JP5880170B2 - Generating method, generating program, and generating apparatus - Google Patents

Description

  The present invention relates to a generation method, a generation program, and a generation apparatus.

  A conventional method for searching for a physiologically active compound that binds to a target protein in a living body has been disclosed (for example, see Patent Document 1 below). The conventional method gives parameters such as the number of atoms, atom type, bond type, and number of ring structures to the query that is the query molecule, and narrows down the molecules that satisfy the condition from the database to determine whether it can bind to the target protein. To do.

Japanese Patent No. 3928000

  However, in the above-described conventional method, it is necessary to specify parameters such as an atom type and a bond type for a query that is a query molecule prior to a search. Therefore, the user has to materialize the query, and there is a problem that the efficiency of query generation is reduced. In addition, the search omission due to this complicated query generation and the candidate compound that may bind to the target protein sterically due to the two-dimensional structure screening may be missed, so that an efficient compound search cannot be performed. There's a problem.

  An object of the present invention is to improve the efficiency of generating the two-dimensional structure data of a compound.

  According to one aspect of the present invention, three-dimensional abstract skeleton data obtained by combining a plurality of vertex data (abstract atoms) whose types of atoms are undefined is acquired, and each vertex data in the acquired abstract skeleton data is acquired. Based on the bond relationship, the hybrid attribute type of the atom corresponding to each vertex data is specified, and the hybrid attribute of the atom corresponding to the two vertex data to be combined selected from the vertex data group in which the hybrid attribute type is specified By combining the types, the bond type between the atoms corresponding to the two vertex data is specified, and the specified bond type is given to the skeleton data indicating the bond between the two vertex data constituting the abstract skeleton data. By performing two-dimensional transformation on the abstract skeleton data in which the mixed attribute type of the atom corresponding to each vertex data is assigned to each vertex data, 2 Method of generating a source structure data, generating program, and generating apparatus is proposed.

  Further, according to one aspect of the present invention, two-dimensional compound structure data indicating a two-dimensional molecular structure of a compound is specified from a database, and each of vertex data indicating atoms constituting the specified two-dimensional compound structure data is specified. Is converted into vertex data indicating the corresponding hybrid attribute type based on the connection relationship with other vertex data, the converted two-dimensional compound structure data is associated with the two-dimensional compound structure data, A generation method, a generation program, and a generation apparatus for storing are proposed.

  According to one aspect of the present invention, it is possible to increase the efficiency of generating the two-dimensional structure data of a compound. In addition, there is an effect that it is possible to comprehensively search for compound data that may be sterically bound to the target protein.

FIG. 1 is an explanatory diagram showing an example of a compound search. FIG. 2 is a block diagram of a hardware configuration example of the generation apparatus according to the embodiment. FIG. 3 is a block diagram illustrating a functional configuration example of the generation device. FIG. 4 is an explanatory diagram showing an example of abstract skeleton data. FIG. 5 is an explanatory diagram showing an example of the data structure of the vertex data group of the abstract skeleton data. FIG. 6 is an explanatory diagram illustrating a data structure example of a skeleton data group of abstract skeleton data. FIG. 7 is an explanatory diagram illustrating an example of a join type identification table. FIG. 8 is an explanatory diagram showing an example of the data structure of the vertex data group after two-dimensional conversion. FIG. 9 is an explanatory diagram showing an example of two-dimensional structure data. FIG. 10 is an explanatory diagram of an example of the contents stored in the DB. FIG. 11 is an explanatory diagram of an example of the first conversion rule table. FIG. 12 is an explanatory diagram of an example of the second conversion rule table. FIG. 13 is an explanatory diagram illustrating an example of conversion of two-dimensional compound structure data by the conversion unit. FIG. 14 is an explanatory diagram illustrating an example of the storage contents of the DB after storage by the storage unit. FIG. 15 is a flowchart illustrating an example of a query generation processing procedure by the generation device. FIG. 16 is a flowchart showing a detailed processing procedure example of the mixed attribute type specifying process (step S1502) from the abstract skeleton data shown in FIG. FIG. 17 is a flowchart showing a detailed processing procedure example of the first mixed attribute type determination process (step S1601) shown in FIG. FIG. 18 is a flowchart showing a detailed processing procedure example of the second mixed attribute type determination process (step S1602) shown in FIG. FIG. 19 is a flowchart showing a detailed processing procedure example of the inter-atom bond type specifying process (step S1503) shown in FIG. FIG. 20 is a flowchart illustrating an example of a DB generation processing procedure by the generation device. FIG. 21 is a flowchart showing a detailed processing procedure example of the hybrid attribute type specifying process (step S2003) from the designated two-dimensional compound structure data shown in FIG. FIG. 22 is a flowchart showing a detailed processing procedure example of the third mixed attribute type determination process (step S2101) shown in FIG. FIG. 23 is a flowchart showing a detailed processing procedure example of the fourth mixed attribute type determination process (step S2102) shown in FIG. FIG. 24 is a flowchart illustrating an example of a compound search processing procedure by the generation device.

Exemplary embodiments of a generation method, a generation program, and a generation apparatus according to the present invention will be described below in detail with reference to the accompanying drawings. In the present embodiment, the mixed attribute type is represented as follows.
Aromatic: AR
Sp Hybridization (hereinafter “Sp”): S1
Sp2 Hybridization (hereinafter “Sp2”): S2
Sp3 Hybridization (hereinafter “Sp3”): S3
Sp2 or Sp3 Hybridization: SS

<Example of compound search>
FIG. 1 is an explanatory diagram showing an example of a compound search. Queries are necessary to search for compounds. In the present embodiment, the abstract skeleton data 101 is the original data of the query. The abstract skeleton data 101 is three-dimensional molecular structure data in which the type of atom is undefined. The three-dimensional active structure data of the cocrystal may be used as the abstract skeleton data 101. The vertex data of the abstract skeleton data 101 indicates atoms. In the present embodiment, for example, in order to generate a query corresponding to a compound having a new structure without designing a compound having a new structure, attention is paid to the mixed attribute type of atoms, and the vertex data is extracted from the skeleton of the abstract skeleton data 101. The atomic hybrid attribute type in is specified.

  When the hybrid attribute type of atoms in each vertex data is specified, the bond type between the vertex data is also specified from the combination of the hybrid attribute types of the vertex data to be combined. Then, two-dimensional structure data 110 serving as a query is obtained by two-dimensionally transforming the abstract skeleton data 101 in which the hybrid attribute type and the coupling type are specified. In this way, a query is generated simply by providing the abstract skeleton data 101 without the user being aware of parameters such as the number of atoms, atom type, bond type, and number of ring structures.

  Further, two-dimensional compound structure data 102 is stored in the compound library. In the present embodiment, also for the two-dimensional compound structure data 102, vertex data indicating each atom is converted into vertex data indicating a hybrid attribute type. Note that the bond type between atoms in the two-dimensional compound structure data 102 is known.

  As a result, the query and the specified two-dimensional compound structure data 120 in which the hybrid attribute type is specified can be compared, and the specified two-dimensional compound structure data 120 including the query is searched. When the specified two-dimensional compound structure data 120 is searched, the two-dimensional compound structure data 102 before conversion is specified. Thus, the compound search is executed without the user being aware of the parameters such as the atom type and the bond type. Therefore, the efficiency of the compound search can be improved. Thereafter, the searched two-dimensional compound structure data 102 is converted into a three-dimensional structure to be a candidate compound, and the possibility of binding with the three-dimensional structure data of the target protein can be evaluated. Since the three-dimensional compound structure data that is a candidate compound has the same three-dimensional skeleton as the abstract skeleton data 101 that is the generation source of the query, the interaction with the target protein can be used for the calculation as it is.

(Example of hardware configuration of generation device)
FIG. 2 is a block diagram of a hardware configuration example of the generation apparatus according to the embodiment. In FIG. 2, the generation apparatus includes a CPU (Central Processing Unit) 201, a ROM (Read Only Memory) 202, a RAM (Random Access Memory) 203, a magnetic disk drive 204, a magnetic disk 205, an optical disk drive 206, and the like. An optical disk 207, a display 208, an I / F (Interface) 209, a keyboard 210, a mouse 211, a scanner 212, and a printer 213. Each component is connected by a bus 200.

