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Atomic properties and adjacency matrix for each target mol are used #155

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Atomic properties and adjacency matrix for each target mol are used #155

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4d00278
Atomic properties and adjacency matrix for each target mol are used
DaniDelHoyo Feb 26, 2026
a1b886b
Add noCache option to command line arguments
DaniDelHoyo Mar 2, 2026
6cb2b91
fixCacheArg
DaniDelHoyo Mar 2, 2026
0abcf78
fixCacheArg
DaniDelHoyo Mar 2, 2026
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4 changes: 4 additions & 0 deletions spyrmsd/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,9 @@
parser.add_argument(
"-n", "--nosymm", action="store_false", help="No graph isomorphism"
)
parser.add_argument(
"-k", "--noCache", action="store_false", help="Compute the isomorphism for each molecule"
)
parser.add_argument(
"-g",
"--graph-backend",
Expand Down Expand Up @@ -77,6 +80,7 @@
center=args.center,
minimize=args.minimize,
strip=not args.hydrogens,
cache= args.noCache
)

for RMSD in RMSDlist:
Expand Down
32 changes: 17 additions & 15 deletions spyrmsd/rmsd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -210,9 +210,9 @@ def symmrmsd(
coordsref: np.ndarray,
coords: Union[np.ndarray, List[np.ndarray]],
apropsref: np.ndarray,
aprops: np.ndarray,
apropsList: Union[np.ndarray, List[np.ndarray]],
amref: np.ndarray,
am: np.ndarray,
amList: Union[np.ndarray, List[np.ndarray]],
center: bool = False,
minimize: bool = False,
cache: bool = True,
Expand All @@ -230,12 +230,12 @@ def symmrmsd(
Coordinates of other molecule
apropsref: np.ndarray
Atomic properties for reference
aprops: np.ndarray
Atomic properties for other molecule
apropsList: List[np.ndarray]
Atomic properties for other molecules
amref: np.ndarray
Adjacency matrix for reference molecule
am: np.ndarray
Adjacency matrix for other molecule
amList: List[np.ndarray]
Adjacency matrix for other molecules
center: bool
Centering flag
minimize: bool
Expand Down Expand Up @@ -271,7 +271,7 @@ def symmrmsd(
best_isomorphism: Any = []
isomorphism = None

for c in coords:
for i, c in enumerate(coords):
if not cache:
# Reset isomorphism
isomorphism = None
Expand All @@ -280,9 +280,9 @@ def symmrmsd(
coordsref,
c,
apropsref,
aprops,
apropsList[i],
amref,
am,
amList[i],
center=center,
minimize=minimize,
isomorphisms=isomorphism,
Expand All @@ -297,9 +297,9 @@ def symmrmsd(
coordsref,
coords,
apropsref,
aprops,
apropsList,
amref,
am,
amList,
center=center,
minimize=minimize,
isomorphisms=None,
Expand Down Expand Up @@ -358,6 +358,8 @@ def rmsdwrapper(

cref = molecule.coords_from_molecule(molref, center)
cmols = [molecule.coords_from_molecule(mol, center) for mol in mols]
apropsList = [mol.atomicnums for mol in mols]
amList = [mol.adjacency_matrix for mol in mols]

RMSDlist = []

Expand All @@ -366,21 +368,21 @@ def rmsdwrapper(
cref,
cmols,
molref.atomicnums,
mols[0].atomicnums,
apropsList,
molref.adjacency_matrix,
mols[0].adjacency_matrix,
amList,
center=center,
minimize=minimize,
cache=cache,
)
else: # No symmetry
for c in cmols:
for i, c in enumerate(cmols):
RMSDlist.append(
rmsd(
cref,
c,
molref.atomicnums,
mols[0].atomicnums,
apropsList[i],
center=center,
minimize=minimize,
)
Expand Down