def CalculateSPANR(ChargeCoordinates):
"""
#################################################################
The span R (SPAN) is a size descriptor defined as
the radius of the smallest sphere, centred on the centre
of mass, completely enclosing all atoms of a molecule
[G.A. Arteca, Molecular Shape Descriptors in Reviews in
Computational Chemistry - Vol. 9, K.B. Lipkowitz, D. Boyd (Eds.),
VCH Publishers, New York (NY), pp. 191-253, 1991]
--->SPAN
#################################################################
"""
temp = []
for coords in ChargeCoordinates:
temp.append([
descriptors3D.get_atomicMass(coords[3]),
[coords[0], coords[1], coords[2]]
])
masscenter = _GetMassCenter(temp)
res = []
for i in temp:
res.append(GetAtomDistance(i[1], masscenter))
return round(float(max(res)), 3)
def CalculateRadiusofGyration(ChargeCoordinates):
"""
#################################################################
Calculation of Radius of gyration.
--->rygr
#################################################################
"""
temp = []
for coords in ChargeCoordinates:
temp.append([
descriptors3D.get_atomicMass(coords[3]),
[coords[0], coords[1], coords[2]]
])
nAT = len(temp)
masscenter = _GetMassCenter(temp)
result = 0.0
for i in range(nAT):
dis = GetAtomDistance(temp[i][1], masscenter)
result = result + temp[i][0] * scipy.power(dis, p=2)
return round(
scipy.sqrt(float(result / descriptors3D.get_MW(ChargeCoordinates))), 3)
def CalculateAtomicNumberMoRSE(lcoordinates):
"""
#################################################################
The calculation of 3-D MoRse descriptors
based on atomic number.
#################################################################
"""
R=_GetR(n=30)
temp=[]
mass = [descriptors3D.get_atomicMass(coords[3]) for coords in lcoordinates]
for i in lcoordinates:
#if i[0]!='H':
temp.append([float(i[0]),float(i[1]),float(i[2])])
DM=_GetGementricalDistanceMatrix(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['MoRSE'+'N'+str(kkk+1)]=round(res/144,3)
return RDFresult
def CalculateMassRDF(lcoordinates):
"""
The calculation of radial distribution function (RDF)
descriptors based on atomic mass.
"""
mass = [descriptors3D.get_atomicMass(coords[3]) for coords in lcoordinates]
R = _GetR(n=30)
temp = []
for i in lcoordinates:
#if i[0]!='H':
temp.append([float(i[0]), float(i[1]), float(i[2])])
DM = GetGementricalDistanceMatrix(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['RDF' + 'M' + str(kkk + 1)] = round(res / 144, 3)
return RDFresult
def GetInertiaMatrix(ChargeCoordinates):
"""
#################################################################
Get Inertia matrix based on atomic mass and optimized coordinates.
#################################################################
"""
temp = []
for coords in ChargeCoordinates:
temp.append([
descriptors3D.get_atomicMass(coords[3]),
[coords[0], coords[1], coords[2]]
])
#
# masscenter=_GetMassCenter(temp)
#
# for i,j in enumerate(temp):
# temp[i][1]=[d-masscenter[k] for k,d in enumerate(j[1])]
nAT = len(temp)
InertiaMatrix = scipy.zeros((3, 3))
res11 = 0.0
res22 = 0.0
res33 = 0.0
res12 = 0.0
res23 = 0.0
res13 = 0.0
for i in range(nAT):
res11 = res11 + temp[i][0] * (math.pow(temp[i][1][1], 2) +
math.pow(temp[i][1][2], 2))
res22 = res22 + temp[i][0] * (math.pow(temp[i][1][0], 2) +
math.pow(temp[i][1][2], 2))
res33 = res33 + temp[i][0] * (math.pow(temp[i][1][0], 2) +
math.pow(temp[i][1][1], 2))
res12 = res12 + temp[i][0] * (temp[i][1][0] * temp[i][1][1])
res13 = res13 + temp[i][0] * (temp[i][1][0] * temp[i][1][2])
res23 = res23 + temp[i][0] * (temp[i][1][1] * temp[i][1][2])
InertiaMatrix[0, 0] = res11
InertiaMatrix[1, 1] = res22
InertiaMatrix[2, 2] = res33
InertiaMatrix[0, 1] = res12
InertiaMatrix[0, 2] = res13
InertiaMatrix[1, 2] = res23
InertiaMatrix[1, 0] = res12
InertiaMatrix[2, 0] = res13
InertiaMatrix[2, 1] = res23
return InertiaMatrix
def CalculateAverageSPANR(ChargeCoordinates):
"""
#################################################################
The average span R (SPAM) is the root square of
the ratio of SPAN over the number of atoms.
--->ASPAN
#################################################################
"""
temp = []
for coords in ChargeCoordinates:
temp.append([
descriptors3D.get_atomicMass(coords[3]),
[coords[0], coords[1], coords[2]]
])
nAT = len(temp)
masscenter = _GetMassCenter(temp)
res = []
for i in temp:
res.append(GetAtomDistance(i[1], masscenter))
return round(math.pow(float(max(res)) / nAT, 0.5), 3)
def CalculateGravitational3D1(ChargeCoordinates):
"""
#################################################################
Calculation of Gravitational 3D index.
--->grav1
#################################################################
"""
temp = []
for coords in ChargeCoordinates:
temp.append([
descriptors3D.get_atomicMass(coords[3]),
[coords[0], coords[1], coords[2]]
])
nAT = len(temp)
result = 0.0
for i in range(nAT - 1):
for j in range(i + 1, nAT):
dis = GetAtomDistance(temp[i][1], temp[j][1])
result = result + temp[i][0] * temp[j][0] / scipy.power(dis, p=2)
return round(float(result) / 100, 3)