def build_ligand_properties(self):
lp = LigandProperities()
lt = LigandType.objects.get(name = 'small molecule')
lp.ligand_type = lt
lp.smiles = None
lp.inchikey = None
lp.sequence= None
lp.mw = None
lp.rotatable_bonds = None
lp.hacc = None
lp.hdon = None
lp.logp = None
lp.save()
self.logger.info("Could not create ligand, empty is returned")
return lp
def main_func(self, positions, iteration, count, lock):
# print(positions,iteration,count,lock)
ligands = self.ligand_dump
while count.value < len(ligands):
with lock:
l = ligands[count.value]
count.value += 1
if count.value % 10000 == 0:
print('{} Status {} out of {}'.format(
datetime.datetime.strftime(datetime.datetime.now(),
'%Y-%m-%d %H:%M:%S'),
count.value, len(ligands)))
if 'logp' not in l:
# temp skip to only use "full" annotated ligands
continue
lp = LigandProperities.objects.filter(
inchikey=l['inchikey']).first()
ligand = None
if lp:
# Check if inchikey is there
ligand = Ligand.objects.filter(
name=l['name'], properities=lp).prefetch_related(
'properities__ligand_type', 'properities__web_links',
'properities__vendors').first()
# The name with corresponding inchikey is there, assume all is good and skip.
# Will add links to make sure they're there.
if not ligand:
if lp:
print(l['name'], 'is there! (but not by name, only inchi')
ligand = Ligand()
ligand.properities = lp
ligand.name = l['name']
ligand.canonical = l['canonical']
ligand.ambigious_alias = l['ambigious_alias']
ligand.save()
else:
# No ligand seems to match by inchikey -- start creating it.
# Make LigandProperities first
lt, created = LigandType.objects.get_or_create(
slug=l['ligand_type__slug'],
defaults={'name': l['ligand_type__name']})
lp = LigandProperities()
lp.inchikey = l['inchikey']
lp.smiles = l['smiles']
lp.mw = l['mw']
lp.logp = l['logp']
lp.rotatable_bonds = l['rotatable_bonds']
lp.hacc = l['hacc']
lp.hdon = l['hdon']
lp.ligand_type = lt
lp.save()
ligand = Ligand()
ligand.properities = lp
ligand.name = l['name']
ligand.canonical = l['canonical']
ligand.ambigious_alias = l['ambigious_alias']
ligand.save()
# create links - impossible to make duplicates so no need to check if there already
if ligand.properities.web_links.count() < len(l['web_links']):
for link in l['web_links']:
wr = WebResource.objects.get(slug=link['web_resource'])
wl, created = WebLink.objects.get_or_create(
index=link['index'], web_resource=wr)
ligand.properities.web_links.add(wl)
# create vendors - impossible to make duplicates so no need to check if there already
if ligand.properities.vendors.count() < len(l['vendors']):
for link in l['vendors']:
lv = LigandVendors.objects.get(slug=link['vendor_slug'])
check = LigandVendorLink.objects.filter(
sid=link['sid']).exists()
if not check:
lvl = LigandVendorLink()
lvl.sid = link['sid']
lvl.vendor = lv
lvl.lp = ligand.properities
lvl.vendor_external_id = link['vendor_external_id']
lvl.url = link['url']
lvl.save()
def main_func(self, positions, iteration,count,lock):
# print(positions,iteration,count,lock)
ligands = self.ligand_dump
while count.value<len(ligands):
with lock:
l = ligands[count.value]
count.value +=1
if count.value % 10000 == 0:
print('{} Status {} out of {}'.format(
datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S'), count.value, len(ligands)))
if 'logp' not in l:
# temp skip to only use "full" annotated ligands
continue
lp = LigandProperities.objects.filter(inchikey=l['inchikey']).first()
ligand = None
if lp:
# Check if inchikey is there
ligand = Ligand.objects.filter(name=l['name'], properities=lp).prefetch_related('properities__ligand_type','properities__web_links','properities__vendors').first()
# The name with corresponding inchikey is there, assume all is good and skip.
# Will add links to make sure they're there.
if not ligand:
if lp:
print(l['name'],'is there! (but not by name, only inchi')
ligand = Ligand()
ligand.properities = lp
ligand.name = l['name']
ligand.canonical = l['canonical']
ligand.ambigious_alias = l['ambigious_alias']
ligand.save()
else:
# No ligand seems to match by inchikey -- start creating it.
# Make LigandProperities first
lt, created = LigandType.objects.get_or_create(slug=l['ligand_type__slug'],defaults = {'name':l['ligand_type__name']})
lp = LigandProperities()
lp.inchikey = l['inchikey']
lp.smiles = l['smiles']
lp.mw = l['mw']
lp.logp = l['logp']
lp.rotatable_bonds = l['rotatable_bonds']
lp.hacc = l['hacc']
lp.hdon = l['hdon']
lp.ligand_type = lt
lp.save()
ligand = Ligand()
ligand.properities = lp
ligand.name = l['name']
ligand.canonical = l['canonical']
ligand.ambigious_alias = l['ambigious_alias']
ligand.save()
# create links - impossible to make duplicates so no need to check if there already
if ligand.properities.web_links.count()<len(l['web_links']):
for link in l['web_links']:
wr = WebResource.objects.get(slug=link['web_resource'])
wl, created = WebLink.objects.get_or_create(index=link['index'], web_resource=wr)
ligand.properities.web_links.add(wl)
# create vendors - impossible to make duplicates so no need to check if there already
if ligand.properities.vendors.count()<len(l['vendors']):
for link in l['vendors']:
lv = LigandVendors.objects.get(slug = link['vendor_slug'])
check = LigandVendorLink.objects.filter(sid=link['sid']).exists()
if not check:
lvl = LigandVendorLink()
lvl.sid = link['sid']
lvl.vendor = lv
lvl.lp = ligand.properities
lvl.vendor_external_id = link['vendor_external_id']
lvl.url = link['url']
lvl.save()
