BJWiley23

Results 23 issues of BJWiley23

Hi, Really scratching my head here with my mocha input. I have the phased annotated of my unphased file and I don't get any variants written to the allelic shift...

Hi, I tested building on following 2 systems and get same resolve errors at bottom for build. 1. Centos 7 Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f) Maven home: /export/home/bwiley4/tools/apache-maven-3.6.3 Java version: 11.0.10,...

Hi, When I run my docking without --flexres it runs "as much" as expected and I'll get a some values like -11.34 kcal/mol or -10.21 kcal/mol for say two molecules....

Hi, I have question about calculating e3fp.fingerprint.metrics.tanimoto coefficients of stereoisomers. I have made 50 conformers for following molecules with hydrogens. There are some locations in the matrix created from call...

Hey Brandon, I was running poltype for 90 atom molecule and the `esp` from Psi4 keep getting killed with the basis used in poltype, so need to use less memory...

There is one torsion parameter that was added to tinker [here](https://github.com/TinkerTools/tinker/commit/5c37bcd20cae2d215e99c8b066658eabf4bce9a2#diff-efc5d62366693141f795c79f47c5535dab174acb157f47f9021d9f63ec45632e) that is missing from poltypes2's [amoebabio18.prm](https://github.com/TinkerTools/poltype2/blob/master/ParameterFiles/amoebabio18.prm) for C-terminal threonines. There were actually 8 more updates as well since then...

Hi, I was potentially trying to use pygamer so I could create a geometric graph somehow with torch_geometric. I ran into one problem in that I have a GLUT3/B-glucose (protein...

Based on #88 The cwl-upgrader tool only updates the input workflow file (or any file that is the input, i.e if the tool is an input it works) to v1.2...

I tested pulling out one of the patches after running `ers.computeSegmentation` and then pulled out a submesh from for instance: ``` submesh = pymesh.submesh(mesh, np.where(patch_labels==2)[0], 0) ``` And I expected...

Does this plugin work on newer MacOS platforms? I see the extension is loaded but no Autocomplete with for me. ![image](https://user-images.githubusercontent.com/26236052/218343514-7c244fc5-e943-44dd-b4dc-b5e2d783a299.png)