Problem with Python API and CLI

[nicolasrincont]

Hi,

I'm new to OpenFE and I'm trying to follow along the tutorials. When I try the Python API I have the following problem:
import openfe

from rdkit import Chem

Path to the folder containing .sdf files

sdf_folder = "inputs/"

Collect molecules from all sdf files

supp = []
for file in os.listdir(sdf_folder):
if file.endswith(".sdf"):
sdf_path = os.path.join(sdf_folder, file)
supplier = Chem.SDMolSupplier(sdf_path, removeHs=False)
supp.append(supplier)

ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]

---

AttributeError Traceback (most recent call last)
Cell In[38], line 17
14 supplier = Chem.SDMolSupplier(sdf_path, removeHs=False)
15 supp.append(supplier)
---> 17 ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]

AttributeError: module 'openfe' has no attribute 'SmallMoleculeComponent'

And when I try on CLI I get this:
openfe plan-rbfe-network -M ligands/ -p 35A_MD.pdb -o network_setup --n-protocol-repeats 3
Usage: openfe [OPTIONS] COMMAND [ARGS]...
Try 'openfe -h' for help.

Error: No such command 'plan-rbfe-network'.

Do you know what could be the issue?

Best,
Nicolás

[IAlibay]

@nicolasrincont could you give us the output from your conda/mamba environment? something like mamba list

[nicolasrincont]

@IAlibay I think the installation is ok now. But now I have this error:

ArgumentError Traceback (most recent call last)
Cell In[8], line 16
13 supplier = Chem.SDMolSupplier(sdf_path, removeHs=False)
14 supp.append(supplier)
---> 16 ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]

File /work3/nrite/openfe_env/lib/python3.13/site-packages/gufe/components/explicitmoleculecomponent.py:109, in ExplicitMoleculeComponent.from_rdkit(cls, rdkit, name)
106 @classmethod
107 def from_rdkit(cls, rdkit: RDKitMol, name: str = ""):
108 """Create a Component, copying from an RDKit Mol"""
--> 109 return cls(rdkit=Chem.Mol(rdkit), name=name)

ArgumentError: Python argument types in
Mol.init(Mol, SDMolSupplier)
did not match C++ signature:
init(_object* self, RDKit::ROMol mol, bool quickCopy=False, int confId=-1)
init(_object* self, std::__cxx11::basic_string<char, std::char_traits, std::allocator > pklString, unsigned int propertyFlags)
init(_object* self, std::__cxx11::basic_string<char, std::char_traits, std::allocator > pklString)
init(_object* self)

[IAlibay]

@nicolasrincont I think the issue is now with your code. Essentially you're passing a suppplier rather than the actual rdmols to SmallMoleculeComponent.

Try this instead:

rdmols = []
for file in os.listdir(sdf_folder):
    if file.endswith(".sdf"):
        sdf_path = os.path.join(sdf_folder, file)
        supplier = Chem.SDMolSupplier(sdf_path, removeHs=False)
        for mol in supplier:
            rdmols.append(mol)

ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in rdmols]

[nicolasrincont]

Hi @IAlibay. It worked, thanks!
Now I seem to have a problem with my pdb file:

ValueError Traceback (most recent call last)
Cell In[21], line 5
2 from openfe import SolventComponent, ProteinComponent
3 from openff.units import unit
----> 5 protein = ProteinComponent.from_pdb_file('35A_MD.pdb')
7 # Note: the distance from the solute to add water is not defined here but in the
8 # the relevant RBFE solver method
9 solvent = SolventComponent(positive_ion='Na', negative_ion='Cl',
10 neutralize=True, ion_concentration=0.15*unit.molar)

File /work3/nrite/openfe_env/lib/python3.13/site-packages/gufe/components/proteincomponent.py:182, in ProteinComponent.from_pdb_file(cls, pdb_file, name)
166 """
167 Create ProteinComponent from PDB-formatted file.
168
(...) 179 the deserialized molecule
180 """
181 openmm_PDBFile = PDBFile(pdb_file)
--> 182 return cls._from_openmmPDBFile(openmm_PDBFile=openmm_PDBFile, name=name)

File /work3/nrite/openfe_env/lib/python3.13/site-packages/gufe/components/proteincomponent.py:298, in ProteinComponent._from_openmmPDBFile(cls, openmm_PDBFile, name)
295 default_valence = periodicTable.GetDefaultValence(atomic_num)
297 if connectivity == 0: # ions
--> 298 fc = _get_ion_charge(atom_name)
299 elif default_valence > connectivity: # negative charge
...
283 res_n = a.GetMonomerInfo().GetResidueName()
284 res_ind = int(a.GetMonomerInfo().GetResidueNumber())
--> 285 raise ValueError(f"Unknown ion: {ion_key} in residue {res_n} at index {res_ind}.")

ValueError: Unknown ion: N in residue GLH at index 167.

I checked the pdb file but I don't understand where is the error coming from.

[ijpulidos]

I does seem that now the problem is with the PDB, I would check if this residue is in a "well known" protonation state, and since the tutorial is using an OpenMM based protocol, it may be helpful to c heck with pdbfixer if there are any missing residues/atoms and if it can read the pdb properly at all.

[nicolasrincont]

Hi. I'm trying to gather the results from this folder:

Using this command: openfe gather quickrun_results/ --report dg -o final_results.tsv --allow-partial

However, I get this error: No results JSON files found.

Do you know what could be the problem?