WO2004088565A1 - Peripheral equipment on a molecular modeling computer system and a method of designing the same - Google Patents

Peripheral equipment on a molecular modeling computer system and a method of designing the same Download PDF

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Publication number
WO2004088565A1
WO2004088565A1 PCT/KR2003/001630 KR0301630W WO2004088565A1 WO 2004088565 A1 WO2004088565 A1 WO 2004088565A1 KR 0301630 W KR0301630 W KR 0301630W WO 2004088565 A1 WO2004088565 A1 WO 2004088565A1
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WO
WIPO (PCT)
Prior art keywords
molecule
user
molecules
gloves
moving
Prior art date
Application number
PCT/KR2003/001630
Other languages
French (fr)
Inventor
Chang-No Yoon
Myung-Whan Chi
Original Assignee
Korea Institute Of Science And Technology
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Publication date
Application filed by Korea Institute Of Science And Technology filed Critical Korea Institute Of Science And Technology
Priority to AU2003256103A priority Critical patent/AU2003256103A1/en
Publication of WO2004088565A1 publication Critical patent/WO2004088565A1/en

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Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/011—Arrangements for interaction with the human body, e.g. for user immersion in virtual reality
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/011—Arrangements for interaction with the human body, e.g. for user immersion in virtual reality
    • G06F3/014—Hand-worn input/output arrangements, e.g. data gloves
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/016—Input arrangements with force or tactile feedback as computer generated output to the user
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/03—Arrangements for converting the position or the displacement of a member into a coded form
    • G06F3/033—Pointing devices displaced or positioned by the user, e.g. mice, trackballs, pens or joysticks; Accessories therefor
    • G06F3/0338—Pointing devices displaced or positioned by the user, e.g. mice, trackballs, pens or joysticks; Accessories therefor with detection of limited linear or angular displacement of an operating part of the device from a neutral position, e.g. isotonic or isometric joysticks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/03—Arrangements for converting the position or the displacement of a member into a coded form
    • G06F3/033—Pointing devices displaced or positioned by the user, e.g. mice, trackballs, pens or joysticks; Accessories therefor
    • G06F3/0354—Pointing devices displaced or positioned by the user, e.g. mice, trackballs, pens or joysticks; Accessories therefor with detection of 2D relative movements between the device, or an operating part thereof, and a plane or surface, e.g. 2D mice, trackballs, pens or pucks
    • G06F3/03543—Mice or pucks

Definitions

  • the present invention relates to a method of designing peripheral equipment for molecular modeling system on a computer.
  • it relates to a method of designing peripheral equipment, for helping a user to comprehend the system intuitively and handle it without much difficulty, on a molecular modeling system in which molecules, composed of several thousands or several tens of thousand of atoms, can be displayed on a computer coordinate system with various displaying styles for easy comprehension of a user and molecular movements can be temporally displayed by calculating the molecular motions and interactions.
  • a molecular modeling is to represent a molecular structure in a stereo-view by using a computer or the like for the purpose of promoting user' s comprehension on natural-scientific phenomena in a molecular level.
  • To represent a molecular structure in a stereo- view one should receive an input for the three- dimensional coordinates of the atoms constituting a molecule, decide a display style according to a user's convenience, and display the structure on a computer screen by setting a both eye's separate coordinate system.
  • the present invention is proposed to meet the necessity described above. It is therefore the object of the present invention to provide intuitive input/output devices on a molecular modeling system to display a molecular structure on a computer and assist a user to comprehend various characteristics of the molecule at once.
  • a user have to go through numbers of input steps with a keyboard and/or a mouse, the standard input devices of a conventional computer system. Therefore, it is another object of the present invention to provide a method of designing peripheral equipment comprising gloves, a spatial location tracking instrument, and a force feedback joystick to reduce the input steps.
  • the present invention presents a method of designing peripheral equipment characterized in that: system control and input for user selective options can be performed by standard keyboard and mouse input devices; when a molecule is being loaded, the control of the molecule can be carried out by mouse, gloves, spatial location tracking instrument, and force feedback joystick, and the viewpoint can be controlled by force feedback joystick; the screen can be outputted in a stereo- view; the interaction force between molecules can be outputted through force feedback joystick; some portion of a molecule can be selected by mouse and/or gloves for displaying partial deformation of the molecule; relative locations of two molecules can be decided by gloves; and when a user is observing the interaction between two molecules, the system shows how to use the gloves, spatial location tracking instrument, and force feedback joystick and gives some information such as the present condition and the predicted route to the user.
  • FIG. 1 is a block diagram illustrating the method of designing peripheral equipment on a system for molecular modeling in accordance with the present invention .
  • FIG. 2 is a view illustrating the input/output devices used in the present invention.
  • FIG. 3 is a view illustrating an example of screen display when a user is observing the interaction between two molecules in accordance with an embodiment of the present invention.
  • a force displaying section 70 a molecule/viewpoint moving section
  • serial (or USB) communication 201 a fixed molecule
  • FIG. 1 is a block diagram illustrating the method of designing peripheral equipment on a system for molecular modeling in accordance with the present invention.
  • the system comprises a user(l ⁇ ), a computer coordinate system(20), a molecular DB(30), a force feedback joystick control section(40), a force calculation section(50) for calculating the interaction force between molecules, a force displaying section( ⁇ ), a molecule/viewpoint moving section(70), a screen displaying section(80), a keyboard ( 110 ) , a mouse ( 120 ) , gloves(130), and a spatial location tracking instrument ( 140 ) .
