JP3010700B2 - Molecular data display - Google Patents

Description

Description: TECHNICAL FIELD The present invention relates to a novel molecular data display device for visually displaying the progress, etc., as a result of molecular dynamics calculation.

<Prior art and problems to be solved by the invention> It is known that a simulation by molecular dynamics calculation can be performed to know how a biopolymer moves over time. I have.

By the way, the simulation by molecular dynamics calculation is solved by numerically integrating the Newton's equation of motion for all atoms in the system at the same time, and although the principle itself is not difficult, the biopolymer is extremely large. It is very difficult to grasp the behavior of the biopolymer based on the obtained data because the amount of data obtained becomes extremely large because of the structure composed of the atoms.

Specifically, a great deal of effort is required to confirm the flexibility of biopolymers, and a great deal of effort is needed to understand changes in various energy values due to changes in molecular structure. And

In addition, a great deal of information is needed to understand the molecular structure after escape from the local minimum energy range, and to understand the bond length, bond angle, dihedral angle, hydrogen bond, etc. for any target atom together with the molecular structure at each time point. Requires effort.

<Object of the Invention> The present invention has been made in view of the above problems, and has as its object to provide a molecular data display device capable of easily grasping the behavior of a biopolymer obtained by molecular dynamics calculation. The purpose is.

<Means for Solving the Problems> In order to achieve the above object, a molecular data display device according to a first aspect of the present invention includes a molecular data holding unit for holding molecular data, and a condition setting for molecular dynamics calculation. Condition setting means for performing, molecular dynamics calculation means for performing molecular dynamics calculation using the molecular data selected from the molecular data holding means and the set conditions as inputs, and a molecular model for each predetermined time obtained by the molecular dynamics calculation. A molecular model holding means for sequentially holding frames of an animation image composed of line drawings, an energy value holding means for sequentially holding energy values obtained corresponding to each molecular model, and a condition that molecular dynamics calculation is completed. A molecular model reading means for sequentially reading out each frame from the molecular model holding means, and an energy value storing in synchronization with the reading of the molecular model. Energy value reading means for reading an energy value from the holding means;
Energy graph creating means for creating an energy graph based on the maximum and minimum values of the read energy values, molecular model display means for displaying each read frame, and displaying the energy graph Energy value display means for highlighting an energy value corresponding to the issued molecular model.

According to a second aspect of the present invention, there is provided a molecular data display device for storing molecular data, a condition setting device for setting conditions for molecular dynamics calculation, and molecular data selected and set from the molecular data storage device. Molecular dynamics calculation means for performing a molecular dynamics calculation using the input conditions as input, and molecular model holding means for sequentially storing a molecular model obtained at predetermined time intervals obtained by the molecular dynamics calculation as a frame of an animation image composed of line drawings. An energy value holding means for sequentially holding energy values obtained corresponding to each molecular model; and an energy for reading an energy value from the energy value holding means and forming an energy graph based on the maximum value and the minimum value of the energy value・ Graph creation means, molecular model display means for displaying each read frame, and energy Energy value display means for displaying a graph, energy graph designation means for designating a desired point on the energy graph, and a coma corresponding to the point designated by the energy graph designation means read out from the molecular model holding means for the molecular model And a molecular model reading means for supplying to the display means.

<Operation> With the molecular data display device of the first invention, the molecular dynamics calculation is performed by the molecular dynamics calculation means using the molecular data selected from the molecular data holding means and the conditions set by the condition setting means as inputs. Then, the molecular models at predetermined time intervals obtained by the molecular dynamics calculation are sequentially stored in the molecular model storing means as frames of an animation image composed of line drawings, and the energy value obtained for each molecular model is stored as an energy value. Each of the frames is sequentially held by the holding unit, and each frame is sequentially read by the molecular model reading unit on condition that the molecular dynamics calculation is completed, and the energy value is read by the energy value reading unit in synchronization with the reading of each frame. . Then, each read frame is displayed by the molecular model display means. In addition, a graph is created by the energy graph creating means based on the maximum value and the minimum value of the energy value obtained by the molecular dynamics calculation, and the energy graph is displayed and read out by the energy value displaying means. The energy value corresponding to the generated molecular model is highlighted.

