Hi
What are the standalone tools available for conversion of 2D molecules to 3D molecules for the large number of 2D molecules?
Thank you.
Pipeline pilot by Accelrys (Currently BIOVIA) can do that. But it is not open source.
You can also use MarvinSpace from ChemAxon, which is also free. I've used it to convert 2D SDF libraries to 3D.
I would recommend rdkit to this task, it also has implementations of UFF and MMFF94 for geometry optimization.
You can use de Open Babel with this command: babel -isdf molecule.sdf -opdb molecule.pdb --gen3D
I'm assuming that you have a SDF file with a 2D molecule (if this molecule is in another format, you can change the code)
When you use --gen3D the Open Babel calculate the 3D coordinates.
Using RDKit, this code can help you:
import os, sys, glob
import os.path
import shutil
from rdkit import *
from rdkit import Chem
from rdkit.Chem import AllChem
from shutil import copyfile
for filename in glob.glob(os.path.join("", "*.sdf")):
try:
f = open(filename, 'r')
print(filename)
m = Chem.ForwardSDMolSupplier(f)
for mol in m:
mol2=Chem.AddHs(mol)
AllChem.EmbedMolecule(mol2)
x = AllChem.EmbedMolecule(mol2)
if(x
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