  • a user (10) can input user-selective options into the system and/or control the molecules loaded onto the computer coordinate system(20) from molecular DB(30) by using the keyboard ( 110 ) , mouse(120), gloves (130), spatial location tracking instrument ( 140 ) , and the force feedback j oystick ( 150 ) .
  • a computer coordinate system(20) establishes a three-dimensional coordinate system in a computer ( 100 ) , and when a molecule is loaded from the molecular DB(30), the molecule is constituted on the computer coordinate system(20) .
  • the system sets the coordinates of the moving molecule azimuth (206) , moving molecule traj ectory ( 205 ) being passed, and the predicted route (204) that work to be the reference points for checking the current location of the molecule and/or the glove pointer (203) displayed on the screen displaying section (80) in FIG. 3.
  • the system transforms the coordinates according to the characteristics and requirements of the devices.
  • the transformation results are transmitted to the screen displaying section(80), and if a user has selected the option of loading two molecules and diminishing the interaction force between molecules, the results are also transmitted to the force calculation section(50) for calculating the interaction force between molecules.
  • a molecular database is composed of the information on the kinds and locations of the atoms constituting a molecule, their roles in the molecule, and other molecular characteristics for each molecule.
  • a force feedback joystick control section(40) controls the force feedback j oystick ( 150 ) when a user (10) is giving an input by using the force feedback j oystick ( 150 ) or the system is indicating the force to the user.
  • a conventional force feedback j oystick ( 150 ) is manufactured by imitating a gaming joystick, especially a fighter control stick, and thus it is generally able to control only two degrees of freedom.
  • additional gaming input devices are equipped to be easily handled, and thus an input of 6- degrees-of-freedom can be achieved by combining these additional input devices, and then this input signal is transmitted to the molecule/viewpoint moving section ( 70 ) .
  • the system when indicating the force, the system sends signals to the two main shafts of the force feedback j oystick ( 150 ) , able to indicate the force, to indicate the strength of the force to the user according to the direction and the strength transmitted from the force displaying section( ⁇ ).
  • the force calculation section (50) first loads a molecule (fixed molecule) to the computer coordinate system(20), fixes the location, establishes virtual three-dimensional grids, and when the second molecule (moving molecule) is loaded, pre-calculates the effect of the fixed molecule to the surrounding grid points to calculate the interaction force between the molecules in real-time base. And then, when the coordinates of the center-of-mass (COM) of the moving molecule moves into the three-dimensional grids, it calculates the vector-value of the interaction force between the molecules and informs the value to the force displaying section( ⁇ ).
  • COM center-of-mass
  • the force displaying section( ⁇ ) constitutes a plane with the two axes of the force feedback joystick ( 150 ) to indicate an arbitrary force vector obtained by the computer coordinate system(20). Then, it projects the arbitrary force vector onto the plane to obtain a new force vector, assigns the strength and the direction of the new force according to the vector value proportional to the strength of the force indicated by the force feedback j oystick ( 150 ) , and transmits them to the force feedback joystick control section(40) .
  • the molecule/viewpoint moving section (70) assigns the user' s input to the viewpoint movement so that the user can observe the molecule in various angles. And, if a user has selected the option of loading two molecules and diminishing the interaction force between molecules, it assigns the user's input to the COM point of moving molecule and transmits the movement of the molecule to the computer coordinate system (20) .
  • a screen displaying section(80) receives the current coordinates of the subjects, to be displayed on the screen, from computer coordinate system(20) and projects them onto a two-dimensional screen.
  • the overall subjects on the computer coordinate system(20) are being displayed by orthogonal projection technique or perspective projection technique according to the user selection.
  • the screen to display the screen in a stereo-view according to the user selection, it separates the contents projected to the screen into the contents corresponding to the viewpoint coordinates of left eye and those corresponding to the viewpoint coordinates of right eye and alternately outputs the separated projected contents, fitting for each eye respectively, on the screen.
  • the user for watching the screen fit for corresponding eye, the user (10) screens one eye according to the screen display period by wearing a stereo viewer (16) for synchronizing the period.
  • the user (10) assigns the distance between two eyes, the focal distance of two eyes' seeing, and the like.
  • a keyboard ( 110 ) is used for character input like a filename.
  • a mouse (120) is used for controlling the system operation and the molecule with the mouse pointer appeared on the screen, left/right buttons, and a wheel being combined together.
  • a menu of selective options for mouse pointer is provided on the screen, and when molecules are loaded from the molecular DB(30), the movement of the molecules for observing them are controlled by mouse ( 120 ) .
  • an in situ rotation of a molecule i. e., the opposite directional viewpoint
  • the approach of the viewpoint to the molecule is controlled by rolling the wheel .
  • An atom can be selected by the left button of the mouse, and the amino-acid in the molecule, where the atom belongs, can be selected by the right button of the mouse.
  • the gloves (130) comprise a left glove (130a) and a right glove (130b) and help the user to handle the molecules intuitively when the molecules are loaded from the molecular DB(30) .
  • a user simply grabs the molecules, and then rotates and/or drags them to put them on the location he (or she) wants to observe.
  • a user can grab and control two molecules at the same time to decide the relative locations of the two molecules.
  • the user can select the amino-acid in the molecule to which the portion belongs.
  • two ports (141) of the spatial location tracking instrument ( 140 ) are assigned to each of the left and right gloves (130a, 130b).
  • FIG. 2 is a view illustrating the system and the peripheral equipment in accordance with the present invention.
