28/5/24 starting on OpenBabelReader

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):