  Here, the CPU 201 controls the entire generation apparatus. The ROM 202 stores a program such as a boot program. The RAM 203 is used as a work area for the CPU 201. The magnetic disk drive 204 controls reading / writing of data with respect to the magnetic disk 205 according to the control of the CPU 201. The magnetic disk 205 stores data written under the control of the magnetic disk drive 204.

  The optical disk drive 206 controls reading / writing of data with respect to the optical disk 207 according to the control of the CPU 201. The optical disk 207 stores data written under the control of the optical disk drive 206, or causes the computer to read data stored on the optical disk 207.

  The display 208 displays data such as a document, an image, and function information as well as a cursor, an icon, or a tool box. As the display 208, for example, a liquid crystal display, a plasma display, or the like can be adopted.

  An interface (hereinafter abbreviated as “I / F”) 209 is connected to a network 214 such as a LAN (Local Area Network), a WAN (Wide Area Network), and the Internet through a communication line. Connected to other devices. The I / F 209 controls an internal interface with the network 214 and controls data input / output from an external device. For example, a modem or a LAN adapter may be employed as the I / F 209.

  The keyboard 210 includes keys for inputting characters, numbers, various instructions, and the like, and inputs data. Moreover, a touch panel type input pad or a numeric keypad may be used. The mouse 211 performs cursor movement, range selection, window movement, size change, and the like. A trackball or a joystick may be used as long as they have the same function as a pointing device.

  The scanner 212 optically reads an image and takes in the image data into the generation apparatus. The scanner 212 may have an OCR (Optical Character Reader) function. The printer 213 prints image data and document data. As the printer 213, for example, a laser printer or an ink jet printer can be employed. Note that at least one of the optical disk drive 206, the optical disk 207, the display 208, the keyboard 210, the mouse 211, the scanner 212, and the printer 213 may be omitted.

<Functional configuration example of generation device>
FIG. 3 is a block diagram illustrating a functional configuration example of the generation device. The generation apparatus 300 includes an acquisition unit 301, a mixed attribute type identification unit 302, a combination type identification unit 303, and a generation unit 304, and generates the two-dimensional structure data 110 serving as a query. The generation apparatus 300 includes a specification unit 305, a detection unit 306, a conversion unit 307, and a storage unit 308, and generates the specified two-dimensional compound structure data 120 in which the hybrid attribute type is specified. In addition, the generation apparatus 300 includes a search unit 309, an extraction unit 310, and an output unit 311 and executes a compound search using a compound library.

  The acquisition unit 301, the mixed attribute type identification unit 302, the combination type identification unit 303, the generation unit 304, the designation unit 305, the detection unit 306, the conversion unit 307, the storage unit 308, the search unit 309, the extraction unit 310, and the output unit 311 Specifically, for example, by causing the CPU 201 to execute a program stored in a storage device such as the ROM 202, the RAM 203, the magnetic disk 205, and the optical disk 207 shown in FIG. Realize. Further, the compound library specifically realizes its functions by a storage device such as the ROM 202, the RAM 203, the magnetic disk 205, and the optical disk 207 shown in FIG.

  First, the acquisition unit 301 acquires the abstract skeleton data 101 stored in the storage device. As described above, the abstract skeleton data 101 is three-dimensional molecular structure data in which the type of atom is undefined. An example of the abstract skeleton data 101 is shown in FIG.

  FIG. 4 is an explanatory diagram illustrating an example of the abstract skeleton data 101. The abstract skeleton data 101 shown in FIG. 4 is configured by combining 30 pieces of vertex data p1 to p30 whose types of atoms are undefined, and connecting vertex data. Specifically, for example, the abstract skeleton data 101 is configured by combining 30 vertex data p1 to p30 by link data r1 to r34.

  FIG. 5 is an explanatory diagram showing an example of the data structure of the vertex data group of the abstract link data 101. In the data structure 500 of the vertex data group, the abstract skeleton data 101 has, for each vertex data, a three-dimensional coordinate value, a combination destination, and a hybrid attribute type. The joining destination is the vertex data of the other side to be joined. The hybrid attribute type has not yet been set. Since (A) in FIG. 5 shows an initial state, the hybrid attribute type is not yet determined.

  FIG. 6 is an explanatory diagram showing an example of the data structure of the link data group of the abstract skeleton data 101. In the data structure 600 of the link data group, the abstract skeleton data 101 has a vertex data pair to be combined and a connection type for each link data. Since (A) of FIG. 6 shows an initial state, the coupling type is not yet determined.

  Returning to FIG. 3, the hybrid attribute type specifying unit 302 specifies the mixed attribute type of the atom corresponding to each vertex data based on the connection relationship of each vertex data in the abstract skeleton data 101 acquired by the acquisition unit 301. Specifically, for example, the hybrid attribute type identification unit 302 includes a selection unit 321, a determination unit 322, and a determination unit 323.

  The selection unit 321 selects, from among a plurality of vertex data, a hybrid attribute type that has not yet been determined and a circular coupled vertex data group (hereinafter, “circular coupled vertex data group”). Specifically, for example, by referring to the data structure of the abstract skeleton data 101, the circularly coupled vertex data group is selected. In the example of FIG. 4, for example, the vertex data p1 to p6, p5 to p10, p13 to p18, p22 to p27, and p26 to p30 are selected as the circularly coupled vertex data group, respectively.

  The determination unit 322 determines whether or not each vertex data of the circularly coupled vertex data group selected by the selection unit 321 exists on the same plane. Specifically, for example, the determination unit 322 determines whether or not the coordinate values of the circularly coupled vertex data group are on the same plane. More specifically, the determination unit 322 generates a plane including three pieces of vertex data of the vertex data group using a plane equation. Then, it is determined whether or not the remaining vertex data is located on the generated plane.

  When the determination unit 322 determines that the data exists on the same plane, the determination unit 323 aromatically determines the mixed attribute type of the atom corresponding to each vertex data in the cyclic bond vertex data group. In the example of FIG. 4, the vertex data p1 to p6, p5 to p10, p13 to p18, p22 to p27, and p26 to p30 correspond to the vertex data p1 to p6, p5 to p10, p13 to p18, and p22 to p27. The atomic hybrid attribute type is determined aromatically. The data structure of FIG. 5B shows a state determined from the initial state to an aromatic (indicated by “AR” in FIG. 5).

  Through a series of processes by the selection unit 321, the determination unit 322, and the determination unit 323, the mixed attribute type of the atom corresponding to each vertex data of the circular bond vertex data group is specified as aromatic or non-aromatic. be able to.

  Further, the selection unit 321 combines the first vertex data whose hybrid attribute type is undetermined, the second vertex data and the third vertex data that are combined with the first vertex data, and the second vertex data. Four connected vertex data composed of the fourth vertex data to be matched is selected. Specifically, for example, after the selection unit 321 specifies whether the atomic mixed attribute type corresponding to each vertex data of the circular bond vertex data group is aromatic or non-aromatic, the 4-connected vertex data group Select.

  In the example of FIG. 4, the vertex data p10 to p13 are selected as the 4-connected vertex data. Among the vertex data p10 to p13, which is the 4-connected vertex data group, the vertex data p11 is the first vertex data whose hybrid attribute type is undetermined, and the vertex data p12 is combined with the first vertex data. 2 vertex data, the vertex data p10 is the third vertex data combined with the first vertex data, and the vertex data p13 is the fourth vertex data combined with the second vertex data. . Among the vertex data p10 to p13, which is a 4-connected vertex data group, the mixed attribute type of atoms corresponding to the vertex data p10 and p13 has already been determined aromatically.

