numbers in the example of FIG. 3, they may be symbols. Further, the bond atom pair data is preferably expressed as a combination of atom numbers.

Next, the molecular structure drawing creating program 10 stored in the molecular structure drawing creating storage medium 1 is loaded into the information processing device 2.
The outline of the processing when it is executed at 0 will be described. As shown in FIG. 4, the operator operates the mouse 71 or the keyboard 7
When the user operates 2 to input the information of the molecular structure diagram, the bond table 62 of the compound for which the molecular structure diagram is created is created in the main storage device 50.

The mouse 71 is used to manually input the molecular structure diagram of the compound on the display 70 using the mouse 71. The numbers of the atoms of the handwritten molecular structure diagram C are stored in the main storage device 50. It is written in the column of the atom number of the bond table 62 created in. Further, bond atom pair data indicating the bond relationship of each atom in the molecular structure diagram C is written in the bond atom pair column of the bond table 62. In this way, with the input by the mouse 71, the binding table 62 for identifying the compound is created from the handwritten molecular structure diagram C.
However, at this stage, data (bonding atom pair, bond species, element name data) indicating the bond state of atoms is extracted from the handwritten molecular structure diagram C and written in the bond table 62. Nothing is written in the dimensional coordinate field.

In addition, the keyboard 72 is used to input a symbol string that specifies a binding table name corresponding to a predetermined compound using the keyboard 72. Then, based on the input symbol data 31a, the bond table 62 specified by this bond table name is read from the bond table file 61, and bond atom pair data and the like are extracted (recognized by the information processing device 20. ).

In this way, the mouse 71 and the keyboard 72 are
Whichever is used, a connection table 62 is obtained, and based on each data of this connection table 62, the calculation (annular portion coordinate calculation routine 14a, chained portion coordinate calculation routine 14b) described later is performed.
Etc.) is performed. As will be described later, the above calculation for obtaining the two-dimensional coordinates of atoms is performed based on the bond atom pair data, and the bond species and element name data are mainly used when creating image data of the molecular structure diagram.

The two-dimensional coordinate data obtained by this calculation is written in the two-dimensional coordinate column of the binding table 62, and the aesthetically excellent molecular structure diagram D is obtained based on the written two-dimensional coordinate data. Created. The created molecular structure diagram D can be displayed on the display 70 or output from the printer 73.

The joining table 62 thus obtained is stored by specifying the joining table name in the joining table file 61 in the hard disk device 60 as required. The keyboard 72
The input may be performed by directly writing the data indicating the bond state of atoms into the bond table created in the main storage device 50. Further, an input device such as an image scanner or an optical card reader (OCR) for optically reading figures or characters may be used as the input device to accept the input of the binding table data.

In particular, when the molecular structure diagram C is input by hand using the mouse 71 and the molecular structure diagram D obtained by the calculation is displayed on the display 70, the molecular structure diagram C is first displayed on the display 70. Is displayed, and then the molecular structure diagram D is displayed. As described above, the distorted molecular structure diagram C by handwriting is replaced with the aesthetically excellent distorted molecular structure diagram D, and the handwritten figure is reshaped.

Next, the molecular structure diagram creation program 10 stored in the molecular structure diagram creation storage medium 1 is loaded into the information processing device 2.
The flow of processing when it is executed at 0 will be described in detail. As shown in FIG. 2, when the molecular structure drawing creating storage medium 1 is inserted into the storage medium reader 40, the molecular structure drawing creating program 10 stored in the program area A of the molecular structure drawing creating storage medium 1 is executed. , Read by the storage medium reader 40. The molecular structure drawing creation program 10 read by the storage medium reader 40 is stored in the main storage device 50.
And is stored in the main storage device 50. Then,
When the operator inputs an operation start command using the keyboard, the molecular structure drawing program 1 under the control of the OS 51
The main routine 11 of 0 is started.

As shown in the flowchart of FIG. 5, the main routine 11 first extracts bond atom pair data recorded in the atom pair table 62b of the bond table 62 (S1).
0). This extraction is performed by calling the atom pair data extraction routine 12. Next, the plurality of extracted bond atom pair data are classified into bond atom pair data that forms the ring portion and bond atom pair data that forms the chain portion (S20). This classification is performed by calling the classification routine 13. Further, the two-dimensional coordinates of each atom in the ring portion are calculated based on the bond atom pair data forming the ring portion (S30). This calculation is performed by calling the annular portion coordinate calculation routine 14a.

