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KULL-Centre · Jan 25, 2024 · 4001785 · 4001785
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diff --git a/Fig2.png b/Fig2.png
diff --git a/Fig_1_S4_S5_S6_S7.ipynb b/Fig_1_S4_S5_S6_S7.ipynb
diff --git a/Fig_3.ipynb b/Fig_3.ipynb
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diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -1 +1,13 @@
-# _2023_Montepietra_FRET
+# Data analyses using FRETpredict
+
+This repository contains Python code, [Jupyter](http://jupyter.org) Notebooks, and data for reproducing the results presented in the manuscript _FRETpredict: A Python package for FRET efficiency predictions using rotamer libraries_
+
+### Usage
+
+To open the Notebooks, install [Miniconda](https://conda.io/miniconda.html) and make sure all required packages are installed by issuing the following terminal commands
+
+```bash
+    conda env create -f environment.yml
+    source activate fret
+    jupyter-notebook
+```
diff --git a/Clusters_populations.csv → data/Clusters_populations.csv b/Clusters_populations.csv → data/Clusters_populations.csv
diff --git a/results_HiSiaP_closed.npy → data/results_HiSiaP_closed.npy b/results_HiSiaP_closed.npy → data/results_HiSiaP_closed.npy
diff --git a/results_HiSiaP_open.npy → data/results_HiSiaP_open.npy b/results_HiSiaP_open.npy → data/results_HiSiaP_open.npy
diff --git a/results_MalE_350_C1R.npy → data/results_MalE_350_C1R.npy b/results_MalE_350_C1R.npy → data/results_MalE_350_C1R.npy
diff --git a/results_MalE_350_L1R.npy → data/results_MalE_350_L1R.npy b/results_MalE_350_L1R.npy → data/results_MalE_350_L1R.npy
diff --git a/results_MalE_closed.npy → data/results_MalE_closed.npy b/results_MalE_closed.npy → data/results_MalE_closed.npy
diff --git a/results_MalE_closed_El_false.npy → data/results_MalE_closed_El_false.npy b/results_MalE_closed_El_false.npy → data/results_MalE_closed_El_false.npy
diff --git a/results_MalE_open.npy → data/results_MalE_open.npy b/results_MalE_open.npy → data/results_MalE_open.npy
diff --git a/results_MalE_open_El_false.npy → data/results_MalE_open_El_false.npy b/results_MalE_open_El_false.npy → data/results_MalE_open_El_false.npy
diff --git a/results_MalE_open_different_probe.npy → data/results_MalE_open_different_probe.npy b/results_MalE_open_different_probe.npy → data/results_MalE_open_different_probe.npy
diff --git a/results_MalE_open_el_off.npy → data/results_MalE_open_el_off.npy b/results_MalE_open_el_off.npy → data/results_MalE_open_el_off.npy
diff --git a/results_MalE_open_r0_647_647.npy → data/results_MalE_open_r0_647_647.npy b/results_MalE_open_r0_647_647.npy → data/results_MalE_open_r0_647_647.npy
diff --git a/results_SBD2_closed.npy → data/results_SBD2_closed.npy b/results_SBD2_closed.npy → data/results_SBD2_closed.npy
diff --git a/results_SBD2_open.npy → data/results_SBD2_open.npy b/results_SBD2_open.npy → data/results_SBD2_open.npy
diff --git a/results_pairs_ACTR_0M_20.npy → data/results_pairs_ACTR_0M_20.npy b/results_pairs_ACTR_0M_20.npy → data/results_pairs_ACTR_0M_20.npy
diff --git a/results_pairs_ACTR_0M_30.npy → data/results_pairs_ACTR_0M_30.npy b/results_pairs_ACTR_0M_30.npy → data/results_pairs_ACTR_0M_30.npy
diff --git a/results_pairs_ACTR_0M_save_30.npy → data/results_pairs_ACTR_0M_save_30.npy b/results_pairs_ACTR_0M_save_30.npy → data/results_pairs_ACTR_0M_save_30.npy
diff --git a/results_pairs_ACTR_0M_ws_20.npy → data/results_pairs_ACTR_0M_ws_20.npy b/results_pairs_ACTR_0M_ws_20.npy → data/results_pairs_ACTR_0M_ws_20.npy
diff --git a/results_pairs_ACTR_0M_ws_30.npy → data/results_pairs_ACTR_0M_ws_30.npy b/results_pairs_ACTR_0M_ws_30.npy → data/results_pairs_ACTR_0M_ws_30.npy
diff --git a/results_pairs_ACTR_2_5M_20.npy → data/results_pairs_ACTR_2_5M_20.npy b/results_pairs_ACTR_2_5M_20.npy → data/results_pairs_ACTR_2_5M_20.npy
diff --git a/results_pairs_ACTR_2_5M_30.npy → data/results_pairs_ACTR_2_5M_30.npy b/results_pairs_ACTR_2_5M_30.npy → data/results_pairs_ACTR_2_5M_30.npy
diff --git a/results_pairs_ACTR_2_5M_ws_20.npy → data/results_pairs_ACTR_2_5M_ws_20.npy b/results_pairs_ACTR_2_5M_ws_20.npy → data/results_pairs_ACTR_2_5M_ws_20.npy
diff --git a/results_pairs_ACTR_5M_20.npy → data/results_pairs_ACTR_5M_20.npy b/results_pairs_ACTR_5M_20.npy → data/results_pairs_ACTR_5M_20.npy
diff --git a/results_pairs_ACTR_5M_30.npy → data/results_pairs_ACTR_5M_30.npy b/results_pairs_ACTR_5M_30.npy → data/results_pairs_ACTR_5M_30.npy
diff --git a/results_pairs_ACTR_5M_ws_20.npy → data/results_pairs_ACTR_5M_ws_20.npy b/results_pairs_ACTR_5M_ws_20.npy → data/results_pairs_ACTR_5M_ws_20.npy
diff --git a/results_pp11.npy → data/results_pp11.npy b/results_pp11.npy → data/results_pp11.npy
diff --git a/results_pp11_ws.npy → data/results_pp11_ws.npy b/results_pp11_ws.npy → data/results_pp11_ws.npy
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,14 @@
+name: fret
+dependencies:
+  - python=3.8
+  - jinja2
+  - notebook
+  - numpy
+  - pandas
+  - scipy
+  - matplotlib
+  - seaborn
+  - conda-forge::mdtraj
+  - pip
+  - pip:
+    - mdanalysis==2.0.0
diff --git a/lib/A35_C1R_cutoff10_weights.txt b/lib/A35_C1R_cutoff10_weights.txt
diff --git a/lib/A35_C1R_cutoff20_weights.txt b/lib/A35_C1R_cutoff20_weights.txt
diff --git a/lib/A35_C1R_cutoff30_weights.txt b/lib/A35_C1R_cutoff30_weights.txt