JP2878624B2 - Display device and display method of molecular structure diagram - Google Patents

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a molecular structure diagram display device and a display method for displaying a molecular structure diagram which is easy to visually recognize and which is aesthetically excellent on a display.

[0002]

2. Description of the Related Art Conventionally, in order to display a molecular structure diagram of a compound on a display, it has been general to use a molecular structure diagram handwritten on a display by a human using a mouse or the like as it is. For a molecular structure diagram having a simple structure, it was also possible to automatically create a molecular structure diagram by calculation and display the created molecular structure diagram on a display.

[0003]

However, when any of the above-mentioned conventional methods is used, if the structure is complicated such as a condensed ring, particularly a condensed ring sharing three or more atoms, aesthetically, It has been difficult to display an excellent, particularly highly symmetric, molecular structure diagram on a display.

That is, when a molecular structure diagram having a complicated structure is created by handwriting, the shape is often distorted, which is a problem. In addition, when a molecular structure diagram having a complicated structure is automatically created, it takes a long processing time and sometimes the shape is distorted.

The present invention solves such a problem, and even if the molecular structure diagram has a complicated structure such as a condensed ring, it automatically creates an aesthetically superior molecular structure diagram with high symmetry in particular. It is an object of the present invention to provide a display device and a display method of a molecular structure diagram which can be displayed by using the method.

[0006]

[0007]

[0008]

According to the present invention, there is provided an apparatus for displaying a molecular structure diagram, comprising: input means for receiving an input of bonding atom pair data indicating a bonding relationship between atoms constituting a compound; Processing means for creating a molecular structure diagram of the compound based on the bond atom pair data, a display on which the molecular structure diagram of the compound created by the processing means is displayed, and a molecular structure of the compound on the display A display device for a molecular structure diagram, comprising: a display control unit for displaying a diagram, wherein the processing unit includes a condensed ring based on the bonding atom pair data received by the input unit. In order to form a set of single rings having the minimum number of ring members necessary to represent all atoms and bonds constituting the condensed ring, the condensed ring is divided into a plurality of single rings. Means, extraction means for extracting a combination of monocycles which share three or more atoms and condensed with each other from the plurality of monocycles, and each bond in the combination of monocycles is A shared covalent bond A and another non-shared non-covalent bond B
Classifying means, and the length of the non-covalent bond B and the angle between the bonds B are equal for each ring,
Coordinate calculation means for obtaining two-dimensional coordinates of each atom constituting the combination of the single ring, and a molecular structure diagram creating means for creating a molecular structure diagram of the compound from the two-dimensional coordinates of each atom,
It has. Here, the processing means, based on the bonding atom pair data received by the input means, classifies whether each atom constituting the compound belongs to a cyclic portion or a chain portion. And a ring determining means for determining whether a ring composed of atoms classified into the cyclic portion belongs to a condensed ring or a single ring.

[0009]

[0010]

According to the method for displaying a molecular structure diagram of the present invention, a molecular structure diagram of a compound is displayed on the display by using a molecular structure diagram display device provided with an input means, a processing means, a display, and a display control means. In the method of displaying a molecular structure diagram to be displayed, a first step in which input of bond atom pair data indicating a bond relationship of each atom constituting the compound is received by the input means, and the step in which the input is accepted in the first step A second step of creating a molecular structure diagram of the compound by the processing means based on the bond atom pair data;
And a third step of displaying the molecular structure diagram of the compound prepared in the second step on a display by the display control means, wherein the second step is performed in the first step. Based on the bonding atom pair data, when the compound contains a condensed ring, a single ring set having a minimum number of minimum ring members necessary to represent all atoms and bonds constituting the condensed ring. A dividing step of dividing the condensed ring into a plurality of monocycles by the processing means, and treating the combination of the monocycles, which share three or more atoms among the plurality of monocycles and are fused together, And extracting each bond in the single ring combination into a covalent bond A shared in the single ring combination and another non-covalent bond B in the single ring combination. And a two-dimensional coordinate of each atom constituting the combination of the single rings so that the length of the non-covalent bond B and the angle between the bonds B are equal for each ring. And the two-dimensional coordinates of each atom,
Creating a molecular structure diagram of the compound by the processing means. here,
In the second step, the processing means classifies, based on the bonding atom pair data received in the first step, whether each atom constituting the compound belongs to a cyclic portion or a chain portion. A ring determination step, and a ring determination step of determining by the processing unit whether a ring composed of atoms classified into the cyclic portion belongs to a condensed ring or a single ring. Good.

The number of bonds extending from each atom constituting the condensed ring, which is counted in the condensed ring, is the number of bonds forming a ring, ie, a ring, and the number of bonds not forming a ring such as a side chain. Is not included. The length of the connection and the degree of the identity of the angle between the connections depend on the visual sensitivity of the operator, but the resolution level of an output device such as a display or a printing device is sufficient.

[0013]

[0014]

[0015]

According to the molecular structure diagram display device of the present invention, the input means accepts bond atom pair data indicating the bond relationship of each atom constituting the compound. The bond atom pair data is passed to the processing means, and the processing means creates a molecular structure diagram of the compound based on the bond atom pair data. In particular, the bond atom pair data is data of a compound consisting of only a condensed ring, and is included in a set of rings having a minimum number of minimum members necessary to represent all atoms constituting the condensed ring and a bond. In a combination of the above, when an arbitrary pair of rings share three or more atoms and are fused to each other, each bond in the pair of rings is shared with a bond A in which the atoms are shared by the pair of rings. The molecular structure diagram is created such that the length of the bond B and the angle between the bonds B are equal to each other for each ring separately from the bond B that is not formed. Then, the molecular structure diagram of the compound created by the processing means is passed to the display control means,
In the display control means, a molecular structure diagram of the compound is displayed on a display.