  In this case, the determination unit 323 determines the mixed attribute type of the atom corresponding to the first vertex data based on the positional relationship of the four connected vertex data selected by the selection unit 321. Specifically, for example, the determination unit 322 refers to the coordinate value of the 4-connected vertex data and determines whether the 4-connected vertex data is arranged on a straight line. If the determination unit 322 determines that the elements are arranged on a straight line, the determination unit 323 determines that the mixed attribute type of the atom corresponding to the first vertex data is “S1”. In the above example, when the vertex data p10 to p13, which is a 4-connected vertex data group, are on a straight line, the mixed attribute type of the atom corresponding to the vertex data p11 is determined to be “S1”.

  When it is determined by the determination unit 322 that they are not arranged on a straight line, the determination unit 322 determines whether the four-connected vertex data exists on the same plane. Specifically, for example, the determination unit 322 determines whether or not the coordinate values of the four connected vertex data are on the same plane. More specifically, the determination unit 322 generates a plane including three vertex data selected from the four connected vertex data by a plane equation. Then, it is determined whether or not the remaining one vertex data is located on the generated plane.

  When it is determined by the determination unit 322 that the determination unit 322 is present on the same plane, the determination unit 323 determines the mixed attribute type of the atom corresponding to the first vertex data as one of the mixed attribute types S2 and S3. In the above example, when the vertex data p10 to p13, which is a 4-connected vertex data group, are on the same plane, the mixed attribute type of the atom corresponding to the vertex data p11 is determined to be “SS”.

  On the other hand, when the determination unit 322 determines that the two do not exist on the same plane, the determination unit 323 determines that the mixed attribute type of the atom corresponding to the first vertex data is “S3”. In the above example, when the vertex data p10 to p13, which is a 4-connected vertex data group, are not on the same plane, the mixed attribute type of the atom corresponding to the vertex data p11 is determined to be “S3”. In the data structure 500 of FIG. 5C, any one of “S1”, “SS”, and “S3” is determined for the vertex data whose hybrid attribute type is undetermined from the state of FIG. 5B. It shows the state that was done.

  Through a series of processes by the selection unit 321, the determination unit 322, and the determination unit 323, the mixed attribute type of the atom corresponding to the first vertex data among the four connected vertex data is changed to “S1”, “SS”, “S3”. It can be determined to any of "."

  Returning to FIG. 3, the bond type specifying unit 303 is a combination of mixed attribute types of atoms corresponding to two vertex data to be combined selected from the vertex data group whose hybrid attribute type is specified by the hybrid attribute type specifying unit 302. Thus, the bond type between the atoms corresponding to the two vertex data is specified. Specifically, for example, the bond type specifying unit 303 specifies a bond type between atoms corresponding to two vertex data to be bonded by referring to a bond type specifying table.

  FIG. 7 is an explanatory diagram illustrating an example of a join type identification table. In the bond type specifying table 700, “aromatic”, “single” (by combining the mixed attribute type of the atom corresponding to one vertex data to be combined and the mixed attribute type of the atom corresponding to the other vertex data ( The bond type is specified from “single bond”, “double” (double bond), and “triple” (triple bond). FIG. 6B shows the data structure after specifying the coupling type.

  Further, the hybrid attribute type for the vertex data p19 and p20 is both “SS”. Accordingly, the link data r21 to r23 having the vertex data p19 and p20 as the coupling partners are processed as follows.

  In the case of the link data r21, the mixed attribute type of the atom corresponding to the vertex data p18 is “AR”. Therefore, when the mixed attribute type of the atom corresponding to the vertex data p19 is S2, there is no possibility of coupling. Accordingly, in this case, the hybrid attribute type “SS” corresponding to the vertex data p19 is determined to be “S3”. Since the combination of “AR” and “S3” is “single” (single connection), the connection type of the link data r21 is determined to be single connection.

  In the case of the link data r23, the mixed attribute type of the atom corresponding to one vertex data p20 to be combined is “SS”, and the mixed attribute type of the atom corresponding to the other vertex data p21 is “S3”. . In the case of this combination, since “SS” is “S2” or “S3”, it is “single” (single link), so the link data r23 is determined to have a single bond type. .

  In the case of the link data r22, the mixed attribute type of the atom corresponding to one vertex data p19 to be combined is changed from “SS” to “S3”, and the mixed attribute type of the atom corresponding to the other vertex data p20. Is “SS”. In the case of this combination, since “SS” is “S2” or “S3”, it is “single” (single link), so the link data r22 is determined to have a single bond type. .

  Returning to FIG. 3, the generation unit 304 adds the connection type specified by the connection type specification unit 303 to the link data indicating the connection between the two vertex data constituting the abstract skeleton data 101, and each vertex data is assigned to each vertex. Two-dimensional structure data 110 is generated by performing two-dimensional conversion on the abstract link data 101 to which the mixed attribute type of atoms corresponding to the data is assigned. The generated two-dimensional structure data 110 becomes a compound search query. Specifically, for example, the generation unit 304 converts a three-dimensional coordinate value stored in the data structure 500 of the vertex data group of the abstract skeleton data 101 into a two-dimensional coordinate value.

  FIG. 8 is an explanatory diagram showing an example of the data structure of the vertex data group after two-dimensional conversion. When performing two-dimensional conversion, among vertex data groups connected in a ring shape, vertex data groups having a hybrid attribute type of aromatic are located on the same plane. Therefore, the generation unit 304 performs coordinate conversion so that the vertex data groups connected in a circular manner are parallel to each other, that is, are positioned on the same plane. In the example of FIG. 4, the circular coupling vertex data p1 to p6, p5 to p10, p13 to p18, and p22 to p27 are arranged on the same plane.

  In addition, with respect to the cyclic coupling vertex data group whose hybrid attribute type is not aromatic, the generation unit 304 is configured such that any link data is positioned on the same plane as the cyclic coupling vertex data group whose hybrid attribute type is aromatic. Transform coordinates. In the example of FIG. 4, for the circular connection vertex data p26 to p30 whose hybrid attribute type is not aromatic, the link data r30 is arranged on the same plane as the circular connection vertex data p22 to p27 whose hybrid attribute type is aromatic. Will be.

  In addition, the generation unit 304 performs coordinate transformation on the remaining vertex data on the same plane as the circular coupled vertex data group in which the hybrid attribute type is aromatic so that the length of the link data is maintained. As a result, the abstract skeleton data 101 expressed in three dimensions is two-dimensionally converted. The two-dimensional conversion is not limited to the conversion example described above, and other known methods may be employed.

  As described above, the generation unit 304 uses the link data group combination types illustrated in FIG. 6B, the vertex data group converted coordinate values illustrated in FIG. 8, the combination destination, and the hybrid attribute type. Two-dimensional structure data 110 can be generated.

FIG. 9 is an explanatory diagram showing an example of the two-dimensional structure data 110. In FIG. 9, since there is one vertex data with the hybrid attribute type “SS”, two two-dimensional structure data 110 of SS = S2 and SS = S3 are actually generated. In FIG. 9, since there is only one vertex data having the hybrid attribute type “SS”, two types of two-dimensional structure data 110 are obtained. However, when the number of “SS” is N, 2 ^N Street two-dimensional structure data 110 is obtained. As described above, the two-dimensional structure data 110 serving as a compound search query is generated by a series of processes performed by the acquisition unit 301, the hybrid attribute type specification unit 302, the binding type specification unit 303, and the generation unit 304.

  Next, a function for generating the two-dimensional compound structure data 102 will be described. The generation apparatus 300 includes a DB 320, a specification unit 305, a detection unit 306, a conversion unit 307, and a storage unit 308, and generates the two-dimensional compound structure data 102 in which the hybrid attribute type is specified. A DB (Data Base) 320 is a compound library that stores the two-dimensional compound structure data 102.

  FIG. 10 is an explanatory diagram showing an example of the contents stored in the DB 320. Two-dimensional compound structure data 102 is stored in the DB 320. The two-dimensional compound structure data 102 is data indicating the two-dimensional molecular structure of the compound. In the two-dimensional compound structure data 102, atoms and molecules constituting the compound are specified, and the bond type between the atoms is also specified.

