def _CalculateGearyAutocorrelation(mol, lag=1, propertylabel="m"):
"""
#################################################################
**Internal used only**
Calculation of Geary autocorrelation descriptors based on
different property weights.
Usage:
res=_CalculateGearyAutocorrelation(mol,lag=1,propertylabel='m')
Input: mol is a molecule object.
lag is the topological distance between atom i and atom j.
propertylabel is the weighted property.
Output: res is a numeric value.
#################################################################
"""
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 + numpy.square(temp1 - temp2)
index = index + 1
else:
res = res + 0.0
if sum(tempp) == 0 or index == 0:
result = 0
else:
result = (res / index / 2) / (sum(tempp) / (Natom - 1))
return round(result, 3)
def _CalculateMoreauBrotoAutocorrelation(mol, lag=1, propertylabel="m"):
"""
#################################################################
**Internal used only**
Calculation of Moreau-Broto autocorrelation descriptors based on
different property weights.
Usage:
res=_CalculateMoreauBrotoAutocorrelation(mol, lag=1,propertylabel='m')
Input: mol is a molecule object.
lag is the topological distance between atom i and atom j.
propertylabel is the weighted property.
Output: res is a numeric value.
#################################################################
"""
Natom = mol.GetNumAtoms()
GetDistanceMatrix = Chem.GetDistanceMatrix(mol)
res = 0.0
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 * temp2
else:
res = res + 0.0
return round(numpy.log(res / 2 + 1), 3)
def _GetBurdenMatrix(mol, propertylabel="m"):
"""
#################################################################
*Internal used only**
Calculate Burden matrix and their 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 test_pymolecule():
from rdkit import Chem
from openbabel import pybel
from PyBioMed.PyMolecule.AtomProperty import (
AtomProperty,
GetAbsoluteAtomicProperty,
GetRelativeAtomicProperty,
)
from PyBioMed.PyMolecule.estate import GetEstate
from PyBioMed.PyMolecule.constitution import GetConstitutional
from PyBioMed.PyMolecule.fingerprint import CalculateECFP4Fingerprint
from PyBioMed.PyMolecule.connectivity import GetConnectivity
from PyBioMed.PyMolecule.charge import GetCharge
from PyBioMed.PyMolecule.bcut import GetBurden
from PyBioMed.PyMolecule.basak import Getbasak
from PyBioMed.PyMolecule.geary import GetGearyAuto
from PyBioMed.PyMolecule.kappa import GetKappa
from PyBioMed.PyMolecule.moe import GetMOE
from PyBioMed.PyMolecule.molproperty import GetMolecularProperty
from PyBioMed.PyMolecule.moran import GetMoranAuto
from PyBioMed.PyMolecule.moreaubroto import GetMoreauBrotoAuto
from PyBioMed.PyMolecule.topology import GetTopology
from PyBioMed.PyMolecule.ghosecrippen import GhoseCrippenFingerprint
from PyBioMed.PyMolecule.cats2d import CATS2D
print("...............................................................")
print("testing the AtomProperty module")
for i, j in AtomProperty.items():
print(j)
print(GetAbsoluteAtomicProperty(element="S", propertyname="En"))
print(GetRelativeAtomicProperty(element="S", propertyname="En"))
# ==============================================================================
# Getbasak
# ==============================================================================
print("...............................................................")
print("testing the Getbasak module")
smi5 = [
"CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"
]
for index, smi in enumerate(smi5):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", Getbasak(m))
print(len(Getbasak(m)))
# ==============================================================================
# GetBurden, bcut model
# ==============================================================================
print("...............................................................")
print("testing the bcut module")
smi5 = [
"CCOCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N",
"C"
]
for index, smi in enumerate(smi5):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi, "\n")
print(GetBurden(m))
print(len(GetBurden(m)))
# ==============================================================================
# GetCharge
# ==============================================================================
print("...............................................................")
print("testing the GetCharge module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
smi5 = [
"CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"
]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetCharge(m))
print(len(GetCharge(m)))
# ==============================================================================
# GetConnectivity
# ==============================================================================
print("...............................................................")
print("testing the GetConnectivity module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
smi5 = [
"CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"
]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetConnectivity(m))
print("\t", len(GetConnectivity(m)))
# ==============================================================================
# GetConstitutional
# ==============================================================================
print("...............................................................")