[0016]

[0017]

According to the method for displaying a molecular structure diagram of the present invention, first, in a first step, an input of bond atom pair data indicating a bond relationship between atoms constituting a compound is received. Next, in a second step, a molecular structure diagram of the compound is created based on the bonding atom pair data received in the first step. In particular, the bond atom pair data is data of a compound consisting of only a condensed ring, and is included in a set of rings having a minimum number of minimum members necessary to represent all atoms constituting the condensed ring and a bond. In the combination of
When an arbitrary pair of rings share three or more atoms and are condensed with each other, each bond in the pair of rings is replaced with a bond A whose atoms are not shared with a bond A shared by the pair of rings. B, the molecular structure diagram is created such that the length of the bond B and the angle between the bonds B are equal for each ring. Then, in a third step, the molecular structure diagram of the compound prepared in the second step is displayed on a display.

[0019]

DESCRIPTION OF THE PREFERRED EMBODIMENTS Preferred embodiments of the present invention will be described below with reference to the accompanying drawings.

FIG. 1 is a diagram showing a configuration of a display device of a molecular structure diagram according to an embodiment of the present invention. As shown in FIG.
The molecular structure diagram display device 1 displays the image data 10 of the molecular structure diagram.
a working memory 11 for temporarily storing symbol data 11a and the like, a main storage device 20 for storing an operating system (OS) 21 and a molecular structure diagram display program 22, and a connection table. A hard disk device 30 in which a file 31 is stored.

A display 40 for displaying a molecular structure diagram, a mouse 50 as a pointing device for receiving an input of a handwritten figure, a keyboard 60 for receiving input of symbol data such as a chemical formula, and a printer 70 for outputting a molecular structure diagram And a CPU 80 for controlling the execution of the molecular structure diagram display program 22 and the like. In addition to the mouse 50, the pointing device includes a tablet, a digitizer, a light pen, and the like. Any of these devices may be provided instead of the mouse 50.

The molecular structure diagram display program 22 obtains two-dimensional coordinate data of each atom constituting the compound from the bond atom pair data of the compound, creates a molecular structure diagram from these two-dimensional coordinate data, and displays it on the display 40. This is the program to be displayed. This molecular structure diagram display program 22
Input unit 100a, processing unit 100b, and display control unit 100c
And a main routine 100 for controlling the processing.
And an atom pair data extraction routine 101 for extracting atom pair data indicating a bonding relationship between atoms constituting the compound, and a classification routine 102 for classifying each atom constituting the compound into a cyclic portion and a chain portion. ing. Further, the molecular structure diagram display program 22 includes a cyclic part coordinate calculation routine 103 for obtaining two-dimensional coordinate data of each atom classified into a cyclic part.
And a chain part coordinate calculation routine 104 for obtaining two-dimensional coordinate data of each atom classified into a chain part, and a molecular structure diagram creation routine 105 for creating a molecular structure diagram.

Further, a molecular structure diagram display program 22
Are a chain determination routine 106 for determining whether each atom pair data belongs to a ring or a chain, a ring detection routine 107 for detecting a ring, and a chain detection for detecting a chain. And a routine 108.

The hard disk device 30 stores a connection table file 31 capable of recording a plurality of connection tables 32. As shown in FIG. 2A and FIG.
2 has an atom table 32a and an atom pair table 32b. The atom table 32a includes columns for writing the atom number, the two-dimensional coordinates (X coordinate / Y coordinate) of the atom, the element name (generally, an element symbol is used), and the attribute (FIG. 2). (A), the atom pair table 32b stores the bond atom pair data and the bond type (for example,
A single bond is 1, a double bond is 2, and a column for writing a structure is provided (see FIG. 2B). Here, the atom number is a number for identifying each atom constituting the compound by a computer, and is a number in the example of FIG. 2A, but may be a symbol. Also, the bond atom pair data is preferably expressed as a combination of atom numbers.

Next, an outline of a method for displaying a molecular structure diagram using the molecular structure diagram display device 1 will be described. As shown in FIG. 3, the operator operates the mouse 50 or the keyboard 60 to display the binding table 32 of the compound whose molecular structure is to be created.
Can be created in the main storage device 20.

The input by the mouse 50 is for manually inputting the molecular structure diagram of the compound on the display 40 using the mouse 50. The number of each atom of the handwritten molecular structure diagram A is stored in the main storage device 20. Is written in the column of the atom number in the bonding table 32 created in the step (1). Further, the bonding atom pair data indicating the bonding relationship of each atom in the molecular structure diagram A is written in the column of the bonding atom pair in the bonding table 32. Thus, with the input by the mouse 50, the binding table 32 for specifying the compound is created from the handwritten molecular structure diagram A.
At this stage, however, data (bonding atom pairs, bonding species, and element name data) indicating the bonding state of atoms is extracted from the handwritten molecular structure diagram A and written into the bonding table 32.
Nothing has yet been written in the two-dimensional coordinate column of the connection table 32.

The keyboard 60 is used to input a symbol string for specifying a binding table name corresponding to a predetermined compound by using the keyboard 60. Based on the input symbol data 11a, this binding table is input. The binding table 32 specified by the name is read from the binding table file 31,
Bonded atom pair data and the like are extracted.

