Open Babel...

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.

Thank you all for your answers

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

hello everyone how can i convert my 3D sdf file into 2sdf file?

You can try Schrodinger, Biovia Discovery Studio, BioSolveit.