CN113611376A - Method and device for constructing molecular structure, computer equipment and storage medium - Google Patents
Method and device for constructing molecular structure, computer equipment and storage medium Download PDFInfo
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Abstract
The application relates to a molecular structure construction method, a molecular structure construction device, a computer device and a storage medium. The method comprises the following steps: responding to the triggering operation of the construction plug-in of the molecular structure, displaying a construction page of the molecular structure, and displaying a plurality of construction entries of a plurality of molecular structure types in the construction page; responding to the triggering operation of a construction entrance of a target molecular structure type in multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input area of parameters required by constructing the molecular structure of the target molecular structure type on the parameter input page; receiving a target parameter through a parameter input area; and acquiring and displaying the target molecular structure conforming to the target parameters. The method can realize the automatic construction of various molecular structures.
Description
Technical Field
The present application relates to the field of computer technologies, and in particular, to a method and an apparatus for constructing a molecular structure, a computer device, and a storage medium.
Background
The construction of molecular structures is a method for visually expressing the spatial conformation of molecules, and can provide specific and clear visual models for users (e.g., molecular simulators and experimenters).
Conventionally, a user can construct a molecular structure by using existing software such as Materials Studio (a material calculation software), GaussView (a software that can be used for constructing a molecular structure), Pymol (a molecular three-dimensional structure display software), and the like. Or, the user can also realize the operation of building the molecular structure through a World Wide Web (global area network) end webpage. However, the existing software requires local installation and has certain limitations. For example, Materials Studio focuses on material science architecture; pymol focuses on life sciences. Most of the web terminals are molecular structure display plug-ins, and the requirements of users cannot be met at the present stage of molecular structure building. Therefore, the construction mode of the molecular structure in the traditional technology has the problem of incomplete functions.
Disclosure of Invention
In view of the above, it is necessary to provide a method, an apparatus, a computer device, and a storage medium for constructing a molecular structure, which can efficiently and comprehensively construct the molecular structure, in order to solve the above-described technical problems.
In a first aspect, an embodiment of the present application provides a method for constructing a molecular structure, where the method includes:
displaying a building page of the molecular structure in response to a triggering operation of a building plug-in for the molecular structure, and displaying a plurality of building entries of a plurality of molecular structure types in the building page;
responding to triggering operation of a construction entrance of a target molecular structure type in multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input area of parameters required for constructing a molecular structure under the target molecular structure type on the parameter input page;
receiving a target parameter through the parameter input area;
and acquiring and displaying the target molecular structure conforming to the target parameters.
In one embodiment, the molecular structure types include any of common molecules, crystal structures, surface structures, disordered structures, polymer structures, nanostructures, polypeptide structures, and nucleic acid structures.
In one embodiment, after acquiring and displaying the target molecule structure meeting the target parameter, the method further includes:
in response to a save operation directed to the target molecular structure, saving the target molecular structure;
and displaying the historically constructed molecular structure, the target molecular structure and molecular structure related information corresponding to each molecular structure.
In one embodiment, the method further comprises:
responding to the downloading operation of the target molecular structure, and displaying a plurality of candidate file formats;
and responding to the selection operation of a target file format in a plurality of candidate file formats, and downloading the target molecular structure in the target file format.
In one embodiment, the method further comprises:
and responding to the modification operation of the target molecular structure, and adjusting the target molecular structure to generate the adjusted target molecular structure.
In one embodiment, after receiving the target parameter through the parameter input area, the method further includes:
and sending a construction request of a molecular structure to a server, wherein the construction request carries the target molecular structure type and the target parameter, and the construction request is used for indicating the server to generate the target molecular structure under the target molecular structure type according to the target parameter and sending the target molecular structure to a terminal.
In one embodiment, the construction plug-in of the molecular structure is a plug-in applied to a webpage end, and is generated based on molecular data three-dimensional representation JSimol.
In a second aspect, an embodiment of the present application provides an apparatus for constructing a molecular structure, the apparatus including:
the building page display module is used for responding to the triggering operation of the building plug-in of the molecular structure, displaying a building page of the molecular structure, and displaying a plurality of building entries of a plurality of molecular structure types in the building page;
the input page display module is used for displaying a parameter input page of a target molecular structure type in response to the triggering operation of a construction entrance of the target molecular structure type in multiple molecular structure types, and displaying a parameter input area of parameters required for constructing the molecular structure of the target molecular structure type on the parameter input page;
the parameter receiving module is used for receiving target parameters through the parameter input area;
and the structure display module is used for acquiring and displaying the target molecular structure conforming to the target parameters.
In a third aspect, an embodiment of the present application provides a computer device, which includes a memory and a processor, where the memory stores a computer program, and the processor implements the method for constructing a molecular structure according to any one of the embodiments of the first aspect when executing the computer program.
In a fourth aspect, embodiments of the present application provide a computer-readable storage medium, on which a computer program is stored, where the computer program, when executed by a processor, implements the method for constructing a molecular structure according to any one of the embodiments of the first aspect.