As described above, the mouse 50 and the keyboard 60
By using any one of the above, the connection table 32 is obtained, and based on each data of the connection table 32, calculations (to be described later, a circular portion coordinate calculation routine 103, a chain portion coordinate calculation routine 104)
Etc.) is performed. As described later in detail, the above calculation for obtaining the two-dimensional coordinates of the atoms is performed based on the bond atom pair data, and the bond species and element name data are mainly used at the time of creating image data of a molecular structure diagram. . The two-dimensional coordinate data obtained by this operation is written in the two-dimensional coordinate column of the connection table 32, and an aesthetically superior molecular structure diagram B is created based on the written two-dimensional coordinate data. . The created molecular structure diagram B is
It is displayed on the display 40 by the instruction of 0.

The binding table 32 thus obtained is written and stored in the binding table file 31 in the hard disk drive 30 by designating the binding table name as necessary. The input from the keyboard 60 may be performed by directly writing the data indicating the bonding state of the atoms into the bonding table in the main storage device 20. Further, an apparatus for optically reading figures and characters, such as an image scanner or an optical card reader (OCR), may be used as the input device of the present invention to receive the input of the connection table data.

In particular, when the molecular structure diagram A is inputted by handwriting using the mouse 50 and the molecular structure diagram B obtained by the calculation is displayed on the display 40, the molecular structure diagram A is first displayed on the display 40. Is displayed, and then the molecular structure diagram B is displayed. In this way, the handwritten distorted molecular structure diagram A is replaced with the aesthetically superior undistorted molecular structure diagram B, and the handwritten figure is shaped (reshaped).

Next, a method of displaying a molecular structure diagram using the molecular structure diagram display device 1 will be described in detail. First, OS
Under the control of 21, the main routine 100 of the molecular structure diagram display program 22 is started.

As shown in the flowchart of FIG. 4, the main routine 100 includes an input unit 100a and a processing unit 100b.
And a display control unit 100c.
S10, the processing unit 100b has S20 to S60, and the display control unit 100c has S70. Then, by causing the input unit 100a to be executed under the control of the CPU 80, the input unit 100a functions as an input unit that receives input of bond atom pair data indicating a bond relationship between atoms constituting the compound. Further, the processing unit 100b is
The processing unit 100b
Functions as a processing unit for creating a molecular structure diagram of a compound based on bond atom pair data. Further, by causing the display control unit 100c to execute under the control of the CPU 80, the display control unit 100c functions as a display control unit that displays the molecular structure diagram of the compound on the display 40.

Main routine 1 having such a function
00 first extracts bond atom pair data recorded in the atom pair table 32b of the bond table 32 (S10). This extraction is performed by calling an atom pair data extraction routine 101. Next, the extracted plurality of bond atom pair data is classified into bond atom pair data forming a cyclic portion and bond atom pair data forming a chain portion (S20). This classification is performed by calling a classification routine 102. Further, two-dimensional coordinates of each atom of the cyclic portion are calculated based on the bonding atom pair data constituting the cyclic portion (S30). This calculation is performed by calling the annular part coordinate calculation routine 103.

Next, two-dimensional coordinates of each atom of the chain portion are calculated based on the bond atom pair data constituting the chain portion (S40). This calculation is performed by the chain part coordinate calculation routine 10.
4 is called. Then, the chain portion is moved and rotated to couple the annular portion and the chain portion (S50). Specifically, as shown in FIGS. 5A to 5C, the annular portion 1
18 and the predetermined connection 119 of the chain 110
The coordinate conversion is performed on the two-dimensional coordinate data of each atom of the chain-like portion 110 obtained in the processing of S40 so that 11 coincides. In particular, each bond 11 extending from a bond portion atom 112
The chain portion 11 is adjusted while adjusting the branch angles θ _{1 to} θ _{3 of 1,} 113 and 114 to be equal (θ ₁ = θ ₂ = θ ₃ ).
Rotate 0.

The two-dimensional coordinate data of each atom obtained in the processing of S30 to S50 is written in the X-coordinate and Y-coordinate columns of the bonding table 32 created in the main storage device 20.

Next, image data 10a indicating the molecular structure is created based on the two-dimensional coordinate data of each atom written in the X coordinate and Y coordinate columns of the bonding table 32 (S6).
0). The creation of the image data is performed by calling the molecular structure diagram creation routine 105. Then, the image data 10a of the created molecular structure diagram is displayed on the display 40 (S70).

S10 corresponds to the first step,
S20 to S60 correspond to the second step. further,
S70 corresponds to a third step.

Next, the atomic pair data extraction routine 101 will be described. The atom pair data extraction routine 101
This is a subroutine called by the processing of S10 of the main routine 100. As shown in the flowchart of FIG. 6, the atom pair data extraction routine 101 first causes the display 40 to display an input method selection screen (S
101). In accordance with this display screen, the operator
Is selected (S102), the display 4
At 0, a screen for drawing a molecular structure diagram is displayed. Next, when the operator uses the mouse 50 to manually input a molecular structure diagram showing the structure of a predetermined compound, the input of the handwritten graphic data is accepted (S103). The connection table 32 is stored in the main storage device 20 based on the handwritten graphic data.
(S104).

Next, the input of the handwritten figure data by the mouse 50 will be specifically described. First, when the operator clicks the mouse 50, data on one of the atoms forming the bonded atom pair is input. Next, when the operator moves the mouse 50 and clicks the mouse 50, data on one atom and the other atom forming a bonded atom pair is input. Then, the click for inputting data on the other atom is regarded as a click for designating one atom of the next bonded atom pair when the next click is subsequently performed. In this manner, a pair of bonding atom pairs can be designated by two consecutive mouse clicks. That is, when the operator continues to specify the bond atom pairs while shifting the atoms one by one, all the bond atom pairs constituting the compound are input.

