def create_or_update_residue(protein_conformation, segment, schemes, residue,
b_and_c):
logger = logging.getLogger('build')
rns_defaults = {
'protein_segment': segment
} # default numbering scheme for creating generic numbers
# default numbering scheme
ns = settings.DEFAULT_NUMBERING_SCHEME
ns_obj = ResidueNumberingScheme.objects.get(slug=ns)
rvalues = {}
rvalues['protein_segment'] = segment
rvalues['amino_acid'] = residue['aa']
rvalues['generic_number'] = None
rvalues['display_generic_number'] = None
sequence_number = residue['pos']
numbers = residue['numbers']
if 'generic_number' in numbers:
numbers = format_generic_numbers(
protein_conformation.protein.residue_numbering_scheme, schemes,
sequence_number, numbers['generic_number'], numbers['bw'], b_and_c)
# print(numbers)
# print(residues,numbers)
# main generic number
if 'generic_number' in numbers:
gnl = numbers['generic_number']
if gnl in schemes[ns]['generic_numbers']:
rvalues['generic_number'] = schemes[ns]['generic_numbers'][gnl]
else:
try:
gn, created = ResidueGenericNumber.objects.get_or_create(
scheme=ns_obj, label=gnl, defaults=rns_defaults)
# if created:
# logger.info('Created generic number {}'.format(gn.label))
except IntegrityError:
gn = ResidueGenericNumber.objects.get(scheme=ns_obj, label=gnl)
rvalues['generic_number'] = schemes[ns]['generic_numbers'][
gnl] = gn
# equivalent to main generic number
if 'equivalent' in numbers:
try:
gn_equivalent, created = ResidueGenericNumberEquivalent.objects.get_or_create(
default_generic_number=rvalues['generic_number'],
scheme=protein_conformation.protein.residue_numbering_scheme,
defaults={'label': numbers['equivalent']})
# if created:
# logger.info('Created generic number equivalent {} ({}) for scheme {}'.format(
# numbers['equivalent'], numbers['generic_number'],
# protein_conformation.protein.residue_numbering_scheme))
except IntegrityError:
gn_equivalent = ResidueGenericNumberEquivalent.objects.get(
default_generic_number=rvalues['generic_number'],
scheme=protein_conformation.protein.residue_numbering_scheme)
# display generic number
if 'display_generic_number' in numbers:
ns = protein_conformation.protein.residue_numbering_scheme.slug
gnl = numbers['display_generic_number']
if gnl in schemes[ns]['generic_numbers']:
rvalues['display_generic_number'] = schemes[ns]['generic_numbers'][
gnl]
else:
try:
gn, created = ResidueGenericNumber.objects.get_or_create(
scheme=protein_conformation.protein.
residue_numbering_scheme,
label=gnl,
defaults=rns_defaults)
# if created:
# logger.info('Created display generic number {}'.format(gn.label))
except IntegrityError:
gn = ResidueGenericNumber.objects.get(
scheme=protein_conformation.protein.
residue_numbering_scheme,
label=gnl)
rvalues['display_generic_number'] = schemes[ns]['generic_numbers'][
gnl] = gn
# UPDATE or CREATE the residue
# bulk_r = Residue(protein_conformation=protein_conformation,sequence_number=sequence_number,defaults = rvalues)
bulk_r = Residue(protein_conformation=protein_conformation,
sequence_number=sequence_number,
amino_acid=rvalues['amino_acid'],
display_generic_number=rvalues['display_generic_number'],
generic_number=rvalues['generic_number'],
protein_segment=segment)
# r, created = Residue.objects.update_or_create(protein_conformation=protein_conformation,
# sequence_number=sequence_number, defaults = rvalues)
# alternative generic numbers
# r.alternative_generic_numbers.clear() # remove any existing relations
bulk_add_alt = []
if (numbers and 'alternative_generic_numbers' in numbers):
for alt_scheme, alt_num in numbers[
'alternative_generic_numbers'].items():
if alt_num in schemes[alt_scheme]['generic_numbers']:
argn = schemes[alt_scheme]['generic_numbers'][alt_num]
else:
try:
argn, created = ResidueGenericNumber.objects.get_or_create(
scheme=ResidueNumberingScheme.objects.get(
slug=alt_scheme),
label=alt_num,
defaults=rns_defaults)
except IntegrityError:
argn = ResidueGenericNumber.objects.get(
scheme=ResidueNumberingScheme.objects.get(
slug=alt_scheme),
label=alt_num)
schemes[alt_scheme]['generic_numbers'][alt_num] = argn
try:
bulk_add_alt.append(argn)
# r.alternative_generic_numbers.add(argn)
except IntegrityError:
print('argn already added?')
