Output ligand inserted in pdb

[ss199514]

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Description of the Change

The new changes will allow qFit-ligand script to output a ligand inserted PDB model

We must be able to understand the purpose of your change from this description. If we can't get a good idea of the benefits of the change from the description here, the pull request may be closed at the maintainers' discretion.

[stephaniewankowicz]

Let's re-write this using qFit infrastructure. We have functions that output file (.tofile()) and combine PDB values. If you look in qFit protein, we put HETATMS into a variable, then combine them with the protein output and finally output multiconformer_model2.pdb. We should follow the same in qFit ligand.