  • input devices comprise standard input devices of a keyboard ( 110 ) and a mouse (120) and additional input devices of gloves (130), a spatial location tracking instrument ( 140 ) , and a force feedback j oystick ( 150 ) .
  • output devices comprise a force feedback j oystick ( 150 ) and a stereo viewer(160) for stereo-view screen output.
  • the gloves (130a, 130b), the spatial location tracking instrument ( 140 ) , and the force feedback j oystick (150 ) can be connected to the computer ( 100 ) through serial (or USB) communication ( 170 ) .
  • a wheel mouse is used for the mouse (120) for back- and-forth movement of the viewpoint.
  • the left and right gloves (130a, 130b) transmit the information on the states of bending/stretching of user's fingers periodically to the computer ( 100 ) .
  • the spatial location tracking instrument ( 140 ) comprises a port (142) for producing a magnetic field area, two ports (141) for tracking the movement in the magnetic field, and a main body for checking the states of the ports (141, 142) in real-time base and transmitting them to the computer ( 100 ) periodically.
  • the ports (141) of the spatial location tracking instrument ( 140 ) is assigned to each of the two gloves (130a, 130b) respectively to obtain the information on the location and the rotation of the user' s hands .
  • a force feedback j oystick ( 150 ) is used for moving the viewpoint when the user (10) moves the viewpoint to observe the molecule loaded from the molecular DB(30) and for indicating the interaction force between the molecules .
  • the system makes it possible that the user's viewpoint or the COM point of a certain molecule can be moved to a desired direction on the computer coordinate system(20) by single control of the force feedback j oystick ( 150 ) .
  • a user can effectively observe a molecule and objectively comprehend the molecular interaction.
  • a molecular modeling system it is preferable for a molecular modeling system that a user can deform a molecule and constitutes a new molecule by combining two or more molecules .
  • the present invention also presents a combined-operation method of the peripheral equipment of the present invention to implement the molecular deformation and/or the molecular compounding.
  • a user For observing a molecular interaction, a user (10) uses the gloves (130), a spatial location tracking instrument ( 140) , a force feedback j oystick ( 150 ) , and a mouse (120) as input devices and a screen, a stereo viewer(l ⁇ ), and the force feedback j oystick ( 150 ) as output devices .
  • the user loads a fixed molecule (201) to the computer coordinate system(20), and then loads a moving molecule (202 ) to be moved in the surrounding space of the fixed molecule (201 ) .
  • the COM point of the moving molecule (202 ) becomes to be the point where the input from the force feedback j oystick ( 150 ) is being applied, In addition, the force applied to this point is outputted through the force feedback j oystick ( 150 ) .
  • the viewpoint is located at the upper direction of the axis, orthogonal to the line connecting the COM point of the fixed molecule (201 ) and the COM point of the moving molecule ( 202 ) , of the computer coordinate system(20) on the screen and looking at the COM point of the fixed molecule ( 201 ) .
  • the COM points of the molecules become to be the points where the inputs from the gloves (130a, 130b) are being applied respectively, and the viewpoint is located on the axis, orthogonal to the line connecting the COM points of two molecules (201, 202), on the screen and looking at the center point of the line connecting the COM points of two molecules.
  • FIG. 3 is a view illustrating the information obtained by using the peripheral equipment in accordance with the present invention when a user is observing a molecular interaction.
  • the screen displays a fixed molecule (201 ) and a moving molecule (202 ) constituted on the computer coordinate system(20), the moving molecule traj ectory ( 205) being passed, the predicted route(204) displayed by calculating the interaction force between the fixed and moving molecules, the moving molecule azimuth (206) , the attractive/repulsive force indication ( 207 ) of the force applied to the moving molecule from the other molecule, and the glove pointer (203) representing the locations of the hands of the glove-using user and the states of the hands being grabbed or opened.
  • the rotation and the locative movement of the moving molecule (202 ) is being carried out by using the glove pointer(203) .
  • the locative movement is being implemented by carrying out reverse locative movement of the subject and the viewpoint instead of moving the fixed molecule (201) .
  • the movement of the moving molecule ( 202 ) by input devices is corresponding to the movement of the COM point .
  • the rotation of the moving molecule ( 202 ) should be classified into a rotation interlocked to the viewpoint and a rotation unrelated to the viewpoint so that the user can decide the moving molecule azimuth at desired viewpoint location.
  • the force feedback j oystick ( 150 ) takes charge for giving input so that the viewpoint can rotate along when the moving molecule ( 202 ) is being rotated.
  • the mouse (120) takes charge for giving input .
  • the interaction force between the molecules is being calculated in real-time base and outputted through the force feedback j oystick ( 150 ) .
  • the attractive/repulsive force indication (207 ) on the screen indicates whether the force applied to the moving molecule by the fixed molecule is attractive or repulsive .
  • the system calculates the vector value of the current interaction force to display it on the screen, and then recalculates the vector value of the force to be applied to the endpoint of the displayed vector to successively display the force vector on the screen .
  • a predicted route (204) of the moving molecule (202 ) is being displayed on the screen, and the moving molecule traj ectory ( 205 ) , through which the user(l ⁇ ) has moved the moving molecule ( 202 ) , is being displayed on the screen.
  • the trajectory of the moving molecule ( 202 ) azimuth being changed is being displayed together on the screen.
  • the user can record the relative locations of the two molecules on a desired screen into a file.
  • the user can control the relative locations of the two molecules, loaded to the computer coordinate system(20), by using the two gloves (130a, 130b) and connect the two molecules to constitute a new molecule.
