def dump4molviewer(filename='kripo-phar-molviewer.json'):
"""Dumps each pharmacophore/residue pairs to a json file which can be viewed with the 3d-e-chem molviewer
```python
from tests.pharmacohore.test_from_site import dump4molviewer
dump4molviewer()
```
"""
rows = []
ligand_expo = LigandExpoDb('tests/fixtures/ligand-expo.db').as_dict()
ligand = ligands(pdb_from_file('tests/fixtures/3HEG.prepped.pdb'),
ligand_expo)[0]
for residue in residues:
block = residue.values[0]
features = residue.values[1]
site = prep_site(block, ligand.atomium_mol)
label = site.residue().name() + str(len(list(site.residue().atoms())))
row = {
'id': label,
'label': label,
'protein': {
'data': site.ligand().model().to_file_string('pdb'),
'format': 'pdb',
},
'pharmacophore': {
'data': as_phar(label, feat2points(features)),
'format': 'phar',
},
}
rows.append(row)
with open(filename, 'w') as f:
json.dump(rows, f)
def dump_artificial_pdb_with_all_residues(all_res_site_pdb='all_res_site.pdb'):
"""
```python
from tests.pharmacohore.test_from_site import dump_artificial_pdb_with_all_residues
dump_artificial_pdb_with_all_residues('all_res_site_pdb')
```
"""
ligand = ligands(pdb_from_file('tests/fixtures/3HEG.prepped.pdb'))[0]
block = ""
for residue in residues:
block += residue.values[0]
site = prep_site(block, ligand.atomium_mol)
block_with_ligand = site.ligand().model().to_file_string('pdb')
with open(all_res_site_pdb, 'w') as f:
f.write(block_with_ligand)
def yasara_fragment2_3heg_bax(ligand_expo_dict_fixture):
filename = 'tests/fixtures/3HEG.frag2.pdb'
pdb = pdb_from_file(filename)
ligand = ligands(pdb, ligand_expo_dict_fixture)[0]
frags = ligand.fragments()
return frags[0]
def test_protonate_pdb_2muv():
unprotonated = pdb_from_file('tests/fixtures/2MUV.pdb',
hydrogenate=False,
clean=False)
protonated = protonate_pdb(unprotonated)
assert len(protonated.model().atoms(element='H')) == 982
def prep_pdb(opath, npath):
"""Speed up tests by using already hydrogenated and cleaned pdbs"""
pdb = pdb_from_file(opath)
pdb.save(npath)
def pdb_2muv():
# NMR and multi model
filename = 'tests/fixtures/2MUV.prepped.pdb'
return pdb_from_file(filename, hydrogenate=False, clean=False)
def pdb_3rze():
# multiple ligands
filename = 'tests/fixtures/3RZE.prepped.pdb'
return pdb_from_file(filename, hydrogenate=False, clean=False)
def pdb_5is0():
# electron microscopy
filename = 'tests/fixtures/5IS0.prepped.pdb'
return pdb_from_file(filename, hydrogenate=False, clean=False)
def pdb_3heg():
filename = 'tests/fixtures/3HEG.prepped.pdb'
return pdb_from_file(filename, hydrogenate=False, clean=False)