The number of the atom is written in the column of the atom number of the atom table 32a in correspondence with the data on the input atom (for example, 1, 2, 3,... In the order of input of the atom). Further, the input data on the bonding relationship between the atoms is written in the column of the bonded atom pair in the atom pair table 32b. 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 32a. Similarly, when the operator inputs the multiplicity of the bond connecting the bond atom pairs, the multiplicity of the bond is written in the column of the bond type in the atom pair table 32b.

In the process of S102, the operator operates the keyboard 6
When input by 0 is selected, a symbol string input screen is displayed on the display 40. When the operator uses the keyboard 60 to input a symbol string of a binding table name that specifies a predetermined compound, the input of the symbol data 11a is accepted (S105). Then, the data of the binding table specified by the symbol data 11a is read from the binding table file 31 (S106), and the binding table 32 is extracted in the main storage device 20 (S107).

Further, after the processing of S104 and S107 is completed, the bond atom pair data is extracted from the atom pair table 32b of the bond table 32 created by these processes (S1).
08). Then, after the processing of S108 ends, the atomic pair data extraction routine 101 ends, and the main routine 100
The process returns to S20.

Next, the classification routine 102 will be described. The classification routine 102 is the same as the S in the main routine 100.
This is a subroutine called by the process of 20.
As shown in the flowchart of FIG.
In 2, in step S201, it is determined whether each bond atom pair data created by the atom pair data extraction routine 101 belongs to a cyclic structure or a chain structure. This judgment is
This is performed by calling the chain determination routine 106. Then, the determination result is set as the structure data of the atom pair table of the bonding table 32 stored in the main storage device 20 as described later.

Next, an annular portion is detected (S202). This detection is performed by calling the annular portion detection routine 107. Further, a chain portion is detected (S203). This detection is performed by calling the chain portion detection routine 108. S2
By the processes of 02 and S203, each bond atom pair data is classified into a cyclic portion and a chain portion as described later.
For example, as shown in FIG. 8, 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 parts 140 and 150. Then, after the end of the process of S203, the classification routine 102 is ended, and the process returns to S30 of the main routine 100.

Next, the annular part coordinate calculation routine 103 will be described. The annular part coordinate calculation routine 103 is a subroutine called by the processing of S30 of the main routine 100. As shown in the flowchart of FIG. 9, the annular part coordinate calculation routine 103 first determines whether the annular part classified by the classification routine 102 has a single ring structure (S301). In this process, assuming that the number of atoms is Na and the number of bonds is Nb, N = Nb−Na + 1, and that if N is 1 it is determined to be a single ring, and if N is more than 1 (integer), it is a condensed ring. Is determined. Incidentally, N is 0 in the case of a chain portion.

Here, the terms used in the present invention will be explained. First, the `` ring '' or `` single ring '' performs an operation of starting from one atom of an arbitrary starting bond and tracing the bond one after another, without tracing the starting bond and the bond once traversed and its atom, When the other atom of the starting bond can be reached, it should be understood as a loop formed by the starting bond and the bond followed. For example, assuming that the atom 1 of the bonding atom pair (1, 2) in FIG. 2 is one of the starting bonds, the bonds that can be traced from the atom 1 are the bonding (6, 1) and the bonding (1, 7). . Where the join (6,1)
If one is selected, the joins (5,6), (4,5),
By tracing the bonds one after another (3, 4) and (2, 3), the other atom 2 of the starting bond can be reached without tracing the starting bond and the bond once traversed and its atoms. Therefore, it can be said that the compound in FIG. 2 has a ring structure formed by the starting bond (1, 2) and the bond following the starting bond.

Further, the “ring portion” is to be understood as a collection of bonds forming all “rings” including an arbitrary bond. As described above, the “cyclic portion” is classified into a single ring (N = 1) and a condensed ring (N> 1).

If it is determined in step S301 that the structure has a single ring structure, two-dimensional coordinates of each vertex are obtained as a regular n-gon (in the case of an n-membered ring) (S302). Further, when it is determined that the condensed ring structure is obtained in the process of S301, a small ring set (SSSR: Smallest Set of rings) having a minimum number of ring members necessary for expressing all atoms and bonds constituting the condensed ring structure is required. Smallest
Rings) (S303). The set of rings having the minimum necessary minimum number of members can be obtained by using an exclusive OR method which is a known technique. This exclusive OR method is described in the literature `` 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, A set of N (= Nb-Na + 1) or more mutually independent single rings (independent single ring set) is created, where Nb is the number of bonds. Here, “mutually independent” means that one or more bonds included in only one of the two rings are present.

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

(3) If the single ring obtained in (2) is different from any of the single rings constituting the independent single ring set, this is added to form a new independent single ring set.

(4) Returning to (2), processing is performed for all combinations of N or more single rings, and the processing is repeated until a new single ring cannot be obtained.

(5) From (1) to (4), all mutually independent monocycles could be obtained. Therefore, among the obtained independent monocycle sets, N
By selecting the individual, the SSSR is obtained.

SS obtained by this exclusive OR method
As an example of SR, the condensed ring 160 shown in FIG.
Is divided into a set of four single rings 161-163. Similarly, the condensed ring 170 shown in FIG. 10B is divided into a set of three single rings 171 to 173. That is, SSS
The exclusive OR method for finding R is a calculation method in which all single rings that can be traced in a condensed ring are extracted, and N pieces are extracted from the single rings in ascending order of the number of ring members to form a set.