print("testing the GetConstitutional module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
smi5 = [
"CCCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCCCCN", "c1ccccc1N"
]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetConstitutional(m))
print(len(GetConstitutional(m)))
# ==============================================================================
# GetEstate
# ==============================================================================
print("...............................................................")
print("testing the GetEstate module")
smi5 = [
"COCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCOCCN", "c1ccccc1N"
]
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
# print '\t',CalculateEstateFingerprint(m)
# print '\t',CalculateEstateValue(m)
# print '\t',CalculateMaxAtomTypeEState(m)
# print '\t', CalculateMinAtomTypeEState(m)
print(GetEstate(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("fingerprint......")
ms = [
Chem.MolFromSmiles("CCOC=N"),
Chem.MolFromSmiles("NC1=NC(=CC=N1)N1C=CC2=C1C=C(O)C=C2"),
]
m2 = [pybel.readstring("smi", "CCOC=N"), pybel.readstring("smi", "CCO")]
res1 = CalculateECFP4Fingerprint(ms[0])
print(res1)
res2 = CalculateECFP4Fingerprint(ms[1])
print(res2)
# print CalculateSimilarityRdkit(res1[2],res2[2])
# print CalculateSimilarityPybel(res1,res2)
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetGearyAuto module")
smi5 = [
"COCCCC", "CCC(C)CC", "CC(C)CCC", "CC(C)C(C)C", "CCOCCN", "c1ccccc1N"
]
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
## print '\t',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print(GetGearyAuto(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetKappa module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetKappa(m))
print("\t", len(GetKappa(m)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMOE module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetMOE(m))
print("\t", len(GetMOE(m)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMolecularProperty module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetMolecularProperty(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMoranAuto module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
## print '\t',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print(GetMoranAuto(m))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetMoreauBrotoAuto module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
## print '\t',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print(len(GetMoreauBrotoAuto(m)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the GetTopology module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-]"]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print(index + 1)
print(smi)
print("\t", GetTopology(m))
print("\t", len(GetTopology(m)))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the CATS2D module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-]"]
for i in smis:
mol = Chem.MolFromSmiles(i)
cats = CATS2D(mol, PathLength=10, scale=3)
print("\t", cats)
print("\t", len(cats))
# ==============================================================================
#
# ==============================================================================
print("...............................................................")
print("testing the ghoseFP module")
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-]"]
for i in smis:
mol = Chem.MolFromSmiles(i)
ghoseFP = GhoseCrippenFingerprint(mol)
print("\t", ghoseFP)
print("\t", len(ghoseFP))
print("testing the ghose_count module")
for i in smis:
mol = Chem.MolFromSmiles(i)
ghose_count = GhoseCrippenFingerprint(mol, count=True)
print("\t", ghose_count)
print("\t", len(ghose_count))
def test_pymolecule():
from rdkit import Chem
import pybel
from PyBioMed.PyMolecule.AtomProperty import AtomProperty, GetAbsoluteAtomicProperty, GetRelativeAtomicProperty
from PyBioMed.PyMolecule.estate import GetEstate
from PyBioMed.PyMolecule.constitution import GetConstitutional
from PyBioMed.PyMolecule.fingerprint import CalculateECFP4Fingerprint
from PyBioMed.PyMolecule.connectivity import GetConnectivity
from PyBioMed.PyMolecule.charge import GetCharge
from PyBioMed.PyMolecule.bcut import GetBurden
from PyBioMed.PyMolecule.basak import Getbasak
from PyBioMed.PyMolecule.geary import GetGearyAuto
from PyBioMed.PyMolecule.kappa import GetKappa
from PyBioMed.PyMolecule.moe import GetMOE
from PyBioMed.PyMolecule.molproperty import GetMolecularProperty
from PyBioMed.PyMolecule.moran import GetMoranAuto
from PyBioMed.PyMolecule.moreaubroto import GetMoreauBrotoAuto
from PyBioMed.PyMolecule.topology import GetTopology
from PyBioMed.PyMolecule.ghosecrippen import GhoseCrippenFingerprint
from PyBioMed.PyMolecule.cats2d import CATS2D
print '...............................................................'
print 'testing the AtomProperty module'
for i, j in AtomProperty.items():
print j
print GetAbsoluteAtomicProperty(element='S', propertyname='En')
print GetRelativeAtomicProperty(element='S', propertyname='En')
#==============================================================================
# Getbasak
#==============================================================================
print '...............................................................'
