From 8e279bd925910de8c4c1cc1506f95087a96401dd Mon Sep 17 00:00:00 2001
From: m-julian <52214154+m-julian@users.noreply.github.com>
Date: Wed, 24 Apr 2024 23:56:19 +0300
Subject: [PATCH] add parent dir and docstring update

---
 .../ichor/core/files/xyz/trajectory.py          | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/ichor_core_subpackage/ichor/core/files/xyz/trajectory.py b/ichor_core_subpackage/ichor/core/files/xyz/trajectory.py
index b1424e62..c670fa71 100644
--- a/ichor_core_subpackage/ichor/core/files/xyz/trajectory.py
+++ b/ichor_core_subpackage/ichor/core/files/xyz/trajectory.py
@@ -149,7 +149,13 @@ def rmsd(self, ref=None):
 
         return [ref.rmsd(point) for point in self]
 
-    def to_dir(self, system_name: str, every: int = 1, center=False) -> Path:
+    def to_dir(
+        self,
+        system_name: str,
+        every: int = 1,
+        center: bool = False,
+        parent_dir: Path = None,
+    ) -> Path:
         """Writes out every nth timestep to a separate .xyz file to a given directory
 
         :param system_name: The name of the system. This will be the name of the
@@ -157,6 +163,8 @@ def to_dir(self, system_name: str, every: int = 1, center=False) -> Path:
         :param every: An integer value that indicates the nth step at which an
             xyz file should be written. Default is 1. If
             a value eg. 5 is given, then it will only write out a .xyz file for every 5th timestep.
+        :param center: Whether or not to subtract mean of coordinates from atomic coordinates, defaults to False
+        :param parent_dir: A path to a parent directory where the inner directory will be created.
 
         :returns: The Path object to the made directory
         """
@@ -166,7 +174,12 @@ def to_dir(self, system_name: str, every: int = 1, center=False) -> Path:
 
         # capitalize system name
         system_name = system_name.upper()
-        root_path = Path(system_name).with_suffix(default_root_suffix)
+        if parent_dir:
+            if not parent_dir.exists():
+                parent_dir.mkdir()
+            root_path = parent_dir / Path(system_name).with_suffix(default_root_suffix)
+        else:
+            root_path = Path(system_name).with_suffix(default_root_suffix)
 
         mkdir(root_path, empty=True)
         for i, atoms_instance in enumerate(self):