  Returning to FIG. 3, the designation unit 305 designates the two-dimensional compound structure data 102 indicating the two-dimensional molecular structure of the compound from the DB 320. Specifically, the designation unit 305 designates, from the DB 320, the two-dimensional compound structure data 102 in which the vertex data indicating the atoms is not converted to the hybrid attribute type. Specifically, for example, the specifying unit 305 does not associate the two-dimensional compound structure data in which the mixed attribute type of the atom corresponding to the vertex data is specified (hereinafter, specified two-dimensional compound structure data 120) in the DB 320. The two-dimensional compound structure data 102 is designated.

  The detection unit 306 includes cyclic compound data indicating a cyclic compound from two-dimensional compound structure data, a pair of vertex data coupled by a triple bond, a pair of vertex data coupled by a double bond, 1 A pair of vertex data connected by a double connection is detected. The detected data is converted into data indicating a hybrid attribute type with reference to a first conversion rule table and a second conversion rule table described later.

  The conversion unit 307 converts each of the vertex data indicating the atoms constituting the two-dimensional compound structure data 102 specified by the specifying unit 305 to a vertex indicating the corresponding hybrid attribute type based on the connection relationship with other vertex data. Convert to data. Specifically, for example, the conversion unit 307 converts the two-dimensional compound structure data 102 by referring to the following conversion rule table.

  FIG. 11 is an explanatory diagram of an example of the first conversion rule table. The first conversion rule table 1100 defines conversion rules for the two-dimensional compound structure data 102 of the cyclic compound. Specifically, for example, when the conversion source data in the left column is detected by the detection unit 306, it is converted into converted data in the right column.

  FIG. 12 is an explanatory diagram showing an example of the second conversion rule table 1200. The second conversion rule table 1200 defines a conversion rule that focuses on the bond type of two atoms that are connected. Specifically, for example, when the conversion source data in the left column is detected by the detection unit 306, it is converted into converted data in the right column.

  FIG. 13 is an explanatory diagram illustrating an example of conversion of the two-dimensional compound structure data 102 by the conversion unit 307. The conversion unit 307 converts the two-dimensional compound structure data 102 by referring to the first conversion rule table 1100 and the second conversion rule table 1200. The two-dimensional compound structure data on the right side of FIG. 13 is the specified two-dimensional compound structure data 120, and the mixed attribute type of each atom is specified.

  Returning to FIG. 3, the storage unit 308 associates the two-dimensional compound structure data 102 with the two-dimensional compound structure data converted by the conversion unit 307 and stores the data in the database. Specifically, for example, the storage unit 308 stores the specified two-dimensional compound structure data 120 in the DB 320 in association with the two-dimensional compound structure data 102 that is the conversion source.

  FIG. 14 is an explanatory diagram illustrating an example of storage contents of the DB 320 after being stored by the storage unit 308. In FIG. 14, two-dimensional compound structure data 102 that is a conversion source and specified two-dimensional compound structure data 120 are stored in association with each other. Therefore, when the identified two-dimensional compound structure data 120 is hit by the query, the two-dimensional compound structure data 102 associated with the identified two-dimensional compound structure data 120 is extracted from the DB 320.

  As described above, the specified two-dimensional compound structure data 120 is generated by a series of processes by the designation unit 305, the conversion unit 307, and the storage unit 308, and is associated with the conversion source two-dimensional compound structure data 102 in the DB 320. Can be stored.

  Returning to FIG. 3, the generation apparatus 300 includes a search unit 309, an extraction unit 310, and an output unit 311, and executes a compound search using the DB 320. First, the search unit 309 searches the specified two-dimensional compound structure data 120 including the two-dimensional structure data 110 generated by the generation unit 304 from the DB 320. Specifically, for example, the search unit 309 searches for the specified two-dimensional compound structure data 120 that includes (completely matches) the two-dimensional structure data 110 serving as a query.

  The extraction unit 310 extracts the two-dimensional compound structure data 102 associated with the specified two-dimensional compound structure data 120 searched by the search unit 309 from the DB 320. Further, the extraction unit 310 extracts the two-dimensional compound structure data 102 corresponding to the extraction condition from the two-dimensional compound structure data 102 associated with the specified two-dimensional compound structure data 120 searched by the search unit 309. It is good as well. As the extraction conditions, for example, conditions such as a structure including a substituent or a functional group, or a structure including a specific substituent or a specific functional group are set. Thereby, the extracted two-dimensional compound structure data 102 can be narrowed down.

  In addition, as an extraction condition, a condition such as a structure from a query to a combination of a predetermined number of link data is set. The predetermined number can be arbitrarily set by the user. For example, a structure up to one bond can be used. Even if the two-dimensional compound structure data 102 includes the query, if the molecular structure other than the query is large, the two-dimensional compound structure data 102 may not fit in the target protein. Can be limited in size.

  The output unit 311 outputs the two-dimensional compound structure data 102 extracted by the extraction unit 310. Examples of output formats include display on the display 208, printing on the printer 213, transmission to an external device, and storage in a storage device in the generation device 300. As described above, the two-dimensional compound structure data 102 associated with the specified two-dimensional compound structure data 120 can be obtained by a series of processes performed by the search unit 309, the extraction unit 310, and the output unit 311.

<Generation processing procedure>
Next, a generation processing procedure performed by the generation apparatus 300 will be described using a flowchart. The flowcharts of FIGS. 15 to 19 show processing procedures for query generation by the acquisition unit 301, the hybrid attribute type specification unit 302, the combination type specification unit 303, and the generation unit 304. The flowcharts of FIGS. 20 to 23 show the processing procedure of DB generation by the designation unit 305, the conversion unit 307, and the storage unit 308. The flowchart in FIG. 24 shows a processing procedure of compound search by the search unit 309, the extraction unit 310, and the output unit 311.

  FIG. 15 is a flowchart illustrating an example of a query generation processing procedure performed by the generation apparatus 300. The generating apparatus 300 first reads the abstract link data 101 by the acquisition unit 301 (step S1501), and executes the hybrid attribute type specifying process from the abstract link data 101 by the hybrid attribute type specifying unit 302 (step S1502). Details of the mixed attribute type specifying process (step S1502) from the abstract link data 101 will be described with reference to FIG.

  Next, the generating apparatus 300 performs the bond type specifying process between atoms by the bond type specifying unit 303 (step S1503). Details of the inter-atom bond type specifying process (step S1503) will be described with reference to FIG. Then, the generation apparatus 300 generates secondary original structure data to be a query by using the generation unit 304 (step S1504). As a result, the query generation process ends.

  FIG. 16 is a flowchart showing a detailed processing procedure example of the hybrid attribute type specifying process (step S1502) from the abstract skeleton data 101 shown in FIG. The generating apparatus 300 uses the hybrid attribute type specifying unit 302 to execute a first hybrid attribute type determination process (step S1601), and then executes a second hybrid attribute type determination process (step S1602). Details of the first hybrid attribute type determination process (step S1601) will be described with reference to FIG. Details of the second hybrid attribute type determination process (step S1602) will be described with reference to FIG.

  FIG. 17 is a flowchart showing a detailed processing procedure example of the first mixed attribute type determination process (step S1601) shown in FIG. The generation apparatus 300 determines whether there is an unselected circular coupled vertex data group from the abstract skeleton data 101 (step S1701). When there is an unselected circular connection vertex data group (step S1701: Yes), the generation apparatus 300 selects an unselected circular connection vertex data group by the selection unit 321 (step S1702). Next, the generating apparatus 300 determines whether or not each vertex data of the selected circularly coupled vertex data group is on the same plane by the determination unit 322 (step S1703). If not on the same plane (step S1703: NO), the process returns to step S1701.

  On the other hand, if they are on the same plane (step S1703: Yes), the generation apparatus 300 causes the determination unit 323 to change the mixed attribute type of the atom corresponding to each vertex data of the cyclic bond vertex data group to aromatic (AR). Determination is made (step S1704). The determined hybrid attribute type is stored in the vertex data group data structure 500 in association with the corresponding vertex data. Thereafter, the process returns to step S1701. In step S1701, if there is no unselected circular combination vertex data group (step S1701: No), the process proceeds to the second hybrid attribute type determination process (step S1602).

