Loading deepchem/featurizers/atomic_coordinates.py +0 −2 Original line number Diff line number Diff line Loading @@ -248,8 +248,6 @@ class NeighborListAtomicCoordinates(Featurizer): return (bohr_coords, neighbor_list) # TODO(rbharath): This shares a lot of code with NeighborListAtomicCoordinates. # Is there some elegant way to refactor to avoid code duplication? class NeighborListComplexAtomicCoordinates(ComplexFeaturizer): """ Adjacency list of neighbors for protein-ligand complexes in 3-space. Loading deepchem/featurizers/grid_featurizer.py +0 −13 Original line number Diff line number Diff line Loading @@ -51,35 +51,22 @@ def load_molecule(molecule_file, remove_hydrogens=True, """ if ".mol2" in molecule_file: ###################################################### DEBUG print("mol2 file") ###################################################### DEBUG obConversion = ob.OBConversion() obConversion.SetInAndOutFormats(str("mol2"), str("mol2")) ob_mol = ob.OBMol() obConversion.ReadFile(ob_mol, str(molecule_file)) elif ".sdf" in molecule_file: ###################################################### DEBUG print("sdf file") ###################################################### DEBUG obConversion = ob.OBConversion() obConversion.SetInAndOutFormats(str("sdf"), str("sdf")) ob_mol = ob.OBMol() obConversion.ReadFile(ob_mol, str(molecule_file)) elif ".pdb" in molecule_file: ###################################################### DEBUG print("pdb file") ###################################################### DEBUG obConversion = ob.OBConversion() obConversion.SetInAndOutFormats(str("pdb"), str("pdb")) ob_mol = ob.OBMol() obConversion.ReadFile(ob_mol, str(molecule_file)) else: raise ValueError("Unrecognized file type") ###################################################### DEBUG print("ob_mol.NumAtoms()") print(ob_mol.NumAtoms()) ###################################################### DEBUG if calc_charges: gasteiger = ob.OBChargeModel.FindType(str("gasteiger")) Loading examples/BACE.ipynb→examples/broken/BACE.ipynb +0 −0 File moved. View file examples/Multitask Networks on MUV.ipynb→examples/broken/Multitask Networks on MUV.ipynb +0 −0 File moved. View file examples/protein_ligand_complex_notebook.ipynb→examples/broken/protein_ligand_complex_notebook.ipynb +0 −0 File moved. View file Loading
deepchem/featurizers/atomic_coordinates.py +0 −2 Original line number Diff line number Diff line Loading @@ -248,8 +248,6 @@ class NeighborListAtomicCoordinates(Featurizer): return (bohr_coords, neighbor_list) # TODO(rbharath): This shares a lot of code with NeighborListAtomicCoordinates. # Is there some elegant way to refactor to avoid code duplication? class NeighborListComplexAtomicCoordinates(ComplexFeaturizer): """ Adjacency list of neighbors for protein-ligand complexes in 3-space. Loading
deepchem/featurizers/grid_featurizer.py +0 −13 Original line number Diff line number Diff line Loading @@ -51,35 +51,22 @@ def load_molecule(molecule_file, remove_hydrogens=True, """ if ".mol2" in molecule_file: ###################################################### DEBUG print("mol2 file") ###################################################### DEBUG obConversion = ob.OBConversion() obConversion.SetInAndOutFormats(str("mol2"), str("mol2")) ob_mol = ob.OBMol() obConversion.ReadFile(ob_mol, str(molecule_file)) elif ".sdf" in molecule_file: ###################################################### DEBUG print("sdf file") ###################################################### DEBUG obConversion = ob.OBConversion() obConversion.SetInAndOutFormats(str("sdf"), str("sdf")) ob_mol = ob.OBMol() obConversion.ReadFile(ob_mol, str(molecule_file)) elif ".pdb" in molecule_file: ###################################################### DEBUG print("pdb file") ###################################################### DEBUG obConversion = ob.OBConversion() obConversion.SetInAndOutFormats(str("pdb"), str("pdb")) ob_mol = ob.OBMol() obConversion.ReadFile(ob_mol, str(molecule_file)) else: raise ValueError("Unrecognized file type") ###################################################### DEBUG print("ob_mol.NumAtoms()") print(ob_mol.NumAtoms()) ###################################################### DEBUG if calc_charges: gasteiger = ob.OBChargeModel.FindType(str("gasteiger")) Loading
examples/Multitask Networks on MUV.ipynb→examples/broken/Multitask Networks on MUV.ipynb +0 −0 File moved. View file
examples/protein_ligand_complex_notebook.ipynb→examples/broken/protein_ligand_complex_notebook.ipynb +0 −0 File moved. View file
