refactored to be able to install package

Signed-off-by: Marcel Müller <[email protected]>

pyproject.toml

@@ -0,0 +1,12 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.mypy]
+check_untyped_defs = true
+disallow_any_generics = true
+disallow_incomplete_defs = true
+disallow_untyped_defs = true
+warn_redundant_casts = true
+warn_unreachable = true
+warn_unused_ignores = true

setup.cfg

@@ -0,0 +1,41 @@
+[metadata]
+name = getrandompcmol
+version = attr: getrandompcmol.__version__.__version__
+long_description = file: README.md
+long_description_content_type = text/markdown
+author = "Marcel Müller"
+license = GPL-3.0
+license_files = LICENSE
+classifiers =
+    License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Topic :: Scientific/Engineering
+    Typing :: Typed
+
+[options]
+packages = find:
+install_requires =
+    numpy
+python_requires = >=3.8
+include_package_data = True
+package_dir =
+    =src
+
+[options.packages.find]
+where = src
+
+[options.entry_points]
+console_scripts =
+    getrandompcmol = getrandompcmol:console_entry_point
+
+[options.extras_require]
+dev =
+    black
+    pre-commit
+    pylint

setup.py

@@ -0,0 +1,4 @@
+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()

src/getrandompcmol/__init__.py

@@ -0,0 +1,10 @@
+"""
+GetRandomPCMol
+=======
+
+Dummy command line tool to square a number.
+"""
+
+from .__version__ import __version__
+from .miscelleanous import chdir, create_directory
+from .randommols import console_entry_point, main

src/getrandompcmol/__version__.py

@@ -0,0 +1,5 @@
+"""
+Module containing the version string.
+"""
+
+__version__ = "0.1.0"

src/getrandompcmol/miscelleanous.py

@@ -0,0 +1,46 @@
+"""
+Miscelleanous functions that are used in the project.
+"""
+
+from __future__ import annotations
+
+import os
+
+
+def create_directory(name: str) -> bool:
+    """
+    Creates a directory with the given name if it does not exist already.
+    """
+    if not os.path.exists(name):
+        os.mkdir(name)
+        exist = False
+    else:
+        print(f"Directory {name} already exists.")
+        exist = True
+
+    # check if the new directory exists and raise an error and stop execution if not
+    try:
+        if not os.path.exists(name):
+            raise FileNotFoundError(f"Directory {name} does not exist.")
+    except FileNotFoundError as e:
+        print(f"Error: {e}")
+        raise SystemExit(1) from e
+    return exist
+
+
+# define a function which goes back to the original working directory if it is called
+def chdir(dirname: str) -> None:
+    """
+    Change the active directory.
+    """
+    try:
+        os.chdir(str(dirname))
+        # print("Current working directory: {0}".format(os.getcwd()))
+    except FileNotFoundError:
+        print(f"Directory: {dirname} does not exist")
+    except NotADirectoryError:
+        print(f"{dirname} is not a directory")
+    except PermissionError:
+        print(f"You do not have permissions to change to {dirname}")
+
+    return None

randommols.py → src/getrandompcmol/randommols.py

@@ -1,31 +1,30 @@
 #!/usr/bin/env python
 
+"""
+This script generates random molecules from PubChem and optimizes them with xTB.
+"""
+from __future__ import annotations
+
 import argparse as ap
 import os
 import subprocess
 
 from numpy.random import RandomState
 
+from .miscelleanous import chdir, create_directory
+
 
-def main(arguments):
+def main(arguments: ap.Namespace) -> None:
+    """
+    Main function of the script.
+    """
     # get number of compounds from command line
     numcomp = arguments.numcomp
 
     ### GENERAL PARAMETERS ###
     maxcid = 10000000
     maxnumat = 50
 
-    class bcolors:
-        HEADER = "\033[95m"
-        OKBLUE = "\033[94m"
-        OKCYAN = "\033[96m"
-        OKGREEN = "\033[92m"
-        WARNING = "\033[93m"
-        FAIL = "\033[91m"
-        ENDC = "\033[0m"
-        BOLD = "\033[1m"
-        UNDERLINE = "\033[4m"
-
     # set the seed
     print(f"Generating random numbers between 1 and {maxcid:d} ...")
     seed = RandomState(2009)
@@ -35,8 +34,8 @@ class bcolors:
     pwd = os.getcwd()
 
     # run PubGrep for each value and set up a list with successful downloads
-    comp = []
-    molname = []
+    comp: list[int] = []
+    molname: list[str] = []
     for i in values:
         print(f"\nDownloading CID {i:7d} ...")
         try:
@@ -82,30 +81,21 @@ class bcolors:
             else:
                 print(" " * 3 + f"Downloaded {i:7d} successfully after xTB conversion.")
 
