def check_arom(self, resRings, ligRings, centerMol, resRingCenter,
ligRingCenter, aromDist):
'''
Checks for an interaction between the set of rings of a residue and a
ligand. Uses temporary center atoms to make the distance comparisons
'''
# Loop over the residue rings
for resRing in resRings:
# For each ring, define its center using a temp atom
centerMol.SetCoords(resRingCenter, resRing[0])
# Loop over the ligand's rings
for ligRing in ligRings:
# Get the center of the ligand ring
centerMol.SetCoords(ligRingCenter, ligRing[0])
# Get the distance
dist = oechem.OEGetDistance(centerMol, resRingCenter,
centerMol, ligRingCenter)
# If under cutoff, return 1
if dist <= aromDist:
return "1"
# If no aromatic interaction was found, return 0
return "0"
def check_inter(self, molA, molB, patternA, patternB, distCutoff):
'''
Function looping over the atoms of a residue and the ligand
Depending on the pattern arguments, it will check for a type of
interaction, and return 1 as soon as it found it, otherwise return 0
'''
# Look for pattern in residue
try:
for matchA in patternA.Match(molA):
for atomA in matchA.GetTargetAtoms():
# Look for pattern in ligand
for matchB in patternB.Match(molB):
for atomB in matchB.GetTargetAtoms():
# Check distance between those atoms
dist = oechem.OEGetDistance(
molA, atomA, molB, atomB)
if dist <= distCutoff:
return "1"
except SystemError:
pass
# Interaction not found between this residue and the ligand
return "0"
def _calc_properties(mol: oechem.OEMol) -> danceprops.DanceProperties:
"""
Calculates properties of the given molecule and returns a
DanceProperties object holding them.
Based on Victoria Lim's am1wib.py - see
https://github.com/vtlim/misc/blob/master/oechem/am1wib.py
"""
props = danceprops.DanceProperties()
for conf in mol.GetConfs():
charged_copy = oechem.OEMol(conf)
results = oequacpac.OEAM1Results()
if not AM1.CalcAM1(results, charged_copy):
logging.debug(
f"failed to assign partial charges to {mol.GetTitle()}")
return props
DanceGenerator._add_charge_props(mol, charged_copy, results)
# Sum bond orders, bond lengths, and bond angles
for atom in charged_copy.GetAtoms(oechem.OEIsInvertibleNitrogen()):
nbors = list(atom.GetAtoms()) # (neighbors)
ang1 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[0], atom, nbors[1]))
ang2 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[1], atom, nbors[2]))
ang3 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[2], atom, nbors[0]))
props.tri_n_bond_angle = ang1 + ang2 + ang3
for nbor in nbors:
bond_order = results.GetBondOrder(atom.GetIdx(),
nbor.GetIdx())
bond_length = oechem.OEGetDistance(charged_copy, atom,
nbor)
element = nbor.GetAtomicNum()
props.tri_n_bonds.append(
danceprops.DanceTriNBond(bond_order, bond_length,
element))
props.tri_n_bond_order += bond_order
props.tri_n_bond_length += bond_length
break # terminate after one trivalent nitrogen
break # terminate after one conformation
return props
def check_hbond(self, molA, molB, patternA, patternB, distCutoff,
angleCutUp, angleCutLow):
'''
Function checking hbond interaction between a residue and the ligand
Checks for angle between:
donor electronegative atom - donor proton - acceptor
'''
# Look for pattern in residue
try:
for matchA in patternA.Match(molA):
for atomA in matchA.GetTargetAtoms():
if str(atomA).split()[1] == 'H':
protonA = atomA
# Look for pattern in ligand
for matchB in patternB.Match(molB):
for acceptorB in matchB.GetTargetAtoms():
# Check distance between those atoms
dist = oechem.OEGetDistance(
molA, protonA, molB, acceptorB)
# if the distance meets the cutoff, check angle
if dist <= distCutoff:
#print dist, protonA, acceptorB, \
# molA.GetTitle(), molB.GetTitle()
# Get the electronegative atom linked to
# the proton
for donorA in protonA.GetAtoms():
pass
#print donorA
# Check angle: donorA, protonA, acceptorB
angle = oechem.OEGetAngle(
molA, donorA, molA, protonA, molB,
acceptorB)
#print angle, angleCutUp, angleCutLow
# Compare angle to cutoffs
if angle <= angleCutUp and \
angle >= angleCutLow:
return "1"
except SystemError:
pass
# Interaction not found between this residue and the ligand
return "0"
def check_catPi(self, mol, catPattern, rings, centerMol, ringCenter,
catPiDist, catPiAngleUp, catPiAngleLow):
'''
Check for the cation-Pi interactions, loops over the rings of one
molecule, and loops over the cations of the other
'''
# Loop over the rings
for ring in rings:
# Get the center of that ring
centerMol.SetCoords(ringCenter, ring[0])
# Loop over the cations of this 'molecule'
for catMatch in catPattern.Match(mol):
for cation in catMatch.GetTargetAtoms():
# Check distance between center of ring and cation
dist = oechem.OEGetDistance(centerMol, ringCenter, mol,
cation)
#print cation, mol.GetTitle(), dist
# Check for distance threshold
if dist <= catPiDist:
# Calculate the vector between the ring's
# center and the cation (residue)
ringCenterCoords = centerMol.GetCoords(ringCenter)
cationCoords = mol.GetCoords(cation)
vecRingCation = self.defineVector(
ringCenterCoords, cationCoords)
# check the angle between the ring's normal,
# and the vector between the ring's center
# and the cation
angle = self.vectorAngle(vecRingCation, ring[2])
if angle <= catPiAngleUp or angle >= catPiAngleLow:
return "1"
# If the interaction was not found, return 0
return "0"