def GetGeometric(mol):
"""
#################################################################
Wrapper for Geometrical descriptors
#################################################################
"""
filename='temp'
ChargeCoordinates=_ReadCoordinates(filename)
res={}
res['W3DH']=Calculate3DWienerWithH(ChargeCoordinates)
res['W3D']=Calculate3DWienerWithoutH(ChargeCoordinates)
res['Petitj3D']=CalculatePetitjean3DIndex(ChargeCoordinates)
res['GeDi']=CalculateGemetricalDiameter(ChargeCoordinates)
res['grav']=CalculateGravitational3D1(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 GetMoRSEUnweighted(mol):
"""
#################################################################
Obtain all unweighted 3D-Morse descriptors .
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateUnweightMoRSE(ChargeCoordinates)
return result
def GetMoRSESandersonElectronegativity(mol):
"""
#################################################################
Obtain all 3D-Morse descriptors baed on Sanderson Electronegativity schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateSandersonElectronegativityMoRSE(ChargeCoordinates)
return result
def GetMoRSEVDWVolume(mol):
"""
#################################################################
Obtain all 3D-Morse descriptors baed on VDW Volume schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateVDWVolumeMoRSE(ChargeCoordinates)
return result
def GetMoRSEPolarizability(mol):
"""
#################################################################
Obtain all 3D-Morse descriptors baed on polarizability schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculatePolarizabilityMoRSE(ChargeCoordinates)
return result
def GetMoRSEAtomicNumber(mol):
"""
#################################################################
Obtain all 3D-Morse descriptors baed on atomic number schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateAtomicNumberMoRSE(mol, ChargeCoordinates)
return result
def GetMoRSEMass(mol):
"""
#################################################################
Obtain all 3D-Morse descriptors baed on mass schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateMassMoRSE(mol, ChargeCoordinates)
return result
def GetRDFUnweighed(mol):
"""
#################################################################
Obtain all Unweighed radial distribution function descriptors.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateUnweightRDF(ChargeCoordinates)
return result
def GetRDFSandersonElectronegativity(mol):
"""
#################################################################
Obtain all radial distribution function descriptors based
onSanderson Electronegativity schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateSandersonElectronegativityRDF(ChargeCoordinates)
return result
def GetRDFPolarizability(mol):
"""
#################################################################
Obtain all radial distribution function descriptors based
on Polarizability schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculatePolarizabilityRDF(ChargeCoordinates)
return result
def GetRDFMass(mol):
"""
#################################################################
Obtain all radial distribution function descriptors based
on Mass schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateMassRDF(mol, ChargeCoordinates)
return result
def GetRDFVDWVolume(mol):
"""
#################################################################
Obtain all radial distribution function descriptors based
on VDW Volume schems.
#################################################################
"""
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
result = CalculateVDWVolumeRDF(ChargeCoordinates)
return result
def GetMoRSE(mol):
"""
#################################################################
Obtain all 3D-Morse descriptors baed on different weighted schems.
#################################################################
"""
result = {}
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
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 GetAtomCoordinateMatrix():
"""
#################################################################
Get the atom coordinate matrix
#################################################################
"""
ChargeCoordinates = _ReadCoordinates(_filename)
nAtom = len(ChargeCoordinates)
CoordinateMatrix = scipy.zeros([nAtom, 3])
AtomLabel = []
for i, j in enumerate(ChargeCoordinates):
CoordinateMatrix[i, :] = [j[1], j[2], j[3]]
AtomLabel.append(j[0])
return scipy.matrix(CoordinateMatrix), AtomLabel
def GetRDF(mol):
"""
#################################################################
Obtain all radial distribution function descriptors based
on different weighted schems.
#################################################################
"""
result = {}
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
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(RadiusProbe=1.5, n_sphere_point=960):
"""
#################################################################
Get the list form for all atoms in a molecule.
It includes the atom symbol, charge and partial solvent-accessible
surface areas.
Note that this is list form whose element is still list form of each atom.
#################################################################
"""
ChargeCoordinates = _ReadCoordinates(filename)
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
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 _GetHTMLDoc():
"""
#################################################################
Write HTML documentation for this module.
#################################################################
"""
import pydoc
pydoc.writedoc('morse')
############################################################################
if __name__ == "__main__":
from GeoOpt import GetARCFile
mol = 'C1C=CCCS1'
inputmol = pybel.readstring('smi', mol)
GetARCFile(inputmol)
#filename='temp'
ChargeCoordinates = _ReadCoordinates()
print CalculateVDWVolumeMoRSE(ChargeCoordinates)
print len(GetMoRSE(inputmol))
result.update(CalculatePolarizabilityRDF(ChargeCoordinates))
result.update(CalculateSandersonElectronegativityRDF(ChargeCoordinates))
result.update(CalculateVDWVolumeRDF(ChargeCoordinates))
return result
def _GetHTMLDoc():
"""
#################################################################
Write HTML documentation for this module.
#################################################################
"""
import pydoc
pydoc.writedoc('rdf')
############################################################################
if __name__ == "__main__":
import pybel
from GeoOpt import GetARCFile
mol = 'C1C=CCCS1'
inputmol = pybel.readstring('smi', mol)
GetARCFile(inputmol)
filename = 'temp'
ChargeCoordinates = _ReadCoordinates(filename)
res = CalculateVDWVolumeRDF(ChargeCoordinates)
print res
print len(GetRDF(inputmol))
