def test_get_violation(self):
I=cx_validation('test.cif')
print (I.get_violation('DSS',31))
self.assertEqual(0,I.get_violation('DSS',31))
self.assertEqual(1,I.get_violation('DSS',29))
self.assertEqual(1,I.get_violation('EDC',20))
self.assertEqual(0,I.get_violation('EDC',29))
def test_get_xl_data_2(self):
"""Test AtomSiteHandler"""
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_ihm_cross_link_list.id
_ihm_cross_link_list.group_id
_ihm_cross_link_list.entity_description_1
_ihm_cross_link_list.entity_id_1
_ihm_cross_link_list.seq_id_1
_ihm_cross_link_list.comp_id_1
_ihm_cross_link_list.entity_description_2
_ihm_cross_link_list.entity_id_2
_ihm_cross_link_list.seq_id_2
_ihm_cross_link_list.comp_id_2
_ihm_cross_link_list.linker_type
_ihm_cross_link_list.dataset_list_id
1 1 foo 1 2 THR foo 1 3 CYS DSS 97
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 foo
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
self.assertEqual('DSS',I.get_xl_data()['Linker_Name'].unique()[0])
self.assertEqual('1',I.get_xl_data()['Res1_Entity_ID'].unique()[0])
self.assertEqual(2,I.get_xl_data()['Res1_Seq_ID'].unique()[0])
self.assertEqual('1',I.get_xl_data()['Res2_Entity_ID'].unique()[0])
self.assertEqual(3,I.get_xl_data()['Res2_Seq_ID'].unique()[0])
self.assertEqual('A',I.get_xl_data()['Res1_Chain'].unique()[0])
self.assertEqual('A',I.get_xl_data()['Res2_Chain'].unique()[0])
def test_process_ambiguity(self):
lst=pd.DataFrame([['C_4',23],['C_4',11],['C_5',22]],columns=['XL_ID','dist'])
I=cx_validation('test.cif')
self.assertEqual(22,I.process_ambiguity(lst)['dist'].values[0])
self.assertEqual(11,I.process_ambiguity(lst)['dist'].values[1])
self.assertEqual('C_5',I.process_ambiguity(lst)['XL_ID'].values[0])
self.assertEqual('C_4',I.process_ambiguity(lst)['XL_ID'].values[1])
def test_get_atom_model_dict(self):
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_ihm_model_list.model_id
_ihm_model_list.model_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 . 1 1 1
#
loop_
_ihm_model_group.id
_ihm_model_group.name
_ihm_model_group.details
1 "Cluster 1" .
#
loop_
_ihm_model_group_link.group_id
_ihm_model_group_link.model_id
1 1
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_asym_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.label_entity_id
_atom_site.auth_asym_id
_atom_site.B_iso_or_equiv
_atom_site.pdbx_PDB_model_num
_atom_site.ihm_model_id
ATOM 1 CA CA . SER 1 A 54.401 -49.984 -35.287 . 1 A . 1 1
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
atom=I.get_atom_model_dict()[1]
self.assertEqual(1,I.get_xyzrseq_atoms(atom)['Seq'].unique()[0])
self.assertEqual('A',I.get_xyzrseq_atoms(atom)['Chain'].unique()[0])
self.assertEqual('CA',I.get_xyzrseq_atoms(atom)['Atom'].unique()[0])
self.assertEqual(54.401,I.get_xyzrseq_atoms(atom)['X'].unique()[0])
self.assertEqual('A_1',I.get_xyzrseq_atoms(atom)['Res_ID'].unique()[0])
def test_get_xyzrseq_spheres(self):
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_ihm_model_list.model_id
_ihm_model_list.model_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 . 1 1 1
#
loop_
_ihm_model_group.id
_ihm_model_group.name
_ihm_model_group.details
1 "Cluster 1" .