  FIG. 18 is a flowchart showing a detailed processing procedure example of the second mixed attribute type determination process (step S1602) shown in FIG. First, the generation apparatus 300 determines whether there is vertex data whose hybrid attribute type is undetermined (step S1801). When there is vertex data whose hybrid attribute type is undetermined (step S1801: Yes), the generation apparatus 300 selects one undetermined vertex data by the selection unit 321 (step S1802).

  Next, the generating apparatus 300 detects vertex data (hereinafter, “joining vertex data”) that is the joining destination of the selected vertex data (hereinafter, “selected vertex data”) (step S1803). Then, the generation device 300 specifies 4-connected vertex data centered on the selected vertex data and the join destination vertex data (step S1804). In the generation apparatus 300, the determination unit 322 determines whether or not the 4-connected vertex data is on a straight line (step S1805). If it is on a straight line (step S1805: YES), the generating apparatus 300 determines the mixed attribute type of the atom corresponding to the selected vertex data to “S1” by the determining unit 323 (step S1806). The determined hybrid attribute type is stored in the vertex data group data structure 500 in association with the selected vertex data. Thereafter, the process returns to step S1801.

  On the other hand, if it is determined in step S1805 that it is not on a straight line (step S1805: No), the generation apparatus 300 determines whether the four-connected vertex data is on the same plane by the determination unit 322 (step S1805). S1807). If they are on the same plane (step S1807: YES), the generation apparatus 300 determines the mixed attribute type of the atom corresponding to the selected vertex data as “SS” (step S1808). The determined hybrid attribute type is stored in the vertex data group data structure 500 in association with the selected vertex data. Thereafter, the process returns to step S1801.

  On the other hand, when it is determined in step S1807 that they are not on the same plane (step S1807: No), the generating apparatus 300 determines the mixed attribute type of the atom corresponding to the selected vertex data as “S3” (step S1809). . The determined hybrid attribute type is stored in the vertex data group data structure 500 in association with the selected vertex data. Thereafter, the process returns to step S1801. If it is determined in step S1801 that there is no vertex data for which the hybrid attribute type has not been determined (step S1801: No), the second hybrid attribute type determination process (step S1602) is terminated, and the interatomic region of FIG. The process proceeds to the combination type specifying process (step S1503). Thereby, the mixed attribute type of the atom corresponding to each vertex data is specified from the abstract skeleton data 101.

  FIG. 19 is a flowchart showing a detailed processing procedure example of the inter-atom bond type specifying process (step S1503) shown in FIG. First, the generation apparatus 300 determines whether or not an unselected vertex data pair to be combined exists in the abstract skeleton data 101 (step S1901). If there is an unselected vertex data pair to be combined (step S1901: Yes), a pair of unselected vertex data pairs to be combined is selected (step S1902).

  Next, the generating apparatus 300 refers to the join type specification table 700 shown in FIG. 7 and links data that joins the selected vertex data pairs according to the mixed attribute types of the selected vertex data pairs to be joined. Are identified (step S1903). The identified join type is stored in the data structure 600 of the link data group in association with the link data that joins the selected vertex data pair. Thereafter, the process returns to step S1901.

  In step S1901, if there is no unselected vertex data pair to be combined (step S1901: No), the inter-atom bond type specifying process (step S1503) is terminated, and the query generation (step S1504) in FIG. Transition. Thereby, the connection type of each link data is specified.

  Further, for example, in the selection in step S1902, the generation apparatus 300 preferentially selects from vertex data pairs that do not include the hybrid attribute type “SS”. When there is no vertex data pair that does not include the hybrid attribute type “SS”, the generation apparatus 300 selects a vertex data pair whose hybrid attribute type of any one of the vertex data is “SS”. If there is no vertex data pair in which the hybrid attribute type of any one of the vertex data is “SS”, the generation apparatus 300 uses the vertex data pair in which the hybrid attribute type of both vertex data pairs to be combined is “SS”. Select.

  By performing such preferential selection, the hybrid attribute type of the vertex data whose hybrid attribute type was initially “SS” may be fixed to “S2” or “S3”. For example, the vertex data p19 is initially “SS”, but since the hybrid attribute type of the atom corresponding to the vertex data of the bond destination is “AR”, “S2” becomes a hybrid attribute type that cannot be obtained, It will be confirmed to “S3”.

  In this way, the query generation process allows the user to obtain a query that can be used for compound search without being aware of the atom type or bond type parameters.

  FIG. 20 is a flowchart illustrating an example of a DB generation processing procedure performed by the generation apparatus 300. The generating apparatus 300 first determines whether there is unspecified two-dimensional compound structure data 102 in the DB 320 (step S2001). When there is undesignated two-dimensional compound structure data 102 (step S2001: Yes), the generation apparatus 300 designates one undesignated two-dimensional compound structure data 102 by the designation unit 305 (step S2002). Next, the generating apparatus 300 uses the detection unit 306 and the conversion unit 307 to execute a hybrid attribute type specifying process from the designated two-dimensional compound structure data 102 (hereinafter, “designated two-dimensional compound structure data 102”) ( Step S2003). Details of the hybrid attribute type specifying process (step S2003) from the designated two-dimensional compound structure data 102 will be described with reference to FIG.

  Thereafter, the generation device 300 uses the storage unit 308 to specify the specified two-dimensional compound structure data 120 obtained by the hybrid attribute type specifying process (step S2003) from the specified two-dimensional compound structure data 102, with the specified two-dimensional compound structure data. The data is stored in the DB 320 in association with the data 102 (step S2004). Then, the process returns to step S2001. In step S2001, if there is no unspecified two-dimensional compound structure data 102 (step S2001: No), the DB generation process is terminated. Thereby, the DB 320 in which the two-dimensional compound structure data 102 and the specified two-dimensional compound structure data 120 are associated with each other can be generated.

  FIG. 21 is a flowchart showing a detailed processing procedure example of the hybrid attribute type specifying process (step S2003) from the designated two-dimensional compound structure data 102 shown in FIG. The generating apparatus 300 first executes a third hybrid attribute type determination process (step S2101), and then executes a fourth hybrid attribute type determination process (step S2102). Details of the third hybrid attribute type determination process (step S2101) will be described with reference to FIG. Details of the fourth mixed attribute type determination process (step S2102) will be described with reference to FIG.

  FIG. 22 is a flowchart showing a detailed processing procedure example of the third mixed attribute type determination process (step S2101) shown in FIG. In the generation apparatus 300, first, the detection unit 306 detects cyclic compound data indicating an unselected cyclic compound in the designated two-dimensional compound structure data 102 (step S2201). When unselected cyclic compound data is detected (step S2201: Yes), the generating apparatus 300 selects unselected cyclic compound data (step S2202). Then, the generation apparatus 300 refers to the first conversion rule table 1100 by the conversion unit 307, and converts the vertex data constituting the selected cyclic compound data into vertex data indicating the corresponding hybrid attribute type ( Step S2203). Specifically, for example, the corresponding hybrid attribute type is associated with the data structure (not shown) of the vertex data. Thereafter, the process returns to step S2201.

  If unselected cyclic compound data is not detected in step S2201 (step S2201: No), the process proceeds to the fourth hybrid attribute type determination process (step S2102). Thus, the hybrid attribute type of the cyclic compound data is specified by the third hybrid attribute type determination process (step S2101).

  FIG. 23 is a flowchart showing a detailed processing procedure example of the fourth mixed attribute type determination process (step S2102) shown in FIG. First, in the generation apparatus 300, the detection unit 306 detects vertex data pairs that are coupled by triple bonds in the designated two-dimensional compound structure data 102 (step S2301). When a vertex data pair that is coupled by triple coupling is detected (step S2301: Yes), the generation apparatus 300 refers to the second conversion rule table 1200 by the conversion unit 307, and detects the detected vertex data pair. The vertex data pair indicating the corresponding hybrid attribute type is converted (step S2302).

