From d5db0a1e4a7a2703f33bc8130795042300d3e672 Mon Sep 17 00:00:00 2001 From: Stefano De Castro Date: Thu, 15 Jan 2026 19:22:06 -0800 Subject: [PATCH] Updating README --- AlphaFlex/README.md | 8 ++++---- README.md | 12 ++++++++++++ 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/AlphaFlex/README.md b/AlphaFlex/README.md index 9c46410..f32430b 100644 --- a/AlphaFlex/README.md +++ b/AlphaFlex/README.md @@ -40,13 +40,13 @@ Augments the `AlphaFlex_database_Jul2024.json` file with additional information Using this information, an `idr_type_summary.txt` file will be given that outlines the distribution of each protein into AlphaFlex defined categories. -Usage: `python step_1_case_label.py` +Usage: `python Step_1_case_label.py` ## Step 1B: Subset Label `(Output Directory: Step_1_Labeling)` Creates an `id_lists` directory containing a list of proteins in each category within a specified length subset. The lists will contain the IDs of each protein for subsequent processing. -Usage: `python step_1B_subset_label.py` +Usage: `python Step_1B_subset_label.py` ## Step 2: Template Creation `(Output Directory: Step_2_Templates)` @@ -56,7 +56,7 @@ Tails and Loops have templates made by `mk_ldr_template.py` which keeps all regi Linkers have templates made by `mk_flex_template.py` which designates the 2 adjacent folded domains as separate objects and randomly shifts them within a certain distance of one another (mimicking the flexibility of non-interacting folded domains). -Usage: `python step_2_mk_ldr_template.py` +Usage: `python Step_2_mk_ldr_template.py` ## Step 3: IDR Conformer Generation `(Output Directory: Step_3_Raw_Conformers)` @@ -64,7 +64,7 @@ Generates `X` conformers (Default `X` = 10) for each previously created template Generation of IDR conformers is done through the use of `sample_ldr.py`. -Usage: `python step_3_sample_conformer.py`. +Usage: `python Step_3_sample_conformer.py`. ## Step 4: Stitching and Minimization `(Output Directory: Step_4_Final_Models)` diff --git a/README.md b/README.md index cf60784..22cc381 100644 --- a/README.md +++ b/README.md @@ -62,6 +62,8 @@ Then proceed into `openfold/` activate the OpenFold environment using the follow mamba env create -n openfold_env -f environment.yml ``` +> Note: This can also be run with `conda env create -n openfold_env -f environment.yml` + Install other dependencies required by IDPForge using the following command: ``` bash @@ -70,6 +72,16 @@ conda install einops mdtraj -c conda-forge It is also recommended to uninstall flash-attn via `pip uninstall flash-attn` when starting out if this installation pathway is chosen. +Once flash-attn is uninstalled, proceed into `IDPForge/` and `openfold/` and install IDPForge and openfold as modules in the environment using the following commands: + +``` bash +cd IDPForge/ +pip install -e . +cd openfold/ +pip install -e . +``` +> Note: If `pip install -e .` does not work, proceed with `pip install . --no-build-isolation` instead. + This makes the environment fully ready for use. > Note: For more information on OpenFold installation, please refer to the installation guide. https://openfold.readthedocs.io/en/latest/Installation.html