def GetGeometric(mol: pybel.Molecule, arc_file: str) -> dict:
"""Get all (20) geometrical descriptors.
:param mol: the molecule
:param arc_file: Path to MOPAC .arc file
"""
res = {}
ChargeCoordinates = _ReadCoordinates(arc_file)
res['W3DH'] = Calculate3DWienerWithH(ChargeCoordinates)
res['W3D'] = Calculate3DWienerWithoutH(ChargeCoordinates)
res['Petitj3D'] = CalculatePetitjean3DIndex(ChargeCoordinates)
res['GeDi'] = CalculateGeometricalDiameter(ChargeCoordinates)
res['TE'] = CalculateTopoElectronic(ChargeCoordinates)
res['grav1'] = CalculateGravitational3D1(mol, ChargeCoordinates)
# res['grav2'] = CalculateGravitational3D2(mol, ChargeCoordinates)
res['rygr'] = CalculateRadiusofGyration(mol, ChargeCoordinates)
res['Harary3D'] = CalculateHarary3D(ChargeCoordinates)
res['AGDD'] = CalculateAverageGeometricalDistanceDegree(ChargeCoordinates)
res['SEig'] = CalculateAbsEigenvalueSumOnGeometricMatrix(ChargeCoordinates)
res['SPAN'] = CalculateSPANR(mol, ChargeCoordinates)
res['ASPAN'] = CalculateAverageSPANR(mol, ChargeCoordinates)
res['MEcc'] = CalculateMolecularEccentricity(mol, ChargeCoordinates)
res.update(CalculatePrincipalMomentofInertia(mol, ChargeCoordinates))
res.update(CalculateRatioPMI(mol, ChargeCoordinates))
return res
def GetMoRSEVDWVolume(arc_file: str) -> dict:
"""Get all 3D-Morse descriptors from VDW Volume schemes.
:param arc_file: Path to MOPAC .arc file
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateVDWVolumeMoRSE(ChargeCoordinates)
return result
def GetMoRSESandersonElectronegativity(arc_file: str) -> dict:
"""Get all 3D-Morse descriptors from Sanderson Electronegativity schemes.
:param arc_file: Path to MOPAC .arc file
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateSandersonElectronegativityMoRSE(ChargeCoordinates)
return result
def GetMoRSEPolarizability(arc_file: str) -> dict:
"""Get all 3D-Morse descriptors from polarizability schemes.
:param arc_file: Path to MOPAC .arc file
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculatePolarizabilityMoRSE(ChargeCoordinates)
return result
def GetMoRSEAtomicNumber(mol: Chem.Mol, arc_file: str) -> dict:
"""Get all 3D-Morse descriptors from atomic number schemes.
:param arc_file: Path to MOPAC .arc file
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateAtomicNumberMoRSE(mol, ChargeCoordinates)
return result
def GetMoRSEMass(mol: Chem.Mol, arc_file: str) -> dict:
"""Get all 3D-Morse descriptors from on mass schemes.
:param arc_file: Path to MOPAC .arc file
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateMassMoRSE(mol, ChargeCoordinates)
return result
def GetMoRSEUnweighted(arc_file: str) -> dict:
"""Get all unweighted 3D-Morse descriptors.
:param arc_file: Path to MOPAC .arc file
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateUnweightMoRSE(ChargeCoordinates)
return result
def GetRDF(mol, arc_file):
"""Obtain all (180) RDF descriptors with different (un)weighted schemes."""
result = {}
ChargeCoordinates = _ReadCoordinates(arc_file)
result.update(CalculateUnweightRDF(ChargeCoordinates))
result.update(CalculateChargeRDF(ChargeCoordinates))
result.update(CalculateMassRDF(mol, ChargeCoordinates))
result.update(CalculatePolarizabilityRDF(ChargeCoordinates))
result.update(CalculateSandersonElectronegativityRDF(ChargeCoordinates))
result.update(CalculateVDWVolumeRDF(ChargeCoordinates))
return result
def GetChargeSA(arc_file, RadiusProbe=1.5, n_sphere_point=960):
"""Get atom symbol, charge and partial solvent-accessible surface areas for all atoms.
:param arc_file: Path to MOPAC .arc file
:param RadiusProbe: radius of the probe used to calculate SASA
:param n_sphere_point: number of points per atom to calculate SASA
"""
ChargeCoordinates = _ReadCoordinates(arc_file)
atoms = GetAtomClassList(ChargeCoordinates)
FASA = asa.calculate_asa(atoms, RadiusProbe, n_sphere_point)
res = []
for i in range(len(FASA)):
res.append([ChargeCoordinates[i][0], ChargeCoordinates[i][4], FASA[i]])
return res
def GetMoRSE(mol: Chem.Mol, arc_file: str) -> dict:
"""Get all (210) 3D-Morse descriptors with different (un)weighted schemes.
:param arc_file: Path to MOPAC .arc file
"""
result = {}
ChargeCoordinates = _ReadCoordinates(arc_file)
result.update(CalculateUnweightMoRSE(ChargeCoordinates))
result.update(CalculateChargeMoRSE(ChargeCoordinates))
result.update(CalculateMassMoRSE(mol, ChargeCoordinates))
result.update(CalculateAtomicNumberMoRSE(mol, ChargeCoordinates))
result.update(CalculatePolarizabilityMoRSE(ChargeCoordinates))
result.update(CalculateSandersonElectronegativityMoRSE(ChargeCoordinates))
result.update(CalculateVDWVolumeMoRSE(ChargeCoordinates))
return result
def GetRDFVDWVolume(mol, arc_file):
"""Obtain all RDF descriptors with VDW Volume schemes."""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateVDWVolumeRDF(ChargeCoordinates)
return result
def GetRDFSandersonElectronegativity(mol, arc_file):
"""Obtain all RDF descriptors with Sanderson Electronegativity schemes."""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateSandersonElectronegativityRDF(ChargeCoordinates)
return result
def GetRDFPolarizability(mol, arc_file):
"""Obtain all RDF descriptors with Polarizability schemes."""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculatePolarizabilityRDF(ChargeCoordinates)
return result
def GetRDFMass(mol, arc_file):
"""Obtain all RDF descriptors with Mass schemes."""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateMassRDF(mol, ChargeCoordinates)
return result
def GetRDFUnweighed(mol, arc_file):
"""Obtain all Unweighed RDF descriptors."""
ChargeCoordinates = _ReadCoordinates(arc_file)
result = CalculateUnweightRDF(ChargeCoordinates)
return result