Next, the two-dimensional coordinates of each atom in the chain portion are calculated based on the bond atom pair data forming the chain portion (S40). This calculation is performed by the chain portion coordinate calculation routine 14
Call b. Then, the chain portion is moved / rotated to couple the annular portion and the chain portion (S50). Specifically, as shown in FIGS. 6A to 6C, the annular portion 1
The coordinate conversion is performed on the two-dimensional coordinate data of each atom of the chain portion 110 obtained in the process of S40 so that the predetermined bond 101 of 00 and the predetermined bond 111 of the chain portion 110 match. In particular, the chain portion 110 is rotated while adjusting so that the branch angles θ _{1 to} θ _{3 of the} respective bonds 111, 113, 114 extending from the atom 112 of the bond portion are equal (θ ₁ = θ ₂ = θ ₃ ). Let

The two-dimensional coordinate data of each atom obtained by the processing of S30 to S50 is written in the X coordinate and Y coordinate columns of the binding table 62 created in the main storage device 50.

Next, based on the two-dimensional coordinate data of each atom written in the X-coordinate and Y-coordinate columns of the bond table 62, the image data 30a showing the molecular structure is created (S6).
0). This image data is created by calling the molecular structure drawing creation routine 15. Then, the image data 30a of the created molecular structure diagram is displayed on the display 70 (S70).

Next, the atom pair data extraction routine 12 will be described. The atom pair data extraction routine 12 is a subroutine called by the processing of S10 of the main routine 11. As shown in the flowchart of FIG. 7, the atom pair data extraction routine 12 first displays the input method selection screen on the display 70 (S10).
1). When the operator selects input with the mouse 71 according to this display screen (S102), a screen for molecular structure drawing is displayed on the display 70. Next, when the operator uses the mouse 71 to manually input a molecular structure diagram showing the structure of a predetermined compound, the input of the handwritten graphic data is accepted (S103). Then, the combination table 62 is created in the main storage device 50 based on the handwritten graphic data (S104).

Next, the input of handwritten graphic data with the mouse 71 will be specifically described. First, when the operator clicks the mouse 71, data on one atom forming the bond atom pair is input. Next, when the operator moves the mouse 71 and clicks the mouse 71, data on one atom and the other atom forming a bond atom pair is input. Then, the click for inputting the data for the other atom is regarded as a click for designating one atom of the next bond atom pair when the next click is subsequently made. In this way, a pair of bond atom pairs can be designated by two consecutive clicks of the mouse 71. That is, the operator continues to specify the bond atom pairs while shifting the atoms one by one, whereby all the bond atom pairs constituting the compound are input.

The atom number is written in the atom number column of the atom table 62a in correspondence with the input atom data. Further, the input data regarding the bond relation of the atoms is written in the column of the bond atom pair of the atom pair table 62b. Furthermore, when the operator inputs the element name of each atom, the element name is written in the element name column of the atom table 62a. Similarly, when the operator inputs the bond multiplicity connecting the bond atom pairs, the bond multiplicity is written in the bond type column of the atom pair table 62b.

In step S102, the operator operates the keyboard 7
When the input by 2 is selected, the symbol string input screen is displayed on the display 70. When the operator uses the keyboard 72 to input a symbol string of a binding table name that specifies a predetermined compound, the input of the symbol data 31a is accepted (S105). Then, the data of the joining table specified by the symbol data 31a is read from the joining table file 61 (S106), and the joining table 62 is created in the main storage device 50 (S107).

Further, after the processes of S104 and S107 are completed, the bond atom pair data is extracted from the atom pair table 62b of the bond table 62 created by these processes (S10).
8). Then, after the processing of S108 is completed, the atom pair data extraction routine 12 is completed and S20 of the main routine 11 is completed.
Return to processing.

Next, the classification routine 13 will be described. The classification routine 13 is S20 of the main routine 11.
It is a subroutine called by the processing of. FIG.
As shown in the flowchart of FIG. 5, in the classification routine 13, first, it is determined whether each bond atom pair data created by the atom pair data extraction routine 12 belongs to a ring structure or a chain structure (S201). This determination is made by calling the ring chain determination routine 16. And the judgment result is
As will be described later, it is set as structure data of the atom pair table of the bond table 62 stored in the main storage device 50.

