aa5d761c03ea31df01ff51ec3634dd89cd73bec1,oddt/toolkits/extras/rdkit_fixer.py,,UFFConstrainedOptimize,#Any#Any#Any#Any#Any#,138

Before Change

    else:
        fixed_atoms = list(all_atoms.difference(moving_atoms))
    // extract submolecules containing atoms within cutoff
    pos = np.array(mol.GetConformer(-1).GetPositions())
    mask = (cdist(pos, pos[moving_atoms]) <= cutoff).any(axis=1)
    amap = np.where(mask)[0].tolist()

After Change

    else:
        fixed_atoms = list(all_atoms.difference(moving_atoms))
    // extract submolecules containing atoms within cutoff
    mol_conf = mol.GetConformer(-1)
    pos = np.array([mol_conf.GetAtomPosition(i)
                   for i in range(mol_conf.GetNumAtoms())])
    mask = (cdist(pos, pos[moving_atoms]) <= cutoff).any(axis=1)
    amap = np.where(mask)[0].tolist()

    // expand to whole residues

Instances