  • the user can also select an atom and/or an amino- acid, constituting a protein molecule, by using the mouse (120) to obtain desired information. Or, he (or she) can substitute a certain amino-acid for the selected amino-acid to deform the molecule.
  • the left button of the mouse (120) is used for selecting an atom located at the mouse pointer location
  • the right button is used for selecting an amino-acid containing the atom located at the mouse pointer location.
  • a selected portion in a molecule is being displayed by bright color, and when the user want to erase the selected portion, he (or she) can simply select it one more time.
  • a user can select an amino-acid, constituting a protein molecule, by using the gloves (130).
  • the user can select the amino-acid by grabbing the portion where the glove pointer (203) is located, and when releasing, he (or she) simply grabs the same amino-acid.
  • the information on the amino-acid is being displayed on the screen, and the system prepares for substitution of the amino-acid according to the user selection.
  • the system decides the overall shape of the changed molecule and carries out the calculation for obtaining the coordinates of the atoms constituting the new molecule.
  • the present invention provides intuitive input/output devices to a molecular modeling system so that a user can display a molecule on a computer and comprehend various characteristics of the molecule at once.
  • a user have to go through numbers of input steps with a keyboard and/or a mouse, the standard input devices of a conventional computer system.
  • the number of input steps can be reduced by combined-using the peripheral equipment of the present invention comprising gloves, a spatial location tracking instrument, and a force feedback joystick.
  • a user can eliminate the inconvenience occurring at the input stage and handle a molecule accurately.
  • the system effectively assists a user to easily obtain the information on the molecule.

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  • Engineering & Computer Science (AREA)
  • General Engineering & Computer Science (AREA)
  • Theoretical Computer Science (AREA)
  • Human Computer Interaction (AREA)
  • Physics & Mathematics (AREA)
  • General Physics & Mathematics (AREA)
  • Position Input By Displaying (AREA)
  • User Interface Of Digital Computer (AREA)

Abstract

The present invention relates to a method of designing peripheral equipment for molecular modeling system on a computer. In more detail, it relates to a method of designing peripheral equipment that provides intuitive input/output devices to a molecular modeling system so that a user can display a molecule on a computer and comprehend various characteristics of the molecule at once. By separating the screens corresponding to left/right eyes respectively, the present invention makes it possible to output a stereo-view of a molecule. In addition, for assisting a user to easily handle two or more molecules on a computer, the present invention provides gloves, a spatial location tracking instrument, and a force feedback joystick, which transfers the interaction force between two molecules to the user, as input devices in addition to the conventional computer input devices, a keyboard and a mouse.

Description

PERIPHERAL EQUIPMENT ON A MOLECULAR MODELING COMPUTER SYSTEM AND A METHOD OF DESIGNING THE SAME
[Technical Field of the Invention]
The present invention relates to a method of designing peripheral equipment for molecular modeling system on a computer. In more detail, it relates to a method of designing peripheral equipment, for helping a user to comprehend the system intuitively and handle it without much difficulty, on a molecular modeling system in which molecules, composed of several thousands or several tens of thousand of atoms, can be displayed on a computer coordinate system with various displaying styles for easy comprehension of a user and molecular movements can be temporally displayed by calculating the molecular motions and interactions.
[Description of the Prior Art]
A molecular modeling is to represent a molecular structure in a stereo-view by using a computer or the like for the purpose of promoting user' s comprehension on natural-scientific phenomena in a molecular level. To represent a molecular structure in a stereo- view, one should receive an input for the three- dimensional coordinates of the atoms constituting a molecule, decide a display style according to a user's convenience, and display the structure on a computer screen by setting a both eye's separate coordinate system.
For assisting a user to observe the shape and motion of a molecule, which are invisible and only acknowledged theoretically, with easy comprehension, one should load all the locations and characteristics of the atoms constituting the molecule on a computer, output various molecular characteristics, the user wants to observe, in the form of user's selection, and constitute a system being equipped with input devices that assist the user to easily handle the molecule.
In addition, it is also required to provide a method for a user to effectively use the input devices to improve the user's productivity in using the system.
[Description of the Invention]
The present invention is proposed to meet the necessity described above. It is therefore the object of the present invention to provide intuitive input/output devices on a molecular modeling system to display a molecular structure on a computer and assist a user to comprehend various characteristics of the molecule at once. In particular, to indicate an interaction force between molecules, to decide relative locations of two molecules, to display a partial deformation of a molecule, or to couple the molecules on a three- dimensional coordinate system, a user have to go through numbers of input steps with a keyboard and/or a mouse, the standard input devices of a conventional computer system. Therefore, it is another object of the present invention to provide a method of designing peripheral equipment comprising gloves, a spatial location tracking instrument, and a force feedback joystick to reduce the input steps.
To achieve the object mentioned above, the present invention presents a method of designing peripheral equipment characterized in that: system control and input for user selective options can be performed by standard keyboard and mouse input devices; when a molecule is being loaded, the control of the molecule can be carried out by mouse, gloves, spatial location tracking instrument, and force feedback joystick, and the viewpoint can be controlled by force feedback joystick; the screen can be outputted in a stereo- view; the interaction force between molecules can be outputted through force feedback joystick; some portion of a molecule can be selected by mouse and/or gloves for displaying partial deformation of the molecule; relative locations of two molecules can be decided by gloves; and when a user is observing the interaction between two molecules, the system shows how to use the gloves, spatial location tracking instrument, and force feedback joystick and gives some information such as the present condition and the predicted route to the user.
