text: user9040: I am currently working on identifying effective antiviral compounds against the corona virus. I have downloaded the Covid-19 AntiViral Candidate Compounds Dataset from the www.cas.org webpage, the link to which I have provided below. Me and a few other doctors are using Docking software to predict the docking capacity of these anti-viral compounds. Docking software requires the anti-viral compounds to be in the .pdb file format only then is it recognized by Automated docking software. Is there any way I can convert the .sdf file containing the anti-viral compounds to .pdb file or is there a way of obtaining the .pdb files for list of anti-viral compounds.
  Thank you for your time and patience,
  Anas Hussain. 
  Anti-Viral Candidate Compounds Dataset
  https://www.cas.org/covid-19-antiviral-compounds-dataset
  
  user4622: Use OpenBabel.
  Something like babel -isdf file_in.sdf -opdb file_out.pdb.
  
  user6322: 
  Bizarrely, Obabel seems to have written a PDB that was incorrectly spaced for the OP as seen in Error pasing the following line in pdb
  
  If you can use python, rdkit is a great package for cheminformatics —best installed via conda though.
  It allows you do all sorts of things, such as match substructures, embed conformers, edit compounds, compute advanced parameters and many forms of shape & colour finger-/foot-printings.
  Given a multi-compound sdf you can read each individual molecule and write them out as PDBs.
  from rdkit import Chem
  with i, mol in enumerate(Chem.SDMolSupplier('in.sdf')):
      Chem.MolToPDBFile(f'out_{i}.pdb')
  
  We can be fancier with the output name
  from rdkit import Chem
  import re
  with mol in Chem.SDMolSupplier('in.sdf'):
      # The headerline of a mol file is retrieved oddly.
      name = mol.GetProp('_Name')
      # make filename safe
      slugify = lambda name: re.sub(r'[\W_.-]+', '-', name)
      Chem.MolToPDBFile(f'{slugify(name)}.pdb')
  
  To specify what name (e.g. CA) each atom gets and what is the residue name, chain and residue position —information absent in the sdf, it gets a bit odd.
    names = [' CA ', ' CB ', ' CG ', ' CD '] # say
    for i, atom in enumerate(mol.GetAtoms()):
          info = Chem.AtomPDBResidueInfo(names[i], # or whatever.
                                         residueName='LIG')
  
  For more see this blog post.
  
original_text: 9040: <p>I am currently working on identifying effective antiviral compounds against the corona virus. I have downloaded the Covid-19 AntiViral Candidate Compounds Dataset from the www.cas.org webpage, the link to which I have provided below. Me and a few other doctors are using Docking software to predict the docking capacity of these anti-viral compounds. Docking software requires the anti-viral compounds to be in the .pdb file format only then is it recognized by Automated docking software. <strong>Is there any way I can convert the .sdf file containing the anti-viral compounds to .pdb file or is there a way of obtaining the .pdb files for list of anti-viral compounds</strong>.</p>
  
  <p><em>Thank you for your time and patience,
  Anas Hussain.</em> </p>
  
  <p><strong>Anti-Viral Candidate Compounds Dataset</strong>
  <a href="https://www.cas.org/covid-19-antiviral-compounds-dataset" rel="nofollow noreferrer">https://www.cas.org/covid-19-antiviral-compounds-dataset</a></p>
   4622: <p>Use <a href="http://openbabel.org/wiki/Main_Page" rel="nofollow noreferrer">OpenBabel</a>.</p>
  <p>Something like <code>babel -isdf file_in.sdf -opdb file_out.pdb</code>.</p>
   6322: <blockquote>
  <p>Bizarrely, Obabel seems to have written a PDB that was incorrectly spaced for the OP as seen in <a href="https://bioinformatics.stackexchange.com/questions/13586/error-pasing-the-following-line-in-pdb/13595">Error pasing the following line in pdb</a></p>
  </blockquote>
  <p>If you can use python, <code>rdkit</code> is a great package for cheminformatics —best installed via conda though.</p>
  <p>It allows you do all sorts of things, such as match substructures, embed conformers, edit compounds, compute advanced parameters and many forms of shape &amp; colour finger-/foot-printings.</p>
  <p>Given a multi-compound sdf you can read each individual molecule and write them out as PDBs.</p>
  <pre><code>from rdkit import Chem
  with i, mol in enumerate(Chem.SDMolSupplier('in.sdf')):
      Chem.MolToPDBFile(f'out_{i}.pdb')
  </code></pre>
  <p>We can be fancier with the output name</p>
  <pre><code>from rdkit import Chem
  import re
  with mol in Chem.SDMolSupplier('in.sdf'):
      # The headerline of a mol file is retrieved oddly.
      name = mol.GetProp('_Name')
      # make filename safe
      slugify = lambda name: re.sub(r'[\W_.-]+', '-', name)
      Chem.MolToPDBFile(f'{slugify(name)}.pdb')
  </code></pre>
  <p>To specify what name (<em>e.g.</em> <code>CA</code>) each atom gets and what is the residue name, chain and residue position —information absent in the sdf, it gets a bit odd.</p>
  <pre><code>  names = [' CA ', ' CB ', ' CG ', ' CD '] # say
    for i, atom in enumerate(mol.GetAtoms()):
          info = Chem.AtomPDBResidueInfo(names[i], # or whatever.
                                         residueName='LIG')
  </code></pre>
  <p>For more see <a href="http://blog.matteoferla.com/2020/03/atom-names-purely-in-rdkit.html" rel="nofollow noreferrer">this blog post</a>.</p>
  