build(deps): add requirements.txt file

Freezes dependency versions so that future releases of those dependencies
don't leave LigandMPNN in a broken state. Fixes #11 and #13

README.md

@@ -10,8 +10,7 @@ bash get_model_params.sh "./model_params"
 
 #setup your conda/or other environment
 #conda create -n ligandmpnn_env python=3.11
-#pip3 install torch
-#pip install prody
+#pip3 install -r requirements.txt
 
 python run.py \
         --seed 111 \
@@ -25,8 +24,7 @@ To run the model you will need to have Python>=3.0, PyTorch, Numpy installed, an
 For example to make a new conda environment for LigandMPNN run:
 ```
 conda create -n ligandmpnn_env python=3.11
-pip3 install torch
-pip install prody
+pip3 install -r requirements.txt
 ```
 
 ### Main differences compared with [ProteinMPNN](https://github.com/dauparas/ProteinMPNN) code

requirements.txt

@@ -0,0 +1,27 @@
+biopython==1.79
+filelock==3.13.1
+fsspec==2024.3.1
+Jinja2==3.1.3
+MarkupSafe==2.1.5
+mpmath==1.3.0
+networkx==3.2.1
+numpy==1.23.5
+nvidia-cublas-cu12==12.1.3.1
+nvidia-cuda-cupti-cu12==12.1.105
+nvidia-cuda-nvrtc-cu12==12.1.105
+nvidia-cuda-runtime-cu12==12.1.105
+nvidia-cudnn-cu12==8.9.2.26
+nvidia-cufft-cu12==11.0.2.54
+nvidia-curand-cu12==10.3.2.106
+nvidia-cusolver-cu12==11.4.5.107
+nvidia-cusparse-cu12==12.1.0.106
+nvidia-nccl-cu12==2.19.3
+nvidia-nvjitlink-cu12==12.4.99
+nvidia-nvtx-cu12==12.1.105
+ProDy==2.4.1
+pyparsing==3.1.1
+scipy==1.12.0
+sympy==1.12
+torch==2.2.1
+triton==2.2.0
+typing_extensions==4.10.0