Therefore, the molecular model that changes with time can be displayed as an animation, and by highlighting the corresponding energy value in the energy graph, not only the energy value corresponding to the molecular model but also the energy values before and after the relevant time point can be displayed. Can also be easily recognized.

With the molecular data display device of the second invention, when the molecular model and the energy value are displayed in the same manner as in the second invention, an arbitrary point in the energy graph is designated by the energy graph designation means. In this case, the corresponding frame is read from the molecular model holding means by the molecular model reading means and supplied to the molecular model display means to display the read molecular model.

Therefore, it is possible to arbitrarily read and display the molecular model in which the energy value is locally minimized, the molecular model in which the energy value is changing from the local minimum value to the next local minimum value, and grasp the optimized structure. Can be easily achieved.

<Example> Hereinafter, an example will be described in detail with reference to the accompanying drawings.

FIG. 1 is a block diagram showing one embodiment of the molecular data display device of the present invention, based on the molecular data selected from the molecular data holding unit (1) and the conditions set by the condition setting unit (2). A molecular dynamics calculation is performed by the molecular dynamics calculation unit (3), and the structure data indicating the molecular structure and the corresponding energy values and the like are stored in the structure file (4) and the energy file (5), respectively, at predetermined time intervals. . Then, the data conversion unit (6) reads out the structure data from the structure file (4) and the corresponding energy value from the energy file (5), and creates an intermediate file (7) in which the two are integrated. The processing by the data conversion unit (6) may be performed after the molecular dynamics calculation is completed, but may be started before the molecular dynamics calculation is completed. In addition, the video registration unit (8)
Data is sequentially read from the intermediate file (7) to create line drawing data determined based on the structure data, and is sequentially registered in the video file (9). After the registration of all the line drawing data to the video file (9) is completed, the line drawing reading unit (10
The line drawing data is sequentially read from the video file (9) according to a), and the line drawing is displayed by the line drawing display section (10b).
In addition, in the apparatus for displaying based on the molecular dynamics calculation result, as shown in FIG. 2, in addition to the line drawing (A),
Although the polygon (B) represented by the menu image is also displayed at the same time, in this embodiment, only the line drawing is registered in the video file (9), and the polygon is not registered.

Therefore, after performing the molecular dynamics calculation, it is sufficient to sequentially read out the line drawing data from the video file (9) and display the line drawing (A) on the line drawing display section (10b), and an animation display that faithfully shows the behavior of the molecule. Can be achieved. Since the polygon data is not registered in the video file (9), only the line drawing (A) needs to be updated for each frame, and the display speed can be increased. However, if the animation display speed may be slightly reduced, the line drawing data and the corresponding polygon data may be registered in the image file (9).

<Embodiment 2> FIG. 3 is a block diagram showing another embodiment of the molecular data display device of the present invention. The difference from the molecular data display device of FIG. Is created and registered in the video file (9) as an animation video frame together with polygon data such as menu images. Data is sequentially read from the intermediate file (7) by the data registration unit (11) to correspond to each molecular structure Energy values and the like are sequentially registered in a data file (12), and a maximum value and a minimum value are extracted from the energy values read by the energy value reading unit (14a), and a graph is generated based on the maximum value and the minimum value. Point for creating an energy graph by the creating unit (13), reading of frames from the video file (9) by the line drawing reading unit (10a), and line drawing display unit (10b) The energy graph created by the energy graph creation unit (13) is displayed by the energy display unit (14b) in synchronization with the display of the molecular model by (b), and the corresponding point of the energy graph is highlighted; and The only difference is that the control unit (15) controls the line drawing display unit (10b) to display the energy value as text data on condition that reading of new data from the video file (9) is stopped.