#
loop_
_ihm_model_group_link.group_id
_ihm_model_group_link.model_id
1 1
#
loop_
_ihm_sphere_obj_site.id
_ihm_sphere_obj_site.entity_id
_ihm_sphere_obj_site.seq_id_begin
_ihm_sphere_obj_site.seq_id_end
_ihm_sphere_obj_site.asym_id
_ihm_sphere_obj_site.Cartn_x
_ihm_sphere_obj_site.Cartn_y
_ihm_sphere_obj_site.Cartn_z
_ihm_sphere_obj_site.object_radius
_ihm_sphere_obj_site.rmsf
_ihm_sphere_obj_site.model_id
1 1 1 6 A 389.993 145.089 134.782 4.931 . 1
1 1 7 7 A 389.993 145.089 134.782 4.931 . 1
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
spheres=I.get_sphere_model_dict()[1]
self.assertEqual((1,9),I.get_xyzrseq_spheres(spheres)[0].shape)
self.assertEqual((1,8),I.get_xyzrseq_spheres(spheres)[1].shape)
self.assertEqual('A',I.get_xyzrseq_spheres(spheres)[0]['Chain'].unique()[0])
self.assertEqual('A',I.get_xyzrseq_spheres(spheres)[1]['Chain'].unique()[0])
self.assertEqual(389.993,I.get_xyzrseq_spheres(spheres)[0]['X'].unique()[0])
self.assertEqual(145.089,I.get_xyzrseq_spheres(spheres)[1]['Y'].unique()[0])
def test_get_asym_for_entity(self):
"""Test AtomSiteHandler"""
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 foo
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
self.assertEqual('1',list(I.get_asym_for_entity().keys())[0])
self.assertEqual(['A'],list(I.get_asym_for_entity().values())[0])
def run_cx_validation(self, Template_Dict: dict) -> (dict, dict):
if self.I.check_for_cx(self.I.get_dataset_comp()):
Template_Dict['cx'] = ["True"]
I_cx = cx.cx_validation(self.mmcif_file)
xl_df = I_cx.get_xl_data()
model_df = I_cx.get_df_for_models()
cx_fit = I_cx.get_violation_plot(model_df)
for key, value in cx_fit.items():
Template_Dict['Cx Fit ' + str(key)] = value
try:
Template_Dict['validation_input'].extend(
utility.get_cx_data_fits(cx_fit))
except:
Template_Dict['validation_input'] = utility.get_cx_data_fits(
cx_fit)
else:
cx_fit = dict()
return cx_fit, Template_Dict
def test_get_sphere_model_dict(self):
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_ihm_model_list.model_id
_ihm_model_list.model_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 . 1 1 1
#
loop_
_ihm_model_group.id
_ihm_model_group.name
_ihm_model_group.details
1 "Cluster 1" .
#
loop_
_ihm_model_group_link.group_id
_ihm_model_group_link.model_id
1 1
#
loop_
_ihm_sphere_obj_site.id
_ihm_sphere_obj_site.entity_id
_ihm_sphere_obj_site.seq_id_begin
_ihm_sphere_obj_site.seq_id_end
_ihm_sphere_obj_site.asym_id
_ihm_sphere_obj_site.Cartn_x
_ihm_sphere_obj_site.Cartn_y
_ihm_sphere_obj_site.Cartn_z
_ihm_sphere_obj_site.object_radius
_ihm_sphere_obj_site.rmsf
_ihm_sphere_obj_site.model_id
1 1 1 6 A 389.993 145.089 134.782 4.931 . 1
2 1 7 7 B 406.895 142.176 135.653 3.318 1.34 1
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
self.assertEqual(2,len(I.get_sphere_model_dict()[1]) )
def test_get_violation_plot(self):
lst=pd.DataFrame([['C_4',0],['C_4',1],['C_5',1]],columns=['XL_ID','Satisfied'])
model_df={1:lst}
I=cx_validation('test.cif')
self.assertEqual(66,int(I.get_violation_plot(model_df)[1]))
def test_label_inter_intra_2(self):
lst=pd.DataFrame([['C_4','D_5']],columns=['Res1','Res2'])
I=cx_validation('test.cif')
self.assertEqual(0,int(I.label_inter_intra(lst)['Intra'].values[0]))
def test_get_distance(self):
lst=pd.DataFrame([[4,5,6,1,2,3]],columns=['Res1_X','Res1_Y','Res1_Z',
'Res2_X','Res2_Y','Res2_Z'])
I=cx_validation('test.cif')
self.assertEqual(5,int(I.get_distance(lst)['dist'].values[0]))
def test_get_atom_model_dict(self):
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_ihm_model_list.model_id
_ihm_model_list.model_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 . 1 1 1
#
loop_
_ihm_model_group.id
_ihm_model_group.name
_ihm_model_group.details
1 "Cluster 1" .
