def test_info_10(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') molsys = msm.convert(molsys, to_form='molsysmt.Trajectory') df = msm.info(molsys) true_dict = { 'form': { 0: 'molsysmt.Trajectory' }, 'n_atoms': { 0: 3983 }, 'n_groups': { 0: None }, 'n_components': { 0: None }, 'n_chains': { 0: None }, 'n_molecules': { 0: None }, 'n_entities': { 0: None }, 'n_structures': { 0: 1 } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_17(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='component', indices=2, output='long_string') true_output = '2/A-C@2/water@1' assert output == true_output
def test_info_22(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='entity', indices=0, output='short_string') true_output = 'TRIOSEPHOSPHATE ISOMERASE@0' assert output == true_output
def test_info_13(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='atom', indices=[10, 11, 12, 13], output='short_string') true_output = ['CA-11@10', 'C-12@11', 'O-13@12', 'CB-14@13'] assert np.all(output == true_output)
def test_remove_2(): molsys = msm.demo['Trp-Cage']['1l2y.pdb'] molsys = msm.convert(molsys, to_form='molsysmt.Trajectory') molsys = msm.remove(molsys, structure_indices=range(1,38)) df = msm.info(molsys) true_dict = {'form': {0: 'molsysmt.Trajectory'}, 'n_atoms': {0: 304}, 'n_groups': {0: None}, 'n_components': {0: None}, 'n_chains': {0: None}, 'n_molecules': {0: None}, 'n_entities': {0: None}, 'n_structures': {0: 1}} true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_remove_1(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') molsys = msm.remove(molsys, selection='chain_index==[1,2,3]') df = msm.info(molsys) true_dict = {'form': {0: 'molsysmt.MolSys'}, 'n_atoms': {0: 1906}, 'n_groups': {0: 248}, 'n_components': {0: 1}, 'n_chains': {0: 1}, 'n_molecules': {0: 1}, 'n_entities': {0: 1}, 'n_proteins': {0: 1}, 'n_structures': {0: 1}} true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_24(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') df = msm.info(molsys, target='component', selection='molecule_type=="protein"') true_dict = { 'index': { 0: 0, 1: 1 }, 'n atoms': { 0: 1906, 1: 1912 }, 'n groups': { 0: 248, 1: 249 }, 'chain index': { 0: 0, 1: 1 }, 'molecule index': { 0: 0, 1: 0 }, 'molecule type': { 0: 'protein', 1: 'protein' }, 'entity index': { 0: 0, 1: 0 }, 'entity name': { 0: 'TRIOSEPHOSPHATE ISOMERASE', 1: 'TRIOSEPHOSPHATE ISOMERASE' } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_11(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') molsys = msm.convert(molsys, to_form=['molsysmt.Topology', 'molsysmt.Trajectory']) df = msm.info(molsys) true_dict = { 'form': { 0: ['molsysmt.Topology', 'molsysmt.Trajectory'] }, 'n_atoms': { 0: 3983 }, 'n_groups': { 0: 662 }, 'n_components': { 0: 167 }, 'n_chains': { 0: 4 }, 'n_molecules': { 0: 166 }, 'n_entities': { 0: 2 }, 'n_waters': { 0: 165 }, 'n_proteins': { 0: 1 }, 'n_structures': { 0: 1 } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_7(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') df = msm.info(molsys, target='entity') true_dict = { 'index': { 0: 0, 1: 1 }, 'name': { 0: 'TRIOSEPHOSPHATE ISOMERASE', 1: 'water' }, 'type': { 0: 'protein', 1: 'water' }, 'n atoms': { 0: 3818, 1: 165 }, 'n groups': { 0: 497, 1: 165 }, 'n components': { 0: 2, 1: 165 }, 'n chains': { 0: 2, 1: 2 }, 'n molecules': { 0: 1, 1: 165 } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_6(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') df = msm.info(molsys, target='molecule', selection='molecule_type!="water"') true_dict = { 'index': { 0: 0 }, 'name': { 0: 'TRIOSEPHOSPHATE ISOMERASE' }, 'type': { 0: 'protein' }, 'n atoms': { 0: 3818 }, 'n groups': { 0: 497 }, 'n components': { 0: 2 }, 'chain index': { 0: np.array([0, 1], dtype=object) }, 'entity index': { 0: 0 }, 'entity name': { 0: 'TRIOSEPHOSPHATE ISOMERASE' } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_1(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') df = msm.info(molsys, target='atom', indices=[9, 10, 11, 12], output='dataframe') true_dict = { 'index': { 0: 9, 1: 10, 2: 11, 3: 12 }, 'id': { 0: 10, 1: 11, 2: 12, 3: 13 }, 'name': { 0: 'N', 1: 'CA', 2: 'C', 3: 'O' }, 'type': { 0: 'N', 1: 'C', 2: 'C', 3: 'O' }, 'group index': { 0: 1, 1: 1, 2: 1, 3: 1 }, 'group id': { 0: 5, 1: 5, 2: 5, 3: 5 }, 'group name': { 0: 'PRO', 1: 'PRO', 2: 'PRO', 3: 'PRO' }, 'group type': { 0: 'aminoacid', 1: 'aminoacid', 2: 'aminoacid', 3: 