module 'spyrmsd.molecule' has no attribute 'load'

[JonasLi-19]

Hello, I met an error when using spyrmsd:

AttributeError: module 'spyrmsd.molecule' has no attribute 'load'

from spyrmsd import molecule
from spyrmsd import rmsd

ref_molecule = molecule.load("reference.mol")
docked_molecule = molecule.load("docked.mol")

# Get the coordinates
ref_coords = ref_molecule.coordinates
docked_coords = docked_molecule.coordinates

# Get the adjacency matrices
ref_adjacency_matrix = ref_molecule.adjacency
docked_adjacency_matrix = docked_molecule.adjacency

# Calculate symmetry-corrected RMSD
symm_rmsd_value = rmsd.symmrmsd(
    ref_coords, docked_coords, ref_adjacency_matrix, docked_adjacency_matrix
)

print(f"Symmetry-corrected RMSD: {symm_rmsd_value}")

[RMeli]

The molecule class has no method load. It only has from_rdkit and from_openbabel constructors to make a spyrmsd.molecule from an already loaded RDKit or Open Babel molecule object.

Did you see this usage somewhere in the documentation? Please see the documentation on how to load molecules: you need to use loadmol from the io module.

[JonasLi-19]

I have tried using rdkit to load sdf file to calculating symmrmsd for two pose, which causes error:

Traceback (most recent call last):
  File "analysis_docked_poses_score_to_csv.py", line 82, in <module>
    coords_ref = ref_molecule.coordinates
AttributeError: 'NoneType' object has no attribute 'coordinates'

Code:

from rdkit import Chem
from rdkit.Chem import AllChem
from spyrmsd import io, rmsd, molecule
from spyrmsd.molecule import Molecule
...
            rd_ref_supplier = Chem.SDMolSupplier(ref_pose)
            rd_mol_docked_supplier = Chem.SDMolSupplier(new_filepath)

            rd_ref = next(rd_ref_supplier, None)
            rd_mol_docked = next(rd_mol_docked_supplier, None)

            ref_molecule = Molecule.from_rdkit(rd_ref)
            mol_docked = Molecule.from_rdkit(rd_mol_docked)
            
            ref_molecule = ref_molecule.strip()
            mol_docked = mol_docked.strip()

            coords_ref = ref_molecule.coordinates
            anum_ref = ref_molecule.atomicnums
            adj_ref = ref_molecule.adjacency_matrix

            coords = mol_docked.coordinates
            anum = mol_docked.atomicnums
            adj = mol_docked.adjacency_matrix

            symm_rmsd_value = rmsd.symmrmsd(
                coords_ref,
                coords,
                anum_ref,
                anum,
                adj_ref,
                adj,
            )

Environment

python 3.8
rdkit 2023.9.3
spyrmsd 0.6.0

[RMeli]

This is the same error you describe in #96. Once you have RDKit installed, you can use spyrmsd.io.load to load molecules without having to use RDKit directly. The from_rdkit constructor is useful mainly if you already have RDKit molecules loaded for something else and want to compute the RMSD.

Let's continue the discussion in #96, since you converged to the same error here.