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Questions tagged [openbabel]

Questions about or related to Open Babel.

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4 votes
0 answers
58 views

Read pymatgen format from something else other than Python?

It seems that the only way that Materials Project can report structures with the new API is through the Pymatgen JSON format. ...
alfC's user avatar
  • 281
5 votes
1 answer
521 views

obabel error OpenAndSetFormat Cannot open

I'm trying to convert .xyz to .sdf with Open Babel on Ubuntu 22.04, but I am getting an error message "Cannot open orca.sdf". ...
Frank's user avatar
  • 195
6 votes
3 answers
1k views

Using OpenBabel's gen3d in a Python notebook

I want to preface this by saying I am really new to computational chemistry and this kind of programming in general, but I am having real trouble figuring out how to use OpenBabel's ...
Meheret's user avatar
  • 103
6 votes
1 answer
338 views

Is it possible to recover the protein structure after conversions PDB->XYZ->PDB?

Let suppose that, for a given reason, a PDB file (with all the residues/chains/heteratom/cofactor/ligand information inside) is converted to a XYZ file. Doing that, all protein information is lost. ...
Camps's user avatar
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2 votes
0 answers
682 views

Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files [closed]

Cross-posted on Chemistry.SE. I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
user3765252's user avatar
6 votes
1 answer
455 views

Alternatives to OpenBabel for converting *large* files?

I have been using OpenBabel as a handy-tool for converting small files without any issues. Now, I am working with graphene-like systems with hundreds or even ...
Camps's user avatar
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5 votes
0 answers
195 views

How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files? [closed]

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
Julio Coll's user avatar
16 votes
2 answers
972 views

What's the best quantum chemistry output parser for the command line?

This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second. I am interested e.g. ...
Susi Lehtola's user avatar
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11 votes
2 answers
468 views

How to canonicalize SMILES written with aromatic bond symbols (:)?

I am using a package called PySmiles and it is returning a dialect of SMILES for aromatic groups that uses aromatic bond symbols e.g. NC:1:N:N:C:[N]1N. RDKit does ...
Cody Aldaz's user avatar
  • 8,017