proLIF 从 pdb 可视化并保存到 output.html

Question

如何使用 pdb 文件中的 proLIF 可视化来可视化受体配体相互作用并保存到 output.html。 这是我的代码，但我不明白我输入了什么，请帮助我

import MDAnalysis as mda
import prolif as plf
from prolif.plotting.network import LigNetwork
from rdkit import Chem
import pandas as pd
import prolif as plf
import MDAnalysis as mda

if __name__ == '__main__':
    prot = mda.Universe("rec.pdb")
    prot = plf.Molecule.from_mda(prot)
    fp = plf.Fingerprint()
    ref = mda.Universe("lig.pdb")
    ref = plf.Molecule.from_mda(ref)
    fp.run_from_iterable([ref], prot)
    df = fp.to_dataframe()
    df.rename({0: "ref"}, inplace=True)
    df.columns = df.columns.droplevel(0)
    df = (pd.concat([df, df])
            .fillna(False)
            .sort_index(axis=1, level=0,
                        key=lambda index: [plf.ResidueId.from_string(x) for x in index])) 
 
    template = Chem.MolFromSmiles("C[NH+]1CC(C(=O)NC2(C)OC3(O)C4CCCN4C(=O)C(Cc4ccccc4)N3C2=O)C=C2c3cccc4[nH]cc(c34)CC21")
    pdbqt_files = sorted(plf.datafiles.datapath.glob("*.pdbqt"))
    lig_suppl = plf.pdbqt_supplier(pdbqt_files, template)

    lmol = plf.Molecule.from_mda(lig_suppl)
    pmol = plf.Molecule.from_mda(prot)

    fp = plf.Fingerprint(["HBDonor", "HBAcceptor", "Cationic", "PiStacking"])
    fp.run_from_iterable(lig_suppl, prot)
    df = fp.to_dataframe(return_atoms=True)
    fp = plf.Fingerprint()
    fp.run_from_iterable(lig_suppl, prot)
    df = fp.to_dataframe(return_atoms=True)

    net = LigNetwork.from_ifp(df, lmol, kind="aggregate", threshold=.3, rotation=270)
    net.save("output.html")