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from rdkit import Chem
from rdkit import rdBase
from rdkit.Chem import rdMolDescriptors as rdMD
from rdkit.Chem import AllChem
from rdkit.Chem.EState import EStateIndices
from rdkit.Chem.EState import AtomTypes
import time
print rdBase.rdkitVersion
print rdBase.boostVersion
def getEState(mol):
return EStateIndices(mol)
def localopt(mol, steps = 500):
if mol.GetNumConformers() == 0:
mol=make3D(mol)
AllChem.MMFFOptimizeMolecule(mol, maxIters = steps)
return mol
def make3D(mol, steps = 50):
mol = Chem.AddHs(mol)
success = AllChem.EmbedMolecule(mol)
if success == -1: # Failed
success = AllChem.EmbedMolecule(mol, useRandomCoords = True)
if success == -1:
raise Error, "Embedding failed!"
mol = localopt(mol, steps)
return mol
def get3D(m,is3d):
if not is3d:
m = Chem.AddHs(m)
AllChem.EmbedMolecule(m)
AllChem.MMFFOptimizeMolecule(m)
r= rdMD.CalcAUTOCORR3D(m)+rdMD.CalcRDF(m)+rdMD.CalcMORSE(m)+rdMD.CalcWHIM(m)+rdMD.CalcGETAWAY(m)
return r
def generateALL():
m = Chem.MolFromSmiles('Cc1ccccc1')
thefile = open('testAC.txt', 'w')
filename="/Users/mbp/Github/rdkit_mine/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf"
suppl = Chem.SDMolSupplier(filename,removeHs=False)
mols = [x for x in suppl]
start = time.time()
for m in mols:
r= get3D(m,True)
for item in r:
thefile.write("%.3f," % item)
thefile.write("\n")
end = time.time()
print end - start
thefile = open('testSMWHIM.txt', 'w')
writer = Chem.SDWriter('3Dsmallmol.sdf')
A=['[H][H]','B','O=O','C','CC','CCC','CCCC','CCCCC','CCCCCC','CO','CCO','CCCO','CCCCO','CCCCCO','CCCCCCO','CCl','CCCl','CCCCl','CCCCCl','CCCCCCl','CCCCCCCl','CBr','CCBr','CCCBr','CCCCBr','CCCCCBr','CCCCCCBr','CI','CCI','CCCI','CCCCI','CCCCCI','CCCCCCI','CF','CCF','CCCF','CCCCF','CCCCCF','CCCCCCF','CS','CCS','CCCS','CCCCS','CCCCCS','CCCCCCS','CN','CCN','CCCN','CCCCN','CCCCCN','CCCCCCN']
for smi in A:
m = Chem.MolFromSmiles(smi)
m=localopt(m,100)
#r=get3D(m,True)
print smi
print "---------"
r=rdMD.CalcWHIM(m)
print "Ei:"+str(r[0])+ "," + str(r[1]) + "," + str(r[2])+ "\n"
print "Gi:"+str(r[5])+ "," + str(r[6]) + "," + str(r[7])+ "\n"
print "SI:"+str(rdMD.CalcSpherocityIndex(m))
print "AS:"+str(rdMD.CalcAsphericity(m))
print "EX:"+str(rdMD.CalcEccentricity(m))
for item in r:
thefile.write("%.3f," % item)
thefile.write("\n")
#m.SetProp("smi", smi)
#writer.write(m)
thefile = open('testBPA.txt', 'w')
writer = Chem.SDWriter('3DBPAmol.sdf')
B=['CN(C)CC(Br)c1ccccc1','CN(C)CC(Br)c1ccc(F)cc1','CN(C)CC(Br)c1ccc(Cl)cc1','CN(C)CC(Br)c1ccc(Cl)cc1','CN(C)CC(Br)c1ccc(I)cc1','CN(C)CC(Br)c1ccc(C)cc1','CN(C)CC(Br)c1cccc(F)c1','CN(C)CC(Br)c1cccc(Cl)c1','CN(C)CC(Br)c1cccc(Br)c1','CN(C)CC(Br)c1cccc(I)c1','CN(C)CC(Br)c1cccc(C)c1','CN(C)CC(Br)c1ccc(F)c(Cl)c1','CN(C)CC(Br)c1ccc(F)c(Br)c1','CN(C)CC(Br)c1ccc(F)c(C)c1','CN(C)CC(Br)c1ccc(Cl)c(Cl)c1','CN(C)CC(Br)c1ccc(Cl)c(Br)c1','CN(C)CC(Br)c1ccc(Cl)c(C)c1','CN(C)CC(Br)c1ccc(Br)c(Cl)c1','CN(C)CC(Br)c1ccc(Br)c(Br)c1','CN(C)CC(Br)c1ccc(Br)c(C)c1','CN(C)CC(Br)c1ccc(C)c(C)c1','CN(C)CC(Br)c1ccc(C)c(Br)c1']
for smi in B:
m = Chem.MolFromSmiles(smi)
m=localopt(m,100)
#r=get3D(m,True)
r=rdMD.CalcWHIM(m)
for item in r:
thefile.write("%.3f," % item)
thefile.write("\n")
#m.SetProp("smi", smi)
#writer.write(m)
A="G1w,G2w,G3w,Gw"
print dir(rdMD)
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