Therefore, in the case of this embodiment, an energy graph is created by the graph creating unit (13) so that the maximum value and the minimum value of the energy value are included in the preset energy value display frame, and the line drawing is created. Readout unit (10a)
Frames are sequentially read from the video file (9), displayed together with the created energy graph, and the corresponding points in the energy graph are highlighted (see FIG. 4).

As a result, the transition of the energy value over the entire range of the molecular dynamics calculation can be easily confirmed, and the corresponding point on the energy graph corresponding to the animated molecular model is highlighted, so that the molecular structure and the energy The correlation with the value can be easily recognized.

Further, since the energy value includes various energies such as kinetic energy and potential energy, the energy value cannot be accurately grasped only by the energy graph. However, in this embodiment, various energy values can be displayed as text data by stopping the animation display, and the energy values can be accurately grasped.

FIG. 5 is a flowchart for explaining a display operation in a state where registration of each frame and creation of an energy graph have been performed. In a step, line drawing data for one frame is read from the video file (9) and displayed as a molecular model. In the step, an energy graph is displayed in a predetermined area, and in the step, the energy graph corresponding to the displayed molecular model is displayed.
A point on the graph is highlighted, and in a step, it is determined whether or not the stop of the animation display is instructed by an operation of a keyboard or the like (not shown). If not, the frame is advanced by one in the step, and the processing of the step is performed as it is. Perform Therefore, if the stop of the animation display is not instructed, the line model data is sequentially read out from the video file (9) and displayed, and the molecular model can be displayed in an animation. Since the point highlighted is moved, it is possible to easily grasp the change in the molecular structure and the change in the energy value in association with each other.

Conversely, if the stop of the animation display is instructed in the above step, the values of kinetic energy, potential energy, etc. are displayed as text data in the step, the molecular model is advanced by one frame in the step, and the animation is performed in the step. After the display is instructed to be restarted, the step processing is performed again. Therefore, by interrupting the animation display, various energy values can be displayed as text data, and the correlation between the corresponding molecular structure and the various energy values can be accurately grasped.

<Embodiment 3> FIG. 6 is a block diagram showing still another embodiment of the molecular data display device of the present invention. The difference from the block diagram of FIG. 3 is that the stop of animation display is instructed. An energy value specification part (16) for specifying an arbitrary point on the energy graph and an energy value specification part (1
The molecular model reading unit (1) reads line drawing data corresponding to a point on the energy graph specified by 6) from the video file (9) and supplies the line drawing data to the line drawing display unit (10b).
7) and a molecular data registration unit (18) for reading molecular data corresponding to the read line drawing data from the intermediate file (7) and registering it in the molecular data holding unit (1). It is.

Therefore, in this embodiment, the same operation as in the second embodiment can be achieved, and an arbitrary point on the energy graph is designated by the energy value designation unit (16) in a state where the stop of the animation display is instructed. Then, the line drawing data corresponding to the designated point can be read from the video file (9) by the molecular model reading section (17) and displayed by the line drawing display section (10b). When the molecular data displayed as a line drawing is to be newly registered as a molecular model, the corresponding molecular data is read from the intermediate file (7) by the molecular data registration unit (18), and the molecular data holding unit (1) Can be registered at

As a result, it is possible to easily select and display the molecular structure that minimizes the energy value and the molecular structure that minimizes the energy value from the energy graph, and, if necessary, displays the corresponding molecular data as necessary. It can be registered in the holding unit (1).

In each of the above embodiments, when the line drawing data is registered as each frame of the animation video, a desired interatomic distance, bond angle, and the like can be registered as one image. In this case, the cause can be more easily investigated in the molecular dynamics calculation process.

<Effects of the Invention> As described above, the first invention can display an animation of a molecular model that changes with time, and highlights a corresponding energy value in an energy graph, thereby obtaining an energy value corresponding to the molecular model. In addition, there is a specific effect that the energy values before and after the relevant point can be easily recognized.

