JP3060651B2 - Registered molecule addition method - Google Patents

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a method for adding a registered molecule, and more particularly, to modeling a molecule by adding a registered molecule to a molecular structure during modeling or the like in a molecular design support system. The present invention relates to a method for adding a registered molecule, which is suitable for such a case.

[0002]

2. Description of the Related Art Conventionally, it has been widely adopted in a molecular design support system to simplify a molecular modeling operation by adding a registered molecule to a molecular structure during modeling or the like. FIG. 11 is a flowchart illustrating an example of a conventional molecule addition method. In step SP1, the process waits until a desired molecule is selected from a plurality of molecules registered in a library, and then bonds the molecules selected in step SP2. Wait until a position is specified, and wait until a molecule addition planned position of a molecular structure such as during modeling is specified in step SP3.
In step SP4, a desired molecule is added to the molecular structure in the middle of modeling or the like by combining the bonding position and the expected molecular addition position, and the molecule added in step SP5 is rotated by a predetermined angle around the bonding axis. Completes a series of processing.

[0003] Therefore, by selecting a molecule already registered in the library and designating a binding position of the selected molecule and a planned molecular addition position of the molecular structure during the modeling or the like, a desired position of the molecular structure during the modeling or the like is specified. The desired molecule can be added to the model, and the modeling operation can be greatly simplified as compared with the case where atoms are added one by one.

[0004]

In the above-described conventional method of adding a registered molecule, the binding position must be specified for both the molecular structure during modeling or the like and the selected molecule. In the modeling of macromolecules or the like in which it is necessary to sequentially add molecules, there is a disadvantage that the amount of work for designating the bonding position is significantly increased. Therefore, there is a strong demand for further reducing the amount of work required to add a selected molecule to a molecular structure during modeling or the like.

[0005]

SUMMARY OF THE INVENTION The present invention has been made in view of the above-mentioned problems, and is intended to improve the workability of adding a registered molecule to a molecular structure during modeling or the like. It is intended to provide a method for adding molecules.

[0006]

According to a first aspect of the present invention, there is provided a registered molecule adding method for registering a molecule in a storage means for storing various molecules. The arrangement of atoms is registered, and in adding the registered molecule to the predetermined molecular structure, after the molecule to be added is selected, the molecule to be added having the predetermined molecular structure is scheduled to be added. When a position is indicated, the dummy atom arrangement position is bonded to the molecule addition expected position, and after the molecule addition expected position of the predetermined molecular structure is indicated, when the molecule to be added is selected, In this method, a designated desired atom arrangement position of a molecule to be added is bonded to the molecule addition expected position, and the dummy atom is replaced with a hydrogen atom.

[0007]

[0008]

[0009]

According to the registered molecule adding method of the first aspect, when a molecule is registered in the storage means for storing various molecules, a molecule in which a dummy atom is arranged at a position where the molecule is to be bonded is registered. In adding the registered molecule to a predetermined molecular structure, when the position to add a molecule of the predetermined molecular structure is designated after the molecule to be added is selected, the dummy atom arrangement position Is linked to the molecule addition expected position, and after the molecule addition expected position of the predetermined molecular structure is designated, if the molecule to be added is selected, the designated desired atom arrangement of the molecule to be added is designated. Since the position is bonded to the expected molecular addition position and the dummy atom is replaced with a hydrogen atom, it is not necessary to specify the bonding position of the molecule to be added, and the registered molecule can be added. Possible to simplify the work required to. Also, when registering a molecule, it is only necessary to place a dummy atom instead of a part of the atoms constituting the molecule. Absent. Further, the present invention can cope with not only the case where a previously registered dummy atom arrangement position is set as a bond position but also a case where a position where atoms other than dummy atoms are arranged is set as a bond position.

[0010]

[0011]

Therefore, it is not necessary to specify the binding position of the molecule to be added, and the operation required for adding the registered molecule can be simplified. Also, when registering a molecule, it is only necessary to place a dummy atom instead of a part of the atoms constituting the molecule. Absent.

[0013]

BRIEF DESCRIPTION OF THE DRAWINGS FIG. FIG. 1 is a flowchart for explaining one embodiment of the registered molecule adding method of the present invention. In step SP1, the process waits until a desired registered molecule is selected from a plurality of registered molecules registered in the library, and then proceeds to step S1.
In P2, it is determined whether or not the selected registered molecule includes a dummy atom. If the selected registered molecule includes a dummy atom, the process waits until a bonding position of a molecular structure during modeling or the like is designated in step SP3. In step SP4, the registered molecule selected by adding the dummy atom arrangement position to the designated bond position of the molecular structure during modeling or the like is added. Conversely, step SP2
If it is determined that the selected registered molecule does not include a dummy atom in step, the process waits until the bonding position of the selected registered molecule is specified in step SP5, and in step SP6, the bonding of the molecular structure during modeling or the like. Wait until the position is specified, and add the selected registered molecule by binding the specified bonding position of the registered molecule to the specified bonding position of the molecular structure being modeled in step SP7. And step SP
After the processing of step 4 or step SP7 is performed, in step SP8, the modeling accompanying the addition of the registered molecule is achieved by rotating the added registered molecule by a desired angle around the bond axis, and a series of processing is performed as it is. finish.

