It has an additional function to read a molecule written in a HIN format.
It is coded in a similar way as Chem.rdmolfiles.MolFromPDBFile to read PDB file.
import rdkit
print(rdkit.version)
from rdkit import Chem
from rdkit.Chem import Descriptors
mol=Chem.rdmolfiles.MolFromHINFile("Ethane.hin")
mass=Descriptors.MolWt(mol)
print(mass)
print(mol.GetNumAtoms())
for conf in mol.GetConformers():
print(conf.GetPositions())
distMat = Chem.Get3DDistanceMatrix(supplHIN)
print(distMat[0,2])
for atom in mol.GetAtoms():
atom_charge = atom.GetFormalCharge()
print("Atom (symbol, atomic numer, valence(imp), valence(exp), charge:",atom.GetSymbol(),atom.GetAtomicNum(),atom.GetImplicitValence(),atom.GetExplicitValence(),atom_charge)
print("Neighbors:",[x.GetAtomicNum() for x in atom.GetNeighbors()])
print("Number of bonds:",mol.GetNumBonds())
for bond in mol.GetBonds():
aid1=bond.GetBeginAtomIdx()
aid2=bond.GetEndAtomIdx()
atom=mol.GetAtomWithIdx(aid1)
aid1_symbol=atom.GetSymbol()
atom=mol.GetAtomWithIdx(aid2)
aid2_symbol=atom.GetSymbol()