Errors in detecting the interaction between pi pi and t-pi.

[zephyrdhb]

In the source code, first search for all aromatic ring distances that meet the requirements of pi_pi_general_dist_cutoff to obtain ligand_receptor_aromatic_dists, and traverse ligand_receptor_aromatic_dists to determine whether the aromatic ring pair is pi-pi. If not, then check if it is t-pi. This will result in the center distance of all t-pi being less than pi_pi_general_dist_cutoff, rather than the set _stacking_closest_dist_cutoff.

Source code:

# Calculate the distances.
ligand_receptor_aromatic_dists = _get_ligand_receptor_aromatic_dists(
    ligand, receptor, pi_pi_general_dist_cutoff
)

pi_interactions = {}
pdb_pistack = Mol()
pdb_pi_t = Mol()
pi_stacking_labels = []
t_stacking_labels = []

# "PI-Stacking Interactions ALIVE AND WELL IN PROTEINS" says distance of 7.5
# A is good cutoff. This seems really big to me, except that pi-pi
# interactions (parallel) are actuall usually off centered. Interesting
# paper. Note that adenine and tryptophan count as two aromatic rings. So,
# for example, an interaction between these two, if positioned correctly,
# could count for 4 pi-pi interactions.
for (
    ligand_aromatic,
    receptor_aromatic,
    dist,
    angle_between_planes,
) in ligand_receptor_aromatic_dists:

    (
        pi_interactions,
        pdb_pistack,
        pi_stacking_labels,
        pi_stacking_detected,
    ) = _pi_stacking(
        ligand,
        receptor,
        ligand_aromatic,
        receptor_aromatic,
        dist,
        angle_between_planes,
        pi_stacking_angle_tol,
        pi_padding,
        pi_interactions,
        pdb_pistack,
        pi_stacking_labels,
    )

    if not pi_stacking_detected:
        pi_interactions, pdb_pi_t, t_stacking_labels = _t_stacking(
            ligand,
            receptor,
            ligand_aromatic,
            receptor_aromatic,
            dist,
            angle_between_planes,
            t_stacking_angle_tol,
            t_stacking_closest_dist_cutoff,
            pi_padding,
            pi_interactions,
            pdb_pi_t,
            t_stacking_labels,
        )