JPH11296570A - Three-dimensional molecule editor device - Google Patents

Abstract

PROBLEM TO BE SOLVED: To easily prepare coordinate information on molecular structure on a virtual three-dimensional space by displaying three-dimensional X, Y and Z coordinate axes and a grid-divided reference surface on a display device and displaying an atom at the position of a designated coordinate and on a grid point existing nearest to it. SOLUTION: The reference surface is initialized for displaying on a graphic display (S1). A molecule editor executing processing is executed (S2). Then, in reference plane grid width changing processing, the re-plotting processing of the reference plane is executed in the case the unit grid width of the reference plane is change (S21). In the position analyzing processing of a mouse pointer, a position where the mouse pointer exists to judge whether to execute atom displaying processing from the position or the execute the rotary operation processing of the reference plane (S22). In atom displaying processing, the processing of displaying the atom on the reference plane is executed (S221). In the rotary operation processing of the reference plane, the rotary displaying processing of the reference plane is executed (S222).

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a three-dimensional molecular editor for creating coordinate information of a molecular structure.

[0002]

2. Description of the Related Art Analyzes of molecular orbital calculations and molecular dynamics calculations have proven to be very useful in understanding the properties and reactivity of molecules. In order to perform these calculations, information on the three-dimensional coordinate values of the molecular structure is required as input data. However, since it is difficult to create coordinate information of a complex molecular skeleton, in recent years, coordinate information of a molecular structure is easily created by assembling molecules in a virtual three-dimensional space on a graphic display. How to do it is important. At present, when assembling molecules in a virtual three-dimensional space on a graphic display, the second and subsequent atoms are Z-matrix methods using relative positional relationships such as distances and angles with other atoms. Often defined by

[0003]

However, in this method, it is difficult to assemble a molecule by specifying three-dimensional coordinate values of atoms. Further, it is difficult to grasp the three-dimensional coordinate values of the molecular structure displayed on the graphic display, which is a two-dimensional plane.

Accordingly, an object of the present invention is to provide a three-dimensional molecular editor device capable of easily creating coordinate information of a molecular structure in a virtual three-dimensional space on a graphic display.

[0005]

In order to achieve the above object, a three-dimensional molecular editor device according to the present invention is a three-dimensional molecular editor device for creating coordinate information of a molecular structure. , Y and Z are displayed along with the coordinate axes indicating the coordinate component directions and the grid-divided reference plane, and the atom is placed on the position of the coordinate designated by the mouse pointer or on the lattice point closest to the designated coordinate. A display control means for displaying is provided. Since a plane serving as a reference for the coordinate position is displayed when assembling the molecular skeleton, it is possible to easily specify the coordinate position of each atom constituting the molecule. The reference plane may be divided and displayed by a unit cell starting from the origin of the three-dimensional coordinates. In this way, the three-dimensional coordinate values of the molecules displayed on the reference plane can be easily grasped. Further, the unit grid width of the reference plane may be freely changed. In this way, a complex molecular structure can be accurately assembled.

[0006]

Embodiments of the present invention will be described below with reference to the drawings. (I) First Embodiment (a) Configuration of Three-Dimensional Molecular Editor Device Hereinafter, a three-dimensional molecular editor device according to a first embodiment of the present invention will be described with reference to the drawings. FIG. 1 is a block diagram showing the configuration of the first embodiment of the three-dimensional molecular editor device of the present invention. As shown in FIG.
The three-dimensional molecular editor device according to the embodiment includes a CPU (display control means) 1, a ROM 2, a RAM 3, a storage device 4 such as a hard disk device, a CRT, a graphic display (display device) 5 such as a TFT liquid crystal panel, a keyboard 6, It is provided with an interface 8 for connecting each of the mouse 7, the storage device 4, the graphic display 5, the keyboard 6, and the mouse 7 to the CPU 1.
The CPU 1 performs various processes according to a control program stored in the ROM 2. The RAM 3 is a so-called work memory used in the operation of the CPU 1. The storage device 4 stores programs executed by the CPU 1 and various data. The graphic display 5 displays images such as characters and figures supplied from the CPU 1.

