From deb5f6ebc1e70345b98e3e62f7039fb2361593c2 Mon Sep 17 00:00:00 2001
From: Logan Ward <ward.logan.t@gmail.com>
Date: Tue, 3 Oct 2023 16:31:48 -0400
Subject: [PATCH] De-duplicate the assemble function

Whoops, forgot I had a whole 'assemble' module
---
 mofa/assemble.py | 21 ++++++++++-----------
 mofa/model.py    | 25 -------------------------
 2 files changed, 10 insertions(+), 36 deletions(-)

diff --git a/mofa/assemble.py b/mofa/assemble.py
index 0ab61eac..25e7bf33 100644
--- a/mofa/assemble.py
+++ b/mofa/assemble.py
@@ -1,19 +1,18 @@
 """Functions for assembling a MOF structure"""
-import ase
+from typing import Sequence
 
+from .model import NodeDescription, LigandDescription, MOFRecord
 
-def assemble_mof(
-        node: object,
-        linker: str,
-        topology: object
-) -> ase.Atoms:
-    """Generate a MOF structure from a recipe
+
+def assemble_mof(nodes: Sequence[NodeDescription], ligands: Sequence[LigandDescription], topology: str) -> MOFRecord:
+    """Generate a new MOF from the description of the nodes, ligands and toplogy
 
     Args:
-        node: Atomic structure of the nodes
-        linker: SMILES string defining the linker object
-        topology: Description of the network structure
+        nodes: Descriptions of each node
+        ligands: Description of the ligands
+        topology: Name of the topology
+
     Returns:
-        Description of the 3D structure of the MOF
+        A new MOF record
     """
     raise NotImplementedError()
diff --git a/mofa/model.py b/mofa/model.py
index 3da4badd..68f0876d 100644
--- a/mofa/model.py
+++ b/mofa/model.py
@@ -102,32 +102,7 @@ def from_file(cls, cif_path: Path | str, **kwargs) -> 'MOFRecord':
 
         return MOFRecord(structure=Path(cif_path).read_text(), **kwargs)
 
-    def replace_ligand(self, new_ligand: ase.Atoms) -> 'MOFRecord':
-        """Create a new MOF by replacing the ligands in this MOF with new
-
-        Args:
-            new_ligand:
-
-        Returns:
-
-        """
-        return assemble_mof(self.nodes, [new_ligand], self.topology)
-
     @cached_property
     def atoms(self) -> ase.Atoms:
         """The structure as an ASE Atoms object"""
         return next(read_cif(StringIO(self.structure), index=slice(None)))
-
-
-def assemble_mof(nodes: Sequence[NodeDescription], ligands: Sequence[LigandDescription], topology: str) -> MOFRecord:
-    """Generate a new MOF from the description of the nodes, ligands and toplogy
-
-    Args:
-        nodes: Descriptions of each node
-        ligands: Description of the ligands
-        topology: Name of the topology
-
-    Returns:
-        A new MOF record
-    """
-    raise NotImplementedError()