'aminoacid' }, 'component index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'chain index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'molecule index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'molecule type': { 0: 'protein', 1: 'protein', 2: 'protein', 3: 'protein' }, 'entity index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'entity name': { 0: 'TRIOSEPHOSPHATE ISOMERASE', 1: 'TRIOSEPHOSPHATE ISOMERASE', 2: 'TRIOSEPHOSPHATE ISOMERASE', 3: 'TRIOSEPHOSPHATE ISOMERASE' } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_24(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') group_index_in_component_0 = msm.get(molsys, target='group', selection='component_index==0', index=True)[69] group_index_in_component_1 = msm.get(molsys, target='group', selection='component_index==1', index=True)[12] df = msm.info( molsys, target='group', indices=[group_index_in_component_0, group_index_in_component_1]) true_dict = { 'index': { 0: 69, 1: 260 }, 'id': { 0: 73, 1: 15 }, 'name': { 0: 'GLY', 1: 'CYS' }, 'type': { 0: 'aminoacid', 1: 'aminoacid' }, 'n atoms': { 0: 4, 1: 6 }, 'component index': { 0: 0, 1: 1 }, 'chain index': { 0: 0, 1: 1 }, 'molecule index': { 0: 0, 1: 0 }, 'molecule type': { 0: 'protein', 1: 'protein' }, 'entity index': { 0: 0, 1: 0 }, 'entity name': { 0: 'TRIOSEPHOSPHATE ISOMERASE', 1: 'TRIOSEPHOSPHATE ISOMERASE' } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_2(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') df = msm.info(molsys, target='atom', selection='group_index==6') true_dict = { 'index': { 0: 45, 1: 46, 2: 47, 3: 48, 4: 49 }, 'id': { 0: 46, 1: 47, 2: 48, 3: 49, 4: 50 }, 'name': { 0: 'N', 1: 'CA', 2: 'C', 3: 'O', 4: 'CB' }, 'type': { 0: 'N', 1: 'C', 2: 'C', 3: 'O', 4: 'C' }, 'group index': { 0: 6, 1: 6, 2: 6, 3: 6, 4: 6 }, 'group id': { 0: 10, 1: 10, 2: 10, 3: 10, 4: 10 }, 'group name': { 0: 'ALA', 1: 'ALA', 2: 'ALA', 3: 'ALA', 4: 'ALA' }, 'group type': { 0: 'aminoacid', 1: 'aminoacid', 2: 'aminoacid', 3: 'aminoacid', 4: 'aminoacid' }, 'component index': { 0: 0, 1: 0, 2: 0, 3: 0, 4: 0 }, 'chain index': { 0: 0, 1: 0, 2: 0, 3: 0, 4: 0 }, 'molecule index': { 0: 0, 1: 0, 2: 0, 3: 0, 4: 0 }, 'molecule type': { 0: 'protein', 1: 'protein', 2: 'protein', 3: 'protein', 4: 'protein' }, 'entity index': { 0: 0, 1: 0, 2: 0, 3: 0, 4: 0 }, 'entity name': { 0: 'TRIOSEPHOSPHATE ISOMERASE', 1: 'TRIOSEPHOSPHATE ISOMERASE', 2: 'TRIOSEPHOSPHATE ISOMERASE', 3: 'TRIOSEPHOSPHATE ISOMERASE', 4: 'TRIOSEPHOSPHATE ISOMERASE' } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_19(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='chain', indices=2, output='long_string') true_output = 'A-C@2' assert output == true_output
def test_info_3(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') df = msm.info(molsys, target='group', indices=[20, 21, 22, 23]) true_dict = { 'index': { 0: 20, 1: 21, 2: 22, 3: 23 }, 'id': { 0: 24, 1: 25, 2: 26, 3: 27 }, 'name': { 0: 'PRO', 1: 'LEU', 2: 'ILE', 3: 'GLU' }, 'type': { 0: 'aminoacid', 1: 'aminoacid', 2: 'aminoacid', 3: 'aminoacid' }, 'n atoms': { 0: 7, 1: 8, 2: 8, 3: 9 }, 'component index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'chain index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'molecule index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'molecule type': { 0: 'protein', 1: 'protein', 2: 'protein', 3: 'protein' }, 'entity index': { 0: 0, 1: 0, 2: 0, 3: 0 }, 'entity name': { 0: 'TRIOSEPHOSPHATE ISOMERASE', 1: 'TRIOSEPHOSPHATE ISOMERASE', 2: 'TRIOSEPHOSPHATE ISOMERASE', 3: 'TRIOSEPHOSPHATE ISOMERASE' } } true_df = DataFrame(true_dict) assert df.data.equals(true_df)
def test_info_15(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='group', indices=3, output='long_string') true_output = 'PRO-7@3/A-A@0/TRIOSEPHOSPHATE ISOMERASE@0' assert output == true_output
def test_info_15(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='group', indices=0, output='short_string') true_output = 'LYS-4@0' assert output == true_output
def test_info_14(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='atom', indices=10, output='long_string') true_output = 'CA-11@10/PRO-5@1/A-A@0/TRIOSEPHOSPHATE ISOMERASE@0' assert output == true_output
def test_info_12(): molsys = msm.convert(msm.demo['TcTIM']['1tcd.msmpk'], to_form='molsysmt.MolSys') output = msm.info(molsys, target='atom', indices=10, output='short_string') true_output = 'CA-11@10' assert output == true_output