dptech-corp · ysyecust · Feb 2, 2024 · Jan 29, 2024 · Jan 29, 2024 · Jan 30, 2024
diff --git a/.github/workflows/ci_tools.yml b/.github/workflows/ci_tools.yml
@@ -1,9 +1,7 @@
 name: Uni-Dock Tools CI/CD
 on:
   push:
-    branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 jobs:
   flake8:
@@ -15,7 +13,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python  ${{ matrix.python-version }}
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
@@ -83,15 +81,15 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.9"]
-    container: 
+    container:
       image: docker.io/dptechnology/unidock:latest
       options: --gpus all
     steps:
     - name: checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         python-version: ${{ matrix.python-version }}
@@ -107,9 +105,9 @@ jobs:
       working-directory: ./unidock_tools
       run: |
         export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
-        python setup.py install
+        conda run -n test python setup.py install
 
     - name: perform unit-test
       run: |
         export PATH=/__w/Uni-Dock/Uni-Dock/3/envs/test/bin:$PATH
-        pytest unidock_tools/tests/ut -v
+        conda run -n test pytest unidock_tools/tests/ut -v
diff --git a/.github/workflows/ci_unidock.yml b/.github/workflows/ci_unidock.yml
@@ -1,14 +1,14 @@
 name: Uni-Dock CI/CD
 on:
   push:
-    branches: [ main ]
+    branches: []
   pull_request:
     branches: [ main ]
 
 jobs:
   unidock_test:
     runs-on: nvidia
-    container: 
+    container:
       image: nvidia/cuda:12.2.0-devel-ubuntu22.04
       options: --gpus all
     steps:
@@ -19,7 +19,7 @@ jobs:
       run: |
         apt-get update
         apt-get install -y build-essential cmake libboost-all-dev ninja-build
-    
+
     - if: ${{ env.ACT }}
       name: Hack container for local development
       run: |
@@ -42,32 +42,29 @@ jobs:
         nvidia-smi
         unidock --version
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.8
+        python-version: '3.10'
 
     - name: perform unit-test
       run: |
         python -m pip install --upgrade pip
-        pip install pytest coverage
-        coverage run -m pytest unidock/test/ut -v
-        coverage xml
+        pip install pytest>=8.0.0 pytest-cov
+        pytest unidock/test/ut -vv --doctest-modules --junitxml=junit/test-results.xml --cov --cov-report term
 
   build_docker_image:
     needs: unidock_test
     runs-on: ubuntu-latest
     steps:
 
     - name: log in to docker hub
-      uses: docker/login-action@v2
+      uses: docker/login-action@v3
+      if: github.event_name == 'push'
       with:
         username: dptechnology
         password: ${{ secrets.DOCKERHUB_PAT }}
 
-    - name: set up QEMU
-      uses: docker/setup-qemu-action@v2
-
     - name: set up docker buildx
       id: buildx
       uses: docker/setup-buildx-action@v2
@@ -86,4 +83,4 @@ jobs:
         tags: dptechnology/unidock:${{ steps.short-sha.outputs.sha }},dptechnology/unidock:latest
         file: Dockerfile
         context: "{{defaultContext}}:unidock"
-        push: true
+        push: ${{ github.event_name == 'push' }}
diff --git a/unidock/CMakeLists.txt b/unidock/CMakeLists.txt
@@ -19,7 +19,7 @@ if(NOT DEFINED CMAKE_CUDA_ARCHITECTURES)
 	set(CMAKE_CUDA_ARCHITECTURES
 		60 # P100
 		70 # V100
-		75 # T4
+		# 75 # T4
 		80 # A100
 		# 89 # RTX 40
 		90 # H100

