def smi2cm(m):
m1 = Chem.MolFromSmiles(m)
m = Chem.AddHs(m1)
AllChem.EmbedMolecule(m,AllChem.ETKDG())
n_atoms = m.GetNumAtoms()
m1=Chem.MolToMolBlock(m)
m1=m1.split()
axis=[]
atom_list=[]
for i in range(0,n_atoms):
axis.append([float(m1[13+16*i]),float(m1[14+i*16]),float(m1[15+16*i])])
atom_list.append(m1[16+16*i])
feat=CoulombMatrix()
mole=(atom_list,axis)
feat.fit([mole])
t=feat.transform([mole])[0]
CM=t.reshape((n_atoms,n_atoms)).tolist()
return CM
name='mol'+ str(mol_no)
xyz_dict[name]=a
index=index+atom_nums+2
mol_no=mol_no-1
atom_list=[]
axis=[]
for j in range(0,len(a)):
atom=a[j].split()
atom_list.append(atom[0])
axis.append([float(atom[1]),float(atom[2]),float(atom[3])])
feat=CoulombMatrix()
mole=(atom_list,axis)
feat.fit([mole])
CM=feat.transform([mole])[0]
t=CM.reshape((atom_nums,atom_nums)).tolist()
CM_dict.append(t)
fd.close()
sio.savemat('CM.mat',{'CM':CM_dict})
else:
#smi to coordination and coulomb matrix
filepath=input("what's sdf filename?")
#get CM
def smi2cm(m):
m1 = Chem.MolFromSmiles(m)
m = Chem.AddHs(m1)
AllChem.EmbedMolecule(m,AllChem.ETKDG())
n_atoms = m.GetNumAtoms()
m1=Chem.MolToMolBlock(m)
m1=m1.split()
]
HCN_CONNS = {
0: {1: '1'},
1: {0: '1', 2: '3'},
2: {1: '3'},
}
if __name__ == "__main__":
# Example of generating the Coulomb matrix with just elements and coords
# for a single example molecule.
feat = CoulombMatrix()
H2 = (H2_ELES, H2_COORDS)
feat.fit([H2])
print("Transformed H2")
print(feat.transform([H2]))
print()
# Example of generating the Coulomb matrix with just elements and coords
# for multiple molecules.
feat = CoulombMatrix()
HCN = (HCN_ELES, HCN_COORDS)
feat.fit([H2, HCN])
print("Transformed H2")
print(feat.transform([H2]))
print("H2 and HCN transformed")
print(feat.transform([H2, HCN]))
print()
# Example of generating the Coulomb matrix with elements, coords, and
# connections.