def test_assign_histidine(): fn = get_fn('4lzt/4lzt_h.pdb') parm = pmd.load_file(fn) his_residues = [ res.name for res in parm.residues if res.name in {'HIS', 'HIE', 'HID', 'HIP'} ] assert his_residues == ['HIS'] pdbfixer = AmberPDBFixer(parm) pdbfixer.assign_histidine() his_residues = [ res.name for res in pdbfixer.parm.residues if res.name in {'HIS', 'HIE', 'HID', 'HIP'} ] assert his_residues == ['HID'] # Do not rename to HIS if this residue does not # have hydrogen. parm2 = pmd.Structure() for resnum, resname in enumerate(['HIE', 'HID', 'HIS']): atom = pmd.Atom(name='C', atomic_number=6) parm2.add_atom(atom, resname, resnum=resnum, chain='A') fixer2 = AmberPDBFixer(parm2) fixer2.assign_histidine() assert ['HIE', 'HID', 'HIS'] == [res.name for res in fixer2.parm.residues]
def test_assign_histidine(): fn = get_fn('4lzt/4lzt_h.pdb') parm = pmd.load_file(fn) his_residues = [ res.name for res in parm.residues if res.name in {'HIS', 'HIE', 'HID', 'HIP'} ] assert his_residues == ['HIS'] pdbfixer = AmberPDBFixer(parm) pdbfixer.assign_histidine() his_residues = [ res.name for res in pdbfixer.parm.residues if res.name in {'HIS', 'HIE', 'HID', 'HIP'} ] assert his_residues == ['HID']