According to the construction method, the construction device, the computer equipment and the storage medium of the molecular structure, the construction plug-in of the molecular structure is deployed in advance, and the generation logics of various molecular structure types are integrated in the construction plug-in, so that a user can flexibly, simply and conveniently construct various molecular structures through the plug-in, and the construction mode of the molecular structure is greatly simplified. And when the triggering operation of the construction plug-in is detected, displaying a construction page, and displaying a plurality of construction entries of a plurality of molecular structure types in the construction page. When the triggering operation of the construction entrance of the target molecular structure type in the multiple molecular structure types is detected, the parameter input page of the target molecular structure type is displayed, so that the target parameters input by a user can be received through the parameter input page, and the target molecular structure conforming to the target parameters is obtained and displayed, thereby realizing the automatic construction of the multiple molecular structures and improving the automation degree of the constructed molecular structure.
Drawings
In order to more clearly illustrate the embodiments of the present specification or the technical solutions in the prior art, the drawings needed to be used in the description of the embodiments or the prior art will be briefly introduced below, it is obvious that the drawings in the following description are only some embodiments described in the specification, and other drawings can be obtained by those skilled in the art without inventive labor.
FIG. 1 is a diagram showing an application environment of a method for constructing a molecular structure according to an embodiment;
FIG. 2 is a schematic flow chart of a method for constructing a molecular structure according to an embodiment;
FIG. 3 is a schematic diagram of a construction page of a molecular structure in one embodiment;
FIG. 4a is a diagram of a parameter entry page for a generic molecular structure in one embodiment;
FIG. 4b is a schematic diagram of a parameter entry page for the crystal structure in one embodiment;
FIG. 4c is a schematic illustration of a parameter entry page for a polymer structure in one embodiment;
FIG. 4d is a diagram of a parameter entry page for a surface structure in one embodiment;
FIG. 5 is a schematic diagram of a constructed molecular structure shown in one example;
FIG. 6 is a diagram of a candidate file format shown in one embodiment;
FIG. 7 is a schematic flow chart of a method for constructing a molecular structure in one embodiment;
FIG. 8 is a schematic flow chart of the construction of each molecular structure in one embodiment;
FIG. 9 is a block diagram showing an apparatus for constructing a molecular structure in one embodiment;
FIG. 10 is a diagram showing an internal structure of a computer device according to an embodiment.
Detailed Description
In order to make the objects, technical solutions and advantages of the present application more apparent, the present application is described in further detail below with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are merely illustrative of the present application and are not intended to limit the present application.
The method for constructing the molecular structure provided by the application can be applied to the application environment shown in FIG. 1. Wherein the terminal 110 communicates with the server 120 through a network. The terminal 110 is disposed with a building plug-in of a molecular structure and application software that can call the building plug-in. The application software may be, but is not limited to, a WEB browser, display software of molecular structure, and the like. The server 120 is pre-deployed with generation logic of a variety of molecular structure types. Specifically, the terminal 110 displays a building page of the molecular structure in response to a user's trigger operation on a building plug-in of the molecular structure, and displays building entries of a plurality of molecular structure types in the building page. The terminal 110 displays a parameter input page of the target molecular structure type in response to a trigger operation for a construction entry of the target molecular structure type, and displays a parameter input region of parameters required for constructing the molecular structure under the target molecular structure type on the parameter input page. The terminal 110 receives the target parameters through the parameter input area, transmits the target molecular structure type and the target parameters to the server 120, so that the server 120 generates a target molecular structure according to the target molecular structure type and the target parameters, and transmits the target molecular structure to the terminal 110. The terminal 110 acquires and displays the target molecular structure.
The terminal 110 may be, but not limited to, various personal computers, notebook computers, smart phones, tablet computers, and portable wearable devices, and the server 120 may be implemented by an independent server or a server cluster formed by a plurality of servers.
In another embodiment, the method for constructing the molecular structure provided by the present application can also be applied to a terminal alone. The terminal is provided with a construction plug-in of a molecular structure, application software capable of calling the construction plug-in and generation logic aiming at each molecular structure type. And the terminal responds to the triggering operation of the user on the construction plug-in of the molecular structure, displays a construction page of the molecular structure, and displays a plurality of construction entries of a plurality of molecular structure types in the construction page. The terminal responds to the triggering operation of the construction entrance of the target molecular structure type, displays a parameter input page of the target molecular structure type, and displays a parameter input area of parameters required by constructing the molecular structure under the target molecular structure type on the parameter input page. And the terminal receives the target parameters through the parameter input area, and generates and displays a target molecular structure according to the target molecular structure type and the target parameters.
In an embodiment, as shown in fig. 2, a method for constructing a molecular structure is provided, which is described by taking the method as an example for being applied to the terminal in fig. 1, and includes the following steps:
step S210, responding to the triggering operation of the building plug-in of the molecular structure, displaying a building page of the molecular structure, and displaying a plurality of building entries of a plurality of molecular structure types in the building page.
The building plug-in of the molecular structure is a program written by an application program interface following a certain specification, and is pre-installed in application software, for example, a WEB page end, and the WEB page end can directly call the building plug-in.
The molecular structure is used to describe the three-dimensional arrangement of atoms in a molecule. The various molecular structure types may be, but are not limited to, ordinary molecular structures, crystal structures, surface structures, polymer structures, and the like.
The triggering operation of the plug-in can be realized by clicking operation.