#
loop_
_ihm_model_group_link.group_id
_ihm_model_group_link.model_id
1 1
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_asym_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.label_entity_id
_atom_site.auth_asym_id
_atom_site.B_iso_or_equiv
_atom_site.pdbx_PDB_model_num
_atom_site.ihm_model_id
ATOM 1 CA CA . SER 1 A 54.401 -49.984 -35.287 . 1 A . 1 1
ATOM 2 CA CA . SER 2 A 54.401 -49.984 -35.287 . 3 A . 1 1
ATOM 3 CA CA . SER 3 A 54.401 -49.984 -35.287 . 3 A . 1 1
loop_
_ihm_cross_link_list.id
_ihm_cross_link_list.group_id
_ihm_cross_link_list.entity_description_1
_ihm_cross_link_list.entity_id_1
_ihm_cross_link_list.seq_id_1
_ihm_cross_link_list.comp_id_1
_ihm_cross_link_list.entity_description_2
_ihm_cross_link_list.entity_id_2
_ihm_cross_link_list.seq_id_2
_ihm_cross_link_list.comp_id_2
_ihm_cross_link_list.linker_type
_ihm_cross_link_list.dataset_list_id
1 1 foo 1 2 THR foo 1 3 CYS DSS 97
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 foo
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
atom=I.get_atom_model_dict()[1]
df=I.get_xyzrseq_atoms(atom)
xl_df=I.get_xl_data()
self.assertEqual((1,11),I.get_complete_df_atomic(xl_df,df).shape)
self.assertEqual(54.401,I.get_complete_df_atomic(xl_df,df)['Res1_X'].unique()[0])
self.assertEqual('2_3',I.get_complete_df_atomic(xl_df,df)['XL_ID'].unique()[0])
self.assertEqual('A_2',I.get_complete_df_atomic(xl_df,df)['Res1'].unique()[0])
def test_get_complete_df_hybrid(self):
fh = """
data_PDBDEV_test
_entry.id PDBDEV_test
loop_
_ihm_model_list.model_id
_ihm_model_list.model_name
_ihm_model_list.assembly_id
_ihm_model_list.protocol_id
_ihm_model_list.representation_id
1 . 1 1 1
#
loop_
_ihm_model_group.id
_ihm_model_group.name
_ihm_model_group.details
1 "Cluster 1" .
#
loop_
_ihm_model_group_link.group_id
_ihm_model_group_link.model_id
1 1
#
loop_
_ihm_sphere_obj_site.id
_ihm_sphere_obj_site.entity_id
_ihm_sphere_obj_site.seq_id_begin
_ihm_sphere_obj_site.seq_id_end
_ihm_sphere_obj_site.asym_id
_ihm_sphere_obj_site.Cartn_x
_ihm_sphere_obj_site.Cartn_y
_ihm_sphere_obj_site.Cartn_z
_ihm_sphere_obj_site.object_radius
_ihm_sphere_obj_site.rmsf
_ihm_sphere_obj_site.model_id
1 1 1 6 A 389.993 145.089 134.782 4.931 . 1
1 1 7 7 A 389.993 145.089 134.782 4.931 . 1
loop_
_ihm_cross_link_list.id
_ihm_cross_link_list.group_id
_ihm_cross_link_list.entity_description_1
_ihm_cross_link_list.entity_id_1
_ihm_cross_link_list.seq_id_1
_ihm_cross_link_list.comp_id_1
_ihm_cross_link_list.entity_description_2
_ihm_cross_link_list.entity_id_2
_ihm_cross_link_list.seq_id_2
_ihm_cross_link_list.comp_id_2
_ihm_cross_link_list.linker_type
_ihm_cross_link_list.dataset_list_id
1 1 foo 1 2 THR foo 1 3 CYS DSS 97
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 foo
"""
with open ('test.cif', 'w') as fd:
fd.write(fh)
I=cx_validation('test.cif')
spheres=I.get_sphere_model_dict()[1]
df_s,df_u=I.get_xyzrseq_spheres(spheres)
df=I.convert_df_unstruc(df_u)
xl_df=I.get_xl_data()
self.assertEqual((1,11),I.get_complete_df_hybrid(xl_df,df).shape)
self.assertEqual(389.993,I.get_complete_df_hybrid(xl_df,df)['Res1_X'].unique()[0])
self.assertEqual('2_3',I.get_complete_df_hybrid(xl_df,df)['XL_ID'].unique()[0])
self.assertEqual('A_2',I.get_complete_df_hybrid(xl_df,df)['Res1'].unique()[0])
