def analyse(uniprot):
print('***************** ANALYSIS *******************************')
p = ProteinAnalyser(taxid='9606', uniprot=uniprot).load()
p.mutation = f'{p.sequence[65]}66W'
p.predict_effect()
p.analyse_structure()
print(p)
import json
json.dump(p.asdict(), open('test.json', 'w'))
def test_ProteinAnalyser():
p = ProteinAnalyser(uniprot='Q86V25').load()
print(p)
p.mutation = Mutation('p.N127W')
p.analyse_structure()
print(p.get_features_near_position())
print(p.get_gnomAD_near_position())
print(p.model.get_structure_neighbours())
print(p.get_superficiality())
def protein_step(self):
"""
Check mutations are valid
"""
self.start_timer()
if self.has(): # this is already done (very unlikely/
protein = system_storage[self.handle]
else:
log.info(
f'Step 1 analysis requested by {User.get_username(self.request)}'
)
uniprot = self.request.params['uniprot']
taxid = self.request.params['species']
mutation_text = self.request.params['mutation']
## Do analysis
mutation = Mutation(mutation_text)
protein = ProteinAnalyser(uniprot=uniprot, taxid=taxid)
protein.load()
protein.mutation = mutation
# assess
if not protein.check_mutation():
log.info('protein mutation discrepancy error')
discrepancy = protein.mutation_discrepancy()
self.reply = {
**self.reply, 'error': 'mutation',
'msg': discrepancy,
'status': 'error'
}
raise VenusException(discrepancy)
else:
system_storage[self.handle] = protein
self.reply['protein'] = self.jsonable(protein)
self.stop_timer()
def protein_step():
uniprot = request.params['uniprot']
taxid = request.params['species']
mutation = Mutation(request.params['mutation'])
protein = ProteinAnalyser(uniprot=uniprot, taxid=taxid)
try:
protein.load()
except FutureWarning:
log.error(
f'There was no pickle for uniprot {uniprot} taxid {taxid}. TREMBL code via API?'
)
#protein.__dict__ = ProteinGatherer(uniprot=uniprot, taxid=taxid).get_uniprot().__dict__
protein.mutation = mutation
if not protein.check_mutation():
log.info('protein mutation discrepancy error')
return {
'error': 'mutation',
'msg': protein.mutation_discrepancy(),
'status': 'error'
}
else:
handle = request.params['uniprot'] + request.params['mutation']
system_storage[handle] = protein
return {'protein': jsonable(protein), 'status': 'success'}
def load_protein(self) -> ProteinAnalyser:
protein = ProteinAnalyser(uniprot=self.uniprot, taxid=self.taxid)
protein.load()
# self.reply['protein'] = self.jsonable(protein)
return protein
print([m for m in p.gnomAD if m.homozygous])
print(' '.join([str(m.description.split()[0]) for m in p.gnomAD]) + ')')
print([m for m in p.gnomAD if m.homozygous])
elif 1 == 0:
iterate_taxon('9606')
#.retrieve_references(ask=False, refresh=False)
#UniprotMasterReader()
#global_settings.startup()
#make_pdb_dex()
#split_gnomAD.gnomAD().write()
#iterate_taxon('9606')
p = ProteinAnalyser(taxid='9606', uniprot='Q9BZ29').load()
p.mutation = 'P23W'
print('check_mutation', p.check_mutation())
print('mutation_discrepancy', p.mutation_discrepancy())
print('predict_effect', p.predict_effect())
print('elmdata', p.elmdata)
print(p.mutation)
# fetch_binders is too slow. Pre-split the data like for gnomAD.
elif 1 == 0:
print('retrieving...')
global_settings.retrieve_references(ask=False, refresh=False)
else:
## dock 9 ops.
#test_ProteinAnalyser()
p = ProteinGatherer(uniprot='Q96N67').load()
p.parse_gnomAD()
pymol.cmd.remove('chain A')
pymol.cmd.save('GNB2_alone.pdb')
native_alone = pyrosetta.rosetta.core.pose.Pose()
pyrosetta.rosetta.core.import_pose.pose_from_file(native_alone,
'GNB2_alone.pdb')
relax(native_alone, 15)
native_alone.dump_pdb('GNB2_alone.r.pdb')
################### phosphorylated ######################################
from Bio.SeqUtils import seq3
from michelanglo_protein import ProteinAnalyser, global_settings
global_settings.startup(
data_folder='/home/matteo/Coding/Michelanglo/protein-data')
p = ProteinAnalyser(taxid=9606, uniprot='P62879').load()
native_phospho = pyrosetta.rosetta.core.pose.Pose()
pyrosetta.rosetta.core.import_pose.pose_from_file(native_phospho,
'GNB2_alone.pdb')
MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
# KinaseMover = pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover
add_variant_type_to_residue = pyrosetta.rosetta.core.pose.add_variant_type_to_residue
pose2pdb = native_phospho.pdb_info().pdb2pose
for record in p.features['PSP_modified_residues']:
change = record['from_residue'] + '-' + record['ptm']
if record['ptm'] == 'ub':
continue
elif record['ptm'] == 'p':
patch = 'phosphorylated'