Calculation method for molecular volume and comparison method for shapes of two molecules

A method for shape comparison between two molecules, comprising steps of:

• (31) loading in three-dimensional structure information for a first molecule and a second molecule and calculating self-overlap volumes of the first and second molecules, the calculation comprising steps of:
• loading in three-dimensional structure information of the first molecule, the three-dimensional structure information comprising type and coordinate values of each atom contained in the first molecule;
• obtaining respective van der Waals radius based on the type of respective atom contained in the first molecule, converting the three-dimensional structure information into a group of Gaussian spheres representing atoms in the first molecule, each of the set of Gaussian spheres having a radius equal to the van der Waals radius of respective atom and a position equal to the coordinate position of respective atom;
• calculating overlap volume for each pair of Gaussian spheres in the first molecule, wherein the ijth pair of Gaussian spheres in the first molecule consists of the/and the jth Gaussian spheres and has a overlap volume vij;
• calculating the weight of each Gaussian sphere in the first molecule, the weight of the ith Gaussian sphere in the first molecule
• w
• i
• =
• v
• i
• v
• i
• +
• k
• 
• ∑
• j
• ≠
• 1
• 
• v
• ij
• ,
• wherein vi is the volume of the ith Gaussian sphere, and k is a constant;
• calculating self-overlap volume of the first molecule
• V
• 1
• =
• ∑
• i
• ∈
• A
• ,
• j
• ∈
• A
• 
• w
• i
• 
• w
• j
• 
• v
• ij
• ,
• wherein A is a set of all Gaussian sphere in the first molecule;
• loading in three-dimensional structure information of the second molecule, the three-dimensional structure information comprising type and coordinate values of each atom contained in the second molecule;
• obtaining respective van der Waals radius based on the type of respective atom contained in the second molecule, converting the three-dimensional structure information into a group of Gaussian spheres representing atoms in the second molecule, each of the set of Gaussian spheres having a radius equal to the van der Waals radius of respective atom and a position equal to the coordinate position of respective atom;
• calculating overlap volume for each pair of Gaussian spheres in the second molecule, wherein the ijth pair of Gaussian spheres in the second molecule consists of the ith and the jth Gaussian spheres and has a overlap volume vij′;
• calculating the weight of each Gaussian sphere in the second molecule, the weight of the ith Gaussian sphere in the second molecule
• w
• i
• ′
• =
• v
• i
• ′
• v
• i
• ′
• +
• k
• ′
• 
• ∑
• j
• ≠
• 1
• 
• v
• ij
• ′
• ,
• wherein vi′ is the volume of the ith Gaussian sphere, and k′ is a constant;
• calculating self-overlap volume of the second molecule
• V
• 2
• =
• ∑
• i
• ∈
• B
• ,
• j
• ∈
• B
• 
• w
• i
• ′
• 
• w
• j
• ′
• 
• v
• ij
• ′
• ,
• wherein B is a set of all Gaussian sphere in the second molecule;
• (32) calculating intermolecular volumes of the first and second molecules in various overlap situations, selecting the maximum intermolecular volume;
• and
• (33) determining the similarity between the first and second molecules based on the volume of the first molecule, the volume of the second molecule and the maximum intermolecular volume, the similarity being the result of the shape comparison between the two molecules.