adding CLI for processed

pyproject.toml

@@ -86,4 +86,5 @@ abfe = [
 ]
 
 [project.scripts]
-aleimi-run = "aleimi.cli:_aleimi"
+aleimi-run = "aleimi.cli:_aleimi"
+aleimi-processed="aleimi.cli:_aleimi_processed"

src/aleimi/cli.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-from aleimi import confgen, boltzmann, extractor, __version__, utils
+from aleimi import confgen, boltzmann, extractor, __version__, utils, processed
 import argparse, os, yaml
 
 """
@@ -12,7 +12,7 @@
     """
 
 
-def _aleimi():
+def _aleimi_run():
     """CLI of ``aleimi``
     """
     parser = argparse.ArgumentParser(description=__doc__,
@@ -85,5 +85,40 @@ def _aleimi():
         extractor.main(f"{mol_name}.arc", f"{mol_name}_boltzmann.csv", **boltzmann_keywords)
 
 
+def _aleimi_processed():
+    """CLI of ``processed``
+    """
+    parser = argparse.ArgumentParser(description=__doc__,
+                                     formatter_class=argparse.RawTextHelpFormatter)
+
+
+    parser.add_argument('--no_sub_dirs',
+                        help ='Should be True if :meth:`aleimi.extractor.main` was used with ``mkdir = True``, by default True',
+                        nargs = "?",
+                        dest = 'no_sub_dirs',
+                        const = False,
+                        default = True,
+                        type=bool)
+    parser.add_argument('-e, --engine',
+                        help ="psi4, gaussian or orca. It depends on the engine defined on :meth:`aleimi.extractor.main` was used with ``engine`` keyword, by default 'psi4'",
+                        dest = 'engine',
+                        default = 'psi4',
+                        type=str)
+
+    parser.add_argument('--xyz_out',
+                        help ='If True, it will write the xyz coordinates of the conformer with the lowest energy, by default False',
+                        nargs = "?",
+                        dest = 'xyz_out',
+                        const = True,
+                        default = False,
+                        type=bool)
+
+    args = parser.parse_args()
+
+    processed(
+        SubDirs=not args.no_sub_dirs,
+        engine=args.engine,
+        xyz_out=args.xyz_out
+    )
 if __name__ == '__main__':
     pass

src/aleimi/extractor.py

@@ -95,15 +95,16 @@ def get_coords(input_file, indx_to_extract):
             if 79*'-' in line:
                 while True:
                     line = f.readline()
-                    if (79*'*' in line) or (len(line) == 0):break
+                    if (79*'*' in line) or (len(line) == 0):
+                        break
 
-                    if 'CELL' in line: 
+                    if 'CELL' in line:
                         cell = int(line.split(':')[1])
 
                     elif 'CARTESIAN COORDINATES' in line and cell in indx_to_extract:
                         utils.ignoreLines(f, 1)
                         cont = 0
-                        chunk = []        
+                        chunk = []   
                         while cont < natoms:
                             chunk.append(f.readline())
                             cont += 1
@@ -135,10 +136,12 @@ def main(
     elif engine == 'gaussian':
         InputExt = '.gjf'
     else:
-        print(f"Warning!: It was used 'in' as generic extension for the input file for the non recognized engine: {engine}")
+        print("Warning!: It was used 'in' as generic extension for the input "
+              f"file for the non recognized engine: {engine}")
         InputExt = '.in'
 
-    indx_to_extract = extract(boltzmann_file, energy_cut=energy_cut, conformer_cut=conformer_cut)
+    indx_to_extract = extract(boltzmann_file, energy_cut=energy_cut,
+                              conformer_cut=conformer_cut)
     names_coords = get_coords(input_file, indx_to_extract)
     for name, coords in names_coords:
         INPUT_obj = templates.INPUT(engine, machine=machine, name=name, coords=coords, **keywords)