where x r i (x g ai ) represents the predicted (true) atomic type of the i-th VP; y r i (y g ai ) represents the predicted (true) coordinates of the i-th VP; τ is the truncation threshold for the coordinate loss; d r ij (d g ai,aj ) is the predicted (true) distance between VP pairs; c r ij (c g ai,j ) is the predicted (true) distance between VPs and spatial atoms; and δ is the threshold for movement constraint.