[Brief Description of the Drawings]
FIG. 1 is a block diagram illustrating the method of designing peripheral equipment on a system for molecular modeling in accordance with the present invention . FIG. 2 is a view illustrating the input/output devices used in the present invention.
FIG. 3 is a view illustrating an example of screen display when a user is observing the interaction between two molecules in accordance with an embodiment of the present invention. <Description of the Numerals on the Main Parts of the Drawings>
10 : a user 20 : a computer coordinate system
30 : a molecular database (DB)
40 : a force feedback joystick control section
50 : a force calculation section
60 : a force displaying section 70 : a molecule/viewpoint moving section
80 : a screen displaying section
100 : a computer
110 : a keyboard
120 : a mouse 130 : gloves
140 : a spatial location tracking instrument
150 : a force feedback joystick
160 : a stereo viewer
170 : serial (or USB) communication 201 : a fixed molecule
202 : a moving molecule
203 : a glove pointer
204 : a predicted route
205 : a moving molecule trajectory 206 : a moving molecule azimuth 207 : an attractive/repulsive force indication
[Detailed Description of the Embodiments]
Hereinafter, referring to appended drawings, the structures and the operation procedures of the embodiments of the present invention are described in detail .
FIG. 1 is a block diagram illustrating the method of designing peripheral equipment on a system for molecular modeling in accordance with the present invention. Referring to FIG. 1, the system comprises a user(lθ), a computer coordinate system(20), a molecular DB(30), a force feedback joystick control section(40), a force calculation section(50) for calculating the interaction force between molecules, a force displaying section(βθ), a molecule/viewpoint moving section(70), a screen displaying section(80), a keyboard ( 110 ) , a mouse ( 120 ) , gloves(130), and a spatial location tracking instrument ( 140 ) .
A user (10) can input user-selective options into the system and/or control the molecules loaded onto the computer coordinate system(20) from molecular DB(30) by using the keyboard ( 110 ) , mouse(120), gloves (130), spatial location tracking instrument ( 140 ) , and the force feedback j oystick ( 150 ) .
In addition, the results are outputted through the screen displaying section(80) or the force feedback j oystick ( 150 ) so that the user can confirm them. A computer coordinate system(20) establishes a three-dimensional coordinate system in a computer ( 100 ) , and when a molecule is loaded from the molecular DB(30), the molecule is constituted on the computer coordinate system(20) . For assisting the user's comprehension, the system sets the coordinates of the moving molecule azimuth (206) , moving molecule traj ectory ( 205 ) being passed, and the predicted route (204) that work to be the reference points for checking the current location of the molecule and/or the glove pointer (203) displayed on the screen displaying section (80) in FIG. 3.
Then, checking the inputs from the input devices, the system transforms the coordinates according to the characteristics and requirements of the devices.
The transformation results are transmitted to the screen displaying section(80), and if a user has selected the option of loading two molecules and diminishing the interaction force between molecules, the results are also transmitted to the force calculation section(50) for calculating the interaction force between molecules.
A molecular database (DB) is composed of the information on the kinds and locations of the atoms constituting a molecule, their roles in the molecule, and other molecular characteristics for each molecule.
A force feedback joystick control section(40) controls the force feedback j oystick ( 150 ) when a user (10) is giving an input by using the force feedback j oystick ( 150 ) or the system is indicating the force to the user.
A conventional force feedback j oystick ( 150 ) is manufactured by imitating a gaming joystick, especially a fighter control stick, and thus it is generally able to control only two degrees of freedom.
However, in addition to the main shaft of the control stick, additional gaming input devices are equipped to be easily handled, and thus an input of 6- degrees-of-freedom can be achieved by combining these additional input devices, and then this input signal is transmitted to the molecule/viewpoint moving section ( 70 ) .
Besides, when indicating the force, the system sends signals to the two main shafts of the force feedback j oystick ( 150 ) , able to indicate the force, to indicate the strength of the force to the user according to the direction and the strength transmitted from the force displaying section(βθ).
If a user has selected the option of loading two molecules and diminishing the interaction force between molecules, the force calculation section (50) first loads a molecule ( fixed molecule) to the computer coordinate system(20), fixes the location, establishes virtual three-dimensional grids, and when the second molecule (moving molecule) is loaded, pre-calculates the effect of the fixed molecule to the surrounding grid points to calculate the interaction force between the molecules in real-time base. And then, when the coordinates of the center-of-mass (COM) of the moving molecule moves into the three-dimensional grids, it calculates the vector-value of the interaction force between the molecules and informs the value to the force displaying section(δθ).
When the vector-value of the force to be indicated by force feedback j oystick ( 150 ) is transmitted from the force calculation section(50), since a conventional force feedback joystick can indicate the force only by two axes, the force displaying section(βθ) constitutes a plane with the two axes of the force feedback joystick ( 150 ) to indicate an arbitrary force vector obtained by the computer coordinate system(20). Then, it projects the arbitrary force vector onto the plane to obtain a new force vector, assigns the strength and the direction of the new force according to the vector value proportional to the strength of the force indicated by the force feedback j oystick ( 150 ) , and transmits them to the force feedback joystick control section(40) .
When a user (10) enters a β-dgrees-of-freedom input by using a force feedback j oystick ( 150 ) and if the user selective option is "ON" for viewpoint control, the molecule/viewpoint moving section (70) assigns the user' s input to the viewpoint movement so that the user can observe the molecule in various angles. And, if a user has selected the option of loading two molecules and diminishing the interaction force between molecules, it assigns the user's input to the COM point of moving molecule and transmits the movement of the molecule to the computer coordinate system (20) .
