10. The computer implemented method of claim 1 , wherein the structured document is indexed by external indexing programs by one of the group consisting of chemical structure, biological sequence, biological structure, 3D shapes and 3D biomolecule structures.
1. A computer implemented method for transforming multiple data types into a single structured document, the method comprising the step of transforming two or more data types into a single structure document to obtain the single structured document stored in a computer readable medium comprised of: a three dimensional structured object component comprising the vector coordinate, and object element type description of a representation of at least one three dimensional object; and a user configured viewing component comprising data representing the three dimensional structured object component's view attributes wherein the graphic component and the viewing component are jointly stored in a single file which can be accessed and viewed by a structured document viewer wherein said viewer may output the stored one or more views without user input and wherein said viewer may allow one or more single user actionable transitions to other stored views to thereby transform multiple data types into a structured document stored in a computer readable medium, and wherein the structured document is comprised of a single multi view file and wherein at least one of the three dimensional objects is a three dimensional representation of a biological or chemical molecule; and wherein the at least one attribute in said structured document is a view other than an initial view of an animation that can be interactively manipulated by the user via a browser graphical user interface; and 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.