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Overhaul MD code to support decoupling of separate run/parsing functionality #37

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merged 15 commits into from
May 1, 2024
Merged

Overhaul MD code to support decoupling of separate run/parsing functionality #37

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ce4b00d
Separate wrapper from result during return
smcolby Apr 22, 2024
a0ea3f8
Remove try/except blocks for geometry parsing
smcolby Apr 22, 2024
3d22c1e
Remove attribute update from atom count method
smcolby Apr 22, 2024
7613c5c
Remove charge kwarg
smcolby Apr 22, 2024
1f3e63b
Improve `finish` method for XTB parser
smcolby Apr 22, 2024
6dc1c3a
Remove extra blank line
smcolby Apr 23, 2024
5f45cd2
Overhaul XTB parser
smcolby Apr 23, 2024
e2a8255
Remove charge attribute in init
smcolby May 1, 2024
2b99d74
Decrease verbosity of if checks
smcolby May 1, 2024
44937f1
Simplify return for XTB when only single geometry type present
smcolby May 1, 2024
f6d0c38
Improve edge case handling when finishing a run
smcolby May 1, 2024
ad395b1
Fix bad attribute reference, return logic for XTB parser
smcolby May 1, 2024
c39a5b5
Add missing import
smcolby May 1, 2024
e4a6bd2
Fix parsing bugs for XTB
smcolby May 1, 2024
2a539e8
Remove charge as kwarg
smcolby May 1, 2024
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8 changes: 3 additions & 5 deletions isicle/geometry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ def __init__(self, **kwargs):
self.__dict__.update(dict.fromkeys(self._defaults, self._default_value))
self.__dict__.update(kwargs)

if self.charge is None:
self.charge = self.get_charge()
# if self.charge is None:
# self.charge = self.get_charge()

def get_basename(self):
"""
Expand Down Expand Up @@ -395,9 +395,7 @@ def get_natoms(self):

"""

natoms = Chem.Mol.GetNumAtoms(self.to_mol())
self.__dict__["natoms"] = natoms
return self.__dict__["natoms"]
return Chem.Mol.GetNumAtoms(self.to_mol())

def get_atom_indices(
self, atoms=["C", "H"], lookup={"C": 6, "H": 1, "N": 7, "O": 8, "F": 9, "P": 15}
Expand Down
2 changes: 1 addition & 1 deletion isicle/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ def load_xyz(path, charge=None):
basename = os.path.splitext(os.path.basename(path))[0]

# Initialize Geometry instance
geom = isicle.geometry.Geometry(mol=mol, charge=charge, basename=basename)
geom = isicle.geometry.Geometry(mol=mol, basename=basename)

return geom

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