Abstract: Systems and methods for visualization of a molecule, comprising a set of particles, are provided. A set of three-dimensional coordinates is obtained, each coordinate describing a position for a corresponding particle. A cost function containing an error in a set of two-dimensional coordinates, where each two-dimensional coordinate corresponds to a three-dimensional coordinate in the set of three-dimensional coordinates, is minimized until an exit condition is achieved. The minimization alters the two-dimensional coordinate values. A set of physical properties SM is obtained, each such property representing a property shared by a pair of particles in the molecule. The coordinates are plotted as nodes of a two-dimensional graph after minimization, connected by a plurality of edges. An edge connects a coordinate pair in the graph that corresponds to a pair of particles in the molecule. A characteristic of the edge is determined by a physical property for the pair of particles.

Abstract: Systems and methods for visualization of a molecule, comprising a set of particles, are provided. A set of three-dimensional coordinates is obtained, each coordinate describing a position for a corresponding particle. A cost function containing an error in a set of two-dimensional coordinates, where each two-dimensional coordinate corresponds to a three-dimensional coordinate in the set of three-dimensional coordinates, is minimized until an exit condition is achieved. The minimization alters the two-dimensional coordinate values. A set of physical properties SM is obtained, each such property representing a property shared by a pair of particles in the molecule. The coordinates are plotted as nodes of a two-dimensional graph after minimization, connected by a plurality of edges. An edge connects a coordinate pair in the graph that corresponds to a pair of particles in the molecule. A characteristic of the edge is determined by a physical property for the pair of particles.

Abstract: Systems and methods for two-dimensional visualization of a molecule, comprising the set of particles {p1, . . . , pN}, are provided. A set of N three-dimensional coordinates {x1, . . . , xN} is obtained, each xi in {x1, . . . , xN} describing a three-dimensional position for a corresponding particle pi in {p1, . . . , pN}. A cost function containing the error in a set of two-dimensional coordinates (c1, . . . , cN), where each ci in (c1, . . . , cN) corresponds to a three-dimensional coordinate xi in {x1, . . . , xN}, is minimized until an exit condition is achieved. The minimization alters the values of (c1, . . . , cN). A set of physical properties SM is obtained, each si,j in SM representing a physical property shared by a pair of particles (pi, pj) in {p1, . . . , pN}. Coordinates (c1, . . . , cN) are plotted as nodes of a two-dimensional graph after minimization. A plurality of edges for the graph is plotted.

Abstract: Systems and methods for two-dimensional visualization of a molecule, comprising the set of particles {p1, . . . , pN}, are provided. A set of N three-dimensional coordinates {x1, . . . , xN} is obtained, each xi in {x1, . . . , xN} describing a three-dimensional position for a corresponding particle pi in {p1, . . . , pN}. A cost function containing the error in a set of two-dimensional coordinates (c1, . . . , cN), where each ci in (c1, . . . , cN) corresponds to a three-dimensional coordinate xi in {x1, . . . , xN}, is minimized until an exit condition is achieved. The minimization alters the values of (c1, . . . , cN). A set of physical properties SM is obtained, each si,j in SM representing a physical property shared by a pair of particles (pi, pj) in {p1, . . . , pN}. Coordinates (c1, . . . , cN) are plotted as nodes of a two-dimensional graph after minimization. A plurality of edges for the graph is plotted.

Abstract: Systems and methods for two-dimensional visualization of a molecule, comprising the set of particles {p1, . . . , pN}, are provided. A set of N three-dimensional coordinates {x1, . . . , xN} is obtained, each xi in {x1, . . . , xN} describing a three-dimensional position for a corresponding particle pi in {p1, . . . , pN}. A cost function containing the error in a set of two-dimensional coordinates (c1, . . . , cN), where each Ci in (c1, . . . , cN) corresponds to a three-dimensional coordinate xi in {x1, . . . , xN}, is minimized until an exit condition is achieved. The minimization alters the values of (c1, . . . , cN). A set of physical properties SM is obtained, each Si,j in SM representing a physical property shared by a pair of particles (pi, pj) in {p1, . . . , pN}. Coordinates (c1, . . . , cN) are plotted as nodes of a two-dimensional graph after minimization. A plurality of edges for the graph is plotted.