[0014] Figure 2 is a diagram illustrating a specific example of the registration molecular addition method of FIG. 1 shows a case of adding the CH ₄ molecule relative CH ₄ molecules. As shown in FIG. 2 (A) CH ₄
If a registered molecule CH ₃ D in which one H is replaced with a dummy atom D is selected in a state where a molecule is being modeled, the designation of the bonding position of the CH ₄ molecule during the modeling is required. It is only necessary to specify the bonding position in response to the above. As shown in FIG. 2 (B), by combining the specified bonding position with the dummy atom arrangement position and removing the dummy atom D, C ₂ H ₆ Modeling can be achieved. However, since the relative rotation angle between the CH ₄ molecule during modeling and the added CH ₃ D molecule is not uniquely determined, the molecule is added by rotating the added molecule around the bond axis as in the conventional method. To achieve the modeling associated with

FIG. 3 is a diagram for explaining another specific example.
_If a registered molecule NH ₂ D in which one H is replaced with a dummy atom D is selected in a state in which a ₂ H ₆ molecule is modeled, the designation of the bonding position of the C ₂ H ₆ molecule during the modeling is required. You. And in response to this request, one C
Is designated as a bonding position, there are a plurality of directions that can be added to the C atom. Therefore, as shown in FIG. 3A, the directions that can be added are displayed by, for example, broken lines, and the direction is selected. Encourage what to do. Next, if a direction is selected, addition of molecules can be achieved in the selected direction as shown in FIG.

FIG. 4 is a flowchart for explaining a process of selecting a molecule registered in the library. The process waits until reading of the registered molecule is specified in step SP1, and a list of file names of the registered molecule is displayed in step SP2. Then, it is determined whether or not the display of the structure diagram of the registered molecule is instructed in step SP3. When the display of the structure diagram of the registered molecule is instructed, the registered data of the registered molecule is sequentially read from the library in step SP4, and a visual display based on the read structural data is performed in step SP5. If the display of the structural diagram of the registered molecule has not been instructed in step SP3, or if the processing in step SP5 has been performed, the process waits until a registered molecule is selected in step SP6, and the registered molecule selected in step SP7 is displayed. Read molecular data from library. However, when the selection based on the structure diagram display of the registered molecule is performed, since the reading of the molecule data has already been read from the library, the process that would be duplicated can be omitted, and the process for picking can be omitted. Since only the ID assignment processing or the like needs to be performed, the subsequent processing can be speeded up.

FIG. 5 is a view for explaining the processing of the flowchart of FIG. 4. When reading of a registered molecule is instructed, a list of file names of registered molecules is displayed as shown in FIG. If the registered molecule can be selected accurately based only on this, picking or the like of the corresponding portion of the file name list display may be performed, and the molecular data of the desired registered molecule can be immediately read from the library. Conversely, if there is a high possibility that the registered molecule cannot be selected accurately only by the file name, the display of the structure diagram of the registered molecule may be instructed. As shown in FIG. Because it gives a visual representation of the structure,
Accurately select registered molecules based on a visual representation of the molecular structure. Although the molecular structure is three-dimensional, visual display of the molecular structure can only be achieved two-dimensionally, so registration is made by displaying the molecular structure in a rotated state as necessary. Molecule selection can be more accurate.

[0018]

[Embodiment 2] FIG. 6 is a block diagram showing an embodiment of a registered molecule adding apparatus according to the present invention. The library 1 holds a plurality of molecule data and corresponding file names and the like, and is registered in the library 1. A registered molecule selection unit 2 for selecting a desired registered molecule from a plurality of registered molecules; a dummy atom presence / absence determining unit 3 for determining whether the selected registered molecule contains a dummy atom; A first bonding position holding unit 4 that holds a specified bonding position of a molecular structure as a first bonding position, and a second bonding position holding unit 5 that holds a dummy atom arrangement position of a selected registered molecule as a second bonding position. A second bond position holding unit 6 for holding the specified bond position of the molecular structure of the selected registered molecule as the second bond position, and a data indicating that the selected registered atom includes a dummy atom. The are held in the first coupling position holding unit 4 in response to the determination result from over atomic existence discriminating unit 3 1
The coupling position and the second coupling position held by the second coupling position holding unit 5
A first registered molecule adding unit 7 for adding a selected registered molecule to a corresponding position in a molecular structure such as during modeling based on a bonding position with a dummy atom removed, and the selected registered atom includes a dummy atom In response to the discrimination result from the dummy atom presence / absence discriminating unit 3 indicating that the first and second bonding positions are not held in the first and second bonding position holding units 4 and 6, respectively. A second registered molecule adding unit 8 for adding the selected registered molecule to a corresponding position in the molecular structure during modeling or the like based on the bonding position, and an additional molecule for rotating the added registered molecule by a desired angle around the bonding axis And a rotating unit 9.

