This module handles the :class:`~ProtoCaller.Ensemble.Protein.Protein` class which keeps track of protein instantiation, missing residue/atom addition, PDB file modification, protonation and parametrisation. More broadly, it contains the PDB file of the protein, the corresponding SDF files of any relevant extra ligands/cofactors and a file containing the FASTA sequence, all downloaded from the Protein Data Bank. If the user supplies these manually, they need to make sure that they provide ProtoCaller with all relevant information.
This class handles calls to various wrappers in the :mod:`~ProtoCaller.Wrappers` module and provides a filtering function, which is a convenient way to remove specific parts of the PDB file if needed. Alternatively, the user can change the :const:`~ProtoCaller.Ensemble.Protein.Protein.pdb_obj` manually using the :mod:`~ProtoCaller.IO` module's capabilities. In this case the PDB file has to be overwritten after any changes to the PDB object.
.. automodule:: ProtoCaller.Ensemble.Protein
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