A screen displaying section(80) receives the current coordinates of the subjects, to be displayed on the screen, from computer coordinate system(20) and projects them onto a two-dimensional screen. At this stage, the overall subjects on the computer coordinate system(20) are being displayed by orthogonal projection technique or perspective projection technique according to the user selection. In addition, to display the screen in a stereo-view according to the user selection, it separates the contents projected to the screen into the contents corresponding to the viewpoint coordinates of left eye and those corresponding to the viewpoint coordinates of right eye and alternately outputs the separated projected contents, fitting for each eye respectively, on the screen.
In this case, for watching the screen fit for corresponding eye, the user (10) screens one eye according to the screen display period by wearing a stereo viewer (16) for synchronizing the period.
For setting the viewpoints of two eyes, the user (10) assigns the distance between two eyes, the focal distance of two eyes' seeing, and the like.
A keyboard ( 110 ) is used for character input like a filename.
A mouse (120) is used for controlling the system operation and the molecule with the mouse pointer appeared on the screen, left/right buttons, and a wheel being combined together. A menu of selective options for mouse pointer is provided on the screen, and when molecules are loaded from the molecular DB(30), the movement of the molecules for observing them are controlled by mouse ( 120 ) . When controlling the movement of molecules by mouse (120), an in situ rotation of a molecule(i. e., the opposite directional viewpoint) can be achieved by combining the left button of the mouse and the movement of the mouse. And the approach of the viewpoint to the molecule is controlled by rolling the wheel .
An atom can be selected by the left button of the mouse, and the amino-acid in the molecule, where the atom belongs, can be selected by the right button of the mouse.
The gloves (130) comprise a left glove (130a) and a right glove (130b) and help the user to handle the molecules intuitively when the molecules are loaded from the molecular DB(30) . A user simply grabs the molecules, and then rotates and/or drags them to put them on the location he (or she) wants to observe.
By using the two gloves (130a, 130b), a user can grab and control two molecules at the same time to decide the relative locations of the two molecules. By grabbing a portion of a molecule by the gloves (130), the user can select the amino-acid in the molecule to which the portion belongs.
To catch the movement of the location of the gloves (130) on the computer coordinate system(20) in real-time base, two ports (141) of the spatial location tracking instrument ( 140 ) are assigned to each of the left and right gloves (130a, 130b).
Therefore, it is required to operate two gloves (130a, 130b) and the spatial location tracking instrument ( 140 ) together for checking the finger movement .
FIG. 2 is a view illustrating the system and the peripheral equipment in accordance with the present invention. Referring to FIG. 2, input devices comprise standard input devices of a keyboard ( 110 ) and a mouse (120) and additional input devices of gloves (130), a spatial location tracking instrument ( 140 ) , and a force feedback j oystick ( 150 ) . And output devices comprise a force feedback j oystick ( 150 ) and a stereo viewer(160) for stereo-view screen output.
Among the devices, the gloves (130a, 130b), the spatial location tracking instrument ( 140 ) , and the force feedback j oystick (150 ) can be connected to the computer ( 100 ) through serial (or USB) communication ( 170 ) .
A wheel mouse is used for the mouse (120) for back- and-forth movement of the viewpoint.
The left and right gloves (130a, 130b) transmit the information on the states of bending/stretching of user's fingers periodically to the computer ( 100 ) .
The spatial location tracking instrument ( 140 ) comprises a port (142) for producing a magnetic field area, two ports (141) for tracking the movement in the magnetic field, and a main body for checking the states of the ports (141, 142) in real-time base and transmitting them to the computer ( 100 ) periodically.
The ports (141) of the spatial location tracking instrument ( 140 ) is assigned to each of the two gloves (130a, 130b) respectively to obtain the information on the location and the rotation of the user' s hands .
A force feedback j oystick ( 150 ) is used for moving the viewpoint when the user (10) moves the viewpoint to observe the molecule loaded from the molecular DB(30) and for indicating the interaction force between the molecules .
By implementing the 6-dgrees-of-freedom input of the movement and rotation along with the three axes of the three dimensional coordinate system with a conventional force feedback j oystick ( 150 ) , the system makes it possible that the user's viewpoint or the COM point of a certain molecule can be moved to a desired direction on the computer coordinate system(20) by single control of the force feedback j oystick ( 150 ) .
By combined-controlling the equipment described above, a user can effectively observe a molecule and objectively comprehend the molecular interaction. Besides, it is preferable for a molecular modeling system that a user can deform a molecule and constitutes a new molecule by combining two or more molecules .
Thus, the present invention also presents a combined-operation method of the peripheral equipment of the present invention to implement the molecular deformation and/or the molecular compounding.
For observing a molecular interaction, a user (10) uses the gloves (130), a spatial location tracking instrument ( 140) , a force feedback j oystick ( 150 ) , and a mouse (120) as input devices and a screen, a stereo viewer(lβθ), and the force feedback j oystick ( 150 ) as output devices .
First, the user loads a fixed molecule (201) to the computer coordinate system(20), and then loads a moving molecule (202 ) to be moved in the surrounding space of the fixed molecule (201 ) .
In case of a user using a force feedback joystick (150) , the COM point of the moving molecule (202 ) becomes to be the point where the input from the force feedback j oystick ( 150 ) is being applied, In addition, the force applied to this point is outputted through the force feedback j oystick ( 150 ) .
