def convert_mdtraj_to_oemol(traj: md.Trajectory) -> oechem.OEMol:
"""
This method converts an mdtraj Trajectory to an OEMol via saving as a PDBfile
and reading in with OpenEye. Although this seems hacky, it seems less error-prone
than trying to manually construct the OEMol.
Parameters
----------
mdtraj: md.Trajectory
The trajectory to turn into an OEMol
Returns
-------
mol : oechem.OEMol
The trajectory represented as an OEMol
"""
# create a temporary file with a PDB suffix and save with MDTraj
pdb_file = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
traj.save(pdb_file.name)
pdb_file.close()
# Now use the openeye oemolistream to read in this file as an OEMol:
ifs = oechem.oemolistream()
ifs.open(pdb_file.name)
ifs.SetFormat(oechem.OEFormat_PDB)
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
# close the stream and delete the temporary pdb file
ifs.close()
os.unlink(pdb_file.name)
return mol
def mdtraj_to_oemol(snapshot: md.Trajectory):
"""
Create an OEMol from an MDTraj file by writing and reading
NOTE: This uses terrible heuristics
Parameters
----------
snapshot : mdtraj.Trajectory
MDTraj Trajectory with a single snapshot
Returns
-------
oemol : openeye.oechem.OEMol
The OEMol
"""
from openeye import oechem
with tempfile.TemporaryDirectory() as tmpdir:
filename = os.path.join(tmpdir, "tmp.pdb")
# Write the PDB file
snapshot.save(filename)
# Read it with OpenEye
with oechem.oemolistream(filename) as ifs:
for mol in ifs.GetOEGraphMols():
return mol
def convert_mdtraj_to_oemol(traj: md.Trajectory) -> oechem.OEMol:
"""
This method converts an mdtraj Trajectory to an OEMol via saving as a PDBfile
and reading in with OpenEye. Although this seems hacky, it seems less error-prone
than trying to manually construct the OEMol.
Parameters
----------
mdtraj: md.Trajectory
The trajectory to turn into an OEMol
Returns
-------
mol : oechem.OEMol
The trajectory represented as an OEMol
"""
#create a temporary file with a PDB suffix and save with MDTraj
pdb_file = tempfile.NamedTemporaryFile(delete=False, suffix=".pdb")
traj.save(pdb_file.name)
pdb_file.close()
#Now use the openeye oemolistream to read in this file as an OEMol:
ifs = oechem.oemolistream()
ifs.open(pdb_file.name)
ifs.SetFormat(oechem.OEFormat_PDB)
mol = oechem.OEMol()
oechem.OEReadMolecule(ifs, mol)
#close the stream and delete the temporary pdb file
ifs.close()
os.unlink(pdb_file.name)
return mol
def test_unitcell():
# make sure that bogus unitcell vecotrs are not saved
top = md.load(get_fn('native.pdb')).restrict_atoms(range(5)).topology
t = Trajectory(xyz=np.random.randn(100, 5, 3), topology=top)
# xtc dcd binpos trr h5 pdb nc lh5
for fn in [temp1, temp2, temp3, temp4, temp5, temp6, temp6, temp8]:
t.save(fn)
f = lambda: eq(md.load(fn, top=top).unitcell_vectors, None)
f.description = 'unitcell preservation in %s' % os.path.splitext(fn)[1]
yield f
def test_unitcell():
# make sure that bogus unitcell vecotrs are not saved
top = md.load(get_fn('native.pdb')).restrict_atoms(range(5)).topology
t = Trajectory(xyz=np.random.randn(100, 5, 3), topology=top)
# xtc dcd binpos trr h5 pdb nc lh5
for fn in [temp1, temp2, temp3, temp4, temp5, temp6, temp6, temp8]:
t.save(fn)
f = lambda: eq(md.load(fn, top=top).unitcell_vectors, None)
f.description = 'unitcell preservation in %s' % os.path.splitext(fn)[1]
yield f
