Removed unnecessary files from GitHub Classroom and added our project…

… files.

get_close_resids.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+import numpy as np
+from scipy.spatial import KDTree
+import MDAnalysis as mda
+
+def binding_resids(pdb_path, ligand_resname, rcut):
+
+    all_atoms = mda.Universe(pdb_path)
+
+    ligand_resname = '7V7'
+
+
+    ligand = all_atoms.select_atoms(f'resname {ligand_resname}')
+    protein = all_atoms.select_atoms('protein')
+
+    pr_tree = KDTree(protein.positions)
+    li_tree = KDTree(ligand.positions)
+
+    rcut = 5.0
+
+    binding_inds = np.unique(np.hstack(li_tree.query_ball_tree(pr_tree,rcut))).astype('int')
+    binding_resids = np.unique(protein[binding_inds].resids)
+    return binding_resids
+
+if __name__ == "__main__":
+
+    pdbfile = "5tzo.pdb"
+    ligand_resname = '7V7'
+    rcut = 5.0 #in angstroms
+
+    close_resids = binding_resids(pdbfile,ligand_resname,rcut)
+
+    print(','.join([str(i) for i in close_resids]))
+    print(f'\n{len(close_resids)}')
+
+

requirements.txt

@@ -1,9 +1,110 @@
-  -e . # package from this repo
-#  numpy
-#  scipy
-#  pandas
-#  matplotlib
-#  matplotlib-inline
-#  ipython
-#  ipykernel
- pytest
+accelerate==0.28.0
+affinity-pred @ git+https://github.com/ORNL/affinity_pred.git@d1258396b8889384f7b0919c07177d9b029f7a05
+aiohttp==3.9.3
+aiosignal==1.3.1
+asttokens==2.4.1
+async-timeout==4.0.3
+attrs==23.2.0
+ax-platform==0.3.7
+botorch==0.10.0
+certifi==2024.2.2
+charset-normalizer==3.3.2
+comm==0.2.2
+contourpy==1.2.0
+cycler==0.12.1
+datasets==2.18.0
+decorator==5.1.1
+dill==0.3.8
+exceptiongroup==1.2.0
+executing==2.0.1
+fasteners==0.19
+filelock==3.13.3
+fonttools==4.50.0
+frozenlist==1.4.1
+fsspec==2024.2.0
+gpytorch==1.11
+GridDataFormats==1.0.2
+huggingface-hub==0.22.1
+idna==3.6
+ipython==8.22.2
+ipywidgets==8.1.2
+jaxtyping==0.2.28
+jedi==0.19.1
+Jinja2==3.1.3
+joblib==1.3.2
+jupyterlab_widgets==3.0.10
+kiwisolver==1.4.5
+linear-operator==0.5.1
+MarkupSafe==2.1.5
+matplotlib==3.8.3
+matplotlib-inline==0.1.6
+mda-xdrlib==0.2.0
+MDAnalysis==2.7.0
+mmtf-python==1.1.3
+mpmath==1.3.0
+mrcfile==1.5.0
+msgpack==1.0.8
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+mypy-extensions==1.0.0
+networkx==3.2.1
+numpy==1.26.4
+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
+opt-einsum==3.3.0
+packaging==24.0
+pandas==2.2.1
+parso==0.8.3
+pexpect==4.9.0
+pillow==10.2.0
+plotly==5.20.0
+prompt-toolkit==3.0.43
+psutil==5.9.8
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pyarrow==15.0.2
+pyarrow-hotfix==0.6
+Pygments==2.17.2
+pyparsing==3.1.2
+pyre-extensions==0.0.30
+pyro-api==0.1.2
+pyro-ppl==1.9.0
+python-dateutil==2.9.0.post0
+pytz==2024.1
+PyYAML==6.0.1
+regex==2023.12.25
+requests==2.31.0
+safetensors==0.4.2
+scikit-learn==1.4.1.post1
+scipy==1.12.0
+six==1.16.0
+stack-data==0.6.3
+sympy==1.12
+tenacity==8.2.3
+threadpoolctl==3.4.0
+tokenizers==0.15.2
+torch==2.2.2
+tqdm==4.66.2
+traitlets==5.14.2
+transformers==4.39.2
+triton==2.2.0
+typeguard==2.13.3
+typing-inspect==0.9.0
+typing_extensions==4.10.0
+tzdata==2024.1
+urllib3==2.2.1
+wcwidth==0.2.13
+widgetsnbextension==4.0.10
+xxhash==3.4.1
+yarl==1.9.4