print 'testing the Getbasak module'
smi5 = [
'CCCCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCCCCN', 'c1ccccc1N'
]
for index, smi in enumerate(smi5):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', Getbasak(m)
print len(Getbasak(m))
#==============================================================================
# GetBurden, bcut model
#==============================================================================
print '...............................................................'
print 'testing the bcut module'
smi5 = [
'CCOCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCCCCN', 'c1ccccc1N',
'C'
]
for index, smi in enumerate(smi5):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi, '\n'
print GetBurden(m)
print len(GetBurden(m))
#==============================================================================
# GetCharge
#==============================================================================
print '...............................................................'
print 'testing the GetCharge module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
smi5 = [
'CCCCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCCCCN', 'c1ccccc1N'
]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetCharge(m)
print len(GetCharge(m))
#==============================================================================
# GetConnectivity
#==============================================================================
print '...............................................................'
print 'testing the GetConnectivity module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
smi5 = [
'CCCCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCCCCN', 'c1ccccc1N'
]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetConnectivity(m)
print '\t', len(GetConnectivity(m))
#==============================================================================
# GetConstitutional
#==============================================================================
print '...............................................................'
print 'testing the GetConstitutional module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
smi5 = [
'CCCCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCCCCN', 'c1ccccc1N'
]
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetConstitutional(m)
print len(GetConstitutional(m))
#==============================================================================
# GetEstate
#==============================================================================
print '...............................................................'
print 'testing the GetEstate module'
smi5 = [
'COCCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCOCCN', 'c1ccccc1N'
]
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
# print '\t',CalculateEstateFingerprint(m)
# print '\t',CalculateEstateValue(m)
# print '\t',CalculateMaxAtomTypeEState(m)
# print '\t', CalculateMinAtomTypeEState(m)
print GetEstate(m)
#==============================================================================
#
#==============================================================================
print '...............................................................'
print "fingerprint......"
ms = [
Chem.MolFromSmiles('CCOC=N'),
Chem.MolFromSmiles('NC1=NC(=CC=N1)N1C=CC2=C1C=C(O)C=C2')
]
m2 = [pybel.readstring("smi", 'CCOC=N'), pybel.readstring("smi", 'CCO')]
res1 = CalculateECFP4Fingerprint(ms[0])
print res1
res2 = CalculateECFP4Fingerprint(ms[1])
print res2
# print CalculateSimilarityRdkit(res1[2],res2[2])
# print CalculateSimilarityPybel(res1,res2)
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetGearyAuto module'
smi5 = [
'COCCCC', 'CCC(C)CC', 'CC(C)CCC', 'CC(C)C(C)C', 'CCOCCN', 'c1ccccc1N'
]
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
## print '\t',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print GetGearyAuto(m)
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetKappa module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetKappa(m)
print '\t', len(GetKappa(m))
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetMOE module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetMOE(m)
print '\t', len(GetMOE(m))
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetMolecularProperty module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetMolecularProperty(m)
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetMoranAuto module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
## print '\t',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print GetMoranAuto(m)
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetMoreauBrotoAuto module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
## print '\t',CalculateEstateFingerprint(m)
## print '\t',CalculateEstateValue(m)
## print '\t',CalculateMaxAtomTypeEState(m)
## print '\t', CalculateMinAtomTypeEState(m)
print len(GetMoreauBrotoAuto(m))
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the GetTopology module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-]']
for index, smi in enumerate(smis):
m = Chem.MolFromSmiles(smi)
print index + 1
print smi
print '\t', GetTopology(m)
print '\t', len(GetTopology(m))
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the CATS2D module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-]']
for i in smis:
mol = Chem.MolFromSmiles(i)
cats = CATS2D(mol, PathLength=10, scale=3)
print '\t', cats
print '\t', len(cats)
#==============================================================================
#
#==============================================================================
print '...............................................................'
print 'testing the ghoseFP module'
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-]']
for i in smis:
mol = Chem.MolFromSmiles(i)
ghoseFP = GhoseCrippenFingerprint(mol)
print '\t', ghoseFP
print '\t', len(ghoseFP)
print 'testing the ghose_count module'
for i in smis:
mol = Chem.MolFromSmiles(i)
ghose_count = GhoseCrippenFingerprint(mol, count=True)
print '\t', ghose_count
print '\t', len(ghose_count)