Next, the highest priority among the determined SSSRs (for a single ring, for example, a 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). Then, the selected single ring is an m-membered ring (m is
In the case of (natural number of 3 or more), two-dimensional coordinates of each vertex are obtained as a regular m-sided polygon (S305). Further, a single ring having the highest priority is selected from the rings condensed with a single ring (specific single ring) for which two-dimensional coordinates have already been determined (S306).

It is preferable that the selection of a single ring in the processing of S304 and S306 is basically performed in accordance with the priority specified in accordance with the number of rings. Further, in a monocyclic ring having the same number of ring members, for example, a ring containing a nitrogen atom is placed at a lower position, or a ring containing a double bond is placed at a higher position. It is also preferable to further subdivide the ranks and rank them. According to the knowledge of the present inventor, when a six-membered ring is selected as the highest order of the basic order, a particularly aesthetically excellent molecular structure diagram can be obtained.

Next, as shown in FIG. 11, a single ring 181 condensed with a single ring (specific single ring) 180 whose two-dimensional coordinates have already been determined is selected, and this single ring 181 is formed into an n-membered ring (n Is
In the case of three or more natural numbers, the two-dimensional coordinates of each atom are determined as n-gons sharing k sides (k = 3 in FIG. 11) with the single ring 180 (S307). Specifically, a single ring 18
Among the sides of the n-sided polygon forming 1, k sides shared with the single ring 180 are defined as a shared side 182, and the other sides are defined as non-shared sides 183. The length of the auxiliary straight line 186 connecting both ends 184 and 185 of the line segment composed of all the shared sides 182 is set to L (L is a known value), and each non-shared side 18
The length of 3 is defined as r (r is a constant value).

At this stage, the two-dimensional coordinates of each atom constituting the single ring 180 have already been obtained.
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 a fixed value that is generally determined by the single ring 180 and the single ring 181 except for the case where exception processing described later is performed. Thus, single rings 180, 181
By setting all sides to a constant value r, the calculation for obtaining the two-dimensional coordinates of each atom can be performed at high speed.

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

That is, in the process of S307, the bond length r and the bond length of all the atoms whose two-dimensional coordinates are unknown among the atoms constituting the single ring fused to the specific ring whose two-dimensional coordinates are known are known. Unknown atoms are arranged such that the angles β are equal, and the two-dimensional coordinates are obtained. S307
The above-mentioned algorithm employed in the above-mentioned method has three consecutive combinations of rings included in the SSSR characterizing a condensed ring.
This is excellent and effective in the case where the structure is particularly complicated, such as a condensed ring in which a combination of rings which are condensed with each other by sharing two or more atoms or a molecular structure diagram including the condensed ring. This is because the two-dimensional coordinates of atoms can be calculated at high speed by using the above-described coordinate calculation method, and the arrangement of atoms is symmetric with respect to the perpendicular bisector of the auxiliary straight line 186. The molecular structure diagram is easy to grasp the structure visually and is excellent in aesthetics.

The shared side 182 is connected to the bond A of the present invention by
The non-shared side 183 corresponds to the connection B of the present invention. Thus, bond B contains a bond where one atom is shared by the two rings but the other atom is not. Further, the condensed ring 160 shown in FIG. 10A has three combinations of rings that share two consecutive atoms and is fused to each other, and the condensed ring 170 shown in FIG. The combination of rings which share three atoms and are fused to each other is 2
Exist.

In the process of S308, when it is determined that the two-dimensional coordinates of all the rings constituting the SSSR have been obtained,
When the processing of S302 is completed, the annular part coordinate calculation routine 103 is terminated and the processing of S of the main routine 100 is terminated.
The process returns to 40.

In general, as the number of bonds extending from each atom increases, the frequency of the atom whose two-dimensional coordinates have been calculated in the processing of S307 overlaps or is very close to the atom whose coordinates have already been determined. Becomes larger. Then, as a countermeasure against such inconvenience, it is necessary to change the length of one bond to shift the position of the atom. Therefore,
Exception processing for changing the length of the connection is incorporated in the annular part coordinate calculation routine 103 (details will not be described). When such exception processing is performed, the connection length is set to a value other than r. Become.

However, considering the above-described relationship between the number of connections and the frequency of proximity, in the annular part coordinate calculation routine 103,
When the number of bonds extending from each atom of the condensed ring to be treated is three or less, treatment is preferably performed so that the lengths of all the bonds become a constant value r. As a result, the calculation for obtaining the two-dimensional coordinates is speeded up, and the number of steps in the annular part coordinate calculation routine 103 can be reduced.

Next, the chain part coordinate calculation routine 104 will be described. The chain part coordinate calculation routine 104 is a subroutine called by the processing of S40 of the main routine 100. As shown in the flowchart of FIG. 12, in the chain part coordinate calculation routine 104, first, all the terminal atoms that are the ends of the chain structure are extracted and extracted from the atoms classified into the chain part. A terminal atom pair having the largest number of bonds included between the terminal atom pairs is selected from among the paired terminal atoms (S401).

As shown in FIG. 13, the terminating atom refers to atoms a to c which are the ends of a chain structure among a plurality of atoms bonded in a chain shape. The term “terminal atom pair” means a combination of these terminal atoms a to c (a, b), (a, c),
(B, c). Here, terminal atom pairs (a, b),
The numbers of bonds included between (a, c) and (b, c) are 3, 10, and 11, respectively. Therefore, in the process of S401, the terminal atom pair (b, c) is selected.