Next, the annular portion is detected (S202). This detection is performed by calling the annular portion detection routine 17.
Further, a chain portion is detected (S203). This detection
This is performed by calling the chain detection routine 18. By the processing of S202 and S203, each bond atom pair data is classified into a ring portion and a chain portion, as described later. For example, as shown in FIG. 9, each bond atom pair data (1,
2), (2, 3), ... (40, 41) are classified into two sets of annular parts 120 and 130 and two sets of chain-like parts 140 and 150. Then, after the processing of S203 ends, the classification routine 13 ends, and the processing returns to S30 of the main routine 11.

Next, the annular portion coordinate calculation routine 14a will be described. The annular portion coordinate calculation routine 14a is a subroutine called by the processing of S30 of the main routine 11. As shown in the flowchart of FIG. 10, the annular part coordinate calculation routine 14a first determines whether the annular part classified by the classification routine 13 has a single ring structure (S301). In this treatment, the number of atoms is Na, the number of bonds is Nb, N = Nb-Na + 1, N is determined to be a single ring, and N is a number (integer) that is a condensed ring. Is determined. Incidentally, N is 0 in the case of a chain portion.

Here, terms used in the present invention will be explained. First, a “ring” or a “monocycle” means starting from one atom of any starting bond and performing the operation of tracing the bonds one after another, without tracing the starting bond and the bond and its atom once traced, When the other atom of the starting bond can be reached, it should be regarded as a loop formed by the starting bond and the traced bond. For example, assuming that atom 1 of the bond atom pair (1, 2) in FIG. 3 is one atom of the starting bond, the bonds that can be traced from atom 1 are bond (6, 1) and bond (1, 7). . Where the join (6,1)
If you select, the bonds (5,6), (4,5),
It is possible to reach the other atom 2 of the starting bond without following the starting bond and the bond which has been once traced and its atom by tracing the bonds in sequence with (3, 4) and (2, 3). Therefore, it can be said that the compound of FIG. 3 has a ring structure formed of the starting bond (1, 2) and the traced bond.

Further, the "ring portion" should be regarded as a group of bonds forming all "rings" formed by including arbitrary bonds. As described above, the “ring portion” is classified into a single ring (N = 1) and a condensed ring (N> 1).

When it is determined in step S301 that the structure is a monocyclic structure, the two-dimensional coordinates of each vertex are obtained as a regular n-sided polygon (in the case of an n-membered ring) (S302). In addition, when it is determined to be a condensed ring structure in the process of S301, a ring set having a minimum number of ring members (SSSR: Smallest Set of the minimum required to express all atoms and bonds that constitute the condensed ring structure). Smallest
Rings) is calculated (S303). This set of rings with the minimum required minimum ring member number can be performed using the exclusive OR method which is a known technique. This exclusive OR method is based on the document "Journal of Chemical Infomation and Computer Scie
nces, Vol. 15, No. 3, 1975 p140-p147 ”.

As can be seen from this document, the outline of the exclusive OR method is as follows.

(1) The number of atoms constituting the ring structure is N
a, and the number of bonds is Nb, a set of N (= Nb-Na + 1) or more independent monocycles (independent monocycle set) is created. Here, “independently from each other” means that there are one or more bonds contained in only one of the two rings.

(2) Subsequently, an arbitrary number of monocycles of N or more (duplication is not allowed) is selected from the independent monocycle set, and one of the bonds included in the selected monocycle subset is selected. If you select a bond that belongs to only one single ring (exclusive OR),
By connecting the selected bonds, another monocycle not included in the subset can be obtained.

(3) When the monocycle obtained in (2) is different from any of the monocycles constituting the independent monocycle set, it is added to form a new independent monocycle set.

(4) Returning to (2), processing is performed for all combinations of N or more monocycles, and repeated until no new monocycle is obtained.

(5) Since all mutually independent monocycles can be obtained by (1) to (4), N from the smallest independent monocyclic set obtained in the order of the number of ring members is N.
The SSSR is obtained by selecting the individual pieces.

SS obtained by this exclusive OR method
Taking SR as an example, the condensed ring 160 shown in FIG.
Is divided into a set of four single rings 161 to 163. Similarly, the condensed ring 170 shown in FIG. 11B is divided into a set of three single rings 171 to 173. That is, SSS
The exclusive OR method for obtaining R is a calculation method in which all the monocyclic rings that can be traced in the condensed ring are extracted, and N pieces are taken out in order from the smallest number of ring members to form a set.

Next, the highest priority among the obtained SSSRs (for example, 6-membered ring> 5-membered ring> 3-membered ring> 4-membered ring> 7-membered ring, ... A single ring (predetermined single ring) having a high priority is selected (S304). And the selected monocycle is an m-membered ring (m is
In the case of a natural number of 3 or more), a two-dimensional coordinate of each vertex is obtained as a regular m-gon (S305). Further, among the rings condensed to the single ring (specific single ring) for which the two-dimensional coordinates have already been obtained, the single ring with the highest priority is selected (S306).