Specifically, when the terminal detects that the user triggers the construction plug-in of the molecular structure in the application software, the construction plug-in is called, and the construction page of the molecular structure is displayed. And displaying construction entries of multiple molecular structure types in a first preset display mode in the construction page of the molecular structure. The first preset display mode may be a sequential display mode, for example, a sequential display mode in a horizontal, vertical, grid, or the like. The building entry of each molecular structure type can display the associated information of each molecular structure type, such as the molecular structure name, the molecular structure diagram, and the like.
Step S220, in response to the trigger operation on the building entry of the target molecular structure type among the multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input region of parameters required for building the molecular structure under the target molecular structure type on the parameter input page.
The target molecular structure type is a type of a molecular structure that a user wants to construct. The triggering operation of the building entrance can be realized by clicking operation.
Specifically, after the terminal detects that the user triggers a target molecular structure type in the multiple molecular structure types, a parameter input page corresponding to the target molecular structure type is displayed. The parameter input page comprises a parameter input area which is configured in advance and is used for constructing the parameters needed by the structure type of the target molecule. The specific content of the required parameters depends on the target molecular structure type, for example, the target molecular structure type is a common molecular structure, and the required parameters may include an atom type; the target molecular structure type is a crystal structure, and the required parameters may include a unit cell size parameter, a space group information parameter, an atom type, an in-cell fractional coordinate, and the like.
In step S230, the target parameter is received through the parameter input area.
Specifically, the parameter input form of the parameter input area may be various, and depending on the specific target molecule structure type and the parameter type, the user may perform operations such as selecting a parameter, manually inputting a parameter, uploading an existing parameter, and the like in the parameter input area.
In one exemplary illustration, the target molecular structure type is a generic molecular structure. The parameter input page corresponding to the common molecular structure comprises an element period table. The periodic table of elements includes a plurality of candidate atoms. And the terminal acquires a target atom selected from the candidate atoms by the user through the parameter input area as a target parameter.
Another exemplary illustration is that the target molecular structure type is a crystal structure. The parameter input page corresponding to the crystal structure includes parameter input areas corresponding to the cell size parameter, the space group information parameter, the atom type, the fractional coordinate in the cell, and the like. The terminal obtains parameters such as a unit cell size parameter, a space group information parameter, an atom type, a fractional coordinate in the unit cell and the like through the parameter input area as target parameters.
Another exemplary illustration is that the target molecular structure type is a disordered structure. The parameter input page corresponding to the unordered structure comprises a file uploading area for uploading the structure file and parameter input areas corresponding to the target density, the box type, the distance between the minimum atoms, the number of molecules in the composition and the like. The terminal takes the structure file, the target density, the box type, the distance between the minimum atoms, the number of molecules in the composition and the like acquired from each parameter input area as target parameters.
Step S240, a target molecular structure conforming to the target parameter is acquired and displayed.
Specifically, when the terminal detects a construction operation (for example, clicking an input completion button) on the parameter input page, the target molecular structure may be generated according to the target molecular structure and the target parameter, and the target molecular structure may be displayed. For example, when the target molecular structure type is a normal molecular structure, the terminal generates the target molecular structure according to the target atom selected by the user. Or, the terminal may also send a construction request of the molecular structure to the server, where the construction request carries the target molecular structure type and the target parameters. And the server responds to the construction request, invokes a generation logic corresponding to the target molecular structure type, and generates the target molecular structure according to the target parameters. And the server sends the generated target molecular structure to the terminal so that the terminal can acquire and display the target molecular structure according with the target parameters.
According to the construction method of the molecular structure, the construction plug-in of the molecular structure is deployed in advance, and the generation logics of various molecular structure types are integrated in the construction plug-in, so that a user can flexibly, simply and conveniently construct various molecular structures through the plug-in, and the construction mode of the molecular structure is greatly simplified. And when the triggering operation of the construction plug-in is detected, displaying a construction page, and displaying a plurality of construction entries of a plurality of molecular structure types in the construction page. When the triggering operation of the construction entrance of the target molecular structure type is detected, the parameter input page of the target molecular structure type is displayed, so that the target parameters input by a user can be received through the parameter input page, and then the target molecular structure conforming to the target parameters is obtained and displayed, the automatic construction of various molecular structures is realized, and the automation degree of constructing the molecular structure is improved.
In one embodiment, the construction plug-in of the molecular structure is a plug-in applied to a webpage end, and is generated based on the molecular data three-dimensional representation JSimol. JSimol is an object-oriented JavaScript library that provides interactive, hardware-accelerated three-dimensional representation of molecular data. The building plug-in of the molecular structure is configured into the plug-in which the webpage end can call, so that a user can automatically build the molecular structure through the webpage end, and the use flexibility of the user is improved.
In one embodiment, the molecular structure type includes any of a general molecular structure, a crystal structure, a surface structure, a polymer structure, a nanostructure, a polypeptide structure, a nucleic acid structure, and the like, without excluding a case where only one molecular structure is included. The building page for a molecular structure then includes multiple building entries for any of a variety of molecular structure types. And responding to the construction entrance triggering operation of each molecular structure type, and displaying a parameter input page corresponding to each molecular structure type by the terminal. Taking various molecular structure types as common molecular structures, crystal structures, polymer structures, and surface structures as examples, fig. 3 exemplarily shows a construction page of the molecular structure. When the terminal detects the trigger operation on the common molecular structure, the parameter input page shown in fig. 4a can be displayed. When the terminal detects the trigger operation on the crystal structure, the parameter input page shown in fig. 4b can be displayed. When the terminal detects a trigger operation on the polymer structure, a parameter input page shown in fig. 4c may be displayed. When the terminal detects the trigger operation on the surface structure, a parameter input page shown in fig. 4d can be displayed. The user can input corresponding target parameters through the parameter input page corresponding to each molecular structure type so as to instruct the terminal and/or the server to generate corresponding target molecular structures.
