restructure and improve tests

ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_2380_002_e-9.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 2380.002
+    activity_type: pIC50
+    activity_unit: 1e-9
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '2'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: PF05053
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: O00255
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF05965
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM

ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_4_9846073_e-6.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 4.9846073
+    activity_type: pIC50
+    activity_unit: 1e-6
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '2'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: PF05053
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: O00255
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF05965
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM

ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_639_39406_e-3.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 639.39406
+    activity_type: pIC50
+    activity_unit: 1e-3
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '2'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: PF05053
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: O00255
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF05965
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM

ippisite/ippidb/tests/test_activity_computation_and_storage_pIC50_6_85_e-0.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 6.85
+    activity_type: pIC50
+    activity_unit: 1e-0
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '2'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: PF05053
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: O00255
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF05965
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM

ippisite/ippidb/tests/test_basic_entry.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 6.85
+    activity_type: pIC50
+    activity_unit: 1e-6
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '2'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: PF05053
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: O00255
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF05965
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: CCC
+diseases:
+- ;toto;1;
+- ;titi;sfddf;
+- ;tata;3232;
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+source: PM

ippisite/ippidb/tests/test_complex_no_pfam.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 6.85
+    activity_type: pIC50
+    activity_unit: 1e-3
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '1'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF00400
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: P61964
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: null
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: C
+diseases: []
+family_name: WD40 (PF00400)
+id_source: '26958703'
+in_silico: true
+pdb_id: 3emh
+source: PM

ippisite/ippidb/tests/test_entry_28.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 3.59
+    activity_type: pKd
+    activity_unit: 1e-9
+    compound_name: '2'
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 1
+  protein_bound_construct: F
+  protein_complex: '1'
+  test_modulation_type: B
+  test_name: biolayer interferometry assay
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: null
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q60795
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF01344
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q9Z2X8
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: ''
+  compound_name: '2'
+  molecule_smiles: c1cc2c(cc1)c(ccc2N(S(=O)(=O)c1ccc(cc1)OC)CC(=O)O)N(S(=O)(=O)c1ccc(cc1)OC)CC(=O)O
+diseases:
+- ;cancer;MONDO:0004992;
+family_name: KEAP1 / NRF2
+id_source: '24512214 '
+in_vitro: true
+pdb_id: 3wn7
+source: PM

ippisite/ippidb/tests/test_simple_heterodimer.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 6.85
+    activity_type: pIC50
+    activity_unit: 1e-3
+    compound_name: 16d
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '1'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF00400
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: P61964
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: null
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: officially 16d
+  compound_name: 16d
+  ligand_id: ABC
+  molecule_smiles: CN1CCN(CC1)C1=C(C=C(C=C1)C1=CC(=CC=C1)CN1CCOCC1)NC(=O)C1=CNC(C=C1C(F)(F)F)=O
+- common_name: officially 14a
+  compound_name: 14a
+  is_macrocycle: false
+  molecule_iupac: N-(2-(4-Methylpiperazin-1-yl)-5-nitrophenyl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide
+- common_name: stuck
+  compound_name: lili
+  is_macrocycle: false
+  molecule_smiles: C1CCC1
+diseases: []
+family_name: WD40 (PF00400)
+id_source: '26958703'
+in_silico: true
+in_vitro: true
+pdb_id: 3emh
+source: PM
+xray: true

ippisite/ippidb/tests/test_simple_stabilized_heterodimer.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 0.25
+    activity_type: pIC50
+    activity_unit: 1e-6
+    compound_name: FC
+    modulation_type: S
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '1'
+  test_modulation_type: I
+  test_name: pull down
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF00244
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: P31947
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: null
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: P03372
+complexChoice: stabilized
+complexType: Stab_Hetero2merAB
+compounds:
+- common_name: fusicoccin
+  compound_name: FC
+  ligand_id: FSC
+  molecule_smiles: COC[C@H]1CC[C@H]2[C@@H](C)[C@@H](O)[C@H](O[C@H]3O[C@H](COC(C)(C)C=C)[C@@H](O)[C@H](OC(C)=O)[C@H]3O)C3=C(C[C@H](O)[C@]3(C)\C=C1/2)[C@H](C)COC(C)=O
+diseases:
+- ;breast cancer;MONDO:0007254;
+family_name: 14-3-3 / ER
+id_source: '23676274'
+in_cellulo: true
+in_vitro: true
+pdb_id: 4jc3
+source: PM
+xray: true