The operation of the registered molecule adding apparatus having the above configuration is as follows. Library 1 by registered molecule selection unit 2
When a desired registered molecule is selected from the above, first, the dummy atom presence / absence determining unit 3 determines whether or not the selected registered molecule contains a dummy atom. When it is determined that the selected registered molecule contains a dummy atom, the designated bond position of the molecular structure during modeling or the like is held in the first bond position holding unit 4 as the first bond position. At the same time, the dummy atom arrangement position of the selected registered molecule is held in the second bond position holding unit 5 as the second bond position.
After that, the first coupling position holding unit 4
Based on the bonding position and the second bonding position held in the second bonding position holding unit 5, the first registered molecule adding unit 7 removes the registered molecule selected at the corresponding position of the molecular structure during modeling or the like from the dummy atom. Add in the state that was done. Conversely, when it is determined that the selected registered molecule does not include a dummy atom, the first bond position holding unit 4 sets the specified bond position of the molecular structure during modeling or the like as the first bond position.
And the designated binding position of the molecular structure of the selected registered molecule is retained in the second binding position holding unit 6 as the second binding position. After that, the first coupling position holding unit 4
Is selected by the second registered molecule adding unit 8 at a corresponding position in the molecular structure during modeling or the like based on the first bonding position held in the second bonding position holding unit 6 and the second bonding position held in the second bonding position holding unit 6 The registered molecules are added with the dummy atoms removed. In either case, the additional molecule rotating unit 9 rotates the added registered molecule by a desired angle around the bond axis, thereby terminating the modeling accompanying the added registered molecule.

As is clear from the above description, when the selected registered molecule does not include a dummy atom, the bonding position of the molecular structure during the modeling or the like and the bonding position of the selected molecule as in the conventional method. Must be specified, but if the selected registered molecule contains a dummy atom, it is only necessary to specify the bonding position of the molecular structure during modeling, etc., so it is necessary to add the registered molecule. Work can be simplified.

[0021]

Embodiment 3 FIGS. 7 and 8 are flow charts for explaining another embodiment of the registered figure adding method according to the present invention. In step SP1, a desired registered molecule is selected from a plurality of registered molecules registered in the library. Is selected, and in step SP2, it is determined whether or not the selected registered molecule includes a dummy atom. If the selected registered molecule includes a dummy atom, two or more dummy atoms are included in step SP3. If it is determined that only one dummy atom is included, the process waits until a bonding position of the molecular structure, such as during modeling, is designated in step SP4, and the modeling is stopped in step SP5. Add selected registered molecule by bonding dummy atom arrangement position to specified bond position of molecular structure such as That. Conversely, if it is determined in step SP3 that two or more dummy atoms are included, the process waits until one of the dummy atoms is selected in step SP6, and in step SP7, the molecular structure during modeling or the like is lost. Wait until the bond position is specified, and add the registered molecule selected by linking the dummy atom arrangement position to the specified bond position of the molecular structure during modeling or the like in step SP8. Also,
If it is determined in step SP2 that the registered molecule selected does not include a dummy atom, the process waits until the bond position of the selected registered molecule is specified in step SP9, and then in step SP10 a molecule that is being modeled or the like. Wait until the binding position of the structure is designated, and add the selected registered molecule by binding the designated binding position of the registered molecule to the designated binding position of the molecular structure being modeled in step SP11. After the processing of step SP5, step SP8 or step SP11 is performed, step SP5 is performed.
At 12, the added registration molecule is rotated by a desired angle about the bond axis to achieve modeling accompanying the addition of the registration molecule, and the series of processing ends.

Therefore, this embodiment can cope with a case where a molecule in which two or more dummy atoms are arranged is registered. When two or more dummy atoms are arranged, the operation is not simplified because the bond position of the registered molecule must be specified. However, generally, two or more dummy atoms are arranged. This is not very inconvenient because the proportion of molecules to be used is not very large.