Basically, the selection of the single ring in the processes of S304 and S306 is preferably performed in accordance with the priority order defined corresponding to the number of members of the ring. Further, in a monocycle having the same number of ring members, for example, a ring containing a nitrogen atom is in a lower rank, or a ring containing a double bond is in a higher rank. It is also preferable to further divide the rank into ranks. According to the knowledge of the inventor of the present application, when a 6-membered ring is selected as the highest basic order, a particularly aesthetically superior molecular structure diagram can be obtained.

Next, as shown in FIG. 12, a monocycle 181 that is condensed with a monocycle (specific monocycle) 180 for which two-dimensional coordinates have already been obtained is selected, and this monocycle 181 is an n-membered ring (n Is
In the case of a natural number of 3 or more), the two-dimensional coordinates of each atom are obtained as an n-gon that shares k sides (k = 2 in FIG. 12) with the monocycle 180 (S307). Specifically, a single ring 18
Among the sides of the n-sided polygon that form one, k sides shared with the single ring 180 are the shared sides 182, and the other sides are the non-shared sides 183. Then, the length of the auxiliary straight line 186 connecting both ends 184 and 185 of the line segment including all the shared sides 182 is set to L (L is a known value), and the length of each non-shared side 183 is r (r is (Predetermined value).

At this stage, the two-dimensional coordinates of each atom constituting the monocycle 180 have already been obtained, and the auxiliary straight line 1
The length L of 86 is a known value obtained from the two-dimensional coordinates of the atoms located at both ends 184 and 185. On the other hand, the length r is independent of the length of each side of the single ring 180,
It is a predetermined value that can be uniquely determined as the single ring 181.

Further, among the interior angles of the (n−k + 1) polygon which is composed of the auxiliary straight line 186 and all the non-shared edges 183,
The interior angle between the auxiliary straight line 186 and the non-shared side 183 is α (radian), and the interior angle between the non-shared sides 183 is β (radian). Then, r · cos {((n−k−1) π− (n
By calculating β that satisfies −k) β) / 2} = L · cos (β / 2), and by calculating α = (n−k−1) (π−β) / 2 (where π is Circularity), two-dimensional coordinates of each atom are obtained. Then, in the process of S306, if there is a single ring that has not been selected, the process returns to S306, and the processes of S306 and S307 are repeated (S30
8).

That is, in the processing of S307, among the atoms constituting the monocycle fused to a specific ring whose two-dimensional coordinates are known, all the atoms whose two-dimensional coordinates are unknown have bond length r and bond The unknown atoms are arranged so that the angles β are equal to each other, and the two-dimensional coordinates thereof are obtained. And
The arrangement of the unknown atoms is symmetrical with respect to the perpendicular bisector of the auxiliary straight line 186.

When it is determined in the processing of S308 that the two-dimensional coordinates of all the single rings have already been obtained, and when the processing of S302 ends, the annular portion coordinate calculation routine 14a is ended and the main routine 11 The process is returned to S40.

Incidentally, S303 corresponds to the first step, and S305 corresponds to the second step. Furthermore, S
306 and S307 correspond to the third step, and S30
8 corresponds to the fourth step.

Next, the chain portion coordinate calculation routine 14b will be described. The chain portion coordinate calculation routine 14b is a subroutine called by the processing of S40 of the main routine 11. As shown in the flowchart of FIG. 13, in the chain portion coordinate calculation routine 14b, first, all the terminal atoms that are the end portions of the chain structure are extracted and extracted from each atom classified into the chain portion. The terminal atom pair having the largest number of bonds contained therein is selected from the pair of terminal atoms (S401).

As shown in FIG. 14, the term "terminal atom" means, among a plurality of atoms bonded in a chain, the atoms a to c which are the ends of the chain structure. The term “terminal atom pair” means a combination of these terminal atoms a to c (a, b), (a, c),
Refers to (b, c). Here, the terminal atom pair (a, b),
The numbers of bonds included between (a, c) and (b, c) are 3, 10 and 11, respectively. Therefore, in the processing of S401, the terminal atom pair (b, c) is selected.

Then, the two-dimensional coordinates of each atom between the selected terminal atom pair are obtained (S402). As shown in FIG. 15, the two-dimensional coordinates of each atom 190 to 197 between the pair of terminal atoms (the pair of the terminal atom 190 and the terminal atom 197) have an angle (for example, 3 depending on the combination of adjacent bond species). When the heavy bonds are adjacent to each other, or when the double bond and the double bond are adjacent to each other, θ ₄ = 180 degrees, and in other cases, θ ₅ = 120 degrees) is used. From the one terminal atom 190, the distance between them is a constant value d,
The other terminal atom 197 is sequentially searched for. This two-dimensional coordinate is determined with consideration so as to satisfy the designation of the cis orientation and the trans orientation (trans orientation if not specified). It is preferable to accept the designation of the cis orientation or the trans orientation in the processing of the atom pair data extraction routine 12.

Next, the terminal atom having the largest number of bonds between the terminal atom for which the two-dimensional coordinate has not been obtained and the atom for which the two-dimensional coordinate has already been obtained (hereinafter referred to as branch point atom) is selected. (S403), two-dimensional coordinates of each atom between the branch point atom and the terminal atom are obtained (S404). As shown in FIG. 16, the two-dimensional coordinates of the atoms 198 to 200 between the branch point atom 192 and the terminal atom 200 are the branch point atom 1
The branching angle depending on the number of atoms bonded to 92 (for example, 3
Θ ₆ = 120 degrees for atomic bonds and θ _{7 for} 4 atomic bonds
= 90 degrees (θ ₇ is not shown). ), The length between atoms is set to a constant value d, and the values are sequentially obtained from the atom 198 toward the terminal atom 200.

If there is an atom that has not been selected in S403, the process returns to S403, and S403 and S40
The process of 4 is repeated (S405). In the process of S405,
When it is determined that the positions of all atoms have been obtained, the chain portion coordinate calculation routine 14b is ended, and the process returns to S50 of the main routine 11.

Note that S401 corresponds to the fifth step, and S402 corresponds to the sixth step. Furthermore, S
403 corresponds to the seventh step, and S404 corresponds to the eighth step.

Next, the molecular structure diagram creation routine 15 will be described. The molecular structure drawing creation routine 15 is a subroutine called by the processing of S60 of the main routine 11. As shown in the flow chart of FIG.
In the molecular structure drawing creation routine 15, first, the main memory 5
Each data of the combination table 62 stored in 0 is read (S601). Then, based on the read two-dimensional coordinate data, element name data, bond atom pair data, and bond species data, image data of the molecular structure diagram is created (S602).

Creation of this image data is performed in the following procedure. First, the two-dimensional coordinate data of each atom is plotted on the image data. Next, each atom plotted based on the bond atom pair data is connected by a straight line. Then, based on the element name data, a symbol indicating the element name is entered on the side of the two-dimensional coordinate position of each atom. Further, based on the bond type data, a plurality of straight lines (one single bond, two double bonds, etc.) are drawn between the atoms in order to express the type of bond.

The image data 30a of the molecular structure diagram thus created is stored in the image memory 30. Then, after the processing of S602 ends, the molecular structure diagram creation routine 1
5 is ended, and the process is returned to S70 of the main routine 11.

Next, the ring chain determination routine 16 will be described. The ring chain determination routine 16 is S of the classification routine 13.
This is a subroutine called by the processing of 201. The ring chain determination routine 16 is executed for each data selected from the bond atom pair data in the bond table 62, and the selected bond atom pair data belongs to either the ring portion or the chain portion. It is to determine whether there is.

Explaining along the flowchart of FIG. 18, the ring chain determination routine 16 first sets the attributes of all atoms in the atom table 62a included in the bond table 62 as follows.
"0" is written (S2011). Then, "1" is written in the attribute column of the first atom constituting the selected bond atom pair to be determined, and "2" is written in the attribute column of the second atom (S2012). Next, "1" is set to the flag of the reserved predetermined area in the main storage device 50 (S20).
13). Further, it is determined whether "1" is set in the flag (S2014). When it is determined in the process of S2014 that "1" is not set in the flag, "chain" is written in the structure column of the atom pair table 62b (S20).
15).

If it is determined in the process of S2014 that the flag is set to "1", the flag is set to "0" (S2016). Then, all the atoms (excluding the atom having the attribute "2" forming the bond atom pair to be determined) that are bonded to the atom having the attribute "1" are extracted (S201).
7). In the process of S2017, if the atom bonded to the atom of the attribute “1” is not extracted (NO), the process of S2015 is performed. In addition, in the process of S2017, when the atom that is bonded to the atom of the attribute “1” is extracted (YES),
Furthermore, for each extracted atom, the following (1)
The calculation of (4) is repeated.

(1) It is determined whether the attribute of the atom is "0" (S2018).

(2) In the process of S2018, if the attribute of the atom is "0", "1" is entered in the attribute column of the atom.
Is written and the flag is set to "1" (S2019).

(3) If the attribute of the atom is not "0" in the process of S2018, the attribute of the atom is "1".
It is determined (S201A).

(4) After the processing of S2019 is completed,
Alternatively, if the attribute is “1” in the process of S201A, the process is returned to S2018, the remaining extracted atoms are repeated, and (1) to
When the calculation of (3) is completed, the process is returned to S2014 (S201B).

(1) for all the extracted atoms
In the process of S201A in the middle of the loop operation of (3), if the attribute of the atom is not “1” (inevitably, the attribute of the atom is “2”), the column of the structure of the atom pair table 62b. The "ring" is written in (S201C). Furthermore, S20
After the processing of 15 or S201C is completed, the remaining bond atom pairs to be determined are selected and the ring chain determination routine 16 is repeatedly executed. Then, after the ring chain determination for all bond atom pairs is completed, the ring chain determination routine 16 is terminated, and the process returns to S202 of the classification routine 13.

Next, the annular portion detection routine 17 will be described. The annular portion detection routine 17 is the classification routine 13
This is a subroutine called by the processing of S202. As shown in the flowchart of FIG. 19, the cyclic part detection routine 17 first creates a partial bond table excluding the bonds consisting of the atom pairs belonging to the chain structure (S202).
1). Next, an arbitrary atom is selected from this partial bond table (S2022). Then, from the selected atoms, all the traceable atoms are selected along the bond given by the bond atom pair data (S2023).

The atom thus selected is given a partial structure number different from the partial structure number already used (if any) (S2024). Furthermore, it is determined whether there is an atom to which the partial structure number is not given (S20
25). If it is determined in S2025 that an atom having no partial structure number is present, an arbitrary atom is selected from the atoms having no partial structure number (S2026), and the process returns to S2023. Also, S2
In the processing of 025, when it is determined that the partial structure numbers have already been given to all the atoms, the ring portion detection routine 1
7 is ended, and the process is returned to S203 of the classification routine 13.

After all, when classifying a compound into a ring portion and a chain portion, if the ring portion detection routine 17 is executed, one ring portion of the compound is recognized by the computer as a set of atoms having the same partial structure number. can do. Further, the type (number) of the cyclic portion contained in the compound corresponds to the type of partial structure number.

Next, the chain portion detection routine 18 will be described. The chain portion detection routine 18 is the classification routine 13
This is a subroutine called by the processing of S203. As shown in the flowchart of FIG. 20, the chain portion detection routine 18 first creates a partial bond table excluding the bonds composed of atom pairs belonging to the cyclic structure (S203).
1). Next, an arbitrary atom is selected from this partial bond table (S2032). Then, from the selected atoms, all the traceable atoms are selected along the bond given by the bond atom pair data (S2033).

The atom thus selected is given a partial structure number different from the partial structure number (if any) already used (S2034). Furthermore, it is determined whether there is an atom to which the partial structure number is not given (S2
035). When it is determined in S2035 that there is an atom to which the partial structure number is not given, an arbitrary atom is selected from the atoms to which the partial structure number is not given (S2036), and the process is returned to S2033. Also, S2
In the processing of 035, when it is determined that the partial structure numbers have already been given to all the atoms, the chain portion detection routine 1
8 is ended, and the process is returned to the end of S203 of the classification routine 13.

After all, when classifying a compound into a cyclic part and a chain part, the chain part detection routine 18 is executed, and one chain part of the compound is calculated as a set of atoms having the same partial structure number. Can be recognized at. Further, the type (number) of chain-like portions contained in the compound corresponds to the type of partial structure number.

Next, the image data 3 displayed on the display 70 by the processing of S70 of the main routine 11.
An example of 0a is shown in FIG. Despite having a very complicated structure, the image data 30a could be created in a very short time of 1 second or less (not including the time for handwriting input by the mouse 71). As described above, the molecular structure drawing creation program 10 stored in the molecular structure drawing creation storage medium 1
Is suitable for quickly and neatly creating a molecular structure diagram of a complicated structure.

The present invention is not limited to the above embodiment, and various modifications can be made. For example, the process of S70 for displaying the image data of the molecular structure diagram on the display 70 is not essential, and may be output to the printer 73 instead of being displayed on the display 70. It may also be stored in the hard disk device 60 as a database.

