def _CalculateMoranAutocorrelation(mol: Chem.Mol, lag: int = 1, propertylabel: str = 'm') -> float:
"""Calculate weighted Moran autocorrelation descriptors.
:param lag: topological distance between atom i and atom j.
:param propertylabel: type of weighted property
"""
Natom = mol.GetNumAtoms()
prolist = []
for i in mol.GetAtoms():
temp = GetRelativeAtomicProperty(i.GetSymbol(), propertyname=propertylabel)
prolist.append(temp)
aveweight = sum(prolist) / Natom
tempp = [numpy.square(x - aveweight) for x in prolist]
GetDistanceMatrix = Chem.GetDistanceMatrix(mol)
res = 0.0
index = 0
for i in range(Natom):
for j in range(Natom):
if GetDistanceMatrix[i, j] == lag:
atom1 = mol.GetAtomWithIdx(i)
atom2 = mol.GetAtomWithIdx(j)
temp1 = GetRelativeAtomicProperty(element=atom1.GetSymbol(), propertyname=propertylabel)
temp2 = GetRelativeAtomicProperty(element=atom2.GetSymbol(), propertyname=propertylabel)
res = res + (temp1 - aveweight) * (temp2 - aveweight)
index += 1
else:
res = res + 0.0
if sum(tempp) == 0 or index == 0:
result = 0
else:
result = (res / index) / (sum(tempp) / Natom)
return round(result, 3)
def _GetBurdenMatrix(mol: Chem.Mol, propertylabel: str = 'm') -> numpy.matrix:
"""Calculate weighted Burden matrix and eigenvalues."""
mol = Chem.AddHs(mol)
Natom = mol.GetNumAtoms()
AdMatrix = Chem.GetAdjacencyMatrix(mol)
bondindex = numpy.argwhere(AdMatrix)
AdMatrix1 = numpy.array(AdMatrix, dtype=numpy.float32)
# The diagonal elements of B, Bii, are either given by
# the carbon normalized atomic mass,
# van der Waals volume, Sanderson electronegativity,
# and polarizability of atom i.
for i in range(Natom):
atom = mol.GetAtomWithIdx(i)
temp = GetRelativeAtomicProperty(element=atom.GetSymbol(), propertyname=propertylabel)
AdMatrix1[i, i] = round(temp, 3)
# The element of B connecting atoms i and j, Bij,
# is equal to the square root of the bond
# order between atoms i and j.
for i in bondindex:
bond = mol.GetBondBetweenAtoms(int(i[0]), int(i[1]))
if bond.GetBondType().name == 'SINGLE':
AdMatrix1[i[0], i[1]] = round(numpy.sqrt(1), 3)
if bond.GetBondType().name == "DOUBLE":
AdMatrix1[i[0], i[1]] = round(numpy.sqrt(2), 3)
if bond.GetBondType().name == "TRIPLE":
AdMatrix1[i[0], i[1]] = round(numpy.sqrt(3), 3)
if bond.GetBondType().name == "AROMATIC":
AdMatrix1[i[0], i[1]] = round(numpy.sqrt(1.5), 3)
# All other elements of B (corresponding non bonded
# atom pairs) are set to 0.001
bondnonindex = numpy.argwhere(AdMatrix == 0)
for i in bondnonindex:
if i[0] != i[1]:
AdMatrix1[i[0], i[1]] = 0.001
return numpy.real(numpy.linalg.eigvals(AdMatrix1))
def CalculatePolarizabilityRDF(ChargeCoordinates):
"""Calculate RDF descriptors with Polarizability schemes."""
R = GetR(n=30)
temp = []
polarizability = []
# ChargeCoordinates=_ReadCoordinates('temp.arc')
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
polarizability.append(GetRelativeAtomicProperty(i[0], 'alapha'))
DM = GetGeometricalDistanceMatrix(temp)
nAT = len(temp)
RDFresult = {}
for kkk, Ri in enumerate(R):
res = 0.0
for j in range(nAT - 1):
for k in range(j + 1, nAT):
res = res + polarizability[j] * polarizability[k] * math.exp(-_beta * math.pow(Ri - DM[j, k], 2))
RDFresult[f'RDFP{kkk + 1}'] = round(res, 3)
return RDFresult
def CalculateVDWVolumeRDF(ChargeCoordinates):
"""Calculate RDF with atomic van der Waals volume shemes."""
R = GetR(n=30)
temp = []
VDW = []
# ChargeCoordinates=_ReadCoordinates('temp.arc')
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
VDW.append(GetRelativeAtomicProperty(i[0], 'V'))
DM = GetGeometricalDistanceMatrix(temp)
nAT = len(temp)
RDFresult = {}
for kkk, Ri in enumerate(R):
res = 0.0
for j in range(nAT - 1):
for k in range(j + 1, nAT):
res = res + VDW[j] * VDW[k] * math.exp(-_beta * math.pow(Ri - DM[j, k], 2))
RDFresult[f'RDFV{kkk + 1}'] = round(res, 3)
return RDFresult
def CalculateVDWVolumeMoRSE(ChargeCoordinates: List[List[float]]) -> dict:
"""Calculate 3D MoRse descriptors from van der Waals volume.
:param ChargeCoordinates: Atomic coordinates and charges as read by chemopy.GeoOpt._ReadCoordinates
"""
R = GetR(n=30)
temp = []
VDW = []
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
VDW.append(GetRelativeAtomicProperty(i[0], 'V'))
DM = GetGeometricalDistanceMatrix(temp)
nAT = len(temp)
RDFresult = {}
for kkk, Ri in enumerate(R):
res = 0.0
for j in range(nAT - 1):
for k in range(j + 1, nAT):
res = res + VDW[j] * VDW[k] * math.sin(
Ri * DM[j, k]) / (Ri * DM[j, k])
RDFresult[f'MoRSEV{kkk + 1}'] = round(res, 3)
return RDFresult