geem-lab / pnictogen Goto Github PK

Some tests at Travis are failing due to:

AttributeError: 'module' object has no attribute 'OBConformerSearch'

It seems that the OpenBabel version provided by Travis (libopenbabel4 amd64 2.3.2+dfsg-1.1 and libopenbabel-dev amd64 2.3.2+dfsg-1.1 at Ubuntu 14.04.5 LTS) has no support for conformer search.

Options such as --charge or --mult would be useful for usage in the command-line.

Templates in examples/templates might be too complex. My plan is to create some kind of repository (https://github.com/dudektria/pnictogen-templates) of complex, specific templates and restrict the examples in examples/templates to simple tests.

Jinja has support for template inheritance. Can we profit from it? How?

I've been thinking about this for a while. Pnictogen and other template systems are great for batch calculations. Often people want to set up an initial calculation with a GUI.

I'd like to think on a good way to click a button from the Avogadro2 GUI to "Generate Template". I think the main thing would be to insert the tokens for charge, spin, and coordinates, right?

Anything else we'd need?

pnictogen_install_log.txt
While trying to install pnictogen through pip the following error happens:

ERROR: Could not find a version that satisfies the requirement pnictogen (fro
[pnictogen_install_log.txt](https://github.com/geem-lab/pnictogen/files/8700307/pnictogen_install_log.txt)
m versions: none)
ERROR: No matching distribution found for pnictogen

Even though when using isavailable it appears as an valid package.

$ isavailable pnictogen
pnictogen is…     available 🎉 on PyPI.

To reproduce:
It's the first time I'm trying to install, so I just ran pip install -U pnictogen

Trying to install locally (pip install -U -e .) also fails

OS: Pop-OS 20.04

A log from the local installation is also uploaded here.

It seems like it's a problem related to the installation of openbabel, which is funny because it is installed locally.

Initially, I thought about sub-classing pybel.Molecule but eventually ended up passing the object to the template engine as is. Since now we want to add support for other parsers (such as cclib), I believe this extra layer of abstraction is unavoidable.

The point is, should we sub-class pybel.Molecule?

All of the boilerplates in examples/boilerplates technically don't need to be there, and all of the defaults are always generated from config.yml.

Tutorials and examples should be moved as well to a documentation.