def CalculateUnweightRDF(ChargeCoordinates):
"""Calculate unweighted RDF descriptors."""
R = GetR(n=30)
temp = []
# ChargeCoordinates=_ReadCoordinates('temp.arc')
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
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 + math.exp(-_beta * math.pow(Ri - DM[j, k], 2))
RDFresult[f'RDFU{kkk + 1}'] = round(res, 3)
return RDFresult
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 CalculateMassRDF(mol, ChargeCoordinates):
"""Calculate RDF descriptors with Mass schemes."""
mol.addh()
mass = [i.atomicmass for i in mol.atoms]
R = GetR(n=30)
temp = []
# ChargeCoordinates=_ReadCoordinates('temp.arc')
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
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 + mass[j] * mass[k] * math.exp(-_beta * math.pow(Ri - DM[j, k], 2))
RDFresult[f'RDFM{kkk + 1}'] = round(res / 144, 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 CalculateUnweightMoRSE(ChargeCoordinates: List[List[float]]) -> dict:
"""Calculate unweighted 3D MoRse descriptors.
:param ChargeCoordinates: Atomic coordinates and charges as read by chemopy.GeoOpt._ReadCoordinates
"""
R = GetR(n=30)
temp = []
# ChargeCoordinates=_ReadCoordinates('temp.arc')
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
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 + math.sin(Ri * DM[j, k]) / (Ri * DM[j, k])
RDFresult[f'MoRSEU{kkk + 1}'] = round(res, 3)
return RDFresult
def CalculateAtomicNumberMoRSE(mol: Chem.Mol,
ChargeCoordinates: List[List[float]]) -> dict:
"""Calculate 3D MoRse descriptors from atomic number.
:param ChargeCoordinates: Atomic coordinates and charges as read by chemopy.GeoOpt._ReadCoordinates
"""
R = GetR(n=30)
temp = []
mass = [i.atomicnum for i in mol.atoms]
for i in ChargeCoordinates:
# if i[0]!='H':
temp.append([float(i[1]), float(i[2]), float(i[3])])
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 + mass[j] * mass[k] * math.sin(
Ri * DM[j, k]) / (Ri * DM[j, k])
RDFresult[f'MoRSEN{kkk + 1}'] = round(res / 144, 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