Merge pull request #43 from RECETOX/wverastegui/issue40

Updated load_template function calling and read_coordinates ()
RECETOX · Nov 13, 2024 · ce11773 · ce11773
2 parents a68517a + 2ffd3ef
commit ce11773
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Showing 2 changed files with 13 additions and 8 deletions.
diff --git a/codes/extract_coords_into_inp_xyz.py b/codes/extract_coords_into_inp_xyz.py
@@ -8,9 +8,9 @@
 import os
 
 
-PBS_TEMPLATE = load_template("templates", "optimization_gamess_template.pbs")
-INP_TEMPLATE = load_template("templates", "gamess_input_template.inp")
-XYZ_TEMPLATE = load_template("templates", "structure_input_template.xyz")
+PBS_TEMPLATE = load_template("optimization_gamess_template.pbs")
+INP_TEMPLATE = load_template("gamess_input_template.inp")
+XYZ_TEMPLATE = load_template("structure_input_template.xyz")
 
 
 def coords_as_dataframe(element_symbol: List[str], x_coord: List[str], y_coord: List[str], z_coord: List[str])  -> pd.DataFrame:
@@ -48,7 +48,12 @@ def read_coordinates(n_atoms: int, gamess_output: List[str], line_number: int) -
     """
     start, end = compute_start_end_indices(n_atoms, line_number, 4)
     data = [line.split() for line in gamess_output[start:end]]
-    element_symbol, x_coord, y_coord, z_coord = zip(*data)
+
+    element_symbol = [line[0] for line in data]
+    x_coord = [line[2] for line in data]
+    y_coord = [line[3] for line in data]
+    z_coord = [line[4] for line in data]
+
     return element_symbol, x_coord, y_coord, z_coord
 
 

diff --git a/codes/write_dirs_files_for_gamess_qcxms.py b/codes/write_dirs_files_for_gamess_qcxms.py
@@ -277,13 +277,13 @@ def write_gamess_input(multiplicity: int, mol: object, molname: str, mol_input_p
             write_gamess_input(multiplicity, mol, molname, mol_input_path)
 
         spectrum_input_path = spectra_dir / ("qcxms" + ".in")
-        qcxms_template = load_template("templates", "qcxms_input_template.in")
+        template = load_template("qcxms_input_template.in")
         if not Path(spectrum_input_path).exists():
             qcxms_params = read_parameters(args.params_filename, ["QC_Program", "QC_Level", "ntraj", "tmax", "tinit", "ieeatm"])
-            write_from_template(parameters=qcxms_params, template=qcxms_template, file=spectrum_input_path)
+            write_from_template(parameters=qcxms_params, template=template, file=spectrum_input_path)
 
         mol_pbs_path = mol_dir / (inchikey + ".pbs")
-        pbs_template = load_template("templates", "optimization_gamess_template.pbs")
+        template = load_template("optimization_gamess_template.pbs")
         if not Path(mol_pbs_path).exists():
             pbs_params = read_parameters(args.params_filename, ["WALLTIME", "NCPUS", "MEM", "SCRATCH_LOCAL", "USER_EMAIL"])
-            write_from_template(parameters={"MOLNAME": inchikey, **pbs_params}, template=pbs_template, file=mol_pbs_path)
+            write_from_template(parameters={"MOLNAME": inchikey, **pbs_params}, template=template, file=mol_pbs_path)