In the embodiment, multiple molecular structure types are integrated in the plug-in, so that the structure types cover from material science to life science, a user can flexibly and simply construct multiple molecular structures through the plug-in, and the construction mode of the molecular structures is greatly simplified.
In one embodiment, after acquiring and displaying the target molecule structure meeting the target parameter in step S240, the method further includes: in response to a save operation for the target molecular structure, saving the target molecular structure; and displaying the historically constructed molecular structure and the target molecular structure, and molecular structure associated information corresponding to each molecular structure.
Wherein, the saving operation can be realized by clicking a saving button.
The historically-constructed molecular structure may be all or part of the molecular structure constructed by the user account at all terminals, or all or part of the molecular structure constructed by the user account locally. The partial molecular structure may be a molecular structure that meets a certain screening condition, for example, a molecular structure that is constructed within a certain time period (for example, 3 months before the current time), or a certain number (for example, 10 molecules constructed before the current time), one or more specified types of molecular structures, or the like.
The molecular structure associated information is some information associated with the molecular structure, and may be, but not limited to, a name of the molecular structure, a type of the molecular structure, a preview page, a unique identifier, a generation time, a belonging project, user account information for constructing the molecular structure, and the like.
Specifically, when the terminal detects that the user performs a saving operation on the target molecular structure, the target molecular structure may be saved to the local database. The terminal may also send a save request to the server to instruct the server to solidify the target molecular structure in a database or a memory of the server. And after the storage is successful, the terminal displays the historically constructed molecular structure and the target molecular structure as well as the molecular structure associated information corresponding to each molecular structure in a second preset display mode. The second preset display mode may be, but is not limited to, a list display, a pull-down menu display, and the like. Fig. 5 is a schematic diagram schematically showing the constructed molecular structures and the target molecular structure in a list display manner.
In this embodiment, after the molecular structure is saved, the molecular structure and the target molecular structure obtained by history construction are displayed, so that the user can quickly know and preview the history of the molecular structure, and the way for the user to use and know information is simplified.
In one embodiment, after acquiring and displaying the target molecule structure meeting the target parameter in step S240, the method further includes: responding to the downloading operation of the target molecular structure, and displaying a plurality of candidate file formats; and responding to the selection operation of the target file format in the plurality of candidate file formats, and downloading the target molecular structure in the target file format.
The candidate file format may be, but not limited to, a format such as mol (a molecular Data file format), mol2 (a molecular Data file format), pdb (Program Data Base, basic Data of a Program), cif (a molecular Data file format), xsd (XML schema Definition, XML structure Definition), and mxf (a customized molecular Data file format).
Specifically, after the target molecular structure is saved, when the terminal detects that the user downloads the target molecular structure, the multiple candidate file formats are displayed in a third preset mode. The third preset mode may be pop-up page display, pull-down menu display, etc. And when the terminal detects that the user selects the candidate file format, taking the selected candidate file format as a target file format, and downloading the target molecular structure to a local database in the target file format. For example, if the target file format is mol, the terminal downloads the target molecular structure to the local database in the form of the mol file format. Continuing with fig. 5, when the terminal detects the user's click operation on the download key, the candidate file format page shown in fig. 6 is displayed.
In the embodiment, by providing a plurality of file formats, a user can select a proper file format to download the molecular structure, so that the use compatibility of molecular construction is improved, the use convenience of the user is improved, and the use experience of the user is improved.
In one embodiment, the build plug-in also supports modification operations on the constructed target molecule structure.
Specifically, the modification operation may be performed by directly performing an operation on the target molecular structure displayed by the terminal, for example, deleting one atom from the general molecular structure, and performing chemical bond type modification on adjacent atoms in the general molecular structure; the original parameters can be modified through the parameter input page, so that the server adjusts the parameters of the target structure according to the new parameters to generate the adjusted target molecular structure.
In this embodiment, by providing the function of re-editing the generated molecular structure, the function of the building plug-in of the molecular structure is more comprehensive, so that a user can obtain a new molecular structure based on the built molecular structure, and the efficiency of building the molecular structure by the user is accelerated.
In one embodiment, as shown in fig. 7, there is provided a method for constructing a molecular structure, comprising the steps of:
step S702, responding to the triggering operation of the building plug-in of the molecular structure in the webpage end, displaying a building page of the molecular structure, and displaying a plurality of building entries of a plurality of molecular structure types in the building page. Wherein, the various molecular structure types comprise common molecular structures, crystal structures, surface structures, disordered structures, polymer structures, nano structures, polypeptide structures and nucleic acid structures. And generating the construction plug-in based on the three-dimensional representation JSim of the molecular data.
