Skip to content

Commit

Permalink
Merge pull request #16 from lunamorrow/reader-and-tests
Browse files Browse the repository at this point in the history 
OpenBabelReader and Tests
  • Loading branch information
@lunamorrow
lunamorrow authored Sep 11, 2024
2 parents c15500b + 491a7f9 commit f35c093
Show file tree
Hide file tree
Showing 7 changed files with 203,829 additions and 11 deletions.
58 changes: 48 additions & 10 deletions mda_openbabel_converter/OpenBabel.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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):
"""
Expand Down
426 changes: 426 additions & 0 deletions mda_openbabel_converter/data/1crn.pdb
View file

Large diffs are not rendered by default.

98 changes: 98 additions & 0 deletions mda_openbabel_converter/data/ChEBI_26355.mol
View file
Original file line number Diff line number Diff line change
@@ -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
Loading

0 comments on commit f35c093

Please sign in to comment.