In this three-dimensional molecular editor device, as shown in FIG. 2, coordinate axes indicating directions of three-dimensional X, Y, and Z coordinate components, and a grid-divided plane are displayed on a graphic display 5. In the following, this grid-divided plane is referred to as a reference plane. The center of this reference plane always represents the origin of the three-dimensional coordinates. In the initial state, the center of the graphic display 5 indicates the origin of the three-dimensional coordinates, the vertical direction is the Y coordinate component direction, the horizontal direction is the X coordinate component direction,
The direction of the line of sight to the graphic display 5 indicates the Z coordinate component direction. The display direction and the unit grid width of the reference plane can be freely set / changed. FIG. 3A shows a reference plane when the unit lattice width is 1 Å and the display direction is the XY plane. In addition,
The Angstrom unit system is a unit system generally used in molecular orbital calculation or molecular dynamics calculation.
FIG. 3B shows an example in which the unit cell width is changed to 2 angstroms.

Next, an example in which one atom is displayed on the reference plane will be described. When displaying an atom on the reference plane, it is performed by designating an arbitrary point on the reference plane with a mouse pointer. There are two modes for displaying atoms on the reference plane. One is a mode for displaying an atom at a position designated by a mouse pointer. FIG. 4 shows an example of a mode in which an atom is displayed at the position of the coordinates designated by the mouse pointer.
Another method is a mode in which atoms are displayed on lattice points that are closest to coordinates specified by the mouse pointer. Switching between these modes is performed by menu operation of the present apparatus. FIG. 5 shows an example of a mode in which atoms are displayed on lattice points closest to the position specified by the mouse pointer.

To change the display direction of the reference plane, the mouse pointer is moved on the graphic display 5. By placing the mouse pointer outside the display area of the reference plane and moving the mouse pointer,
The rotation processing of the reference plane is performed. FIG. 6 shows an example of a rotation operation of the reference plane. “Before” in this figure shows the state before the mouse pointer is moved, and “After” is the reference plane when the cross-shaped mouse pointer is moved diagonally to the upper left on the graphic display 5. Shows the display state of.

(B) Description of the operation of the embodiment FIG. 7 shows a graphic display 5 using a reference plane.
It is a flowchart explaining an example when assembling a molecular skeleton while displaying it three-dimensionally above. First, in the reference plane initial value setting process in step S1, first, a reference plane to be displayed on the graphic display 5 is initialized. The molecule editor executing process in step S2 further includes a reference plane lattice width changing process in step S21 and a step S22.
And mouse pointer position analysis processing. In the reference plane grid width changing process in step S21, a reference plane redrawing process is performed when the unit grid width of the reference plane is changed. In the position analysis processing of the mouse pointer in step S22, the position where the mouse pointer is located is calculated, and it is determined whether to perform the atom display processing in step S221 or the reference plane rotation operation processing in step S222 from the position. I do. In the atom display process of step S221, a process of displaying atoms on the reference plane is performed. In the reference plane rotation operation processing in step S222, a reference plane rotation display processing is performed.

The above will be described in more detail.
In the first reference plane initial value setting process, first, a reference plane to be displayed on the graphic display 5 is initialized. In the initial setting of the reference plane, a process of calculating the center point of the graphic display 5 from a range occupying the virtual three-dimensional space of the graphic display 5 and setting the center point of the reference plane and the starting point of the coordinate axis for the point is performed. Do. Also, with the center point of the reference plane as the starting point, the calculation of the coordinate values of points separated by the unit grid width in the direction of each coordinate axis is repeated, and all the grid point coordinates are calculated.

After calculation of all grid point coordinates is completed, the reference plane is displayed by connecting the grid points with straight lines along the coordinate axes, and the coordinate axes are displayed at the same time. The molecule editor execution process in step S2 is further divided into a reference plane lattice width changing process in step S21 and a mouse pointer position analysis process in step S22. In the reference plane grid width change processing in step S21, first, the currently displayed reference plane is deleted. Next, starting from the center point of the coordinate axis as a starting point, the calculation of the coordinate values of a point at each changed grid width is repeated, and the coordinates of all changed grid points are calculated. After calculation of all grid point coordinates is completed, the reference plane after the change is displayed by connecting each grid point with a straight line.

