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