  Specifically, for example, the corresponding hybrid attribute type is associated with the data structure (not shown) of each vertex data of the vertex data pair. Thereafter, the process returns to step S2301. As a result, the hybrid attribute type for the triple bond is determined in preference to the double bond and the single bond.

  On the other hand, in step S2301, when the vertex data pair that is coupled by triple coupling is not detected (step S2301: No), the generation device 300 causes the detection unit 306 to search for 2 in the designated two-dimensional compound structure data 102. Vertex data pairs that are joined by multiple joining are detected (step S2303). When a vertex data pair that is coupled by double coupling is detected (step S2303: Yes), the generation apparatus 300 refers to the second conversion rule table 1200 by the conversion unit 307, and detects the detected vertex data pair. The vertex data pair indicating the corresponding hybrid attribute type is converted (step S2304).

  Specifically, for example, the corresponding hybrid attribute type is associated with the data structure (not shown) of each vertex data of the vertex data pair. Thereafter, the process returns to step S2303. Thereby, the hybrid attribute type for the double bond is determined with priority over the single bond.

  On the other hand, in step S2303, when the vertex data pair that is coupled by the double coupling is not detected (step S2303: No), the generation device 300 causes the detection unit 306 to select one of the specified two-dimensional compound structure data 102. Vertex data pairs that are joined by multiple joining are detected (step S2305). When a vertex data pair that is joined by single joining is detected (step S2305: Yes), the generation apparatus 300 refers to the second conversion rule table 1200 by the conversion unit 307, and detects the detected vertex data pair. The vertex data pair indicating the corresponding mixed attribute type is converted (step S2306). Specifically, for example, the corresponding hybrid attribute type is associated with the data structure (not shown) of each vertex data of the vertex data pair. Thereafter, the process returns to step S2305.

  On the other hand, in step S2305, when a vertex data pair that is joined by single joining is not detected (step S2305: No), the fourth hybrid attribute type determination process (step S2102) is terminated. As described above, the specified two-dimensional compound structure data 120 in which the hybrid attribute type for the single bond to triple bond is specified is obtained by the fourth hybrid attribute type determination process (step S2102).

  FIG. 24 is a flowchart illustrating an example of a compound search processing procedure performed by the generation apparatus 300. The generation apparatus 300 first reads a query (step S2401), and also reads the extraction condition when the extraction condition is set (step S2402). Then, the generation apparatus 300 determines whether or not the unselected specified two-dimensional compound structure data 120 exists in the DB 320 (step S2403). When there is unselected specified two-dimensional compound structure data 120 (step S2403: Yes), the generation device 300 selects unselected specified two-dimensional compound structure data 120 from the DB 320 (step S2404). Then, the generation apparatus 300 determines whether the selected identified two-dimensional compound structure data 120 includes a query by the search unit 309 (step S2405).

  When not including (step S2405: No), it returns to step S2403. On the other hand, in the case of inclusion (step S2405: Yes), the generation apparatus 300 extracts, from the DB 320, the two-dimensional compound structure data 102 associated with the selected specified two-dimensional compound structure data 120 by the extraction unit 310 ( Step S2406). Then, the process returns to step S2403. On the other hand, in step S2403, when there is no unselected specified two-dimensional compound structure data 120 (step S2403: No), the generation apparatus 300 outputs the extracted two-dimensional compound structure data 102 by the output unit 311 ( Step S2407). This completes the compound search. Thus, the compound search process allows the user to obtain the result of the compound search without being conscious of the atom type and bond type parameters.

  Note that the vertex data corresponding to the query in the two-dimensional compound structure data 102 obtained by the compound search is three-dimensionally converted by applying the coordinate value of the abstract skeleton data 101 that is the generation source of the query. The molecular structure other than the query is three-dimensionally converted based on the atom type and bond type of the two-dimensional compound structure data 102. Thereby, the two-dimensional compound structure data 102 is converted into three-dimensional compound structure data. Thereafter, the three-dimensional compound structure data is given to the three-dimensional structure data of the target protein, and the compound in the target protein is evaluated using a molecular mechanics method or the like.

  As described above, conventionally, in reagent search using a computer, it takes 2-3 minutes to calculate one reagent, and it is based on docking a large reagent database (for example, the sixth power scale of 10). The evaluation takes from six months to a year. That is, in reality, only a part of the reagent structure can be evaluated as in the experiment. On the other hand, in this embodiment, the query used for the compound search is efficiently performed by specifying the hybrid attribute type and the bond type by focusing on the shape of the abstract skeleton data 101 without specifying the atom type or the bond type. Can be generated automatically. Thereby, efficiency of evaluation of a target protein can be achieved.

  In addition, since the hybrid attribute type is determined aromatically depending on whether each of the circular bond vertex data groups is on the same plane, the hybrid attribute type of atoms corresponding to a plurality of vertex data must be determined at a time. It is possible to improve the efficiency of query generation.

  Further, since the hybrid attribute types such as S1, SS, and S3 are determined from the shape of the 4-connected vertex data, the hybrid attribute type is specified even if the atom type is not specified. Therefore, the efficiency of query generation can be improved.

  Further, for the two-dimensional compound structure data 102 to be searched, compound search using a query can be made possible by specifying the hybrid attribute type. Therefore, even if the atom type or bond type is not specified, if there is the abstract skeleton data 101 and the two-dimensional compound structure data 102 in the DB 320, an efficient compound search can be executed. Thereby, efficiency of evaluation of a target protein can be achieved.

  In addition, by setting extraction conditions in the compound search, the extracted two-dimensional compound structure data can be narrowed down, so that an efficient compound search can be executed. Thereby, efficiency of evaluation of a target protein can be achieved.

  In the above-described embodiment, query generation, DB generation, and compound search are realized by one generation apparatus 300. However, query generation, DB generation, and compound search are realized by different computers, and each computer May be a system connected by a network. Moreover, the system which connected the computer which implement | achieves any two among a query production | generation, DB production | generation, and a compound search, and the computer which implement | achieves the remaining one may be used. The DB 320 may use an existing compound library that is open on a network such as the Internet.

  As described above, according to the present embodiment, it is possible to improve the efficiency of query generation, and to improve the efficiency of searching for a compound and thus the evaluation of a target protein.

  Note that the generation method described in this embodiment can be realized by executing a program prepared in advance on a computer such as a personal computer or a workstation. The generation program is recorded on a computer-readable recording medium such as a hard disk, a flexible disk, a CD-ROM, an MO, and a DVD, and is executed by being read from the recording medium by the computer.

  The following additional notes are disclosed with respect to the embodiment described above.

(Supplementary note 1)
From the storage device accessible by the computer, obtain three-dimensional abstract skeleton data in which a plurality of vertex data with undefined atom types are combined,
Based on the connection relationship of each vertex data in the acquired abstract skeleton data, specify the mixed attribute type of the atom corresponding to each vertex data,
A bond type between the atoms corresponding to the two vertex data is identified by a combination of the mixed attribute types of the atoms corresponding to the two vertex data to be combined selected from the vertex data group in which the hybrid attribute type is specified;
The specified link type is given to the link data indicating the bond between the two vertex data constituting the abstract skeleton data, and the mixed attribute type of the atom corresponding to each vertex data is given to each vertex data The two-dimensional structure data is generated by performing two-dimensional transformation on the abstract skeleton data.
A generation method characterized by executing processing.

(Supplementary Note 2) The process of specifying the hybrid attribute type is as follows:
Among the plurality of vertex data, a hybrid attribute type is undetermined, and a circularly coupled vertex data group is selected,
It is determined whether or not each vertex data of the selected circular coupling vertex data group exists on the same plane,
If it is determined that the data exists on the same plane, the mixed attribute type of the atom corresponding to each vertex data of the cyclic bond vertex data group is determined aromatically.
The generation method according to attachment 1, further comprising a process.