At this time, the viewpoint is located at the upper direction of the axis, orthogonal to the line connecting the COM point of the fixed molecule (201 ) and the COM point of the moving molecule ( 202 ) , of the computer coordinate system(20) on the screen and looking at the COM point of the fixed molecule ( 201 ) .
In case of a user using the gloves (130a, 130b), the COM points of the molecules become to be the points where the inputs from the gloves (130a, 130b) are being applied respectively, and the viewpoint is located on the axis, orthogonal to the line connecting the COM points of two molecules (201, 202), on the screen and looking at the center point of the line connecting the COM points of two molecules.
FIG. 3 is a view illustrating the information obtained by using the peripheral equipment in accordance with the present invention when a user is observing a molecular interaction. The screen displays a fixed molecule (201 ) and a moving molecule (202 ) constituted on the computer coordinate system(20), the moving molecule traj ectory ( 205) being passed, the predicted route(204) displayed by calculating the interaction force between the fixed and moving molecules, the moving molecule azimuth (206) , the attractive/repulsive force indication ( 207 ) of the force applied to the moving molecule from the other molecule, and the glove pointer (203) representing the locations of the hands of the glove-using user and the states of the hands being grabbed or opened.
When the user is controlling the moving molecule (202 ) by the force feedback j oystick ( 150 ) or the gloves (130) for the COM point of the moving molecule ( 202 ) to be moved around the surrounding space of the fixed molecule (201 ) on the computer coordinate system(20), the rotation and the locative movement of the moving molecule (202 ) is being carried out by using the glove pointer(203) .
Here, since the COM point of the fixed molecule ( 201 ) is fixed at the computer coordinate system(20), the locative movement is being implemented by carrying out reverse locative movement of the subject and the viewpoint instead of moving the fixed molecule (201) .
The movement of the moving molecule ( 202 ) by input devices is corresponding to the movement of the COM point . Thus, when a user is using a force feedback j oystic ( 150 ) , the rotation of the moving molecule ( 202 ) should be classified into a rotation interlocked to the viewpoint and a rotation unrelated to the viewpoint so that the user can decide the moving molecule azimuth at desired viewpoint location.
In case of a rotation interlocked to the viewpoint, the force feedback j oystick ( 150 ) takes charge for giving input so that the viewpoint can rotate along when the moving molecule ( 202 ) is being rotated. On the other hand, in case of a rotation unrelated to the viewpoint, the mouse (120) takes charge for giving input .
At this stage, the current moving molecule azimuth (206) to the initial azimuth of the fixed molecule (201) is being displayed on screen.
The interaction force between the molecules is being calculated in real-time base and outputted through the force feedback j oystick ( 150 ) . The attractive/repulsive force indication (207 ) on the screen indicates whether the force applied to the moving molecule by the fixed molecule is attractive or repulsive .
Besides, the system calculates the vector value of the current interaction force to display it on the screen, and then recalculates the vector value of the force to be applied to the endpoint of the displayed vector to successively display the force vector on the screen .
Repeating the sequences described above several times, a predicted route (204) of the moving molecule (202 ) is being displayed on the screen, and the moving molecule traj ectory ( 205 ) , through which the user(lθ) has moved the moving molecule ( 202 ) , is being displayed on the screen. At this time, the trajectory of the moving molecule ( 202 ) azimuth being changed is being displayed together on the screen.
Here, the user can record the relative locations of the two molecules on a desired screen into a file. The user can control the relative locations of the two molecules, loaded to the computer coordinate system(20), by using the two gloves (130a, 130b) and connect the two molecules to constitute a new molecule. The user can also select an atom and/or an amino- acid, constituting a protein molecule, by using the mouse (120) to obtain desired information. Or, he (or she) can substitute a certain amino-acid for the selected amino-acid to deform the molecule.
Here, the left button of the mouse (120) is used for selecting an atom located at the mouse pointer location, and the right button is used for selecting an amino-acid containing the atom located at the mouse pointer location.
A selected portion in a molecule is being displayed by bright color, and when the user want to erase the selected portion, he (or she) can simply select it one more time.
A user can select an amino-acid, constituting a protein molecule, by using the gloves (130). Here, the user can select the amino-acid by grabbing the portion where the glove pointer (203) is located, and when releasing, he (or she) simply grabs the same amino-acid.
When an amino-acid is being selected, the information on the amino-acid is being displayed on the screen, and the system prepares for substitution of the amino-acid according to the user selection.
If the user substitutes the selected amino-acid with another amino-acid, the system decides the overall shape of the changed molecule and carries out the calculation for obtaining the coordinates of the atoms constituting the new molecule.
Since those having ordinary knowledge and skill in the art of the present invention will recognize additional modifications and applications within the scope thereof, the present invention is not limited to the embodiments and drawings described above.
[Industrial Applicability]
The present invention provides intuitive input/output devices to a molecular modeling system so that a user can display a molecule on a computer and comprehend various characteristics of the molecule at once.
In particular, to represent an interaction force between molecules, to decide relative locations of two molecules, to display a partial deformation of a molecule, or to couple the molecules on a three- dimensional coordinate system, a user have to go through numbers of input steps with a keyboard and/or a mouse, the standard input devices of a conventional computer system. However, the number of input steps can be reduced by combined-using the peripheral equipment of the present invention comprising gloves, a spatial location tracking instrument, and a force feedback joystick.
Thus, a user can eliminate the inconvenience occurring at the input stage and handle a molecule accurately. By displaying the current molecular state on a stereo-view screen for a user to be able to concentrate on the subject and giving a physical experience on molecular interaction to the user, the system effectively assists a user to easily obtain the information on the molecule.
