Method, system, and computer program product for representing similarity/dissimilarity between chemical compounds

A method for representing similarity/dissimilarity between compounds, comprising the steps of:

• (1) generating an initial configuration of objects for output, the objects representing a plurality of compounds, each object having an initial set of coordinates;
• (2) selecting a subset of compounds from the plurality of compounds;
• (3) refining the coordinates of at least one object that represents a selected compound based on the coordinates of the at least one object, the coordinates of a second object, and a distance between the at least one and second objects so that a distance between the refined coordinates of the at least one object and the coordinates of the second object is more representative of the similarity/dissimilarity of the compounds;
• (4) repeating steps (2) and (3) for additional subsets of compounds;
• and
• (5) outputting the coordinates of at least some of the objects.

A system for representing similarity/dissimilarity between compounds, comprising:

• a module that generates an initial configuration of objects for display on a graphics device, the objects representing a plurality of compounds, each object having an initial set of coordinates;
• a module that selects a subset of compounds from the plurality of compounds;
• a module that refines the coordinates of at least one object that represents a selected compound based on the coordinates of the at least one object, the coordinates of a second object, and a distance between the at least one and second objects so that a distance between the refined coordinates of the at least one object and the coordinates of the second object is more representative of the similarity/dissimilarity of the compounds;
• and
• a module that displays at least some of the objects on the graphics device.

A computer program product for representing similarity/dissimilarity between compounds, comprising a computer useable medium having computer program logic stored therein, wherein the computer program logic comprises:

• means for enabling a computer to generate an initial configuration of objects for display on a graphics device, the objects representing a plurality of compounds, each object having an initial set of coordinates;
• means for enabling a computer to select a subset of compounds from the plurality of compounds;
• means for enabling a computer to refine the coordinates of at least one object that represents a selected compound based on the coordinates of the at least one object, the coordinates of a second object, and a distance between the at least one and second objects so that a distance between the refined coordinates of the at least one object and the coordinates of the second object is more representative of the similarity/dissimilarity of the compounds;
• and
• means for enabling a computer to display at least some of the objects on the graphics device.