Stephane Gagne

icon company Université Laval icon location Quebec, QC icon location Professor in the department of Biochemistry, Microbiology and Bioinformatics at Université Laval.

Results 3 issues of Stephane Gagne

hhblits : some values (No_of_seqs & Neff) are wrong with some combination of parameters

## Expected Behavior Values for "No_of_seqs" & "Neff" in stdout and in result file (.hhr) should be identical. Values for "No_of_seqs" & "Neff" should be correct. ## Current Behavior "No_of_seqs"...

geometric_gnn_101.ipynb : As of Pandas 2.0, the Pandas append() method is no longer supported.

[As of Pandas 2.0, the Pandas append() method is no longer supported](https://pandas.pydata.org/docs/dev/whatsnew/v2.0.0.html#:~:text=Removed%20deprecated%20Series.append()%2C%20DataFrame.append()%2C%20use%20concat()%20instead%20(GH%2035407)). Since running this notebook "as is" will install a 2.x version of pandas, the use of pandas append()...

geometric_gnn_101.ipynb : py3Dmol==1.8.0 does not work in current Google Colab (and in recent local Jupyter)

In geometric_gnn_101.ipynb, the py3Dmol installation specifies version 1.8.0: `!pip install -q py3Dmol==1.8.0` On both my external setup (Google Colab Pro / Chrome 127.0.6533.88) and local setup (jupyterlab 4.0.11 / Chrome...