p4ward.run.md

p4ward.run.md.fix_proteins(*protein_objs, fixed_suffix='_fixed', ignore_extremities=True, ph=7.0)

accepts any number of protein_obj (Path obj) to fix using pdbfixer creates attribute with fixed filepath and makes it active

p4ward.run.md.get_protein_charges(*protein_objs)

p4ward.run.md.minimize_proteins(*protein_objs, maxiterations=0, hydrogens_only, minimized_suffix='_minim')