Python Progam to read SDF (chemistry) file

Question

I want to read sdf file (containing many molecules) and return the weighted adjacency matrix of the molecule. Atoms should be treated as vertices and bond as edges. If i and j vertex are connected by single, double, or triple bond then corresponding entries in the adjacency matrix should be 1,2, and 3 respectively. I need to further obtain a distance vector for each vertex which list the number of vertices at different distance.

Are there any python package available to do this?

Google, first result seems to be exactly that! https://github.com/mbarriault/PySDF — GreenGuerilla, Feb 17 '13 at 15:19
Were you aware of this before or found now just by googling? I also searched but could not find. Thank you. — DurgaDatta, Feb 18 '13 at 04:29

score 3 · Accepted Answer · answered Nov 24 '13 at 02:57

I would recommend Pybel for reading and manipulating SDF files in Python. To get the bonding information, you will probably need to also use the more full-featured but less pythonic openbabel module, which can be used in concert with Pybel (as pybel.ob).

To start with, you would write something like this:

import pybel

for mol in pybel.readfile('sdf', 'many_molecules.sdf'):
  for atom in mol:
    coords = atom.coords
    for neighbor in pybel.ob.OBAtomAtomIter(atom.OBAtom):
      neighbor_coords = pybel.atom(neighbor).coords

score 1 · Answer 2 · answered Mar 20 '23 at 07:53

Why not use the most commonly used package rdkit to process the SDF chemical file? It is really fast and convenient.

suppl = Chem.SDMolSupplier('xxx.sdf') # name the path of the SDF file 
for mol in supply:
    print(mol.GetNumAtoms()) # give the number of atoms in each molecule
    ......                   # do whatever kind of operations you want

score 0 · Answer 3 · answered Mar 22 '13 at 20:40

0

See

http://code.google.com/p/cinfony/

However for your exact problem you will need to consult the documentation.

answered Mar 22 '13 at 20:40

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Is cinfony available for python 3.7? – BND Apr 05 '20 at 05:50

Python Progam to read SDF (chemistry) file

3 Answers3