[0023]

Embodiment 4 FIGS. 9 and 10 are flowcharts for explaining still another embodiment of the registered molecule adding method according to the present invention. In step SP1, a desired registered molecule is selected from a plurality of registered molecules registered in the library. Waiting until a molecule is selected, it is determined in step SP2 whether or not the selected registered molecule contains a dummy atom. If the selected molecule contains a dummy atom, the bond position is specified in step SP3. In step SP4, it is determined whether or not the designated bonding position is a bonding position of a molecular structure during modeling or the like. If it is determined that the specified bonding position is a bonding position of a molecule to be added, the process proceeds to step SP4.
In step SP6, the process waits until the binding position of the molecular structure being modeled or the like is designated, and in step SP6, the selected molecule is selected by binding the designated binding position of the registered molecule to the designated binding position of the molecular structure being modeled. The registered molecule is added. In this case, the dummy atoms are replaced with hydrogen atoms. Conversely, if it is determined in step SP4 that the specified bonding position is a bonding position of a molecular structure during modeling or the like, step SP7
In step (3), the registered molecule selected by adding the dummy atom arrangement position to the designated bond position of the molecular structure during modeling or the like is added. If it is determined in step SP2 that the dummy atom is not included, the process waits until a bonding position of the molecular structure during modeling or the like is designated in step SP8.
Wait until the binding position of the molecule to be added is designated in P9, and in step SP10, the registration selected by joining the designated binding position of the registered molecule to the designated binding position of the molecular structure being modeled. Add molecules. And step SP6, step SP
7 or after the processing in step SP10 is performed, in step SP11, the added registration molecule is rotated by a desired angle around the bond axis to achieve modeling accompanying the registration molecule addition, and a series of processing is performed as it is. finish.

Therefore, in this embodiment, when a registered molecule containing a dummy atom is selected, the dummy atom is not set unconditionally to the bonding position, but the bonding position of the molecule to be added is set first. By designating, any atom can be designated as a bond position, and by designating a bond position of a molecular structure during modeling or the like first, a dummy atom arrangement position can be automatically set as a bond position.

[0025]

As described above, according to the first aspect of the present invention, it is not necessary to specify the bonding position of the molecule to be added, and the operation required for adding the registered molecule can be simplified, and the registered molecule can be registered in advance. In addition to the case where a dummy atom arrangement position is set as a bond position, a unique effect that it is possible to cope with a case where an atom other than a dummy atom is set as a bond position.

[0026]

[Brief description of the drawings]

FIG. 1 is a flowchart illustrating one embodiment of a method for adding a registered molecule of the present invention.

FIG. 2 is a diagram illustrating a specific example of the registered molecule adding method in FIG. 1;

FIG. 3 is a diagram illustrating another specific example of the registered molecule adding method in FIG.

FIG. 4 is a flowchart illustrating a process of selecting a molecule registered in a library.

FIG. 5 is a diagram for explaining the processing of the flowchart in FIG. 4;

FIG. 6 is a block diagram showing one embodiment of the registered molecule adding apparatus of the present invention.

FIG. 7 is a flowchart illustrating a main part of another embodiment of the registered figure adding method according to the present invention.

FIG. 8 is a flowchart illustrating the rest of another embodiment of the registered figure adding method according to the present invention.

FIG. 9 is a flowchart illustrating a main part of still another embodiment of the registered molecule adding method according to the present invention.

FIG. 10 is a flowchart for explaining the remaining part of still another embodiment of the registered molecule adding method of the present invention.

FIG. 11 is a flowchart illustrating an example of a conventional molecule addition method.

[Explanation of symbols]

1 Library 2 Registered molecule selection unit 4 First binding position holding unit 7 First registered molecule addition unit

Continuation of the front page (56) References JP-A-1-161578 (JP, A) Yumasa Takahashi, Shinichi Sasaki, "Development of Structural Design Knowledge Base System for Candidate Structural Design", support for chemical substance design, etc. On the Knowledge-based System for Information Technology (First Phase), 1986-63 (published in 1990), pp. 85-99

Claims (1)

(57) [Claims] In a method of adding a molecule registered in advance to a predetermined molecular structure, when registering a molecule in a storage means for storing various molecules, a dummy atom is arranged at a bonding position of the molecule. Are registered, and in adding the registered molecule to the predetermined molecular structure, after the molecule to be added is selected,
When the position to add a molecule having the predetermined molecular structure is designated
In this case, the dummy atom arrangement position is set to the molecule addition expected position.
Are bonded to each other, and
After the indication, when the molecule to be added is selected,
The designated desired atom arrangement position of the molecule to be added is
Attach to the molecule addition expected position and
Method for adding a registered molecule, which comprises replacing an atom with a hydrogen atom