Consequently, it improves the user's productivity.

Claims

WHAT IS CLAIMED IS:
1. A method of designing peripheral equipment on a molecular modeling computer system characterized in that: system control and input for user selective options can be performed by keyboard and mouse input devices ; when a molecule is being loaded to said system, the control on said molecule can be carried out by mouse; when said molecule is being loaded, the control on said molecule can be carried out by gloves and a spatial location tracking instrument; when said molecule is being loaded, the control on said molecule and the viewpoint can be carried out by a force feedback joystick; the interaction force between molecules can be outputted through said force feedback joystick; some portion of said molecule can be selected by said mouse and/or said gloves for implementing partial deformation of said molecule; relative locations of two molecules, a fixed molecule and a moving molecule, can be decided by said gloves; and when a user is observing the interaction between two molecules, said gloves, said spatial location tracking instrument, and said force feedback joystick can be used in combination.
2. A method of designing peripheral equipment on a molecular modeling computer system as claimed in claim 1, characterized in that said user can select an amino- acid of a protein molecule by using said mouse and said gloves and partially deform said molecule by substituting said selected amino-acid with another amino-acid .
3. A method of designing peripheral equipment on a molecular modeling computer system as claimed in claim 1, characterized in that said gloves comprises a left glove and a right glove so that the relative locations of two molecules (a fixed molecule and a moving molecule) are decided by using said two gloves and said user can connect two .molecules to constitute a molecule.
4. A method of designing peripheral equipment on a molecular modeling computer system as claimed in claim 1, characterized in that, when said user is observing the interaction between two molecules with using said force feedback joystick, the rotation of a moving molecule, whose center-of- mass(COM) is moving around the surrounding space of a fixed molecule in a computer coordinate system, is classified into a rotation interlocked to the viewpoint and a rotation unrelated to the viewpoint so that said user can decide the azimuth of said moving molecule at desired viewpoint location, wherein said force feedback joystick takes charge for input for said rotation interlocked to the viewpoint so that said viewpoint can rotate along when said moving molecule is being rotated; and said mouse takes charge for input for said rotation unrelated to the viewpoint.
5. A method of designing peripheral equipment on a molecular modeling computer system as claimed in claims 1 or 4, characterized in that, when said user is observing the interaction between two molecules with using said force feedback joystick, the viewpoint is located at the upper direction of the axis, orthogonal to the line connecting the COM point of a fixed molecule and the COM point of a moving molecule, in the computer coordinate system on the screen and looking at the COM point of said fixed molecule .
6. A method of designing peripheral equipment on a molecular modeling computer system as claimed in claims 1 or 4, characterized in that, when said user is observing the interaction between two molecules with using said gloves, the COM points of said two molecules become to be the points where the inputs from said gloves are being applied respectively; and the viewpoint is located at the axis orthogonal to the line connecting the COM points of said two molecules on the screen and looking at the center point of said line connecting the COM points of said two molecules.
7. A method of designing peripheral equipment on a molecular modeling computer system as claimed in claim 1, characterized in that the screen of said system displays, in a stereo-view, at least one or more items among a fixed molecule, a moving molecule, a trajectory of moving molecule being passed, a predicted route displayed by calculating the interaction force between said fixed and moving molecules, a moving molecule azimuth, a directional indication of the force applied to said moving molecule from the other molecule, and a glove pointer representing the locations of the hands of the glove-using user and the states of said hands being grabbed or opened.
8. Peripheral equipment on a molecular modeling computer system characterized by comprising: a keyboard for controlling said system and inputting user selective options; a mouse for controlling said system, inputting user selective options, and when a molecule is being loaded on the screen of said system, controlling said molecule and partially selecting said molecule for partial molecular deformation; gloves for controlling a molecule when said molecule is being loaded on the screen of said system, partially selecting said molecule for partial molecular deformation, and deciding the relative locations of a fixed molecule and a moving molecule ; a spatial location tracking instrument for controlling a molecule when said molecule is being loaded on the screen of said system; and a force feedback joystick for controlling a molecule and the viewpoint when said molecule is being loaded on the screen of said system and outputting the interaction force between said molecules.
9. Peripheral equipment on a molecular modeling computer system as claimed in claim 8, characterized in that said gloves comprises a left glove and a right glove, each of which transmits the information on the states of fingers being bent or stretched to the computer periodically, for grabbing and controlling two molecules at the same time to decide the relative locations of said two molecules.
10. Peripheral equipment on a molecular modeling computer system as claimed in claim 9, wherein said spatial location tracking instrument comprises: a port for producing a magnetic field area; two ports for tracking the movement in said magnetic field and obtaining the information on the location and the rotation of user's hands by being assigned to said left and right gloves respectively; and a main body for checking the states of said ports in real-time base and transmitting them to the computer periodically.
11. Peripheral equipment on a molecular modeling computer system as claimed in claim 8, characterized by further comprising a stereo viewer, that screens one eye according to the screen display period or only allows to see a polarized light, for watching the outputted system screen in a stereo-view.
12. Peripheral equipment on a molecular modeling computer system as claimed in claim 8, characterized in that, when a user is partially selecting said molecule using said mouse, a button at one side of said mouse is used for selecting an atom located at a mouse pointer location and the other button at the other side of said mouse is used for selecting an amino-acid to which the atom located at a mouse pointer location belongs
PCT/KR2003/001630 2003-04-04 2003-08-13 Peripheral equipment on a molecular modeling computer system and a method of designing the same WO2004088565A1 (en)

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