At step S22, it is determined whether or not the mouse pointer is within the display area of the reference plane. If the mouse pointer is within the display area, an atom display process at step S221 is performed. If it is outside the display area of the reference plane, step S
A reference surface rotation operation process of 222 is performed. Step S22
In step 1, it is determined whether the mode is a mode in which atoms are displayed at the position of the mouse pointer or a mode in which the atoms are displayed on lattice points that are closest to the mouse pointer. In the former mode, the coordinate position of the mouse cursor is calculated, and the atom is displayed at that point. In the latter mode, after calculating the coordinate position of the mouse cursor, the nearest grid point is calculated, and atoms are displayed on the grid point. Step S222
Then, the rotation direction and the rotation angle are calculated from the relative movement amount and the movement direction of the mouse cursor with respect to the display area of the graphic display 5, and the reference plane is rotated and displayed according to each value.

(II) Second Embodiment Next, a second embodiment to which the present invention is applied will be described with reference to FIG.
This will be described with reference to FIG. This second embodiment is based on 2
The reference plane, which is a dimension, is moved in parallel with each of the three-dimensional coordinate axes (X, Y, Z). FIG. 8A shows an example in which atoms having an X coordinate value of 1 Å, a Y coordinate value of -4 Å, and a Z coordinate value of 4 Å in the three-dimensional coordinates are displayed on the current reference plane. FIG. 8B shows an example in which atoms are displayed on a reference plane translated on the Z axis to the position of Z = 4 angstroms.
In FIG. 8A, since the atoms are not displayed on the reference plane, it is difficult to grasp the three-dimensional coordinate values of the displayed atoms. However, in FIG. Since it is displayed on a point, it can be easily grasped.

[0015]

As described above, the present invention has the following effects. Conventionally, when assembling a molecular structure in a virtual three-dimensional space on a graphic display, there is a restriction that a relative relationship such as a distance or an angle between atoms needs to be known in advance. Accordingly, an atom can be displayed at an arbitrary position on a reference plane without worrying about a dependency relationship with another atom, thereby greatly increasing the degree of freedom in a method of assembling a molecular structure.

In the conventional method, in order to determine the three-dimensional coordinate component of each atom constituting a molecule, it is necessary to calculate the three-dimensional coordinate component from the relative relationship between atoms such as the distance and angle to other atoms. However, since the reference plane in the present invention is divided by a unit cell starting from the origin of the three-dimensional coordinates, the three-dimensional coordinate values of the molecules displayed on the reference plane can be easily grasped. Can be. Further, since the unit lattice width of the reference plane in the present invention can be freely changed,
Complex molecular structures can be assembled accurately.

[Brief description of the drawings]

FIG. 1 is a block diagram showing a configuration of a first embodiment.

FIG. 2 is a diagram illustrating a display example of a reference plane according to the first embodiment.

FIG. 3 is a diagram illustrating an example of changing the unit cell width according to the first embodiment;

FIG. 4 is a diagram illustrating an example of displaying atoms on a reference plane according to the first embodiment.

FIG. 5 is a diagram illustrating another example of the atom display on the reference plane according to the first embodiment.

FIG. 6 is a diagram illustrating an example of a rotation operation of a reference plane according to the first embodiment.

FIG. 7 is a flowchart for explaining the operation of the first embodiment.

FIG. 8 is a diagram illustrating an example of displaying atoms on a reference plane according to the second embodiment.

[Explanation of symbols]

 1 CPU 2 ROM 3 RAM 4 Storage device 5 Graphic display 6 Keyboard 7 Mouse 8 Interface

Claims (3)

[Claims] 1. A three-dimensional molecular editor device for creating coordinate information of a molecular structure, wherein three-dimensional X,
In addition to displaying the coordinate axes indicating the Y and Z coordinate component directions and the grid-divided reference plane, the atom is displayed on the position of the coordinate specified by the mouse pointer or on the lattice point closest to the specified coordinate. A three-dimensional molecular editor device, comprising: 2. The three-dimensional molecular editor device according to claim 1, wherein the display control means divides and displays the reference plane with a unit cell starting from the origin of the three-dimensional coordinates. 3. The three-dimensional molecular editor device according to claim 1, wherein the display control means changes a display direction and a unit cell width of the reference plane according to an input instruction. .