Then, two-dimensional coordinates of each atom between the selected terminal atom pairs are obtained (S402). As shown in FIG. 14, the two-dimensional coordinates of each of the atoms 190 to 197 between the terminal atom pair (the pair of the terminal atom 190 and the terminal atom 197) are represented by angles (for example, 3 When a heavy bond is adjacent or a double bond is adjacent to a double bond, θ ₄ = 180 degrees, and in other cases, θ ₅ = 120 degrees.) The length between them is defined as a constant value r, and is determined in order from one terminal atom 190 to the other terminal atom 197. The determination of the two-dimensional coordinates is performed in consideration of satisfying the designation of the cis orientation and the trans orientation (when there is no designation, the trans orientation). Acceptance of designation of the cis orientation and the trans orientation is preferably performed in the processing of the atom pair data extraction routine 101.

Next, the terminal atom having the largest number of bonds between the terminal atom for which the two-dimensional coordinates have not been obtained and the atom for which the two-dimensional coordinates have already been obtained (hereinafter referred to as a 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. 15, the two-dimensional coordinates of each atom 198 to 200 between the branch point atom 192 and the terminal atom 200 are represented by the branch point atom 1
The branch angle according to the number of atoms bonded to 92 (for example, 3
Θ ₆ = 120 degrees for atomic bonds, θ _{7 for} 4-atom bonds
= 90 degrees (θ ₇ is not shown). ), And the length between the atoms is determined in order from the atom 198 to the terminal atom 200 as a constant value r.

Next, the process of S405 is performed. If there is an atom that has not been selected, the process returns to S403, and the process returns to S403.
Steps 403 and S404 are repeated. When it is determined in the processing of S405 that the positions of all atoms have been obtained,
The chain part coordinate calculation routine 104 ends, and the process returns to S50 of the main routine 100.

Next, the molecular structure diagram creation routine 105 will be described. The molecular structure diagram creation routine 105 is a subroutine called by the processing of S60 of the main routine 100. As shown in the flowchart of FIG. 16, in the molecular structure diagram creation routine 105, first, each data of the connection table 32 stored in the main storage device 20 is read (S601). Then, image data of a molecular structure diagram is created based on the read two-dimensional coordinate data, element name data, bond atom pair data, and bond type data (S602).

The creation of the image data is performed in the following procedure. First, the two-dimensional coordinate data of each atom is plotted on a two-dimensional screen. Next, each atom plotted based on the bonded 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, the number of straight lines between atoms representing bonds is set to the same number as the multiplicity of bonds (one single bond, two double bonds, etc.).

The image data 10a of the molecular structure diagram thus created is stored in the image memory 10 (FIG. 3). Then, after the processing of S602 is completed, the molecular structure diagram creation routine 105 is terminated, and the S
The process returns to 70.

Next, the chain determination routine 106 will be described. The chain determination routine 106 is the classification routine 10
This is a subroutine called by the process in S201 of FIG. This ring chain determination routine 106 is executed for each piece of data selected from the bond atom pair data in the bond table 32, and the selected bond atom pair data belongs to either the cyclic portion or the chain portion. Is determined.

Referring to the flowchart of FIG. 17, the ring chain determination routine 106 firstly stores the attributes of all the atoms in the atom table 32a of the bond table 32 in the
“0” is written (S2011). Then, “1” is written in the column of the attribute of the first atom constituting the selected bonded atom pair to be determined, and “2” is written in the column of the attribute of the second atom, respectively (S2012). Next, "1" is set to the flag of the reserved predetermined area in the main storage device 20 (S20).
13). Further, it is determined whether "1" is set in the flag (S2014). If it is determined in step S2014 that “1” is not set in the flag, “chain” is written in the structure column of the atom pair table 32b (S20).
15).

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

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

(2) If the attribute of the atom is “0” in the process of S2018, “1” is entered in the column of the attribute 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”.
Is determined (S201A).

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

(1) to (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" (necessarily, the attribute of the atom is "2"), the column of the structure of the atom pair table 32b Is written in (S201C). Further, S20
15 or S201C, the remaining bond atom pairs to be determined are selected, and the ring chain determination routine 106 is selected.
Is repeatedly executed. Then, after completing the ring chain determination for all the bonding atom pairs, the ring chain determination routine 106
Is completed, and the process returns to S202 of the classification routine 102.

Next, the annular portion detection routine 107 will be described. The annular part detection routine 107 is a subroutine called by the processing of S202 of the classification routine 102. As shown in the flowchart of FIG. 18, the cyclic part detection routine 107 first creates a partial bond table excluding the bonds composed of the atom pairs belonging to the chain structure (S2).
021). Next, an arbitrary atom is selected from the partial bond table (S2022). And from the selected atoms,
All the atoms that can be traced are selected along the bond given by the bond atom pair data (S2023).

The atom selected in this way is given a partial structure number different from the partial structure number (if any) already used (S2024). Further, it is determined whether there is an atom to which no partial structure number is given (S20).
25). If it is determined in S2025 that there is an atom to which no partial structure number is given, an arbitrary atom is selected from the atoms to which no partial structure number is given (S2026), and the process returns to S2023. Also, S2
If it is determined in step 025 that all atoms have already been assigned partial structure numbers, the cyclic part detection routine 1
07 ends, and the process returns to S203 of the classification routine 102.

Finally, in classifying the compound into a cyclic portion and a chain portion, if the cyclic portion detection routine 107 is executed,
One cyclic portion of a compound can be recognized by a computer as a set of atoms having the same partial structure number. Further, the type (number) of the cyclic portion contained in the compound corresponds to the type of the partial structure number.

Next, the chain portion detection routine 108 will be described. The chain detection routine 108 is a subroutine called by the processing of S203 of the classification routine 102. As shown in the flowchart of FIG. 19, the chain part detection routine 108 first creates a partial bond table excluding the bonds composed of the atom pairs belonging to the cyclic structure (S2).
031). Next, an arbitrary atom is selected from the partial bond table (S2032). And from the selected atoms,
All the atoms that can be traced along the bond given by the bond atom pair data are selected (S2033).

