From 0fae08645c6748ccfacccf7bbbfc35c8d19bb54a Mon Sep 17 00:00:00 2001 From: gph82 Date: Fri, 6 Sep 2024 11:39:50 +0200 Subject: [PATCH] [examples.fetch_example_data] docs --- mdciao/examples/examples.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/mdciao/examples/examples.py b/mdciao/examples/examples.py index 46e76bca..06e38836 100644 --- a/mdciao/examples/examples.py +++ b/mdciao/examples/examples.py @@ -424,7 +424,7 @@ def fetch_example_data(alias_or_url="b2ar@Gs", * 'cov19' * 'ghrelin@ghsr' * 'mor@muor' - * 'Y1' + * 'y1_apo' This data is used in the notebooks: * 01.Tutorial.ipynb (b2ar@Gs) @@ -433,7 +433,7 @@ def fetch_example_data(alias_or_url="b2ar@Gs", * 04.Comparing_CGs_Flares.ipynb (cov19) * 07.EGFR Kinase Inhibitors.ipynb (EGFR) * 08.Manuscript.ipynb (b2ar@Gs) - * 09.Consensus_labels.ipynb (ghrelin@ghsr,b2ar@Gs,mor@muor,Y1) + * 09.Consensus_labels.ipynb (ghrelin@ghsr,b2ar@Gs,mor@muor,y1_apo) which can all be run locally issuing, from the CLI: @@ -485,26 +485,26 @@ def fetch_example_data(alias_or_url="b2ar@Gs", * Analysis of the Dynamics of the Human Growth Hormone Secretagogue Receptor Reveals Insights into the Energy Landscape of the Molecule A. A. Smith, E. M. Pacull, S. Stecher, P. W. Hildebrand, A. Vogel, D. Huster - Angew. Chem. Int. Ed. 2023, 62, e202302003 + Angew. Chem. Int. Ed. 2023, 62, e202302003 ``_ - * Y1 : https://proteinformatics.uni-leipzig.de/mdciao/y1_apo.zip + * y1_apo : https://proteinformatics.uni-leipzig.de/mdciao/y1_apo.zip Neuropeptide Y receptor type 1, Y1 receptor for short, in apo form. Provided kindly by Dr. A. Vogel (1 traj, ca. 11 MB, 528 frames, dt = 50ns) For the associated publication see here: * Towards Probing Conformational States of Y2 Receptor Using Hyperpolarized 129Xe NMR. Schmidt, P.; Vogel, A.; Schwarze, B.; Seufert, F.; Licha, K.; Wycisk, V.; Kilian, W.; Hildebrand, P.W.; Mitschang, L. - Molecules 2023, 28, 1424. [](https://doi.org/10.3390/molecules28031424) + Molecules 2023, 28, 1424. ``_ * mor@muor : https://proteinformatics.uni-leipzig.de/mdciao/muor_199.zip Active mu-opioid receptor bound to the agonist morphine (1 traj, ca. 7 MB, 400 frames, dt = 100ns). Kindly made available for this purpose by the GPCRmd. The GPCRmd's simulation - report can be found [https://www.gpcrmd.org/dynadb/dynamics/id/199/](here) , + report can be found `here `_ , the original publication is: * Dynamic and Kinetic Elements of ยต-Opioid Receptor Functional Selectivity. Kapoor, A., Martinez-Rosell, G., Provasi, D. et al. - Sci Rep 7, 11255 (2017). [](https://doi.org/10.1038/s41598-017-11483-8) + Sci Rep 7, 11255 (2017). ``_ unzip : bool, or str, default is True Try unzipping the file after downloading. If string,