From 162ace202104925cab5f01f714e27ce153c47437 Mon Sep 17 00:00:00 2001
From: bieniekmat <bieniekmat@gmail.com>
Date: Mon, 10 Jul 2023 13:26:59 +0100
Subject: [PATCH] Allowing gnina to fail.

---
 fegrow/package.py | 45 ++++++++++++++++++---------------------------
 1 file changed, 18 insertions(+), 27 deletions(-)

diff --git a/fegrow/package.py b/fegrow/package.py
index 15f8a694..17a22d9d 100644
--- a/fegrow/package.py
+++ b/fegrow/package.py
@@ -1,19 +1,15 @@
 import copy
-import itertools
 import stat
-from typing import Optional, List, Union, Tuple
+from typing import Optional, List, Union
 import os
 import tempfile
 import subprocess
 import re
 from pathlib import Path
 from urllib.request import urlretrieve
-from collections import OrderedDict
 
 import numpy as np
-import matplotlib.pyplot as plt
-from matplotlib.colors import to_hex
-from prody.proteins.functions import showProtein, view3D
+from prody.proteins.functions import view3D
 import py3Dmol
 import rdkit
 from rdkit import Chem
@@ -512,7 +508,7 @@ def _check_download_gnina():
         os.chmod(gnina, mode | stat.S_IEXEC)
 
         # check if it works
-        subprocess.run(["./gnina", "--help"], capture_output=True, cwd=RMol.gnina_dir)
+        subprocess.run(["./gnina", "--help"], capture_output=True, check=True, cwd=RMol.gnina_dir)
 
     def gnina(self, receptor_file):
         """
@@ -537,26 +533,21 @@ def gnina(self, receptor_file):
                 w.write(self, confId=conformer.GetId())
 
         # run the code on the sdf
-        try:
-            process = subprocess.run(
-                [
-                    "./gnina",
-                    "--score_only",
-                    "-l",
-                    tmp.name,
-                    "-r",
-                    receptor.absolute(),
-                    "--seed",
-                    "0",
-                    "--stripH",
-                    "False",
-                ],
-                capture_output=True,
-                check=True,
-                cwd=RMol.gnina_dir,
-            )
-        except subprocess.CalledProcessError as E:
-            raise Exception('Gnina Failed', process.stderr, E)
+        process = subprocess.run(
+            [
+                RMol.gnina_dir / "gnina",
+                "--score_only",
+                "-l",
+                tmp.name,
+                "-r",
+                receptor,
+                "--seed",
+                "0",
+                "--stripH",
+                "False",
+            ],
+            capture_output=True,
+            check=True)
 
         output = process.stdout.decode("utf-8")
         CNNaffinities_str = re.findall(r"CNNaffinity: (-?\d+.\d+)", output)