From 5590d9fd123701a59b50ebe97d7f9657d16f028b Mon Sep 17 00:00:00 2001
From: lunamorrow <luna.morrow2@gmail.com>
Date: Tue, 28 May 2024 21:25:56 +1000
Subject: [PATCH] 28/5/24 starting on OpenBabelReader

---
 mda_openbabel_converter/OpenBabel.py | 50 ++++++++++++++++++++++++++--
 1 file changed, 48 insertions(+), 2 deletions(-)

diff --git a/mda_openbabel_converter/OpenBabel.py b/mda_openbabel_converter/OpenBabel.py
index 2b070e6..838166c 100644
--- a/mda_openbabel_converter/OpenBabel.py
+++ b/mda_openbabel_converter/OpenBabel.py
@@ -5,22 +5,68 @@
 import MDAnalysis as mda
 from MDAnalysis.converters.base import ConverterBase
 from MDAnalysis.coordinates.base import SingleFrameReaderBase
+from MDAnalysis.core.groups import AtomGroup
+
+try:
+    import openbabel as OB
+    from openbabel import OBMol
+except ImportError:
+    print("Cannot find openbabel, install with 'pip install openbabel==2.4.0'")
 
 class OpenBabelReader(SingleFrameReaderBase):
     """
     Convert an OpenBabel OBMol (from the file) to a MDAnalysis AtomGroup
     """
+    @staticmethod
     def _format_hint(thing):
         """
         Base function to check if the reader can actually read this “thing” 
         (i.e., is it a file that can be converted to an OpenBabel OBMol?)
         """
-        pass
+        try:
+            import openbabel as OB
+        except ImportError:
+            return False
+        else:
+            return isinstance(thing, OB.OBMol)
 
-    def __init__(self, filename, **kwargs):
+    def __init__(self, filename: OBMol, **kwargs):
         """
         Converts file to OBMol to AtomGroup
         """
+        self.atoms = []
+        self.n_atoms = 0
+        self.residues = []
+        self.n_residues = 0
+        self.segments = []
+        self.n_segments = 0
+
+        obmol = filename
+
+        # Atoms
+        names = [] 
+        chiralities = []
+        resnums = []
+        resnames = []
+        elements = []
+        masses = []
+        charges = []
+        aromatics = []
+        ids = []
+        atomtypes = []
+        segids = []
+        altlocs = []
+        chainids = []
+        icodes = []
+        occupancies = []
+        tempfactors = []
+
+        for i in range(1, obmol):
+            atom = obmol.GetAtomById(i-1)
+            # need to add handling incase attributes are invalid or null in OBMol
+            names.append(atom.GetType()) #char
+
+
         pass
 
 class OpenBabelConverter(ConverterBase):