From 761f384bf8ec5be7cc3286b598fb23d87a0779ea Mon Sep 17 00:00:00 2001
From: chao1224 <shengchao1224@gmail.com>
Date: Fri, 10 Jan 2025 21:47:44 -0800
Subject: [PATCH] Update environment

---
 README.md                                 | 38 +++++++++++++++++++++--
 environment.yml => legacy/environment.yml |  0
 2 files changed, 35 insertions(+), 3 deletions(-)
 rename environment.yml => legacy/environment.yml (100%)

diff --git a/README.md b/README.md
index 11583f0..0886b48 100644
--- a/README.md
+++ b/README.md
@@ -19,13 +19,45 @@ Authors: Shengchao Liu, Yanjing Li, Zhuoxinran Li, Anthony Gitter, Yutao Zhu, Ji
 ## 1 Environment
 
 ```
-conda env create -f environment.yml
+conda create -n ProteinDT python=3.7
 conda activate ProteinDT
+
+conda install -y numpy networkx scikit-learn
+
+pip install torch==1.10.*
+
+pip install transformers
+pip install lxml
+
+# for TAPE
+pip install lmdb
+pip install seqeval
+
+# for baseline ChatGPT
+pip install openai==0.28.0
+
+# for baseline Galactica
+pip install accelerate
+
+# for visualization
+pip install matplotlib
+
+# for binding editing
+pip install h5py
+pip install torch_geometric==2.0 torch_scatter torch_sparse torch_cluster
+pip install biopython
+
 # for ESM folding
-pip install fair-esm[esmfold]==2.0.0 --no-dependencies
+pip install "fair-esm[esmfold]"
+pip install dm-tree omegaconf ml-collections einops
+pip install fair-esm[esmfold]==2.0.0  --no-dependencies # Override deepspeed==0.5 
+pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git'
+pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'
+
+conda install -c conda-forge -yq mdtraj
+
 # for ProteinDT
 pip install .
-
 ```
 
 
diff --git a/environment.yml b/legacy/environment.yml
similarity index 100%
rename from environment.yml
rename to legacy/environment.yml