diff --git a/unidock/test/ut/test_unidock.py b/unidock/test/ut/test_unidock.py
@@ -10,23 +10,29 @@ class TestUniDock(ut.TestCase):
     def setUp(self):
         self.workdir = Path(f"/tmp/{uuid.uuid4()}")
         self.workdir.mkdir(parents=True, exist_ok=True)
-        self.receptor = os.path.join(os.path.dirname(os.path.dirname(__file__)), "receptor", "1iep_receptor.pdbqt")
-        self.ligand = os.path.join(os.path.dirname(os.path.dirname(__file__)), "ligands", "1iep_ligand.pdbqt")
+        self.receptor = os.path.join(
+            os.path.dirname(os.path.dirname(__file__)),
+            "receptor",
+            "1iep_receptor.pdbqt",
+        )
+        self.ligand = os.path.join(
+            os.path.dirname(os.path.dirname(__file__)), "ligands", "1iep_ligand.pdbqt"
+        )
         self.pocket = [15.19, 53.903, 16.917, 20, 20, 20]
 
     def tearDown(self):
         shutil.rmtree(self.workdir, ignore_errors=True)
 
-    def test_unidock(self):
+    def test_unidock_vina(self):
         cmd = f"unidock --receptor {self.receptor} --gpu_batch {self.ligand} --dir {self.workdir} \
             --center_x {self.pocket[0]} --center_y {self.pocket[1]} --center_z {self.pocket[2]} \
             --size_x {self.pocket[3]} --size_y {self.pocket[4]} --size_z {self.pocket[5]} \
             --scoring vina --search_mode fast --num_modes 1 --seed 181129"
-        resp = subprocess.run(cmd, shell=True, 
-            stdout=subprocess.PIPE, stderr=subprocess.PIPE,
-            encoding="utf-8")
+        resp = subprocess.run(
+            cmd, shell=True, capture_output=True, encoding="utf-8", cwd=self.workdir, check=True,
+        )
         print(resp.stdout)
-        if resp.stderr:
+        if resp.returncode != 0:
             print(resp.stderr)
         result_ligand = os.path.join(self.workdir, "1iep_ligand_out.pdbqt")
         self.assertTrue(os.path.exists(result_ligand))
@@ -37,9 +43,45 @@ def test_unidock(self):
                     score_line = line.strip("\n")
                     break
         self.assertNotEqual(score_line, "")
-        score = float([e for e in score_line[len("REMARK VINA RESULT:"):].split(" ") if e!=""][0])
-        self.assertEqual(score, -10.33)
+        score = float(
+            [e for e in score_line[len("REMARK VINA RESULT:") :].split(" ") if e != ""][
+                0
+            ]
+        )
+        self.assertTrue(-20 <= score <= -1)
+
+    def test_unidock_vinardo(self):
+        cmd = f"unidock --receptor {self.receptor} --gpu_batch {self.ligand} --dir {self.workdir} \
+            --center_x {self.pocket[0]} --center_y {self.pocket[1]} --center_z {self.pocket[2]} \
+            --size_x {self.pocket[3]} --size_y {self.pocket[4]} --size_z {self.pocket[5]} \
+            --scoring vinardo --search_mode fast --num_modes 1 --seed 181129"
+        resp = subprocess.run(
+            cmd,
+            shell=True,
+            capture_output=True,
+            encoding="utf-8",
+            cwd=self.workdir,
+            check=True,
+        )
+        print(resp.stdout)
+        if resp.returncode != 0:
+            print(resp.stderr)
+        result_ligand = os.path.join(self.workdir, "1iep_ligand_out.pdbqt")
+        self.assertTrue(os.path.exists(result_ligand))
+        score_line = ""
+        with open(result_ligand, "r") as f:
+            for line in f.readlines():
+                if line.startswith("REMARK VINA RESULT:"):
+                    score_line = line.strip("\n")
+                    break
+        self.assertNotEqual(score_line, "")
+        score = float(
+            [e for e in score_line[len("REMARK VINA RESULT:") :].split(" ") if e != ""][
+                0
+            ]
+        )
+        self.assertTrue(-20 <= score <= -1)
 