The atom selected in this way is given a partial structure number different from the already used partial structure number (if any) (S2034). Further, it is determined whether there is an atom to which no partial structure number is given (S2).
035). If it is determined in S2035 that there is an atom to which no partial structure number is given, an arbitrary atom is selected from the atoms to which no partial structure number is given (S2036), and the process returns to S2033. Also, S2
In the process of 035, when it is determined that the partial structure numbers have already been assigned to all the atoms, the chain portion detection routine 1
08 is ended, and the process returns to the end of S203 of the classification routine 102.

In the end, in classifying the compound into a cyclic portion and a chain portion, if the chain portion detection routine 108 is executed,
One chain of a compound can be recognized by a computer as a set of atoms having the same partial structure number. The type (number) of the chain portion contained in the compound corresponds to the type of the partial structure number.

Next, examples of the image data 10a and 10b displayed on the display 40 by the processing of S70 of the main routine 100 will be described with reference to FIGS.
(B). 20 (a) and FIG. 20 (b), the bonding atom pair data received in the process of S10 is data of a compound consisting only of a condensed ring, A set of rings having the minimum number of ring members necessary to represent a bond is one five-membered ring and one six-membered ring.
This is a display example in the case where data is for a condensed ring composed of only membered rings and in which the five-membered ring and the six-membered ring share and condense three atoms. The image data 10a is
Molecular structure diagram, image data 10 created assuming that a 5-membered ring is fused to a 6-membered ring preferentially drawn as a regular hexagon
b is a molecular structure diagram created assuming that a 6-membered ring is fused to a 5-membered ring preferentially drawn as a regular pentagon.

In these data, S307 and S
Since the lengths of all bonds are calculated as a constant value r in the process of 309, the lengths of all bonds in the molecular structure diagrams shown in the image data 10a and 10b are all equal. in this way,
Since the length of each bond in the molecular structure diagram is unified to a constant value r, the calculation is speeded up, and the number of steps of the calculation program is reduced.

As described above, the molecular structure diagram display apparatus and the display method according to this embodiment are very suitable for creating and displaying a complex structure molecular structure diagram at a high speed and clearly. It can be said that.

The present invention is not limited to the above embodiment, but can be variously modified. For example, when there is proximity or crossing of atoms, for a bond contained in a chain portion where cis orientation and trans orientation are not specified, change the cis orientation from the cis orientation to the trans orientation, or change the cis orientation from the trans orientation, A process for avoiding intersection may be added.

When a molecular structure having a conventionally determined orientation is included, the orientation of the entire molecular structure diagram may be changed to match the orientation. Thus, molecules that are conventionally oriented include steroids, vitamins and sugars.

[0093]

[0094]

[0095]

[0096]

[0097]

According to the display device for a molecular structure diagram of the present invention, the input means accepts bond atom pair data indicating the bond relationship between the atoms constituting the compound. The bond atom pair data is passed to the processing means, and the processing means creates a molecular structure diagram of the compound based on the bond atom pair data. In particular, the bond atom pair data is data of a compound consisting of only a condensed ring, and is included in a set of rings having a minimum number of minimum members necessary to represent all atoms constituting the condensed ring and a bond. In a combination of the above, when an arbitrary pair of rings share three or more atoms and are fused to each other, each bond in the pair of rings is shared with a bond A in which the atoms are shared by the pair of rings. The molecular structure diagram is created such that the length of the bond B and the angle between the bonds B are equal to each other for each ring separately from the bond B that is not formed. And
The molecular structure diagram of the compound created by the processing unit is passed to the display control unit, and the display control unit causes the display to display the molecular structure diagram of the compound.

As described above, in a pair of rings condensed with each other, the length of the bond and the angle between the bonds where the atoms are not shared by the pair of rings are the same for each ring, so that a molecule having high symmetry is obtained. The calculation for creating the structure diagram can be performed at high speed.

[0099]

[0100]

[0101]

[0102]

According to the method for displaying a molecular structure diagram of the present invention, first, in a first step, input of bond atom pair data indicating a bond relationship between atoms constituting a compound is received. Next, in a second step, a molecular structure diagram of the compound is created based on the bonding atom pair data received in the first step. In particular, the bond atom pair data is data of a compound in which the bond atom pair data is only a condensed ring, and the ring having the minimum number of ring members necessary to represent all the atoms constituting the condensed ring and the bond. In a combination of the rings included in the set of the above, if any pair of rings share three or more atoms and are fused to each other, each bond in the pair of rings is shared by the pair of rings. Combined A
And a bond B that is not shared, a molecular structure diagram is created such that the length of the bond B and the angle between the bonds B are equal for each ring. And in the third step,
The molecular structure diagram of the compound prepared in the second step is displayed on a display.

As described above, in a pair of rings condensed with each other, the length of the bond and the angle between the bonds where the atoms are not shared by the pair of rings are the same for each ring, so that a highly symmetric molecule is formed. The calculation for creating the structure diagram can be performed at high speed.

By using the display device and the display method of the present invention, it is easy to accumulate a large amount of binding table data. Therefore, the present invention is usefully used for constructing a compound structure database. This is because, according to the present invention, even in the case of the rough molecular structure diagram A which is handwritten, accurate and clean shaping processing is performed at high speed, and a connection table is automatically created. Further, by directly inputting the connection table, a larger amount of data can be accumulated.

[Brief description of the drawings]

FIG. 1 is a diagram showing a configuration of a display device of a molecular structure diagram according to an embodiment.