Further, when atoms are close to each other or intersect with each other,
With respect to the bond included in the chain portion in which the cis orientation or the trans orientation is not specified, the treatment for avoiding the proximity or the intersection may be added by changing the cis orientation to the trans orientation or from the trans orientation to the cis orientation.

Furthermore, if atoms come close to each other in the process of obtaining the two-dimensional coordinates of the atoms in the condensed ring, S307
In the processing of 1, the proximity can be avoided by changing the value of r and performing the processing again.

Furthermore, when a molecular structure whose orientation is conventionally determined is included, the orientation of the entire molecular structure diagram may be changed to match it. As such, conventionally oriented molecules include steroids, vitamins and sugars.

[0091]

As described in detail above, if the storage medium for creating a molecular structure diagram of the present invention is used, by executing the program for creating a molecular structure diagram stored in the program area,
A molecular structure diagram is automatically created. In this automatic creation, first, each atom that constitutes the compound is classified into a ring portion and a chain portion based on the bond atom pair data. Then, the two-dimensional coordinates of each atom classified into the ring portion and the two-dimensional coordinates of each atom classified into the chain portion are separately obtained, and a molecular structure diagram is created from these two-dimensional coordinates. .

As described above, by classifying each atom constituting the compound into a ring portion and a chain portion and separately performing calculations on the ring portion and the chain portion, it is easy to visually grasp the structure. Moreover, it is possible to automatically create an aesthetically excellent molecular structure diagram at high speed.

In particular, even a complicated molecular structure diagram such as a single ring or a condensed ring having a large number of ring members can be extremely easily and automatically prepared in a short time.

[Brief description of the drawings]

FIG. 1 is a block diagram showing a data configuration of a storage medium for creating a molecular structure diagram according to an embodiment of the present invention.

FIG. 2 is a block diagram showing a configuration of an information processing device.

FIG. 3 is a diagram showing a structure of a connection table.

FIG. 4 is a diagram showing an outline of processing of a molecular structure drawing creation program.

FIG. 5 is a flowchart showing a flow of processing of a main routine.

6 (a) to 6 (c) are diagrams showing a method of connecting a ring portion and a chain portion.

FIG. 7 is a flowchart showing a processing flow of an atom pair data extraction routine.

FIG. 8 is a flowchart showing a processing flow of a classification routine.

FIG. 9 is a diagram showing a state in which each bond atom pair data is classified into a ring portion and a chain portion.

FIG. 10 is a flowchart showing a processing flow of an annular portion coordinate calculation routine.

11 (a) and (b) are diagrams showing a state in which a condensed ring is divided into a plurality of single rings by an exclusive OR method.

FIG. 12 is a diagram showing the two-dimensional coordinates of each atom constituting a monocycle fused to a specific monocycle.

FIG. 13 is a flowchart showing a processing flow of a chain portion coordinate calculation routine.

FIG. 14 is a diagram showing a pair of terminal atoms that are the ends of a chain structure.

FIG. 15 is a diagram showing two-dimensional coordinates of each atom forming a chain portion.

FIG. 16 is a diagram showing two-dimensional coordinates of each atom forming a chain portion.

FIG. 17 is a flowchart showing a processing flow of a molecular structure diagram creation routine.

FIG. 18 is a flowchart showing a processing flow of a ring chain determination routine.

FIG. 19 is a flowchart showing a processing flow of an annular portion detection routine.

FIG. 20 is a flowchart showing a processing flow of a chain portion detection routine.

FIG. 21 is a diagram showing an example of image data displayed on a display.

[Explanation of symbols]

1 ... Storage medium for creating molecular structure diagram, 10 ... Program for creating molecular structure diagram, 11 ... Main routine, 12 ... Atom pair data extraction routine, 13 ... Classification routine, 14 ... Two-dimensional coordinate operation routine, 14a ... Annular part coordinate operation Routine, 1
4b ... Chain chain coordinate calculation routine, 15 ... Molecular structure diagram creation routine, 16 ... Ring chain determination routine, 17 ... Ring chain detection routine, 18 ... Chain chain detection routine, 20 ... Information processing device, 30 ... Image memory, 31 ... Working memory, 40 ...
Storage medium reader, 50 ... Main storage device, 51 ... Operating system, 60 ... Hard disk device, 61 ... Combination table file, 70 ... Display, 71 ... Mouse, 7
2 ... Keyboard, 73 ... Printer, 80 ... CPU, A ...
Program area, B ... Header area.