(Supplementary note 3) The process to be selected is
The first vertex data whose hybrid attribute type is undetermined, the second vertex data and third vertex data combined with the first vertex data, and the fourth vertex data combined with the second vertex data Select 4 connected vertex data composed of vertex data,
The determining process is as follows:
The generation method according to appendix 2, wherein the mixed attribute type of the atom corresponding to the first vertex data is determined based on the positional relationship of the selected four-connected vertex data.

(Supplementary note 4)
It is determined whether the four connected vertex data are arranged on a straight line,
The determining process is as follows:
4. The generation method according to appendix 3, wherein when it is determined that the elements are arranged on a straight line, a mixed attribute type of an atom corresponding to the first vertex data is determined to be Sp.

(Supplementary Note 5) The determination process is as follows.
If the four connected vertex data are not arranged on a straight line, determine whether or not they exist on the same plane;
The determining process is as follows:
Item 5. The supplementary note 4, wherein when it is determined that the atoms exist on the same plane, the hybrid attribute type of the atom corresponding to the first vertex data is determined to be one of the hybrid attribute types Sp2 or Sp3. Generation method.

(Appendix 6) The determination process is as follows.
If the four connected vertex data are not arranged on a straight line, determine whether or not they exist on the same plane;
The determining process is as follows:
5. The generation method according to appendix 4, wherein when it is determined that they do not exist on the same plane, the mixed attribute type of the atom corresponding to the first vertex data is determined to be Sp3.

(Supplementary note 7)
For each compound, the two-dimensional compound structure data indicating the two-dimensional molecular structure of the compound and the mixed attribute type of the atom corresponding to each vertex data of the two-dimensional compound structure data are specified, and the link between the vertex data The specified 2D compound structure data including the generated 2D structure data is searched from a database in which the specified 2D compound structure data in which the data coupling type is specified is stored in association with each other,
2D compound structure data associated with the identified identified 2D compound structure data is extracted from the database;
Output the extracted 2D compound structure data,
The generation method according to any one of appendices 1 to 6, wherein the process is executed.

(Supplementary note 8) The processing to be extracted is
The generating method according to appendix 7, wherein two-dimensional compound structure data corresponding to an extraction condition is extracted from the database among two-dimensional compound structure data associated with the specified two-dimensional compound structure data. .

(Appendix 9) The computer
Specifying two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database accessible by the computer;
Each of the vertex data indicating the atoms constituting the specified two-dimensional compound structure data is converted into vertex data indicating the corresponding hybrid attribute type based on the binding relationship with the other vertex data,
Associate the specified two-dimensional compound structure data obtained by the conversion with the two-dimensional compound structure data, and store the data in the database.
The process of searching is as follows:
9. The generation method according to appendix 7 or 8, wherein the specified two-dimensional compound structure data including the two-dimensional structure data is searched from the database after storage.

(Appendix 10) The computer
Performing a process of detecting cyclic compound data indicating a cyclic compound from the two-dimensional compound structure data;
The process to convert is
10. The generation method according to appendix 9, wherein each of vertex data indicating atoms constituting the detected cyclic compound data is converted into vertex data indicating a hybrid attribute type corresponding to the cyclic compound.

(Additional remark 11) The said computer performs the process which detects a pair of vertex data couple | bonded by triple bond from the said two-dimensional compound structure data,
The process to convert is
The generation method according to appendix 9, wherein each of the detected pair of vertex data is converted into vertex data indicating Sp.

(Supplementary note 12) The computer
Executing a process of detecting a pair of vertex data linked by a double bond from the two-dimensional compound structure data;
The process to convert is
The generation method according to appendix 9, wherein each of the detected pair of vertex data is converted into vertex data indicating Sp2.

(Supplementary note 13) The computer
Performing a process of detecting a pair of vertex data linked by a single bond from the two-dimensional compound structure data;
The process to convert is
The generation method according to appendix 9, wherein each of the detected pair of vertex data is converted into vertex data indicating Sp3.

(Supplementary note 14)
Specifying two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database accessible by the computer;
Each of the vertex data indicating the atoms constituting the specified two-dimensional compound structure data is converted into vertex data indicating the corresponding hybrid attribute type based on the binding relationship with the other vertex data,
Associating the two-dimensional compound structure data with the converted two-dimensional compound structure data and storing it in the database;
A generation method characterized by executing processing.

(Supplementary note 15)
Performing a process of detecting cyclic compound data indicating a cyclic compound from the two-dimensional compound structure data;
The process to convert is
15. The generation method according to appendix 14, wherein each of vertex data indicating atoms constituting the detected cyclic compound data is converted into vertex data indicating a hybrid attribute type corresponding to the cyclic compound.

(Supplementary Note 16) The computer
Performing a process of detecting a pair of vertex data connected by triple bonds from the two-dimensional compound structure data;
The process to convert is
15. The generation method according to appendix 14, wherein each detected pair of vertex data is converted into vertex data indicating Sp.

(Supplementary Note 17) The computer
Executing a process of detecting a pair of vertex data linked by a double bond from the two-dimensional compound structure data;
The process to convert is
15. The generation method according to appendix 14, wherein each detected pair of vertex data is converted into vertex data indicating Sp2.

(Supplementary note 18)
Performing a process of detecting a pair of vertex data linked by a single bond from the two-dimensional compound structure data;
The process to convert is
15. The generation method according to appendix 14, wherein each detected pair of vertex data is converted into vertex data indicating Sp3.

(Supplementary note 19)
From the storage device accessible by the computer, obtain three-dimensional abstract skeleton data in which a plurality of vertex data with undefined atom types are combined,
Based on the connection relationship of each vertex data in the acquired abstract skeleton data, specify the mixed attribute type of the atom corresponding to each vertex data,
A bond type between the atoms corresponding to the two vertex data is identified by a combination of the mixed attribute types of the atoms corresponding to the two vertex data to be combined selected from the vertex data group in which the hybrid attribute type is specified;
The specified link type is given to the link data indicating the bond between the two vertex data constituting the abstract skeleton data, and the mixed attribute type of the atom corresponding to each vertex data is given to each vertex data The two-dimensional structure data is generated by performing two-dimensional transformation on the abstract skeleton data.
A generation program characterized by causing processing to be executed.

(Supplementary note 20)
Specifying two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database accessible by the computer;
Each of the vertex data indicating the atoms constituting the specified two-dimensional compound structure data is converted into vertex data indicating the corresponding hybrid attribute type based on the binding relationship with the other vertex data,
Associating the two-dimensional compound structure data with the converted two-dimensional compound structure data and storing it in the database;
A generation program characterized by causing processing to be executed.

(Supplementary Note 21) An acquisition unit that acquires, from a storage device, three-dimensional abstract skeleton data obtained by combining a plurality of vertex data whose types of atoms are undefined;
Based on the connection relationship of each vertex data in the abstract skeleton data acquired by the acquisition unit, a hybrid attribute type specifying unit that specifies the hybrid attribute type of the atom corresponding to each vertex data;
The inter-atom corresponding to the two vertex data by combining the hybrid attribute types of the atoms corresponding to the two vertex data to be combined selected from the vertex data group whose hybrid attribute type is specified by the hybrid attribute type specifying unit A connection type specifying part for specifying the connection type of
The link data indicating the bond between the two vertex data constituting the abstract skeleton data is given the bond type specified by the bond type specifying unit, and the vertex data is mixed with atoms corresponding to the vertex data. A generation unit that generates two-dimensional structure data by performing two-dimensional conversion on the abstract skeleton data to which an attribute type is assigned;
A generation apparatus comprising:

(Additional remark 22) The designation | designated part which designates the two-dimensional compound structure data which shows the two-dimensional molecular structure of a compound from a database,
A conversion unit that converts each of vertex data indicating atoms constituting the two-dimensional compound structure data specified by the specification unit into vertex data indicating a corresponding hybrid attribute type based on a binding relationship with other vertex data. When,
A storage unit that associates the two-dimensional compound structure data with the two-dimensional compound structure data after conversion by the conversion unit and stores the data in the database;
A generation apparatus comprising:

101 Abstract skeleton data 102 Two-dimensional compound structure data 110 Two-dimensional structure data 120 Identified two-dimensional compound structure data 300 Generation device 301 Acquisition unit 302 Hybrid attribute type specification unit 303 Binding type specification unit 304 Generation unit 305 Specification unit 306 Detection unit 307 Conversion unit 308 Storage unit 309 Search unit 310 Extraction unit 311 Output unit 321 Selection unit 322 Determination unit 323 Determination unit 700 Join type identification table 1100 First conversion rule table 1200 Second conversion rule table

Claims (17)

Computer
From the storage device accessible by the computer, obtain three-dimensional abstract skeleton data in which a plurality of vertex data with undefined atom types are combined,
Based on the connection relationship of each vertex data in the acquired abstract skeleton data, specify the mixed attribute type of the atom corresponding to each vertex data,
A bond type between the atoms corresponding to the two vertex data is identified by a combination of the mixed attribute types of the atoms corresponding to the two vertex data to be combined selected from the vertex data group in which the hybrid attribute type is specified;
The specified link type is given to the link data indicating the bond between the two vertex data constituting the abstract skeleton data, and the mixed attribute type of the atom corresponding to each vertex data is given to each vertex data The two-dimensional structure data is generated by performing two-dimensional transformation on the abstract skeleton data.
A generation method characterized by executing processing. The process of identifying the hybrid attribute type is:
Among the plurality of vertex data, a hybrid attribute type is undetermined, and a circularly coupled vertex data group is selected,
It is determined whether or not each vertex data of the selected circular coupling vertex data group exists on the same plane,
If it is determined that the data exists on the same plane, the mixed attribute type of the atom corresponding to each vertex data of the cyclic bond vertex data group is determined aromatically.
The generation method according to claim 1, further comprising a process. The process to select is
The first vertex data whose hybrid attribute type is undetermined, the second vertex data and third vertex data combined with the first vertex data, and the fourth vertex data combined with the second vertex data Select 4 connected vertex data composed of vertex data,
The determining process is as follows:
The generation method according to claim 2, wherein a mixed attribute type of an atom corresponding to the first vertex data is determined based on a positional relationship of the selected four-connected vertex data. The determination process is as follows:
It is determined whether the four connected vertex data are arranged on a straight line,
The determining process is as follows:
4. The generation method according to claim 3, wherein if it is determined that the elements are arranged on a straight line, the mixed attribute type of the atom corresponding to the first vertex data is determined to be Sp. The determination process is as follows:
If the four connected vertex data are not arranged on a straight line, determine whether or not they exist on the same plane;
The determining process is as follows:
The hybrid attribute type of the atom corresponding to the first vertex data is determined as one of the hybrid attribute types Sp2 or Sp3 when it is determined that they are on the same plane. The generation method described. The determination process is as follows:
If the four connected vertex data are not arranged on a straight line, determine whether or not they exist on the same plane;
The determining process is as follows:
The generation method according to claim 4, wherein when it is determined that they do not exist on the same plane, a mixed attribute type of an atom corresponding to the first vertex data is determined to be Sp3. The computer is
For each compound, the two-dimensional compound structure data indicating the two-dimensional molecular structure of the compound and the mixed attribute type of the atom corresponding to each vertex data of the two-dimensional compound structure data are specified, and the link between the vertex data The specified 2D compound structure data including the generated 2D structure data is searched from a database in which the specified 2D compound structure data in which the data coupling type is specified is stored in association with each other,
2D compound structure data associated with the identified identified 2D compound structure data is extracted from the database;
Output the extracted 2D compound structure data,
The generation method according to claim 1, wherein processing is executed. The computer is
Specifying two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database accessible by the computer;
Each of the vertex data indicating the atoms constituting the specified two-dimensional compound structure data is converted into vertex data indicating the corresponding hybrid attribute type based on the binding relationship with the other vertex data,
Associate the specified two-dimensional compound structure data obtained by the conversion with the two-dimensional compound structure data, and store the data in the database.
The process of searching is as follows:
8. The generation method according to claim 7, wherein specified two-dimensional compound structure data including the two-dimensional structure data is searched from a database after storage. The computer is
Performing a process of detecting cyclic compound data indicating a cyclic compound from the two-dimensional compound structure data;
The process to convert is
9. The generation method according to claim 8, wherein each of vertex data indicating atoms constituting the detected cyclic compound data is converted into vertex data indicating a hybrid attribute type corresponding to the cyclic compound. The computer executes a process of detecting a pair of vertex data connected by a triple bond from the two-dimensional compound structure data,
The process to convert is
9. The generation method according to claim 8, wherein each of the detected pair of vertex data is converted into vertex data indicating Sp. The computer is
Executing a process of detecting a pair of vertex data linked by a double bond from the two-dimensional compound structure data;
The process to convert is
9. The generation method according to claim 8, wherein each of the detected pair of vertex data is converted into vertex data indicating Sp2. The computer is
Performing a process of detecting a pair of vertex data linked by a single bond from the two-dimensional compound structure data;
The process to convert is
9. The generation method according to claim 8, wherein each of the detected pair of vertex data is converted into vertex data indicating Sp3. Computer
Specifying two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database accessible by the computer;
Each of the vertex data indicating the atoms constituting the specified two-dimensional compound structure data is converted into vertex data indicating the corresponding hybrid attribute type based on the binding relationship with the other vertex data,
Associating the two-dimensional compound structure data with the converted two-dimensional compound structure data and storing it in the database;
A generation method characterized by executing processing. On the computer,
From the storage device accessible by the computer, obtain three-dimensional abstract skeleton data in which a plurality of vertex data with undefined atom types are combined,
Based on the connection relationship of each vertex data in the acquired abstract skeleton data, specify the mixed attribute type of the atom corresponding to each vertex data,
A bond type between the atoms corresponding to the two vertex data is identified by a combination of the mixed attribute types of the atoms corresponding to the two vertex data to be combined selected from the vertex data group in which the hybrid attribute type is specified;
The specified link type is given to the link data indicating the bond between the two vertex data constituting the abstract skeleton data, and the mixed attribute type of the atom corresponding to each vertex data is given to each vertex data The two-dimensional structure data is generated by performing two-dimensional transformation on the abstract skeleton data.
A generation program characterized by causing processing to be executed. On the computer,
Specifying two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database accessible by the computer;
Each of the vertex data indicating the atoms constituting the specified two-dimensional compound structure data is converted into vertex data indicating the corresponding hybrid attribute type based on the binding relationship with the other vertex data,
Associating the two-dimensional compound structure data with the converted two-dimensional compound structure data and storing it in the database;
A generation program characterized by causing processing to be executed. An acquisition unit for acquiring, from a storage device, three-dimensional abstract skeleton data in which a plurality of vertex data with undefined atom types is combined;
Based on the connection relationship of each vertex data in the abstract skeleton data acquired by the acquisition unit, a hybrid attribute type specifying unit that specifies the hybrid attribute type of the atom corresponding to each vertex data;
The inter-atom corresponding to the two vertex data by combining the hybrid attribute types of the atoms corresponding to the two vertex data to be combined selected from the vertex data group whose hybrid attribute type is specified by the hybrid attribute type specifying unit A connection type specifying part for specifying the connection type of
The link data indicating the bond between the two vertex data constituting the abstract skeleton data is given the bond type specified by the bond type specifying unit, and the vertex data is mixed with atoms corresponding to the vertex data. A generation unit that generates two-dimensional structure data by performing two-dimensional conversion on the abstract skeleton data to which an attribute type is assigned;
A generation apparatus comprising: A designation unit for designating two-dimensional compound structure data indicating a two-dimensional molecular structure of the compound from a database;
A conversion unit that converts each of vertex data indicating atoms constituting the two-dimensional compound structure data specified by the specification unit into vertex data indicating a corresponding hybrid attribute type based on a binding relationship with other vertex data. When,
A storage unit that associates the two-dimensional compound structure data with the two-dimensional compound structure data after conversion by the conversion unit and stores the data in the database;
A generation apparatus comprising:

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