def test_view_molsyst_MolSys_with_NLGView_1():
import nglview as nv
molsys = msm.demo['T4 lysozyme L99A']['181l.pdb']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys_2 = nv.show_molsysmt(molsys)
check = ('nglview.NGLWidget'==msm.get_form(molsys_2))
check_n_elements = msm.compare(molsys, molsys_2, comparison='n_elements')
check_n_molecules = msm.compare(molsys, molsys_2, comparison='n_molecules')
check_n_structures = msm.compare(molsys, molsys_2, comparison='n_structures')
assert check and check_n_elements and check_n_molecules and check_n_structures
def test_file_msmpk_to_nglview_NGLWidget():
molsys = msm.demo['T4 lysozyme L99A']['vacuum.msmpk']
molsys_ref = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys = msm.convert(molsys, to_form='nglview.NGLWidget')
check = ('nglview.NGLWidget' == msm.get_form(molsys))
check_n_elements = msm.compare(molsys, molsys_ref, comparison='n_elements')
check_n_molecules = msm.compare(molsys,
molsys_ref,
comparison='n_molecules')
check_n_structures = msm.compare(molsys,
molsys_ref,
comparison='n_structures')
assert check and check_n_elements and check_n_molecules and check_n_structures
def test_view_molsyst_MolSys_with_NGLView_5():
molsys_1 = msm.convert(msm.demo['alanine dipeptide']['vacuum.msmpk'], to_form='molsysmt.MolSys')
molsys_2 = msm.structure.translate(molsys_1, translation='[0.5, 0.0, 0.0] nm')
view = msm.view([molsys_1, molsys_2], concatenate_structures=True, viewer='NGLView')
molsys_concatenated = msm.concatenate_structures([molsys_1, molsys_2])
check_comparison = msm.compare(view, molsys_concatenated, rule='A_eq_B', comparison='info_no_form')
assert check_comparison
def test_get_nglview_NGLWidget_1():
import warnings
warnings.filterwarnings('ignore')
molsys = msm.convert(
[msm.demo['nglview']['1u19.gro'], msm.demo['nglview']['1u19.xtc']],
to_form='molsysmt.MolSys')
view = msm.convert(molsys, to_form='nglview.NGLWidget')
check_comparison = msm.compare(molsys,
view,
comparison='info_no_form',
rule='A_eq_B')
assert check_comparison
def test_copy_1():
molsys = msm.demo['pentalanine']['traj.h5']
molsys = msm.convert(molsys, to_form='molsysmt.MolSys')
molsys_2 = msm.copy(molsys)
output = msm.compare(molsys, molsys_2, comparison='all', rule='A_eq_B')
assert output == True
def test_view_molsyst_MolSys_with_NGLView_3():
molsys = msm.convert(msm.demo['alanine dipeptide']['vacuum.msmpk'], to_form='molsysmt.MolSys')
view = msm.view(molsys, standardize=True, viewer='NGLView')
check_comparison = msm.compare(view, molsys, rule='A_eq_B', comparison='info_no_form')
assert check_comparison