Claims (8)

[Claims] 1. A program area for storing a program is provided, and by reading the program stored in the program area using a predetermined information processing apparatus, the program can be executed by the information processing apparatus. A storage medium, in the program area, an atom pair data extraction routine for extracting bond atom pair data indicating a bond relation between atoms constituting a compound, and the bond atom extracted by the atom pair data extraction routine. Based on the paired data, a classification routine for classifying whether each atom constituting the compound belongs to a cyclic part or a chain part, and the classification routine classified into the cyclic part and / or the chain part. A two-dimensional coordinate calculation routine for obtaining two-dimensional coordinates of each atom, and each of the elements obtained by the two-dimensional coordinate calculation routine Than the two-dimensional coordinates, the molecular structure diagram creating storage medium characterized by a molecular structure diagram generation program is stored which has a molecular structure diagram creation routine for creating a molecular structure diagram, the. 2. The two-dimensional coordinate calculation routine comprises: a first step of dividing the condensed ring into a plurality of single rings when the ring composed of each atom classified into the ring portion is a condensed ring. , A predetermined monocycle is selected from the monocycles divided in the first step, and when the monocycle is an m-membered ring (m is a natural number of 3 or more), each atom is regarded as a regular m-gonal From the second step of obtaining the two-dimensional coordinates of, and a monocycle fused to a specific monocycle for which the two-dimensional coordinates of the atom have already been obtained, are selected from among the monocycles divided in the first step. , If this monocycle is an n-membered ring (n is a natural number of 3 or more), k and the specific monocycle (k is a natural number)
As a n-sided polygon sharing the sides of, the third step of obtaining the two-dimensional coordinates of each atom, and the third step until all the two-dimensional coordinates of each single ring divided in the first step are obtained. 4. A storage medium for creating a molecular structure diagram according to claim 1, further comprising a fourth step of repeating the steps. 3. In the second step, a predetermined single ring is selected in accordance with a priority order defined corresponding to the number of members of each single ring divided in the first step. The storage medium for creating a molecular structure diagram according to claim 2. 4. In the third step, among the sides of the n-sided polygon, k shared with the specific monocycle is used.
The length of an auxiliary straight line connecting both ends of a line segment composed of all the shared edges is set to L (L is a known value), with each side as a shared edge and each of the other edges as a non-shared edge, and Let r (r is a predetermined value) be the length of each side other than the shared side, and be composed of the auxiliary straight line and all the non-shared sides (nk).
Among the interior angles of the +1) polygon, the interior angle between the auxiliary straight line and the non-shared edge is α (radian), and the interior angle between the non-shared edges is β (radian), and r · cos {((n- k−1) π− (n−k) β) /
2} = L · cos (β / 2) is satisfied, and α = (n−k−1) (π−β) / 2 is calculated (π is a circular constant), and these calculations are performed. The storage medium for creating a molecular structure diagram according to claim 2, wherein the two-dimensional coordinates of each atom are obtained from the values. 5. The two-dimensional coordinate calculation routine extracts all terminal atoms that are end portions of a chain structure from each atom classified into the chain portion, and the extracted pair of terminal atoms is extracted. From among the terminal atom pairs having the largest number of bonds contained therein, and two-dimensional coordinates of each atom between the terminal atom pairs selected in the fifth step. A sixth step, and selecting the terminal atom having the largest number of bonds contained between the terminal atom for which the two-dimensional coordinates have not yet been determined and the atom for which the two-dimensional coordinates have already been determined. And the eighth step of obtaining the two-dimensional coordinates of each atom between the terminal atom selected in the seventh step and the atom for which the two-dimensional coordinates have already been obtained. A storage medium for preparing a molecular structure diagram according to claim 1. 6. In the sixth step and the eighth step, the length between atoms is made constant, and the bond angle is changed according to the number of atoms bonded to each atom, in order from one end. The storage medium for creating a molecular structure diagram according to claim 5, wherein two-dimensional coordinates of each atom are obtained. 7. The atomic pair data extraction routine draws a molecular structure diagram of the compound on a display by using a pointing device, and extracts the bonded atom pair data based on the molecular structure diagram. The storage medium for creating a molecular structure diagram according to claim 1, wherein 8. The atom pair data extraction routine extracts the bond atom pair data by reading the predetermined bond atom pair data from a bond table file in which a list of the bond atom pair data is recorded. The storage medium for creating a molecular structure diagram according to claim 1, wherein