FIG. 2 is a diagram showing a configuration of a binding table.

FIG. 3 is a schematic diagram showing a method for displaying a molecular structure diagram according to the present embodiment.

FIG. 4 is a flowchart showing a flow of processing of a main routine.

FIGS. 5A to 5C are diagrams showing a method of connecting an annular portion and a chain portion.

FIG. 6 is a flowchart illustrating a flow of a process of an atom pair data extraction routine.

FIG. 7 is a flowchart illustrating a flow of a process of a classification routine.

FIG. 8 is a diagram showing a state where each bond atom pair data is classified into a cyclic portion and a chain portion.

FIG. 9 is a flowchart illustrating a flow of a process of an annular part coordinate calculation routine.

FIGS. 10A and 10B are diagrams showing a state where a condensed ring is divided into a plurality of single rings by an exclusive OR method.

FIG. 11 is a diagram showing two-dimensional coordinates of each atom constituting a monocyclic ring fused to a specific monocyclic ring.

FIG. 12 is a flowchart illustrating a flow of a chain part coordinate calculation routine.

FIG. 13 is a diagram showing a pair of terminal atoms to be ends of a chain structure.

FIG. 14 is a diagram showing two-dimensional coordinates of each atom constituting a chain portion.

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

FIG. 16 is a flowchart showing the flow of the processing of a molecular structure diagram creation routine.

FIG. 17 is a flowchart illustrating a flow of processing of a chain determination routine;

FIG. 18 is a flowchart illustrating a flow of a process of an annular portion detection routine.

FIG. 19 is a flowchart showing the flow of a chain part detection routine.

FIGS. 20A and 20B are diagrams illustrating examples of image data displayed on a display. FIGS.

[Explanation of symbols]

DESCRIPTION OF SYMBOLS 1 ... Molecular structure diagram display device, 10 ... Image memory, 11 ... Work memory, 20 ... Main storage device, 21 ... Operating system, 22 ... Molecular structure diagram display program, 30 ...
Hard disk drive, 40 display, 50 mouse, 60 keyboard, 70 printer, 80 CP
U.

Continuation of the front page (58) Field surveyed (Int. Cl. ⁶ , DB name) G06F 17/50 C07B 61/00 JICST file (JOIS)

Claims (4)

(57) [Claims] An input unit for receiving an input of bond atom pair data indicating a bond relationship between atoms constituting a compound, and a molecular structure diagram of the compound based on the bond atom pair data received by the input unit. A molecular structure diagram, comprising: a display unit that displays a molecular structure diagram of the compound created by the processing unit; and a display control unit that displays the molecular structure diagram of the compound on the display. A display device, wherein, when the compound includes a condensed ring, based on the bonding atom pair data received by the input unit, the processing unit expresses all atoms and bonds constituting the condensed ring. Dividing means for dividing the condensed ring into a plurality of single rings so as to form a set of single rings having a minimum number of ring members necessary for performing An extracting means for extracting a combination of single rings which are condensed with each other by sharing an atom; each bond in the combination of the single rings is replaced with a covalent bond A shared in the combination of the single rings; Classifying means for classifying the non-covalent bond B into non-covalent bonds, and the two atoms of each atom constituting the combination of the single ring such that the length of the non-covalent bond B and the angle between the bonds B are equal for each ring A molecular structure diagram display device, comprising: coordinate calculation means for calculating dimensional coordinates; and molecular structure diagram creation means for creating a molecular structure diagram of the compound from two-dimensional coordinates of each atom. 2. The process according to claim 1, wherein the processing unit classifies, based on the bonding atom pair data received by the input unit, whether each atom constituting the compound belongs to a cyclic portion or a chain portion. The method according to claim 1, further comprising: a determination unit; and a ring determination unit that determines whether a ring composed of atoms classified into the cyclic portion belongs to a condensed ring or a single ring. Display device for molecular structure diagram. 3. A method for displaying a molecular structure diagram of a compound on a display using a molecular structure diagram display device including an input unit, a processing unit, a display, and a display control unit. A first step of receiving, by the input unit, bond atom pair data indicating a bond relationship between atoms constituting the compound; and, based on the bond atom pair data received in the first step, A second step of creating a molecular structure diagram of the compound by the processing means; and a third step of displaying the molecular structure diagram of the compound created in the second step on a display by the display control means. The second step, based on the bonding atom pair data received in the first step, when the compound contains a condensed ring; A dividing step of dividing the condensed ring into a plurality of single rings by the processing means so as to form a set of a single ring having a minimum number of ring members necessary for expressing all atoms and bonds constituting the condensed ring. And extracting from the plurality of monocycles a combination of monocycles that share three or more atoms and condensed with each other by the processing means; and each bond in the combination of monocycles, A classification step of classifying the covalent bond A shared in the single ring combination into other non-covalent non-covalent bonds B by the processing means; a length of the non-covalent bond B and an angle between the bonds B A coordinate calculation step of obtaining the two-dimensional coordinates of each atom constituting the combination of the single ring by the processing means so that Display method of molecular structure diagram, characterized in that it comprises a molecular structure diagram creating step of creating a molecular structure diagram of the compound by stages. 4. The method according to claim 2, wherein, in the second step, each of the atoms constituting the compound belongs to a cyclic portion or a chain portion based on the bonding atom pair data received in the first step. A ring determination step of classifying by the processing unit; and a ring determination step of determining by the processing unit whether a ring composed of each atom classified into the cyclic portion belongs to a condensed ring or a single ring. The method for displaying a molecular structure diagram according to claim 3, further comprising: