def pi_metal(mol1, mol2, cutoff = 5, tolerance = 30):
"""Returns pairs of ring-metal atoms, which meet pi-metal criteria
Parameters
----------
mol1, mol2 : oddt.toolkit.Molecule object
Molecules to compute ring-metal pairs
cutoff : float, (default=5)
Distance cutoff for Pi-metal pairs
tolerance : int, (default=30)
Range (+/- tolerance) from perfect direction (perpendicular) in which pi-metal are considered as strict.
Returns
-------
r1 : ring_dict-type numpy array
Aligned rings forming pi-metal
m : atom_dict-type numpy array
Aligned metals forming pi-metal
strict_parallel : numpy array, dtype=bool
Boolean array align with ring-metal pairs, informing whether they form 'strict' pi-metal. If false, only distance cutoff is met, therefore the interaction is 'crude'.
"""
r1, m = close_contacts(mol1.ring_dict, mol2.atom_dict[mol2.atom_dict['ismetal']], cutoff, x_column='centroid')
if len(r1) > 0 and len(m) > 0:
angle1 = angle_2v(r1['vector'], m['coords'] - r1['centroid'])
strict = (angle1 > 180 - tolerance) | (angle1 < tolerance)
return r1, m, strict
else:
return r1, m, np.array([], dtype=bool)
def pi_metal(mol1, mol2, cutoff = 5, tolerance = 30):
"""Returns pairs of ring-metal atoms, which meet pi-metal criteria
Parameters
----------
mol1, mol2 : oddt.toolkit.Molecule object
Molecules to compute ring-metal pairs
cutoff : float, (default=5)
Distance cutoff for Pi-metal pairs
tolerance : int, (default=30)
Range (+/- tolerance) from perfect direction (perpendicular) in which pi-metal are considered as strict.
Returns
-------
r1 : ring_dict-type numpy array
Aligned rings forming pi-metal
m : atom_dict-type numpy array
Aligned metals forming pi-metal
strict_parallel : numpy array, dtype=bool
Boolean array align with ring-metal pairs, informing whether they form 'strict' pi-metal. If false, only distance cutoff is met, therefore the interaction is 'crude'.
"""
r1, m = close_contacts(mol1.ring_dict, mol2.atom_dict[mol2.atom_dict['ismetal']], cutoff, x_column='centroid')
if len(r1) > 0 and len(m) > 0:
angle1 = angle_2v(r1['vector'], m['coords'] - r1['centroid'])
strict = (angle1 > 180 - tolerance) | (angle1 < tolerance)
return r1, m, strict
else:
return r1, m, np.array([], dtype=bool)
def pi_stacking(mol1, mol2, cutoff = 5, tolerance = 30):
"""Returns pairs of rings, which meet pi stacking criteria
Parameters
----------
mol1, mol2 : oddt.toolkit.Molecule object
Molecules to compute ring pairs
cutoff : float, (default=5)
Distance cutoff for Pi-stacking pairs
tolerance : int, (default=30)
Range (+/- tolerance) from perfect direction (parallel or perpendicular) in which pi-stackings are considered as strict.
Returns
-------
r1, r2 : ring_dict-type numpy array
Aligned arrays of rings forming pi-stacking
strict_parallel : numpy array, dtype=bool
Boolean array align with ring pairs, informing whether rings form 'strict' parallel pi-stacking. If false, only distance cutoff is met, therefore the stacking is 'crude'.
strict_perpendicular : numpy array, dtype=bool
Boolean array align with ring pairs, informing whether rings form 'strict' perpendicular pi-stacking (T-shaped, T-face, etc.). If false, only distance cutoff is met, therefore the stacking is 'crude'.
"""
r1, r2 = close_contacts(mol1.ring_dict, mol2.ring_dict, cutoff, x_column = 'centroid', y_column = 'centroid')
if len(r1) > 0 and len(r2) > 0:
angle1 = angle_2v(r1['vector'],r2['vector'])
angle2 = angle(r1['vector'] + r1['centroid'],r1['centroid'], r2['centroid'])
strict_parallel = ((angle1 > 180 - tolerance) | (angle1 < tolerance)) & ((angle2 > 180 - tolerance) | (angle2 < tolerance))
strict_perpendicular = ((angle1 > 90 - tolerance) & (angle1 < 90 + tolerance)) & ((angle2 > 180 - tolerance) | (angle2 < tolerance))
return r1, r2, strict_parallel, strict_perpendicular
else:
return r1, r2, np.array([], dtype=bool), np.array([], dtype=bool)
def pi_stacking(mol1, mol2, cutoff = 5, tolerance = 30):
"""Returns pairs of rings, which meet pi stacking criteria
Parameters
----------
mol1, mol2 : oddt.toolkit.Molecule object
Molecules to compute ring pairs
cutoff : float, (default=5)
Distance cutoff for Pi-stacking pairs
tolerance : int, (default=30)
Range (+/- tolerance) from perfect direction (parallel or perpendicular) in which pi-stackings are considered as strict.
Returns
-------
r1, r2 : ring_dict-type numpy array
Aligned arrays of rings forming pi-stacking
strict_parallel : numpy array, dtype=bool
Boolean array align with ring pairs, informing whether rings form 'strict' parallel pi-stacking. If false, only distance cutoff is met, therefore the stacking is 'crude'.
strict_perpendicular : numpy array, dtype=bool
Boolean array align with ring pairs, informing whether rings form 'strict' perpendicular pi-stacking (T-shaped, T-face, etc.). If false, only distance cutoff is met, therefore the stacking is 'crude'.
"""
r1, r2 = close_contacts(mol1.ring_dict, mol2.ring_dict, cutoff, x_column = 'centroid', y_column = 'centroid')
if len(r1) > 0 and len(r2) > 0:
angle1 = angle_2v(r1['vector'],r2['vector'])
angle2 = angle(r1['vector'] + r1['centroid'],r1['centroid'], r2['centroid'])
strict_parallel = ((angle1 > 180 - tolerance) | (angle1 < tolerance)) & ((angle2 > 180 - tolerance) | (angle2 < tolerance))
strict_perpendicular = ((angle1 > 90 - tolerance) & (angle1 < 90 + tolerance)) & ((angle2 > 180 - tolerance) | (angle2 < tolerance))
return r1, r2, strict_parallel, strict_perpendicular
else:
return r1, r2, np.array([], dtype=bool), np.array([], dtype=bool)
def pi_cation(mol1, mol2, cutoff=5, tolerance=30, cation_exact=False):
"""Returns pairs of ring-cation atoms, which meet pi-cation criteria
Parameters
----------
mol1, mol2 : oddt.toolkit.Molecule object
Molecules to compute ring-cation pairs
cutoff : float, (default=5)
Distance cutoff for Pi-cation pairs
tolerance : int, (default=30)
Range (+/- tolerance) from perfect direction (perpendicular)
in which pi-cation are considered as strict.
cation_exact : bool
Requires interacting atoms to have non-zero formal charge.
Returns
-------
r1 : ring_dict-type numpy array
Aligned rings forming pi-stacking
plus2 : atom_dict-type numpy array
Aligned cations forming pi-cation
strict_parallel : numpy array, dtype=bool
Boolean array align with ring-cation pairs, informing whether
they form 'strict' pi-cation. If false, only distance cutoff is met,
therefore the interaction is 'crude'.
"""
cation_map = mol2.atom_dict['isplus']
if cation_exact:
cation_map = cation_map & (mol2.atom_dict['formalcharge'] > 0)
r1, plus2 = close_contacts(mol1.ring_dict,
mol2.atom_dict[cation_map],
cutoff,
x_column='centroid')
if len(r1) > 0 and len(plus2) > 0:
angle1 = angle_2v(r1['vector'], plus2['coords'] - r1['centroid'])
ideal_angle = 30 # angle to normal vector
strict = (((angle1 > ideal_angle - tolerance) &
(angle1 < ideal_angle + tolerance)) |
((angle1 > 180 - ideal_angle - tolerance) &
(angle1 < 180 - ideal_angle + tolerance)))
return r1, plus2, strict
else:
return r1, plus2, np.array([], dtype=bool)
