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