-        try:
-            os.chdir(str(pwd) + "/pubchem_compounds/" + str(i))
-            # print("Current working directory: {0}".format(os.getcwd()))
-        except FileNotFoundError:
-            print(f"Directory: /pubchem_compounds/{i} does not exist")
-        except NotADirectoryError:
-            print(f"/pubchem_compounds/{i} is not a directory")
-        except PermissionError:
-            print(f"You do not have permissions to change to /pubchem_compounds/{i}")
-
         # print the first entry of the fourth line compund of interest in sdf format
         with open(f"{i}.sdf", encoding="UTF-8") as f:
             lines = f.readlines()
             nat = int(lines[3].split()[0])
             print(" " * 3 + f"# of atoms: {nat:8d}")
             if int(nat) > maxnumat:
                 print(
-                    f"""{bcolors.WARNING}Number of
-                    atoms in {i}.sdf is larger than {maxnumat} -
-                    skipping CID {i:7d}{bcolors.ENDC}"""
+                    f"{bcolors.WARNING}Number of \
+atoms in {i}.sdf is larger than {maxnumat} -\
+skipping CID {i:7d}{bcolors.ENDC}"
                 )
-                odir(pwd)
                 continue
 
+        direxists = create_directory(str(i))
+        chdir(str(i))
         try:
             pgout = subprocess.run(
                 ["xtb", f"{i}.sdf", "--opt"],
@@ -117,7 +107,7 @@ class bcolors:
                 f.write(pgout.stdout.decode("utf-8"))
         except subprocess.TimeoutExpired as exc:
             print(" " * 3 + f"Process timed out.\n{exc}")
-            odir(pwd)
+            chdir(pwd)
             continue
         except subprocess.CalledProcessError as exc:
             print(
@@ -131,7 +121,7 @@ class bcolors:
                 f"{bcolors.WARNING}xTB optimization failed - skipping CID %7d{bcolors.ENDC}"
                 % i
             )
-            odir(pwd)
+            chdir(pwd)
             continue
 
         # load fourth entry of a line with ":: total charge" of xtb.out into a variable
@@ -155,7 +145,7 @@ class bcolors:
             )
         except subprocess.TimeoutExpired as exc:
             print(" " * 3 + f"Process timed out.\n{exc}")
-            odir(pwd)
+            chdir(pwd)
             continue
         except subprocess.CalledProcessError as exc:
             print(" " * 3 + "Status : FAIL", exc.returncode, exc.output)
@@ -166,10 +156,10 @@ class bcolors:
                 f"{bcolors.WARNING}mctc-convert failed - skipping CID %7d{bcolors.ENDC}"
                 % i
             )
-            odir(pwd)
+            chdir(pwd)
             continue
 
-        odir(pwd)
+        chdir(pwd)
 
         # grep the name of the molecule from found.results (first entry in first line)
         with open("found.results", encoding="UTF-8") as f:
@@ -178,8 +168,8 @@ class bcolors:
             print(" " * 3 + f"Compound name: {molname[-1]:s}")
 
         print(
-            f"""{bcolors.OKGREEN}Structure of
-%7d successfully generated and optimized.{bcolors.ENDC}"""
+            f"{bcolors.OKGREEN}Structure of\
+ %7d successfully generated and optimized.{bcolors.ENDC}"
             % i
         )
         comp.append(i)
@@ -198,18 +188,24 @@ class bcolors:
     os.remove("found.results")
 
 
-# define a function which goes back to the original working directory if it is called
-def odir(pwdorg):
-    try:
-        os.chdir(str(pwdorg))
-        # print("Current working directory: {0}".format(os.getcwd()))
-    except FileNotFoundError:
-        print("Directory does not exist")
-    except NotADirectoryError:
-        print(f"{pwdorg} is not a directory")
+class bcolors:
+    """
+    Class for colorizing the output.
+    """
 
+    HEADER = "\033[95m"
+    OKBLUE = "\033[94m"
+    OKCYAN = "\033[96m"
+    OKGREEN = "\033[92m"
+    WARNING = "\033[93m"
+    FAIL = "\033[91m"
+    ENDC = "\033[0m"
+    BOLD = "\033[1m"
+    UNDERLINE = "\033[4m"
 
-if __name__ == "__main__":
+
+def console_entry_point() -> int:
+    # parse arguments
     parser = ap.ArgumentParser(description="Generate random molecules from PubChem")
     parser.add_argument(
         "-n",
@@ -221,3 +217,8 @@ def odir(pwdorg):
     )
     args = parser.parse_args()
     main(args)
+    return 0
+
+
+if __name__ == "__main__":
+    console_entry_point()