Step S704, in response to the trigger operation on the building entry of the target molecular structure type among the multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input region of parameters required for building the molecular structure under the target molecular structure type on the parameter input page. The specific contents of the parameter input page and the parameter input area may refer to the above-mentioned embodiments, and are not specifically described herein.
Step S706, receiving the target parameter through the parameter input area of the target molecule structure type.
Step S708, sending a construction request of the molecular structure to the server, wherein the construction request carries the target molecular structure type and the target parameter, and the construction request is used for indicating the server to generate the target molecular structure under the target molecular structure type according to the target parameter and sending the target molecular structure to the terminal.
Step S710, acquiring and displaying a target molecular structure.
Step S712, in response to the saving operation for the target molecular structure, saving the target molecular structure, and displaying the historically constructed molecular structure and the target molecular structure, and the molecular structure association information corresponding to each molecular structure. The specific implementation manner of saving the target file structure may refer to the above embodiments, and is not specifically described herein.
Step S714, in response to the downloading operation of the target molecular structure, displays a plurality of candidate file formats.
In step S716, in response to the selection operation of the target file format in the plurality of candidate file formats, the target molecular structure is downloaded in the target file format. The specific implementation manner of the downloading target file structure may refer to the above embodiments, and is not specifically described herein.
Fig. 8 is a schematic diagram illustrating a construction process of each molecular structure type. Referring to fig. 8, a specific construction process for each molecular structure type is exemplified.
(1) General molecular structure
Firstly, the terminal responds to the click operation of the user on the atoms in the bullet frame of the element period table to obtain the selected target atoms. In this case in the additive atomic mode of the ordinary molecular structure. Then, the terminal responds to the clicking operation on the blank of the modeling page and displays the target atom in the page. Further, the terminal responds to continuous dragging operation of the target atom in the modeling page, and simultaneously and continuously adds a plurality of target atoms.
Further, other types of atoms may be added with reference to the above process.
Further, for common molecular structures, fragment libraries may also be pre-deployed. And when the triggering operation of the user on the fragment library is detected, displaying a fragment library preview window. And responding to the selection operation of the user on the segment, and acquiring the selected target segment. This time in the add fragment structure mode. And the terminal displays the target segment in a blank of the modeling page, or replaces the replacement site atom in the existing structure with the target segment in response to the replacement operation of the replacement site atom in the existing structure.
Further, the terminal can also modify the chemical bond type of the adjacent atom in response to the chemical bond type modification operation of the adjacent atom by the user.
Further, the terminal can also respond to the deletion operation of the user on the atoms to delete the selected atoms.
Further, the terminal may also perform the hydroprocessing for the common molecular structure in response to the hydroprocessing for the common molecular structure by the user.
Further, the terminal can respond to the optimization operation of the user on the common Molecular structure, and carry out the optimization processing of a universal Force field MMFF (Merck Molecular Force field) on the common Molecular structure.
(2) Crystal structure
Firstly, the terminal can obtain the space group information parameter and the cell size parameter input by the user through the parameter input page, and generate the empty cell with the set parameters. Then, the terminal acquires the atom type input by the user, the in-cell fractional coordinates corresponding to the atom type, and the manner of adding the atom to the empty cell (e.g., adding the atom automatically inside the cell). The terminal generates a crystal structure according to the acquired parameters.
Further, the terminal may also adjust the crystal structure in response to a user's editing operation on the crystal structure, for example, to construct a super cell. The super cell structure can be automatically constructed by redefining the crystal lattice, constructing a super cell parameter panel, modifying the cell size parameters and the like.
(3) Surface structure
First, the terminal acquires the constructed crystal structure. The specific construction of the crystal structure can be found by referring to the above examples, which are not specifically described herein. And the terminal acquires the section index, the section thickness and the thickness option input by the user, and calculates the top layer atomic parameter, the OU parameter and the OV parameter according to the section index, the section thickness and the thickness option. Wherein the OU parameter and the OV parameter characterize two lattice vectors of two-dimensional periodicity of atoms arranged on the surface. And automatically generating a surface structure according to the obtained parameters.
(4) Disordered structure
First, the terminal responds to the file uploading operation of the user, and obtains the structure file which is saved as the composition of the unordered structure. The terminal obtains parameters such as target density, box type, distance between minimum atoms, number of molecules in composition, number of finally generated structures and the like input by a user, and automatically generates the disordered structure according to the obtained parameters.
(5) Polymer structure
The terminal obtains the polymer type selected by the user, wherein the polymer type comprises homopolymer, block polymer and random polymer.
When the acquisition user selects a homopolymer, the desired monomer structure type is acquired from the stored monomer structure library. And acquiring polymer information parameters input by a user, wherein the parameters comprise the tacticity, the monomer connection mode, the chain length, the chain number, the dihedral angle between monomer connections and the like. If the tacticity is a random structure, the monomer conformation inversion rate input by the user is also acquired. And generating a click homopolymer structure according to the acquired parameters.
When the block polymer selected by the user is obtained, the number of monomers, the monomer conformation inversion rate and the monomer inversion rate input by the user are obtained for each monomer. The number of superunits, the number of chains, the dihedral angle between monomer links were obtained for the entire block polymer. And automatically generating a block polymer structure according to the acquired parameters.
