当我使用pandas代替dask时,它会抛出另一个错误: PandasTools.WriteSDF(pp, args.output_file, molColName='ID', properties=list(pp.columns)) File "/scratch/micromamba/envs/biotools_py39/lib/python3.9/site-packages/rdkit/Chem/PandasTools.py", line 440, in WriteSDF mol = Chem.Mol(row[1][mol...
> > sdfFile = os.path.join(RDConfig.RDDataDir,'NCI/first_200.props.sdf')>>> frame > = PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',... > includeFingerprints=True, removeHs=False, strictParsing=True) > > > Any guidance is hugely appreciated. > > On the ...
Newest 'rdkit' Questions, I am trying to convert inchi to sdf format using rdkit python library. I am running following line of python code. #convert inchi to sdf def MolFromInchi(id,inchi): mol = Chem.MolFromInchi(inchi) ("cdk2.sdf") The file is read and i also get output for ...
(except for GUI components, which are GPL) Components End User Developer • Command-line scripts • Python programming library • Python interface • C++ programming library • Database extensions General Molecular Functionality Input/Output: SMILES/SMARTS, mol, SDF, TDT “...
radical); constructing an SDF file with OpenBabel (via cclib), and then trying to read the result in RDKit. I have the SMILES string of the radical, but the connectivity is lost in the gaussian output file. So the SDF that gets created by OpenBabel has to ...
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properties >>> suppl = Chem.SDMolSupplier('divscreen.400.sdf') >>> m = suppl.next() >>> list(m.GetPropNames()) ['Formula', 'MolWeight', 'Mol_ID', 'Smiles', 'cdk2_ic50', 'cdk2_inhib', 'cdk_act_bin_1', 'mol_name', 'scaffold', 'sourcepool'] ...
rdkit.Chem.rdmolfiles.MolFromMolBlock(s)/rdkit.Chem.MolFromMolBlock(s) and rdkit.Chem.rdmolfiles.MolToMolBlock(m)/rdkit.Chem.MolToMolBlock(m) convert molecules from and to Mol blocks (SDF format without custom properties). rdkit.Chem.rdmolfiles.SmilesMolSupplier(f)/rdkit.Chem.rdmol...
the following are my code and sdf, atoms 0-37 were constrained. suppl_ref = Chem.SDMolSupplier('test.sdf') mol = suppl_ref[0] molRmHs = Chem.RemoveHs(mol) mp = AllChem.MMFFGetMoleculeProperties(molRmHs) ff = AllChem.MMFFGetMoleculeForceField(molRmHs, mp) constrained_indices = [...
smi2sdf- Convert SMILES to SDF including additional fields if they are named and exist in SMILES file split_pdb- split PDB by chains and save to separate PDB files. Manipulate with Mol objects (calc properties, generate conformers/stereoisomers, filter compounds, etc): ...