The second invention is capable of arbitrarily reading and displaying a molecular model in which the energy value is locally minimized, a molecular model in which the energy value is changing from the local minimum to the next local minimum, and the like. This has a specific effect that the structure can be easily grasped.

[Brief description of the drawings]

FIG. 1 is a block diagram showing an embodiment of the molecular data display device of the present invention, FIG. 2 is a schematic diagram showing an example of simultaneous display of a line drawing and a polygon, and FIG. FIG. 4 is a schematic diagram showing a display example of an energy graph; FIG. 5 is a flowchart for explaining a display operation in a state where registration of each frame and creation of an energy graph are performed; FIG. 6 is a block diagram showing still another embodiment of the molecular data display device of the present invention. (1) ... molecular data storage unit, (2) ... condition setting unit, (3) ... molecular dynamics calculation unit, (8) ... video registration unit, (9) ... video file, (10a) ... Line drawing reading unit, (10b) ... Line drawing display unit, (11) ... Data registration unit, (12) ... Data file, (13) ... Graph creation unit, (14a) ... Energy value reading Section, (14b) ... energy display section, (16) ... energy value designation section, (17) ... molecular model readout section

Continuation of the front page (56) References ・ Synthetic Organic Chemistry Vol. 45 No. 11 pp. 1198-1106 Hiroshi Nakama “Stereo-Conformational Analysis and Molecular Dynamics of Peptides” ・ Applied Physics Vol. 55 No. 5 482− Page 489 Masuhiro Mikami et al. “Visual Simulation of Molecular Systems” ・ PIXEL 87: 107-111 Fumio Kado “Introduction of Computer Graphics Animation System CGMS” (58) Fields surveyed (Int. Cl. ⁷ , DB name) G06F 17/50 JICST file (JOIS)

Claims (2)

(57) [Claims] 1. Molecular data holding means (1) for holding molecular data; condition setting means (2) for setting conditions for molecular dynamics calculation; and molecular data selected from the molecular data holding means (1). A molecular dynamics calculation means (3) for performing a molecular dynamics calculation using the set conditions as inputs, and a molecular model at predetermined time intervals obtained by the molecular dynamics calculation are sequentially held as frames of an animation image composed of line drawings. Model holding means (8) and (9), energy value holding means (11) and (12) for sequentially holding energy values obtained corresponding to each molecular model, and a condition that molecular dynamics calculation is completed. Molecular model reading means (10a) for sequentially reading each frame from the molecular model holding means (9)
And an energy value reading means (14a) for reading an energy value from the energy value holding means (12) in synchronization with the reading of the molecular model, and an energy graph is created based on the maximum value and the minimum value of the read energy values. Energy graph creation means (13), molecular model display means (10b) for displaying each read frame, and energy graph display, with the energy value corresponding to the read molecular model highlighted. And an energy value display means (14b). 2. Molecular data holding means (1) for holding molecular data; condition setting means (2) for setting conditions for molecular dynamics calculation; and molecular data selected from the molecular data holding means (1). A molecular dynamics calculation means (3) for performing a molecular dynamics calculation using the set conditions as inputs, and a molecular model at predetermined time intervals obtained by the molecular dynamics calculation are sequentially held as frames of an animation image composed of line drawings. Model holding means (8) and (9), energy value holding means (11) and (12) for sequentially holding energy values obtained corresponding to the respective molecular models, and energy values from the energy value holding means (12). And an energy graph creating means (13) for creating an energy graph based on the maximum value and the minimum value of the energy value, and displaying each read frame. A child model display means (10b), the energy value display means for displaying the energy graph (14
b), an energy graph designating means (16) for designating a desired point of the energy graph, and a coma corresponding to the point designated by the energy graph designating means (16) from the molecular model holding means (9). Readout means (17) for reading out the molecular model and supplying it to the display means (10b)
And a molecular data display device.