The invention discloses a three-dimensional molecule generation method fusing conditional flow matching and Van der Waals
radius constraint, which comprises the following steps:
processing a molecule training
data set, and extracting a total number of atoms and a training element component
histogram; based on the optimal transmission path interpolation, combining the sampling
time step and the standard
Gaussian noise to construct a
noise coordinate and a target condition velocity field; the
noise coordinates are input into a
continuous flow matching prediction model, node features are extracted through affine transformation modulation, a prediction velocity field is obtained, soft atom
type distribution is generated, and the expected Van der Waals
radius of each atom type is calculated; calculating flow matching loss through a prediction velocity field and a target condition velocity field, calculating a geometric collision penalty term in combination with an expected Van der Waals
radius and a noise coordinate, and constructing a total
loss function training
model parameter; and defining an
ordinary differential equation by using the trained parameters for solving, and outputting a three-dimensional molecular structure file. According to the method, atom space overlapping is inhibited, and the physical rationality and chemical effectiveness of generated molecules are improved.