Merge pull request #16 from lunamorrow/reader-and-tests

OpenBabelReader and Tests

mda_openbabel_converter/OpenBabel.py

@@ -6,35 +6,73 @@
 from MDAnalysis.converters.base import ConverterBase
 from MDAnalysis.coordinates.memory import MemoryReader
 from MDAnalysis.core.groups import AtomGroup
+import numpy as np
+import warnings
+
+HAS_OBABEL = False
 
 try:
- from openbabel import openbabel as OB
- from openbabel import OBMol
+ from openbabel import openbabel as ob
+ from openbabel.openbabel import OBMol, OBAtom, OBMolAtomIter
+ HAS_OBABEL = True
 except ImportError:
- print("Cannot find openbabel, install with 'pip install openbabel==2.4.0'")
+ warnings.warn("Cannot find openbabel, install with `mamba install -c "
+ "conda-forge openbabel`")
+
 
 class OpenBabelReader(MemoryReader):
  """
- Convert an OpenBabel OBMol (from the file) to a MDAnalysis AtomGroup
+ Inherits from MemoryReader and converts OpenBabel OBMol Coordinates to a
+ MDAnalysis Trajectory which is used to build a Universe. This reader
+ does not work in the reverse direction.
  """
+ format = 'OPENBABEL'
+
+ # Structure.coordinates always in Angstrom
+ units = {'time': None, 'length': 'Angstrom'}
+
  @staticmethod
  def _format_hint(thing):
  """
- Base function to check if the reader can actually read this “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?)
  """
- try:
- import openbabel as OB
- except ImportError:
+ if HAS_OBABEL is False:
  return False
  else:
- return isinstance(thing, OB.OBMol)
+ return isinstance(thing, OBMol)
 
  def __init__(self, filename: OBMol, **kwargs):
  """
  Converts file to OBMol to AtomGroup
  """
- pass
+ n_atoms = filename.NumAtoms()
+ # single position
+ if filename.NumConformers() == 1:
+ coordinates = np.array([
+ [(coords := atom.GetVector()).GetX(),
+ coords.GetY(),
+ coords.GetZ()] for atom in OBMolAtomIter(filename)],
+ dtype=np.float32)
+ else:
+ # multiple conformers, such as for a trajectory
+ numConf = filename.NumConformers()
+ coordinates = np.zeros((numConf, n_atoms, 3))
+ for conf_id in range(numConf):
+ filename.SetConformer(conf_id)
+ for atom in OBMolAtomIter(filename):
+ coordinates_inner = np.array([
+ [(coords := atom.GetVector()).GetX(),
+ coords.GetY(),
+ coords.GetZ()] for atom in OBMolAtomIter(filename)],
+ dtype=np.float32)
+ coordinates[conf_id] = coordinates_inner
+ # no coordinates present
+ if not np.any(coordinates):
+ warnings.warn("No coordinates found in the OBMol")
+ coordinates = np.empty((1, n_atoms, 3), dtype=np.float32)
+ coordinates[:] = np.nan
+ super(OpenBabelReader, self).__init__(coordinates, order='fac', **kwargs)
 
 class OpenBabelConverter(ConverterBase):
  """

mda_openbabel_converter/data/ChEBI_26355.mol

@@ -0,0 +1,98 @@
+
+ Marvin 01281309122D 
+
+ 43 50 0 0 0 0 999 V2000
+ 10.0400 -6.3601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.9791 -5.4001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.6887 -4.9827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 12.4191 -5.4001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.3583 -6.3601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.7757 -7.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.3583 -7.7793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 12.4191 -8.7393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.6887 -9.1567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.9791 -8.7393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.0400 -7.7793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.6226 -7.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 12.5444 -6.2140 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 12.5444 -7.9253 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.8539 -7.9253 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.6643 -5.6088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.8674 -5.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.1497 -5.0244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.3632 -4.2275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.7548 -8.5306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 14.5516 -8.7441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.6643 -8.5306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.8674 -8.7441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.2487 -5.0244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.0352 -4.2275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.2383 -4.0140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.7548 -5.6088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 14.5516 -5.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 14.7652 -4.5984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.2487 -9.1149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.0352 -9.9118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.2383 -10.1253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.1497 -9.1149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.3632 -9.9118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 14.1601 -10.1253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.2279 -11.1357 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.0248 -10.9222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.6081 -11.5056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 13.7902 -11.5056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 14.3734 -10.9222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 15.1703 -11.1357 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.8539 -6.2140 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.6887 -7.0697 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 42 1 0 0 0 0
+ 16 1 2 0 0 0 0
+ 1 12 1 0 0 0 0
+ 2 3 1 0 0 0 0
+ 42 2 1 0 0 0 0
+ 24 2 2 0 0 0 0
+ 3 4 2 0 0 0 0
+ 4 13 1 0 0 0 0
+ 18 4 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 13 5 2 0 0 0 0
+ 27 5 1 0 0 0 0
+ 6 7 2 0 0 0 0
+ 7 14 1 0 0 0 0
+ 7 20 1 0 0 0 0
+ 8 9 2 0 0 0 0
+ 33 8 1 0 0 0 0
+ 14 8 1 0 0 0 0
+ 10 9 1 0 0 0 0
+ 15 10 2 0 0 0 0
+ 30 10 1 0 0 0 0
+ 11 12 2 0 0 0 0
+ 15 11 1 0 0 0 0
+ 22 11 1 0 0 0 0
+ 13 43 1 0 0 0 0
+ 43 14 1 0 0 0 0
+ 15 43 1 0 0 0 0
+ 24 16 1 0 0 0 0
+ 16 17 1 0 0 0 0
+ 18 27 2 0 0 0 0
+ 18 19 1 0 0 0 0
+ 20 33 2 0 0 0 0
+ 20 21 1 0 0 0 0
+ 22 30 2 0 0 0 0
+ 22 23 1 0 0 0 0
+ 24 25 1 0 0 0 0
+ 25 26 2 0 0 0 0
+ 27 28 1 0 0 0 0
+ 28 29 2 0 0 0 0
+ 30 31 1 0 0 0 0
+ 31 32 1 0 0 0 0
+ 32 37 1 0 0 0 0
+ 33 34 1 0 0 0 0
+ 34 35 1 0 0 0 0
+ 35 40 1 0 0 0 0
+ 37 36 1 0 0 0 0
+ 37 38 2 0 0 0 0
+ 40 39 1 0 0 0 0
+ 40 41 2 0 0 0 0
+ 42 43 1 0 0 0 0
+M END