 
 if __name__ == "__main__":
-    ut.main()
+    ut.main()
diff --git a/unidock/test/ut/test_unidock_sdf.py b/unidock/test/ut/test_unidock_sdf.py
@@ -10,23 +10,32 @@ class TestUniDockSDF(ut.TestCase):
     def setUp(self):
         self.workdir = Path(f"/tmp/{uuid.uuid4()}")
         self.workdir.mkdir(parents=True, exist_ok=True)
-        self.receptor = os.path.join(os.path.dirname(os.path.dirname(__file__)), "receptor", "1a30_protein.pdbqt")
-        self.ligand = os.path.join(os.path.dirname(os.path.dirname(__file__)), "ligands", "1a30_ligand.sdf")
+        self.receptor = os.path.join(
+            os.path.dirname(os.path.dirname(__file__)), "receptor", "1a30_protein.pdbqt"
+        )
+        self.ligand = os.path.join(
+            os.path.dirname(os.path.dirname(__file__)), "ligands", "1a30_ligand.sdf"
+        )
         self.pocket = [8.729, 25.62, 4.682, 19.12, 16.56, 18.65]
 
     def tearDown(self):
         shutil.rmtree(self.workdir, ignore_errors=True)
 
-    def test_unidock_sdf(self):
+    def test_unidock_sdf_vina(self):
         cmd = f"unidock --receptor {self.receptor} --gpu_batch {self.ligand} --dir {self.workdir} \
             --center_x {self.pocket[0]} --center_y {self.pocket[1]} --center_z {self.pocket[2]} \
             --size_x {self.pocket[3]} --size_y {self.pocket[4]} --size_z {self.pocket[5]} \
             --scoring vina --search_mode fast --num_modes 1 --seed 181129"
-        resp = subprocess.run(cmd, shell=True, 
-            stdout=subprocess.PIPE, stderr=subprocess.PIPE,
-            encoding="utf-8", cwd=self.workdir)
+        resp = subprocess.run(
+            cmd,
+            shell=True,
+            capture_output=True,
+            encoding="utf-8",
+            cwd=self.workdir,
+            check=True,
+        )
         print(resp.stdout)
-        if resp.stderr:
+        if resp.returncode != 0:
             print(resp.stderr)
         result_ligand = os.path.join(self.workdir, "1a30_ligand_out.sdf")
         self.assertTrue(os.path.exists(result_ligand))
@@ -40,9 +49,44 @@ def test_unidock_sdf(self):
                 if not line:
                     break
         self.assertNotEqual(score_line, "")
-        score = float([e for e in score_line[len("ENERGY="):].split(" ") if e!=""][0])
-        self.assertEqual(score, -6.432)
+        score = float(
+            [e for e in score_line[len("ENERGY=") :].split(" ") if e != ""][0]
+        )
+        self.assertTrue(-20 <= score <= -1)
+
+    def test_unidock_sdf_vinardo(self):
+        cmd = f"unidock --receptor {self.receptor} --gpu_batch {self.ligand} --dir {self.workdir} \
+            --center_x {self.pocket[0]} --center_y {self.pocket[1]} --center_z {self.pocket[2]} \
+            --size_x {self.pocket[3]} --size_y {self.pocket[4]} --size_z {self.pocket[5]} \
+            --scoring vinardo --search_mode fast --num_modes 1 --seed 181129"
+        resp = subprocess.run(
+            cmd,
+            shell=True,
+            capture_output=True,
+            encoding="utf-8",
+            cwd=self.workdir,
+            check=True,
+        )
+        print(resp.stdout)
+        if resp.returncode != 0:
+            print(resp.stderr)
+        result_ligand = os.path.join(self.workdir, "1a30_ligand_out.sdf")
+        self.assertTrue(os.path.exists(result_ligand))
+        score_line = ""
+        with open(result_ligand, "r") as f:
+            while True:
+                line = f.readline()
+                if line.startswith("> <Uni-Dock RESULT>"):
+                    score_line = f.readline().strip("\n")
+                    break
+                if not line:
+                    break
+        self.assertNotEqual(score_line, "")
+        score = float(
+            [e for e in score_line[len("ENERGY=") :].split(" ") if e != ""][0]
+        )
+        self.assertTrue(-20 <= score <= -1)
 
 
 if __name__ == "__main__":
-    ut.main()
+    ut.main()
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,7 +19,7 @@ if(NOT DEFINED CMAKE_CUDA_ARCHITECTURES) @@
     	set(CMAKE_CUDA_ARCHITECTURES
 # P100
 # V100
-# T4
+    		# 75 # T4
 # A100
     		# 89 # RTX 40
 # H100
@@ Expand Down @@