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charge, dielx, diely and dielz cannot be used to reproduce the result.

3

**Describe the bug** A clear and concise description of what the bug is. Say if I run an APBS calculation where I export the charge, dielx, diely and dielz. The...

xiki-tempula

@intendo can you please check your past tests for the use of `pytest.raises` vs. `pytest.mark.xfail`? I'd like to follow https://docs.pytest.org/en/6.2.x/assert.html#assertions-about-expected-exceptions and only use `xfail` for things we need to fix....

sobolevnrm

### Discussed in https://github.com/Electrostatics/apbs/discussions/150 Originally posted by **srdjan125** June 8, 2021 Hello, I would like to ask for help because I have several issues which are all connected to main...

sobolevnrm

Convert input format to YAML and front-end to Python

5

- Allow better integration with other codes. - Support more robust input file parsing 

sobolevnrm

Force and energy option descriptions are used in multiple calculation types but are described as specific to "apolar": https://apbs.readthedocs.io/en/latest/using/input/generic/calcforce.html

sobolevnrm

pip install -e . fails on master

7

``` (mmcif) PS: mmcif_pdbx> pip install -e . Obtaining file:///C:/Users/bake113/OneDrive%20-%20PNNL/Documents/Git/mmcif_pdbx Installing build dependencies ... done Getting requirements to build wheel ... error ERROR: Command errored out with exit status 1:...

sobolevnrm

psize.py

3

When using psize.py with my PQR file (psize.py myfile.pqr) it gives: **No ATOM entires in file!** However, when I use the Pymol plugin with the same PQR and the .mol...

sbembenek18

Hey, I'm using the binary install for APBS-3.0.0 (under Centos 7), FYI. Under Apps/APBS-3.0.0/share/apbs/tools/bin 'similarity' is compiled and it does seem to work in general. The segmentation fault occurred for...

sobolevnrm

Cube to/from DX File conversion

7

I'd like to be able to convert between Gaussian Cube File format and DX File format

sbembenek18

The script currently in use: https://github.com/Electrostatics/apbs-rest/blob/master/src/runner/uploader/dx2cube.py Original (from old repo): https://github.com/Electrostatics/apbs-pdb2pqr/blob/b3bfeecbf4cfd04bf53f983e1a8064ef250bf25f/pdb2pqr/dx2cube.py _Originally posted by @Eo300 in https://github.com/Electrostatics/apbs/issues/131#issuecomment-804238791_

sobolevnrm