def test_extract_3():
molsys = msm.demo['T4 lysozyme L99A']['181l.msmpk']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys = msm.extract(molsys,
selection='molecule_type==["water", "protein"]')
output = msm.is_composed_of(molsys, waters=True, proteins=True)
assert output == True
def test_string_pdb_text_to_openmm_Topology():
molsys = msm.convert(msm.demo['T4 lysozyme L99A']['181l.pdb'],
to_form='string:pdb_text')
molsys = msm.convert(molsys,
to_form='openmm.Topology',
selection='molecule_type=="protein"')
is_composed_of = msm.is_composed_of(molsys, proteins=1)
form = msm.get_form(molsys)
assert ('openmm.Topology' == form) and (is_composed_of == True)
def test_extract_1():
molsys = msm.demo['T4 lysozyme L99A']['181l.msmpk']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys = msm.extract(molsys, selection='molecule_type=="small molecule"')
output = msm.is_composed_of(molsys, small_molecules=2)
assert output == True
def test_is_composed_of_1():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
output = msm.is_composed_of(molsys, proteins=True)
assert output == False
def test_is_composed_of_5():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.extract(molsys, selection='molecule_type=="protein"')
output = msm.is_composed_of(molsys, proteins=1, waters=2, ions=2)
assert output == False
def test_is_composed_of_4():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
molsys = msm.extract(molsys, selection='molecule_type=="peptide"')
output = msm.is_composed_of(molsys, peptides=1)
assert output == True
def test_is_composed_of_3():
molsys = msm.convert(msm.demo['chicken villin HP35']['solvated.msmpk'],
to_form='molsysmt.MolSys')
output = msm.is_composed_of(molsys, peptides=1, waters=True, ions=True)
assert output == True