When the obtaining user selects the random polymer, aiming at each monomer, obtaining the monomer occurrence probability, the monomer conformation inversion rate and the monomer turnover rate input by the user. The user-entered chain length, number of chains, dihedral angle between monomer connections are obtained for the entire random polymer. And automatically generating a random polymer structure according to the acquired parameters.
(6) Nano-structure
The terminal acquires the nanostructure type selected by the user. The nanostructure type includes a nanotube structure, a nanodisk structure.
When a nanotube structure selected by a user is obtained, a constructed carbon nanotube or a boron nitride nanotube selected by the user is obtained, and two unit vectors (n, m) input by the user are obtained, wherein n is a unit of force, and m is a unit of length; length. And automatically generating the nanotube structure according to the acquired parameters.
When the acquisition user selects the structure of the nano disc, the carbon nano disc or the boron nitride nano disc selected by the user is acquired, and the length and the width of the nano disc, the number of layers of the nano disc and the distance between the layers input by the user are acquired. And automatically generating the nano disc structure according to the acquired parameters.
(7) Polypeptide structure
Acquiring the amino acid sequence added by the user, and setting phi, psi dihedral angle parameters. Automatically generating a polypeptide structure based on the obtained parameters.
(8) Nucleic acid structures
And acquiring the nucleic acid sequence added by the user and the configured single double-stranded chain. Automatically generating a nucleic acid structure based on the obtained parameters.
It should be understood that, although the steps in the above-described flowcharts are shown in order as indicated by the arrows, the steps are not necessarily performed in order as indicated by the arrows. The steps are not performed in the exact order shown and described, and may be performed in other orders, unless explicitly stated otherwise. Moreover, at least a part of the steps in the above-mentioned flowcharts may include a plurality of steps or a plurality of stages, which are not necessarily performed at the same time, but may be performed at different times, and the order of performing the steps or the stages is not necessarily performed in sequence, but may be performed alternately or alternately with other steps or at least a part of the steps or the stages in other steps.
Based on the above description of the embodiment of the method for constructing a molecular structure, the present disclosure also provides a device for generating a molecular structure. The apparatus may include systems (including distributed systems), software (applications), modules, components, servers, clients, etc. that use the methods described in embodiments of the present specification in conjunction with any necessary apparatus to implement the hardware. Based on the same innovative concept, the embodiments of the present disclosure provide an apparatus in one or more embodiments as described in the following embodiments. Since the implementation scheme of the apparatus for solving the problem is similar to that of the method, the specific implementation of the apparatus in the embodiment of the present specification may refer to the implementation of the foregoing method, and repeated details are not repeated. As used hereinafter, the term "unit" or "module" may be a combination of software and/or hardware that implements a predetermined function. Although the means described in the embodiments below are preferably implemented in software, an implementation in hardware, or a combination of software and hardware is also possible and contemplated.
In one embodiment, as shown in fig. 9, there is provided a molecular structure generating apparatus 900, including: a build page display module 902, an input page display module 904, a parameter receiving module 906, and a structure display module 908, wherein:
a build page display module 902, configured to display a build page of a molecular structure in response to a trigger operation on a build plug-in of the molecular structure, and display a plurality of build entries of a plurality of molecular structure types in the build page; an input page display module 904, configured to display a parameter input page of a target molecular structure type in response to a trigger operation on a construction entry of the target molecular structure type among multiple molecular structure types, and display a parameter input area of parameters required for constructing a molecular structure under the target molecular structure type on the parameter input page; a parameter receiving module 906 for receiving the target parameter through the parameter input area; and a structure display module 908 for acquiring and displaying the target molecule structure according with the target parameter.
In one embodiment, the molecular structure types include any of common molecules, crystal structures, surface structures, disordered structures, polymer structures, nanostructures, polypeptide structures, nucleic acid structures.
In one embodiment, the apparatus 900 further comprises: a saving module for saving the target molecular structure in response to a saving operation for the target molecular structure; and the historical structure display module is used for displaying the molecular structure and the target molecular structure which are constructed historically and the molecular structure related information corresponding to each molecular structure.
In one embodiment, the apparatus 900 further comprises: the format display module is used for responding to the downloading operation of the target molecular structure and displaying a plurality of candidate file formats; and the downloading module is used for responding to the selection operation of the target file format in the plurality of candidate file formats and downloading the target molecular structure in the target file format.
In one embodiment, the apparatus 900 further comprises: and the modification module is used for responding to modification operation on the target molecular structure, and adjusting the target molecular structure to generate an adjusted target molecular structure.
In one embodiment, the apparatus 900 further comprises: the sending module is used for sending a construction request of the molecular structure to the server, the construction request carries the target molecular structure type and the target parameters, the construction request is used for indicating the server to generate the target molecular structure under the target molecular structure type according to the target parameters, and the target molecular structure is sent to the terminal. In one embodiment, the construction plug-in of the molecular structure is a plug-in applied to a webpage end, and is generated based on the molecular data three-dimensional representation JSimol.
For the specific definition of the generating device of the molecular structure, reference may be made to the above definition of the construction method of the molecular structure, which is not described herein again. The respective modules in the above-described molecular structure generation apparatus may be entirely or partially realized by software, hardware, and a combination thereof. The modules can be embedded in a hardware form or independent from a processor in the computer device, and can also be stored in a memory in the computer device in a software form, so that the processor can call and execute operations corresponding to the modules.
