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Fixed issues related to align_selection=None #396

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Fixed issues related to align_selection=None #396

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119 changes: 64 additions & 55 deletions python/BioSimSpace/Metadynamics/CollectiveVariable/_rmsd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,8 +54,8 @@ def __init__(
self,
system,
reference,
align_selection,
rmsd_selection,
align_selection=None,
reference_mapping=None,
hill_width=_Length(0.1, "nanometer"),
lower_bound=None,
Expand All @@ -77,15 +77,15 @@ def __init__(
reference : :class:`System <BioSimSpace._SireWrappers.System>`
The reference system, against which the RMSD will be measured.

rmsd_selection : str
A Sire selection string that defines the atoms to be used
when calculating the RMSD.

align_selection : str
A Sire selection string that defines the atoms to be used
when aligning the two structures. If None, then the RMSD
will be calculated without alignment.

rmsd_selection : str
A Sire selection string that defines the atoms to be used
when calculating the RMSD.

reference_mapping : dict
A dictionary mapping molecule indices in the reference to
those in the system. This must be used when the reference
Expand Down Expand Up @@ -195,19 +195,23 @@ def __init__(

self._reference_mapping = reference_mapping

# Validate alignment selection string.
if not isinstance(align_selection, str):
raise TypeError("'align_selection' must be of type 'str'")
self._align_selection = align_selection
if not align_selection:
self._align_selection = None
self._aligment_atoms = None
else:
# Validate alignment selection string.
if not isinstance(align_selection, str):
raise TypeError("'align_selection' must be of type 'str'")
self._align_selection = align_selection

try:
self._aligment_atoms = _selection_to_atoms(sire_reference, align_selection)
except Exception as e:
msg = "Invalid 'align_selection' string."
if _isVerbose():
raise IOError(msg) from e
else:
raise IOError(msg) from None
try:
self._aligment_atoms = _selection_to_atoms(sire_reference, align_selection)
except Exception as e:
msg = "Invalid 'align_selection' string."
if _isVerbose():
raise IOError(msg) from e
else:
raise IOError(msg) from None

# Validate RMSD selection string.
if not isinstance(rmsd_selection, str):
Expand All @@ -231,9 +235,10 @@ def __init__(

mol_nums = set()

for atom in self._aligment_atoms:
if atom.molecule().number() not in mol_nums:
mol_nums.add(atom.molecule().number())
if self._aligment_atoms:
for atom in self._aligment_atoms:
if atom.molecule().number() not in mol_nums:
mol_nums.add(atom.molecule().number())

for atom in self._rmsd_atoms:
if atom.molecule().number() not in mol_nums:
Expand Down Expand Up @@ -279,7 +284,7 @@ def __init__(
is_align = False
is_rmsd = False
# This atom is used for alignment.
if atom in self._aligment_atoms:
if self._aligment_atoms and atom in self._aligment_atoms:
is_align = True
try:
align_indices[num].append(atom.index())
Expand Down Expand Up @@ -612,22 +617,23 @@ def _compute_initial_rmsd(
if not isinstance(pair[1], int):
raise TypeError("'molecule_pairs' must be a list of integer tuples.")

if not isinstance(align_indices, dict):
raise TypeError("'align_indices' must be a dictionary.")
for key, value in align_indices.items():
if not isinstance(key, _SireMol.MolNum):
raise TypeError(
"Keys of 'align_indices' must be of type 'sire.legacy.Mol.MolMolNum'."
)
if not isinstance(value, list):
raise TypeError(
"Values of 'align_indices' must be lists of 'sire.legacy.Mol.AtomIdx' types."
)
for idx in value:
if not isinstance(idx, _SireMol.AtomIdx):
if align_indices:
if not isinstance(align_indices, dict):
raise TypeError("'align_indices' must be a dictionary.")
for key, value in align_indices.items():
if not isinstance(key, _SireMol.MolNum):
raise TypeError(
"Keys of 'align_indices' must be of type 'sire.legacy.Mol.MolMolNum'."
)
if not isinstance(value, list):
raise TypeError(
"Values of 'align_indices' must be lists of 'sire.legacy.Mol.AtomIdx' types."
)
for idx in value:
if not isinstance(idx, _SireMol.AtomIdx):
raise TypeError(
"Values of 'align_indices' must be lists of 'sire.legacy.Mol.AtomIdx' types."
)

if not isinstance(rmsd_indices, dict):
raise TypeError("'rmsd_indices' must be a dictionary.")
Expand Down Expand Up @@ -672,29 +678,32 @@ def _compute_initial_rmsd(
mol = system[idx_system]
ref = reference[idx_ref]

align_mapping = {}

try:
align_mapping = {
i.value(): i.value()
for i in align_indices[ref._sire_object.number()]
}
except Exception as e:
pass
if align_indices:
align_mapping = {}

if len(align_mapping) > 0:
try:
new_mol = _rmsdAlign(
mol,
ref,
align_mapping,
property_map0=property_map,
property_map1=property_map,
)
except:
ValueError(
"Unable to align 'molecule' to 'reference' based on 'align_mapping'."
)
align_mapping = {
i.value(): i.value()
for i in align_indices[ref._sire_object.number()]
}
except Exception as e:
pass

if len(align_mapping) > 0:
try:
new_mol = _rmsdAlign(
mol,
ref,
align_mapping,
property_map0=property_map,
property_map1=property_map,
)
except:
ValueError(
"Unable to align 'molecule' to 'reference' based on 'align_mapping'."
)
else:
new_mol = mol

rmsd_mapping = {}

Expand Down