ippisite/ippidb/tests/test_stabilizer_204.yaml

+source: PM
+id_source: '23808890'
+in_vitro: true
+xray: true
+pdb_id: 4ihl
+complexChoice: stabilized
+complexType: Stab_Hetero2merAB
+complex:
+  - cc_nb: 1
+    complex_type: Bound
+    domain_pfam_acc: PF00244
+    ppc_copy_nb: 1
+    ppp_copy_nb_per_p: 1
+    uniprot_id: P63104
+  - cc_nb: 1
+    complex_type: Bound
+    domain_pfam_acc: null
+    ppc_copy_nb: 1
+    ppp_copy_nb_per_p: 1
+    uniprot_id: P04049
+family_name: 14-3-3 / C-RAF
+diseases:
+  - ;melanoma;(MONDO_0005105);
+compounds:
+  - common_name: Cotylenin A
+    compound_name: Cotylenin A
+    molecule_smiles: COC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@H](C)[C@@H]3CC[C@](O)(COC)C3=C[C@@]3(C)CCC(C(C)C)=C23)[C@H](O)[C@H]2O[C@H]3O[C@@]12O[C@@]3(C)[C@@H]1CO1
+activity_tests:
+- test_type: BIOCH
+  test_name: Fluorescence Polarization
+  protein_bound_construct: F
+  test_modulation_type: B
+  nb_active_compounds: 1
+  protein_complex: '1'
+  compound_activity_results:
+  - activity_mol: 20
+    activity_type: pKd
+    activity_unit: 1e-10
+    compound_name: Cotylenin A
+    modulation_type: S
\ No newline at end of file

ippisite/ippidb/tests/test_with_all_tests.yaml

+activity_tests:
+- cell_line_name: ''
+  compound_activity_results:
+  - activity_mol: 6.85
+    activity_type: pIC50
+    activity_unit: 1e-3
+    compound_name: toto
+    modulation_type: I
+  is_primary: true
+  nb_active_compounds: 2
+  protein_bound_construct: F
+  protein_complex: '2'
+  test_modulation_type: I
+  test_name: test
+  test_type: BIOCH
+complex:
+- cc_nb: 1
+  complex_type: Partner
+  domain_pfam_acc: PF05053
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: ''
+  uniprot_id: O00255
+- cc_nb: 1
+  complex_type: Bound
+  domain_pfam_acc: PF05965
+  ppc_copy_nb: 1
+  ppp_copy_nb_per_p: 1
+  uniprot_id: Q03164
+complexChoice: inhibited
+complexType: Inhib_Hetero2merAB
+compounds:
+- common_name: super
+  compound_name: toto
+  molecule_smiles: CCC
+cytotox: true
+cytotox_tests:
+- cell_line_name: '1043SK '
+  compound_concentration: '2'
+  compound_cytotox_results:
+  - compound_name: toto
+    toxicity: 'True'
+  test_name: test
+diseases:
+- ''
+- ;titi;sfddf;
+- ;tutu;5456456;
+- ;tutu;5456456;
+- ''
+family_name: Menin (PF05053)
+id_source: '15072770'
+in_silico: true
+pdb_id: 3u85
+pharmacokinetic: true
+pharmacokinetic_tests:
+- administration_mode: IV
+  cell_line_name: '1043SK '
+  compound_pk_results:
+  - auc: '1'
+    c_max: '5.2'
+    clearance: '1.2'
+    compound_name: toto
+    oral_bioavailability: '22'
+    t_demi: '5'
+    t_max: '5'
+    tolerated: 'True'
+    voldistribution: '5.5'
+  concentration: '1.2'
+  dose: '3.5'
+  dose_interval: '2'
+  organism: 1
+  test_name: test
+source: PM

ippisite/ippidb/tests/tests_utils.py

@@ -6,7 +6,7 @@ import re
 from django.test import TestCase
 from openbabel import vectorUnsignedInt, OBFingerprint
 
-from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
+from ippidb.utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
 
 
 class MolSmiTestCase(TestCase):