In one embodiment, a computer device is provided, which may be a terminal, and its internal structure diagram may be as shown in fig. 10. The computer device includes a processor, a memory, a communication interface, a display screen, and an input device connected by a system bus. Wherein the processor of the computer device is configured to provide computing and control capabilities. The memory of the computer device comprises a nonvolatile storage medium and an internal memory. The non-volatile storage medium stores an operating system and a computer program. The internal memory provides an environment for the operation of an operating system and computer programs in the non-volatile storage medium. The communication interface of the computer device is used for carrying out wired or wireless communication with an external terminal, and the wireless communication can be realized through WIFI, an operator network, NFC (near field communication) or other technologies. The computer program is executed by a processor to implement a method of building a molecular structure. The display screen of the computer equipment can be a liquid crystal display screen or an electronic ink display screen, and the input device of the computer equipment can be a touch layer covered on the display screen, a key, a track ball or a touch pad arranged on the shell of the computer equipment, an external keyboard, a touch pad or a mouse and the like.
Those skilled in the art will appreciate that the architecture shown in fig. 10 is merely a block diagram of some of the structures associated with the disclosed aspects and is not intended to limit the computing devices to which the disclosed aspects apply, as particular computing devices may include more or less components than those shown, or may combine certain components, or have a different arrangement of components.
In one embodiment, a computer device is provided, comprising a memory and a processor, the memory having a computer program stored therein, the processor implementing the following steps when executing the computer program:
responding to the triggering operation of the construction plug-in of the molecular structure, displaying a construction page of the molecular structure, and displaying a plurality of construction entries of a plurality of molecular structure types in the construction page; responding to the triggering operation of a construction entrance of a target molecular structure type in multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input area of parameters required by constructing the molecular structure of the target molecular structure type on the parameter input page; receiving a target parameter through a parameter input area; and acquiring and displaying the target molecular structure conforming to the target parameters.
In one embodiment, the molecular structure types include any of common molecules, crystal structures, surface structures, disordered structures, polymer structures, nanostructures, polypeptide structures, nucleic acid structures.
In one embodiment, the processor, when executing the computer program, further performs the steps of:
in response to a save operation for the target molecular structure, saving the target molecular structure; displaying the constructed molecular structure and the target molecular structure, and the molecular structure related information corresponding to each molecular structure.
In one embodiment, the processor, when executing the computer program, further performs the steps of:
responding to the downloading operation of the target molecular structure, and displaying a plurality of candidate file formats; and responding to the selection operation of the target file format in the plurality of candidate file formats, and downloading the target molecular structure in the target file format.
In one embodiment, the processor, when executing the computer program, further performs the steps of:
and responding to the modification operation of the target molecular structure, and adjusting the target molecular structure to generate an adjusted target molecular structure.
In one embodiment, the processor, when executing the computer program, further performs the steps of:
and sending a construction request of the molecular structure to a server, wherein the construction request carries the target molecular structure and the target parameters, and the construction request is used for indicating the server to generate the target molecular structure under the target molecular structure type according to the target parameters and sending the target molecular structure to the terminal.
In one embodiment, the construction plug-in of the molecular structure is a plug-in applied to a webpage end, and is generated based on the molecular data three-dimensional representation JSimol.
In one embodiment, a computer-readable storage medium is provided, having a computer program stored thereon, which when executed by a processor, performs the steps of:
responding to the triggering operation of the construction plug-in of the molecular structure, displaying a construction page of the molecular structure, and displaying a plurality of construction entries of a plurality of molecular structure types in the construction page; responding to the triggering operation of a construction entrance of a target molecular structure type in multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input area of parameters required by constructing the molecular structure of the target molecular structure type on the parameter input page; receiving a target parameter through a parameter input area; and acquiring and displaying the target molecular structure conforming to the target parameters.
In one embodiment, the molecular structure types include any of common molecules, crystal structures, surface structures, disordered structures, polymer structures, nanostructures, polypeptide structures, nucleic acid structures.
In one embodiment, the computer program when executed by the processor implements the steps of:
in response to a save operation for the target molecular structure, saving the target molecular structure; and displaying the historically constructed molecular structure and the target molecular structure, and molecular structure associated information corresponding to each molecular structure.
In one embodiment, the computer program when executed by the processor implements the steps of:
responding to the downloading operation of the target molecular structure, and displaying a plurality of candidate file formats; and responding to the selection operation of the target file format in the plurality of candidate file formats, and downloading the target molecular structure in the target file format.
In one embodiment, the computer program when executed by the processor implements the steps of:
and responding to the modification operation of the target molecular structure, and adjusting the target molecular structure to generate an adjusted target molecular structure.
In one embodiment, the computer program when executed by the processor implements the steps of:
and sending a construction request of the molecular structure to a server, wherein the construction request carries the target molecular structure type and the target parameters, and the construction request is used for indicating the server to generate the target molecular structure under the target molecular structure type according to the target parameters and sending the target molecular structure to the terminal.
In one embodiment, the construction plug-in of the molecular structure is a plug-in applied to a webpage end, and is generated based on the molecular data three-dimensional representation JSimol.
