[Open Babel] Compression using Python API

I'm not able to compress output files when using the python API. I'm using code like this: import openbabel obConversion = openbabel.OBConversion() obConversion.SetInAndOutFormats("pdb", "mol2") mol = openbabel.OBMol() obConversion.ReadFile(mol, "input.pdb.gz") obConversion.AddOption("z") obCo

Re: [Open Babel] Compression using Python API

) So, try obConversion.GENOPTIONS ? Andrew da...@dalkescientific.com On Apr 11, 2019, at 15:31, Tim Dudgeon wrote: Unfortunately that doesn't work either. Still writes uncompressed. On 11/04/2019 14:15, Andrew Dalke wrote: obConversion.AddOp

[Open Babel] protonation using Python

Another Python options question. I can use the protonation option on the CLI: echo "C1=C(NC=N1)C[C@@H](C(=O)O)N" | obabel -i smi -o mol -p 3 But I can't figure it out with the Python API: import openbabel obConversion = openbabel.OBConversion() obConversion.SetInAndOutFormats("smi", "mol") m

[Open Babel] Segmentation fault when writing as gzipped

I'm getting 'Segmentation fault (core dumped)' errors when using gzipped output formats. It seems to depends on what is being written, but when it happens it always happens. e.g. $ obabel data.pdb.gz -O output.mol2.gz -h -z Segmentation fault (core dumped) $ obabel data.pdb.gz -O output.mol2 -

Re: [Open Babel] protonation using Python

relevant docs: http://openbabel.org/api/2.3/classOpenBabel_1_1OBPhModel.shtml Regards, - Noel On Thu, 11 Apr 2019 at 16:11, Tim Dudgeon <mailto:tdudgeon...@gmail.com>> wrote: Another Python options question. I can use the protonation option on the CLI: > echo "C1=C(NC=N1)C[C@@H](C

Re: [Open Babel] How to deal with .mol2 files?

And with NGLViewer. http://nglviewer.org/ngl/ Just drag the mol2 file into the window. On 24/03/2020 19:54, Amanda Loshbaugh wrote: If you would like to /view/ the structure in 3D, you can open mol2 files in PyMOL. Amanda Loshbaugh, PhD Scientist I, Protein and Cell Engineering Lyell Immuno

Re: [Open Babel] Garbled 3D structures from Python

I think I'm using 3.1, but can't be totally sure. How do you ask this from python? I can't see any obvious way. Tim On Tue, Oct 19, 2021 at 7:22 PM Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > I'm having problems when generating 3D molecules using the Python > bindings. > > This may

Re: [Open Babel] Garbled 3D structures from Python

7:52 PM Stefano Forli via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > The easiest way to get the version would be this: > > from openbabel import openbabel as ob > print(ob.OBReleaseVersion()) > > > On 10/22/21 06:46, Tim Dudgeon wrote

[Open Babel] energy and minimisation from Python

I'm using the Python bindings to do various things, and want to be able to do MMF94 energy calculations and minimisations such as these: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#forcefield-energy-and-minimization Is this possible from Python? Tim ___

[Open Babel] charges when generating mol2 format

It seems that the atom charges being generated when converting to mol2 format do not take into account the formal charge on the atoms. $ echo 'CC(=O)Nc1ccc2[nH+]c(C)cc([O-])c2c1' | obabel -i smiles -o mol2 --gen2d @MOLECULE * 16 17 0 0 0 SMALL GASTEIGER @ATOM 1 C 2.5981 -1.

[Open Babel] Thread usage for make3D()

I'm using the mol.make3D() function from Python to generate 3D coordinates. This is working OK, but when I run this in a K8S container running on a host machine with a large number of cores (124) but with the K8S pod restricted to 1 core then what seems to happen is that OBabel tries to spin up a h

[Open Babel] extracting ligands from macromolecular structures

I'm trying to work out how to use openbabel from Python to perform operations such as extracting out ligands from macromolecules in PDB or CIF format. For instance, if I have a ligand that has the residue name of LIG, how do I create a new molecule with just that ligand so that I can write it out i

Re: [Open Babel] extracting ligands from macromolecular structures

65 1.00 >> 0.00 C >> ATOM 19 C ALA A 3 3.451 -4.925 -1.148 1.00 >> 0.00 C >> ATOM 20 O ALA A 3 3.668 -6.018 -1.670 1.00 >> 0.00 O >> ATOM 21 CB ALA A 3 2.461 -5.731 0.981 1.00 >&g

[Open Babel] unable to read CIF

I'm finding that OBabel 3.1.1 seems to be unable to handle some CIF files that have been generated by ACEDRG ( https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html). One such file is attached. When running this code no errors are thrown but the molecule seems to empty (molwt i

[Open Babel] problem with pip install

Problems similar to this have been asked, but I've not seen an answer. In my case I'm trying to pip install openbabel but it's failing. I have a dockerfile like this: FROM python:3.10.12-slim-bullseye RUN apt-get update && apt-get -y install gcc swig &&\ apt-get clean RUN pip install openbabel==