Bug at naming clean files (CleanPDB tool). It was taking the whole fi…

…le name instead of just the protein identifier making the name longer. 2. Adding some printing statements for clarity in case of errors for the user. 3. Fix registry of the path of packed structures. It mapped them originally when they where at the root directory and then moved the file to the files/pdb directory. Next calls of the file was failing because of this

mdagent/tools/base_tools/preprocess_tools/clean_tools.py

@@ -353,7 +353,7 @@ def _run(self, **input_args) -> str:
             file_mode = "w" if add_hydrogens else "a"
             file_name = self.path_registry.write_file_name(
                 type=FileType.PROTEIN,
-                protein_name=name,
+                protein_name=name.split("_")[0],
                 description="Clean",
                 file_format=end,
             )

mdagent/tools/base_tools/preprocess_tools/pdb_tools.py

@@ -127,6 +127,9 @@ def validate_pdb_format(fhandle):
         - 1 if error was found, 0 if no errors were found.
         - List of error messages encountered.
     """
+    # check if filename is in directory
+    if not os.path.exists(fhandle):
+        return (1, ["File not found. Packmol failed to write the file."])
     errors = []
     _fmt_check = (
         ("Atm. Num.", (slice(6, 11), re.compile(r"[\d\s]+"))),
@@ -160,7 +163,7 @@ def _make_pointer(column):
         if not line:
             continue
 
-        if line[0:6] in ("ATOM  ", "HETATM"):
+        if line[0:6] in ["ATOM  ", "HETATM"]:
             # ... [rest of the code unchanged here]
             linelen = len(line)
             if linelen < 80:
@@ -338,10 +341,12 @@ def run_packmol(self, PathRegistry):
         cmd = "packmol < packmol.inp"
         result = subprocess.run(cmd, shell=True, text=True, capture_output=True)
         if result.returncode != 0:
+            print("Packmol failed to run with 'packmol < packmol.inp' command")
             result = subprocess.run(
                 "./" + cmd, shell=True, text=True, capture_output=True
             )
             if result.returncode != 0:
+                print("Packmol failed to run with './packmol < packmol.inp' command")
                 return (
                     "Packmol failed to run. Please check the input file and try again."
                 )
@@ -355,13 +360,13 @@ def run_packmol(self, PathRegistry):
                 os.remove(molecule.filename)
             # name of packed pdb file
             time_stamp = PathRegistry.get_timestamp()[-6:]
+            os.rename(self.final_name, f"files/pdb/{self.final_name}")
             PathRegistry.map_path(
                 f"PACKED_{time_stamp}",
-                f"{self.final_name}",
+                f"files/pdb/{self.final_name}",
                 self.file_description,
             )
             # move file to files/pdb
-            os.rename(self.final_name, f"files/pdb/{self.final_name}")
             return f"PDB file validated successfully. FileID: PACKED_{time_stamp}"
         elif pdb_validation[0] == 1:
             # format pdb_validation[1] list of errors
@@ -486,6 +491,7 @@ def _run(self, **values) -> str:
                 "./" + cmd, shell=True, text=True, capture_output=True
             )
             if result.returncode != 0:
+                print("Packmol is not installed")
                 return (
                     "Packmol is not installed. Please install packmol "
                     "at 'https://m3g.github.io/packmol/download.shtml' and try again."