It will be understood by those skilled in the art that all or part of the processes of the methods of the embodiments described above can be implemented by hardware instructions of a computer program, which can be stored in a non-volatile computer-readable storage medium, and when executed, can include the processes of the embodiments of the methods described above. Any reference to memory, storage, database or other medium used in the embodiments provided herein can include at least one of non-volatile and volatile memory. Non-volatile Memory may include Read-Only Memory (ROM), magnetic tape, floppy disk, flash Memory, optical storage, or the like. Volatile Memory can include Random Access Memory (RAM) or external cache Memory. By way of illustration and not limitation, RAM can take many forms, such as Static Random Access Memory (SRAM) or Dynamic Random Access Memory (DRAM), among others.
The technical features of the above embodiments can be arbitrarily combined, and for the sake of brevity, all possible combinations of the technical features in the above embodiments are not described, but should be considered as the scope of the present specification as long as there is no contradiction between the combinations of the technical features.
The above-mentioned embodiments only express several embodiments of the present application, and the description thereof is more specific and detailed, but not construed as limiting the scope of the invention. It should be noted that, for a person skilled in the art, several variations and modifications can be made without departing from the concept of the present application, which falls within the scope of protection of the present application. Therefore, the protection scope of the present patent shall be subject to the appended claims.
Claims (10)
1. A method of constructing a molecular structure, the method comprising:
displaying a building page of the molecular structure in response to a triggering operation of a building plug-in for the molecular structure, and displaying a plurality of building entries of a plurality of molecular structure types in the building page;
responding to triggering operation of a construction entrance of a target molecular structure type in multiple molecular structure types, displaying a parameter input page of the target molecular structure type, and displaying a parameter input area of parameters required for constructing a molecular structure under the target molecular structure type on the parameter input page;
receiving a target parameter through the parameter input area;
and acquiring and displaying the target molecular structure conforming to the target parameters.
2. The method of claim 1, wherein the molecular structure types include any of a generic molecular structure, a crystal structure, a surface structure, a disordered structure, a polymer structure, a nanostructure, a polypeptide structure, and a nucleic acid structure.
3. The method of any one of claims 1 or 2, wherein after acquiring and displaying the target molecular structure according to the target parameter, further comprising:
in response to a save operation directed to the target molecular structure, saving the target molecular structure;
and displaying the historically constructed molecular structure, the target molecular structure and molecular structure related information corresponding to each molecular structure.
4. The method of claim 1, further comprising:
responding to the downloading operation of the target molecular structure, and displaying a plurality of candidate file formats;
and responding to the selection operation of a target file format in a plurality of candidate file formats, and downloading the target molecular structure in the target file format.
5. The method according to any one of claims 1 or 2, further comprising:
and responding to the modification operation of the target molecular structure, and adjusting the target molecular structure to generate the adjusted target molecular structure.
6. The method of claim 1 or 2, wherein after receiving the target parameter via the parameter input area, further comprising:
and sending a construction request of a molecular structure to a server, wherein the construction request carries the target molecular structure type and the target parameter, and the construction request is used for indicating the server to generate the target molecular structure under the target molecular structure type according to the target parameter and sending the target molecular structure to a terminal.
7. The method according to claim 1 or 2, wherein the construction plug-in of the molecular structure is a plug-in applied to a webpage end, and JSimol is generated based on three-dimensional representation of molecular data.
8. An apparatus for building a molecular structure, the apparatus comprising:
the building page display module is used for responding to the triggering operation of the building plug-in of the molecular structure, displaying a building page of the molecular structure, and displaying a plurality of building entries of a plurality of molecular structure types in the building page;
the input page display module is used for displaying a parameter input page of a target molecular structure type in response to the triggering operation of a construction entrance of the target molecular structure type in multiple molecular structure types, and displaying a parameter input area of parameters required for constructing the molecular structure of the target molecular structure type on the parameter input page;
the parameter receiving module is used for receiving target parameters through the parameter input area;
and the structure display module is used for acquiring and displaying the target molecular structure conforming to the target parameters.
9. A computer device comprising a memory and a processor, the memory storing a computer program, wherein the processor implements the method of constructing a molecular structure according to any one of claims 1 to 7 when executing the computer program.
10. A computer-readable storage medium, on which a computer program is stored, which, when being executed by a processor, implements the method of constructing a molecular structure according to any one of claims 1 to 7.
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Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN114464273A (en) * | 2021-12-22 | 2022-05-10 | 天翼云科技有限公司 | Molecular structure database construction method and device, electronic equipment and storage medium |
| WO2023123022A1 (en) * | 2021-12-29 | 2023-07-06 | 深圳晶泰科技有限公司 | Method and apparatus for acquiring molecular properties, and storage medium |
| WO2023155724A1 (en) * | 2022-02-18 | 2023-08-24 | 北京有竹居网络技术有限公司 | Method and apparatus for designing ligand molecules |
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Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN114464273A (en) * | 2021-12-22 | 2022-05-10 | 天翼云科技有限公司 | Molecular structure database construction method and device, electronic equipment and storage medium |
| WO2023123022A1 (en) * | 2021-12-29 | 2023-07-06 | 深圳晶泰科技有限公司 | Method and apparatus for acquiring molecular properties, and storage medium |
| WO2023155724A1 (en) * | 2022-02-18 | 2023-08-24 | 北京有竹居网络技术有限公司 | Method and apparatus for designing ligand molecules |
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