STRUCTURED DOCUMENTS AND SYSTEMS, METHODS AND COMPUTER PROGRAMS FOR CREATING, PRODUCING AND DISPLAYING THREE DIMENSIONAL OBJECTS AND OTHER RELATED INFORMATION IN THOSE STRUCTURED DOCUMENTS

• US 20070016853A1
• Filed: 07/14/2006
• Published: 01/18/2007
• Est. Priority Date: 07/14/2005
• Status: Active Grant

• Current Assignee: MolSoft LLC
• Original Assignee: MolSoft LLC
• Inventors: TOTROV, MAXIM, BUDAGYAN, LEVON, ORRY, ANDREW, RAUSH, EUGENE, ABAGYAN, Ruben
• Granted Patent: US 7,880,738 B2
• Time in Patent Office: Days
• US Class Current: 715/251
• CPC Class Codes: G06T 19/00 Manipulating 3D models or images for computer graphics
• CPC Class Codes: G06T 2200/24 involving graphical user interfaces [GUIs]

Abstract

A structured document file which includes graphical and non graphical information. The graphical information includes the vector and coordinate description of a representation of at least one three dimensional object and at least one of the following group of view attributes or features: rotation, translation, view angle, lighting, colors, specific graphical representations, labels and parameters. The vector and coordinate description are stored with or independently from the one or more view attributes or features and the vector and coordinate description and the one or more view attributes are stored in a single file which can be accessed and viewed by a structured document viewer. Related authoring tools and viewers are also disclosed.

Claims

1. A structured document stored in a computer readable medium, the structured document comprising:

the vector and coordinate description of a representation of at least one three dimensional object; and

at least one of the following group of view attributes or features;

rotation, translation, view angle, lighting, colors, specific graphical representations, labels and parameters;

wherein the vector and coordinate description are stored with or independently from the one or more view attributes or features; and

wherein the vector and coordinate description and the one or more view attributes are stored in a single file which can be accessed and viewed by a structured document viewer.

2. The structured document of claim 1, further comprising at least one of the following group of three dimensional object related information:

hyperlinked text, sequence alignments, evolutionary trees, chemical spreadsheets, data tables, data plots, and data clustering trees.

3. The structured document of claim 1, wherein the document is stored with at least one other structured document in a relational database which can be indexed and searched.

4. The structured document of claim 1, wherein at least one of the three dimensional objects is a three dimensional representation of a biological or chemical molecule.

5. The structured document of claim 1, wherein the view attributes further include one or more selected from the following group:

graphical representations and colors for each atom, graphical representations and colors for each residue, ball and stick representation, CPK attributes, molecular surface attributes, ribbon attributes, atom label, residue labels, site labels, two dimensional annotations, and three dimensional annotations.

6. The structured document of claim 1, further comprising at least one attribute defining an initial view when the structured document is initially viewed or interfaced with the structured document viewer.

7. The structured document of claim 1, wherein the structured document is restricted to a single computing platform.

8. The structured document of claim 1, wherein the structured document is a binary file viewable on at least one computing platform with a different order of Endians having a structured document viewer without any modification of the structured document prior to being viewed on the structured document viewer.

9. The structured document of claim 1, further comprising view attributes with animations and transitions in a parametric definition stored in the structured document and capable of defining viewing rules of animations or movements selected from at least one of the following group:

rotation around one or more axes, rocking, transitions between viewpoints, changing colors, transparency, clipping, and molecular geometry.

10. The structured document of claim 1, further comprising an instruction for an automatic update from a repository if a newer version of the structured document is available for downloading.

11. The structured document of claim 1, wherein the at least one attribute is an initial view of an animation that can be interactively manipulated by the user via a browser graphical user interface.

12. The structured document of claim 1, further comprising one more parametric animation and movements selected from the following group:

rotation around different axes, rocking, transitions between viewpoints, changing colors, transparency, clipping, and molecular geometry.

13. The structured document of claim 1, wherein the at least one attribute is an initial view of an animation that can be interactively manipulated by the user via a browser graphical user interface.

14. The structured document of claim 1, wherein the structured document is a binary file viewable on at least one computing platform with a different order of Endians having a structured document viewer without any modification of the structured document prior to being viewed on the structured document viewer.

15. The structured document of claim 1, wherein the document is indexed by external indexing programs by one of the following group:

chemical structure, biological sequence, biological structure, 3D shapes and 3D biomolecule structures.

16. The structured document of claim 1, wherein the document has predetermined limitations which allow the user to interact with the document or presentation in restricted to one or more parameters set by the author of the file.

17. The structured document of claim 1, wherein the document further includes at least one function selected from the following group:

write protection, version control, and editing rights, and file rights modification.

18. The structured document of claim 1, wherein at least one of the three dimensional objects is selected from the following group:

real property, tangible property, and intangible property.

19. A computer implemented system for viewing and interacting with structured document, the computer implemented system comprising:

(a) a computational platform with a processor, memory and a storage medium;

(b) a viewer made up of a graphical user interface; and

(c) the structured document comprising

non graphical information and graphical information with the vector and coordinate description of a representation of at least one three dimensional object and at least one of the following group of view attributes or features;

rotation, translation, view angle, lighting, colors, specific graphical representations, labels and parameters;

wherein the vector and coordinate description are stored with or independently from the one or more view attributes or features in a single file, and

wherein the viewer displays the graphic and non graphic information contained in the structured document allowing the user to interact with said information.

20. The computer implemented system of claim 19 wherein the initial appearance of the graphical user interface is predetermined.

21. The computer implemented system of claim 20 wherein the initial predetermined appearance can be modified by the user.

22. The computer implemented system of claim 19 wherein the graphic information is one or more three dimensional objects in a presentation.

23. The computer implemented system of claim 19 wherein the viewer is compatible with at least one of the following group of operating systems selected from the following group:

Windows, MacOS, Linux and Unix.

24. The computer implemented system of claim 19 wherein the viewer is a compiled executable program.

25. The computer implemented system of claim 19 wherein the viewer further displays to the user at least one preview of a full view.

26. The computer implemented system of claim 19 wherein the vector and coordinate description of a representation of at least one three dimensional object is the vector and coordinate description of a representation of at least one three dimensional molecule comprised of connectivity and Cartesian coordinates.

27. The computer implemented system of claim 19 wherein the viewer further displays the one or more molecular representations with one or more associated colors.

28. The computer implemented system of claim 19 wherein the non graphical information includes general information about molecular and atomic structure.

29. The computer implemented system of claim 19 wherein the general information about molecular and atomic structure is selected from the following group:

the van der Waals radii of atoms and atom types of the polymer backbone.

30. A computer implemented method of authoring an structured document file comprising the steps of:

creating a file which to store at least one three dimensional object and related non graphical information, the at least one three dimensional object defining a three dimensional rendering, and

storing the at least one view in a structured document, the structured document comprising;

the vector and coordinate description of a representation of at least one three dimensional object; and

at least one of the following group of view attributes or features;

rotation, translation, view angle, lighting, colors, specific graphical representations, labels and parameters;

wherein the vector and coordinate description are stored independently from the one or more view attributes or features; and

wherein the vector and coordinate description and the one or more view attributes are stored in a single file which can be accessed and viewed by a structured document viewer.

31. The computer implemented method of claim 30 wherein the structured document file is created based on a rendering to a user of the graphical and non graphical information on a graphical user interface at a certain time upon a trigger event initiated by the user.