added another action to test

2 files changed, 60 insertions, 0 deletions

diff --git a/.github/workflows/test-plip-oddt.yaml b/.github/workflows/test-plip-oddt.yaml
new file mode 100644
index 0000000..383a1e2
--- /dev/null
+++ b/.github/workflows/test-plip-oddt.yaml
@@ -0,0 +1,25 @@
+name: Test Curie Functions
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+    if: "! contains(github.event.head_commit.message, 'wip')"
+    strategy:
+      matrix:
+        python-version: [3.8]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        apt update && apt install python3-openbabel openbabel
+        python -m pip install git
+        python3 -m pip install git+https://github.com/navanchauhan/plip oddt
+    - name: Clean Test Data
+      run: cd tests && python test-oddt-plip.py
diff --git a/tests/test-oddt-plip.py b/tests/test-oddt-plip.py
new file mode 100644
index 0000000..b993516
--- /dev/null
+++ b/tests/test-oddt-plip.py
@@ -0,0 +1,35 @@
+from plip.basic import config
+from plip.exchange.webservices import fetch_pdb
+from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
+from plip.structure.preparation import tilde_expansion, PDBComplex
+
+pdbId = "6LU7"
+print("Downloading PDB:",pdbId)
+
+pdbfile, pdbid = fetch_pdb(pdbId.lower())
+
+pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
+create_folder_if_not_exists(config.BASEPATH)
+with open(pdbpath, 'w') as g:
+    g.write(pdbfile)
+
+print("Adding Charges")
+import oddt
+from oddt.docking.AutodockVina import write_vina_pdbqt
+receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1]))
+receptor.calccharges()
+#receptor = next(oddt.toolkits.rdk.readfile("pdb",pdbpath.split("./")[1]))
+#receptor.calccharges()
+
+print("Writing PDBQT")
+path = write_vina_pdbqt(receptor,'.',flexible=False)
+
+smiles = 'CCC(CC)COC(=O)C(C)NP(=O)(OCC1C(C(C(O1)(C#N)C2=CC=C3N2N=CN=C3N)O)O)OC4=CC=CC=C4'
+
+print("Generating Strucutre")
+mol = oddt.toolkit.readstring('smi', smiles)
+mol.make3D()
+print("Adding Charges")
+mol.calccharges()
+
+path2 = write_vina_pdbqt(mol,'.',flexible=False)
\ No newline at end of file