Added a script for automatically cleaning IRC calculations

pyqmmm/cli.py

@@ -282,6 +282,7 @@ def md(
 @click.option("--bond_valence", "-bv", is_flag=True, help="Replace QM optimized atoms in a pdb.")
 @click.option("--orca_scan", "-os", is_flag=True, help="Plots an ORCA scan.")
 @click.option("--orca_neb_restart", "-rneb", is_flag=True, help="Prepare to restart an ORCA NEB.")
+@click.option("--orca_clean_irc", "-circ", is_flag=True, help="Removes remaining files from an IRC calc.")
 @click.option("--combine_nebs", "-cneb", is_flag=True, help="Combines and NEBs.")
 @click.option("--plot_combine_nebs", "-pcneb", is_flag=True, help="Combines and plots NEBs as a single trajectory.")
 @click.option("--extract_energies", "-ee", is_flag=True, help="Extract electronic energies")
@@ -296,6 +297,7 @@ def qm(
     bond_valence,
     orca_scan,
     orca_neb_restart,
+    orca_clean_irc,
     combine_nebs,
     plot_combine_nebs,
     extract_energies,
@@ -371,6 +373,10 @@ def qm(
         files_in_directory = [f for f in os.listdir() if f != 'delete']
         pyqmmm.qm.orca_neb_restart.move_files(files_in_directory)
 
+    if orca_clean_irc:
+        import pyqmmm.qm.orca_clean_irc
+        pyqmmm.qm.orca_clean_irc.main()
+
     if combine_nebs:
         import pyqmmm.qm.combine_nebs
         pyqmmm.qm.combine_nebs.combine_trajectories()

pyqmmm/qm/orca_clean_irc.py

@@ -0,0 +1,99 @@
+#!/usr/bin/env python3
+"""
+orca_irc_cleanup.py
+===================
+
+Utility to purge non‑essential files left over from an ORCA **I**ntrinsic **R**eaction **C**oordinate (IRC) job.
+
+Safety features
+---------------
+1. **IRC verification** – The script aborts unless **at least one** ``*.out`` file in the working directory
+   contains the phrase ``"Storing full IRC trajectory in"`` (case‑sensitive), which ORCA prints only for
+   IRC runs.
+2. **Interactive confirmation** – A simple "Continue? (y/N):" prompt; default is **No**.
+3. **Scope limited to CWD** – Only files directly in the current working directory are affected.
+
+Examples
+--------
+$ cd /path/to/irc_job  # <- run inside the job dir
+$ python orca_irc_cleanup.py
+Identified 8 left over files from the IRC calculation. Continue? (y/N): y
+Deleted 8 files.
+"""
+from __future__ import annotations
+
+import os
+import sys
+from pathlib import Path
+from typing import List, Set
+
+ALLOWED_EXTS: Set[str] = {
+    ".sh", ".out", ".in", ".gbw", ".xyz", ".densities", ".densitiesinfo", ".engrad",
+}
+
+MARKER = "Storing full IRC trajectory in"
+
+
+def is_irc_directory(path: Path) -> bool:
+    """Return *True* if any ``*.out`` file under *path* contains ``MARKER``.
+
+    Parameters
+    ----------
+    path
+        Directory expected to hold ORCA output files.
+
+    Notes
+    -----
+    Reads files line‑by‑line and stops at the first match.
+    """
+    for out_file in path.glob("*.out"):
+        try:
+            with out_file.open("r", errors="ignore") as f:
+                for line in f:
+                    if MARKER in line:
+                        return True
+        except OSError:
+            continue  # unreadable file – just skip
+    return False
+
+
+def find_leftovers(path: Path) -> List[Path]:
+    """Return list of files lacking extensions in ``ALLOWED_EXTS``."""
+    return [p for p in path.iterdir() if p.is_file() and p.suffix.lower() not in ALLOWED_EXTS]
+
+
+def main() -> None:  # noqa: D401
+    """Script entry point."""
+    cwd = Path(".").resolve()
+
+    if not is_irc_directory(cwd):
+        sys.exit("This directory does not appear to be an ORCA IRC calculation (marker not found).")
+
+    leftovers = find_leftovers(cwd)
+    count = len(leftovers)
+    if count == 0:
+        print("No extraneous files found. Nothing to do.")
+        return
+
+    print(f"You are located in: {os.getcwd()}")
+    response = input(
+        f"Identified {count} left over file{'s' if count != 1 else ''} from the IRC calculation. "
+        "Continue? (y/N): "
+    ).strip().lower()
+    if response != "y":
+        print("Aborted.")
+        return
+
+    deleted = 0
+    for fp in leftovers:
+        try:
+            fp.unlink()
+            deleted += 1
+        except Exception as exc:
+            print(f"Could not delete {fp}: {exc}", file=sys.stderr)
+
+    print(f"Deleted {deleted} file{'s' if deleted != 1 else ''}.")
+
+
+if __name__ == "__main__":
+    main()