Code

.gitattributes

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+models/lddmK5_CDv2_BN_de5_do3_co1_vn10_g4_bs50ag2_he0.1_epoch544.ckpt filter=lfs diff=lfs merge=lfs -text

README.md

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 ---
 title: Drugon
-emoji: 👁
-colorFrom: blue
-colorTo: pink
+emoji: 🏃
+colorFrom: gray
+colorTo: indigo
 sdk: gradio
-sdk_version: 5.31.0
-app_file: app.py
 pinned: false
----
-
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+app_file: startup.py
+python_version: 3.11
+sdk_version: 4.44.1
+---

models/lddmK5_CDv2_BN_de5_do3_co1_vn10_g4_bs50ag2_he0.1_epoch544.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:659009a92d5af0493600d19ddd7fcdbdd40672bda3c4d3da653d7e598e6a1d7e
+size 168628628

packages.txt

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+unzip

requirements.txt

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+rdkit==2023.9.5
+
+--extra-index-url https://download.pytorch.org/whl/cu121
+torch==2.2.1 
+torchvision==0.17.1 
+torchaudio==2.2.1
+
+torch_geometric==2.5.3
+-f https://data.pyg.org/whl/torch-2.2.1+cu121.html
+
+torch_scatter==2.1.2
+-f https://data.pyg.org/whl/torch-2.2.1+cu121.html
+
+lightning==2.2.3
+wandb==0.16.6
+
+scipy==1.13.0
+matplotlib==3.8.4
+tqdm==4.66.2
+ipykernel==6.29.4
+prody==2.4.1
+biopython>=1.79
+
+posebusters==0.2.14
+useful_rdkit_utils==0.55
+fcd==1.2.2
+
+webdataset==0.2.86
+notebook==7.2.1
+prolif==2.0.3
+pot==0.9.4
+
+gradio_toggle==2.0.2
+pydantic==2.10.6
+spaces==0.34.0
+modal==1.0.1

startup.py

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+import subprocess
+subprocess.call(['sh', './startup.sh'])
+
+import os
+import sys
+pwd = os.getcwd()
+sys.path.append(f'{pwd}/lddm')
+sys.path.append(f'{pwd}/lddm/drugon')
+os.environ["PATH"] = f'{pwd}/bin' + os.pathsep + os.environ.get("PATH", "")
+model_path = f'{pwd}/models/lddmK5_CDv2_BN_de5_do3_co1_vn10_g4_bs50ag2_he0.1_epoch544.ckpt'
+ketcher_path = f'{pwd}/lddm/drugon/ketcher'
+
+os.chdir('lddm/drugon')
+print("Current directory:", os.getcwd())
+
+users = {}
+print(os.environ.get('AUTH_USERS'))
+for line in os.environ.get('AUTH_USERS').split('\n'):
+    parts = line.split(' ')
+    if len(parts) == 2:
+        users[parts[0]] = parts[1]
+
+def auth(username, password):
+    if username not in users:
+        return False
+    return users[username] == password
+
+print('Ketcher directory exists:', os.path.exists(ketcher_path))
+print('Ketcher js file exists:', os.path.exists(f'{ketcher_path}/static/js/main.adb1c0c5.js'))
+print('Ketcher css file exists:', os.path.exists(f'{ketcher_path}/static/css/main.c3d3c37d.css'))
+
+
+from app import start
+start(checkpoint=model_path, device='cpu', auth=auth, static_paths=['ketcher'])

startup.sh

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+git clone $PRIVATE_REPO_URL
+cd lddm/drugon
+git checkout drugon-modal
+wget https://github.com/epam/ketcher/releases/download/v2.26.0/ketcher-standalone-2.26.0.zip -O ketcher.zip
+unzip ketcher.zip
+mv standalone ketcher
+mkdir -p static/css
+mkdir -p static/js
+ls -l
+
+
+git lfs install
+git clone https://huggingface.co/datasets/igashov/reference_3d_validity_pdb
+ls -l
+ls -l reference_3d_validity_pdb
+
+cd ../../
+mkdir -p bin
+wget https://zenodo.org/records/15113339/files/reduce?download=1 -O bin/reduce
+chmod +x bin/reduce
+pwd
+ls -l