Tomáš Raček

Sure, I think it's a rather good idea, and it would be great if the bindings were on par with the overall functionality as the standalone app has. Originally, ChargeFW2...

Are those ions classified as HETATMs? Or have their own residues like https://www.rcsb.org/ligand/CA or https://www.rcsb.org/ligand/K? What about something similar to --ignore-water but more general like --ignore-residues CA and some equivalent...

Sure. I need to submit the first draft of the thesis next week, however, after that, I'll contact you on email (hopefully I will remember the hack for EEM by...

Hi! Sorry, I totally missed that. Thesis went fine, however, we changed our focus a bit, see our latest project: https://pdbcharges.biodata.ceitec.cz/ and https://doi.org/10.1093/nar/gkaf401.

Ah, I remember now why I put fulfill_requirements in the init! In Python, you can call calculate_charges multiple times and the fulfill_requirements would be executed again. The solution should check...

Well, there is a simple reason... ;-) I just needed some Python bindings quickly for one project in which I worked only with small molecules so I created something really...

Hi, thanks for the report. I updated the cmake requirements and the dockerfile. Please see if that works for you in the current version.

Well, nanoflann should be detected by cmake, so the manual copy would not be necessary. See the Dockerfile using which ChargeFW2 builds correctly with Ubuntu 24.04 packages. Anyway, I made...

This method is included in the C++20 standard. What's your compiler version? GCC 9 or Clang 10 should be OK according to the https://en.cppreference.com/w/cpp/compiler_support#C.2B.2B20_library_features.

The output is not in PDB format but in PQR, which, to my knowledge, has no exact definition. The exact format ChargeFW2 uses conforms to specifications, which are whitespace-delimited: https://docs.mdanalysis.org/1.0.0/documentation_pages/coordinates/PQR.html...