e456cc88392f8cc0587b8d79c08678dab0b36e44,oddt/toolkits/extras/rdkit.py,,MolToPDBQTBlock,#,289

Before Change

                    break  // break the outer loop as well

            if end_branch:
                if len(branch_queue) > 0:
                    pdbqt_lines.append(branch_queue.pop())
                if old_roots:
                    current_root = old_roots.pop()
                else:  // go to next disconnected fragment
                    next_frag = (frag for frag_num, frag in enumerate(frags)
                                 if frag_num not in visited_frags)[0]
                    current_root = frags[next_frag]
                    visited_frags.append(next_frag)

After Change

    mol = Chem.Mol(mol)

    // if flexible molecule contains multiple fragments write them separately
    if flexible and len(Chem.GetMolFrags(mol)) > 1:
        return "".join(MolToPDBQTBlock(frag, flexible=flexible, addHs=addHs,
                                       computeCharges=computeCharges)
                       for frag in Chem.GetMolFrags(mol, asMols=True))

    // Identify donors and acceptors for atom typing
    // Acceptors
    patt = Chem.MolFromSmarts("[$([O;H1;v2]),"
                              "$([O;H0;v2;!$(O=N-*),"
                              "$([O;-;!$(*-N=O)]),"
                              "$([o;+0])]),"

Instances