def _guess_underbound_nitrogen_cn3(structure: Structure,
site_index: int,
neighbors: list,
tolerance: int = 10) -> bool:
"""Check if there is a nitrogen with three neighbors
that likely misses some coordination.
Args:
structure (Structure): pymatgen Structure object
site_index (int): index of the central site that is check
neighbors (list): list of neighboring sites
tolerance (int, optional): Tolerance for angle checks in degree.
Defaults to 10.
Returns:
bool: True if the nitrogen is likely missing some coordination partner
"""
angle_a = structure.get_angle(site_index, neighbors[0].index,
neighbors[1].index)
angle_b = structure.get_angle(site_index, neighbors[0].index,
neighbors[2].index)
angle_c = structure.get_angle(site_index, neighbors[1].index,
neighbors[2].index)
min_angle = np.min([angle_a, angle_b, angle_c])
any_metal = False
for neighbor in neighbors:
if neighbor.site.specie.is_metal:
any_metal = True
num_h = 0
for neighbor in neighbors:
if str(neighbor.site.specie) == "H":
num_h += 1
if min_angle + tolerance < 110:
# let's only do this if one of the neighbors is a metal.
# sometimes the M-N bond is so long that it isn't correctly recognized
# obviously, this now won't detect missing H on a floating NH3
# but this is probably a rare situation
if any_metal and (num_h == 2):
return True
return False
def _guess_underbound_nitrogen_cn2( # pylint:disable=too-many-arguments
structure: Structure,
site_index: int,
neighbors: list,
connected_sites_a: list,
connected_sites_b: list,
tolerance: int = 10,
) -> bool:
"""Check if there is a nitrogen with CN 2 that probably misses
some coordination.
Args:
structure (Structure): pymatgen Structure object
site_index (int): Index of the site on which the check is performed
neighbors (list): List of neighboring sites
connected_sites_a (list): List of neighbor sites for first neighbor
connected_sites_b (list): List of neighbor sites for second neighbor
tolerance (int, optional): Tolerance for angle checks in degree.
Defaults to 10.
Returns:
bool: True if there is a nitrogen that likely misses some coordination.
"""
angle = structure.get_angle(site_index, neighbors[0].index,
neighbors[1].index)
neighbor_species = set(
[str(neighbors[0].site.specie),
str(neighbors[1].site.specie)])
if np.abs(180 - angle) < tolerance:
# sp hybridization if the nitrogen is linear
# this could be a nitride or a nitrosyl
# usually, there is nothing to worry about if this is the case
return False
if angle < 115:
# typically angle around 109.5 degree for sp3 hybridization
# if we only have two neighbors but the nitrogen is likely
# sp3 this is suspicious
# to be sure we will check if it is planar (pyridine) or
# not (piperazine) in the case the two neighbors are carbon
if neighbor_species == set(["C", "C"]):
dihedral_a = structure.get_dihedral(
site_index,
neighbors[0].index,
neighbors[1].index,
connected_sites_a[0].index,
)
dihedral_b = structure.get_dihedral(
site_index,
neighbors[0].index,
neighbors[1].index,
connected_sites_b[0].index,
)
mean_dihedral = np.mean([dihedral_a, dihedral_b])
if (np.abs(mean_dihedral - 180) <
tolerance) or (np.abs(mean_dihedral - 0) < tolerance):
return False
return True
return True
# larger angles should indicate sp2 hybridization
# one case where MOFs might have an issue with sp2
# is an NH2 group planar to the ring where one H is missing
# the heuristic we use to catch this is if one of the neighbors
# is H
if "H" in neighbor_species:
return True
return False