pass
# print('argn already added?')
return [bulk_r, bulk_add_alt]
def handle(self, *args, **options):
self.options = options
if self.options['purge']:
Residue.objects.filter(
protein_conformation__protein__entry_name__endswith='_a',
protein_conformation__protein__family__parent__parent__name=
'Alpha').delete()
ProteinConformation.objects.filter(
protein__entry_name__endswith='_a',
protein__family__parent__parent__name='Alpha').delete()
Protein.objects.filter(
entry_name__endswith='_a',
family__parent__parent__name='Alpha').delete()
# Building protein and protconf objects for g protein structure in complex
scs = SignprotComplex.objects.all()
for sc in scs:
self.logger.info(
'Protein, ProteinConformation and Residue build for alpha subunit of {} is building'
.format(sc))
try:
# Alpha subunit
try:
alpha_protein = Protein.objects.get(
entry_name=sc.structure.pdb_code.index.lower() + '_a')
except:
alpha_protein = Protein()
alpha_protein.entry_name = sc.structure.pdb_code.index.lower(
) + '_a'
alpha_protein.accession = None
alpha_protein.name = sc.structure.pdb_code.index.lower(
) + '_a'
alpha_protein.sequence = sc.protein.sequence
alpha_protein.family = sc.protein.family
alpha_protein.parent = sc.protein
alpha_protein.residue_numbering_scheme = sc.protein.residue_numbering_scheme
alpha_protein.sequence_type = ProteinSequenceType.objects.get(
slug='mod')
alpha_protein.source = ProteinSource.objects.get(
name='OTHER')
alpha_protein.species = sc.protein.species
alpha_protein.save()
try:
alpha_protconf = ProteinConformation.objects.get(
protein__entry_name=sc.structure.pdb_code.index.lower(
) + '_a')
except:
alpha_protconf = ProteinConformation()
alpha_protconf.protein = alpha_protein
alpha_protconf.state = ProteinState.objects.get(
slug='active')
alpha_protconf.save()
pdbp = PDBParser(PERMISSIVE=True, QUIET=True)
s = pdbp.get_structure('struct',
StringIO(sc.structure.pdb_data.pdb))
chain = s[0][sc.alpha]
nums = []
for res in chain:
try:
res['CA']
nums.append(res.get_id()[1])
except:
pass
resis = Residue.objects.filter(
protein_conformation__protein=sc.protein)
num_i = 0
temp_seq2 = ''
pdb_num_dict = OrderedDict()
# Create first alignment based on sequence numbers
for n in nums:
if sc.structure.pdb_code.index == '6OIJ' and n < 30:
nr = n + 6
else:
nr = n
pdb_num_dict[n] = [chain[n], resis.get(sequence_number=nr)]
# Find mismatches
mismatches = []
for n, res in pdb_num_dict.items():
if AA[res[0].get_resname()] != res[1].amino_acid:
mismatches.append(res)
pdb_lines = sc.structure.pdb_data.pdb.split('\n')
seqadv = []
for l in pdb_lines:
if l.startswith('SEQADV'):
seqadv.append(l)
mutations, shifted_mutations = OrderedDict(), OrderedDict()
# Search for annotated engineered mutations in pdb SEQADV
for s in seqadv:
line_search = re.search(
'SEQADV\s{1}[A-Z\s\d]{4}\s{1}([A-Z]{3})\s{1}([A-Z]{1})\s+(\d+)[\s\S\d]{5}([\s\S\d]{12})([A-Z]{3})\s+(\d+)(\s\S+)',
s)
if line_search != None:
if line_search.group(2) == sc.alpha:
if line_search.group(
4).strip() == sc.protein.accession:
if line_search.group(3) == line_search.group(
6):
mutations[int(line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
else:
shifted_mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5),
int(line_search.group(6))
]
else:
# Exception for 6G79
if line_search.group(3) != line_search.group(
6) and 'CONFLICT' in line_search.group(
7):
mutations[int(line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
# Exception for 5G53
if line_search.group(
4).strip() != sc.protein.accession:
mutations[int(line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
remaining_mismatches = []
# Check and clear mismatches that are registered in pdb SEQADV as engineered mutation
for m in mismatches:
num = m[0].get_id()[1]
if num in mutations:
if m[0].get_resname() != mutations[num][0] and m[
1].amino_acid != AA[mutations[num][1]]:
remaining_mismatches.append(m)
elif num in shifted_mutations:
remaining_mismatches.append(m)
else:
remaining_mismatches.append(m)
### sanity check
# print(mutations)
# print(shifted_mutations)
# print(mismatches)
# print(remaining_mismatches)
# pprint.pprint(pdb_num_dict)
# Mismatches remained possibly to seqnumber shift, making pairwise alignment to try and fix alignment
if len(remaining_mismatches
) > 0 and sc.structure.pdb_code.index not in [
'6OIJ', '6OY9', '6OYA'
]:
ppb = PPBuilder()
seq = ''
for pp in ppb.build_peptides(chain, aa_only=False):
seq += str(pp.get_sequence())
pw2 = pairwise2.align.localms(sc.protein.sequence, seq, 2,
-1, -.5, -.1)
ref_seq, temp_seq = str(pw2[0][0]), str(pw2[0][1])
wt_pdb_dict = OrderedDict()
pdb_wt_dict = OrderedDict()
j, k = 0, 0
for i, ref, temp in zip(range(0, len(ref_seq)), ref_seq,
temp_seq):
if ref != '-' and temp != '-':
wt_pdb_dict[resis[j]] = pdb_num_dict[nums[k]]
pdb_wt_dict[pdb_num_dict[nums[k]][0]] = resis[j]
j += 1
k += 1
elif ref == '-':
wt_pdb_dict[i] = pdb_num_dict[nums[k]]
pdb_wt_dict[pdb_num_dict[nums[k]][0]] = i
k += 1
elif temp == '-':
wt_pdb_dict[resis[j]] = i
pdb_wt_dict[i] = resis[j]
j += 1
for i, r in enumerate(remaining_mismatches):
# Adjust for shifted residue when residue is a match
if r[0].get_id()[1] - remaining_mismatches[
i - 1][0].get_id()[1] > 1:
pdb_num_dict[r[0].get_id()[1] -
1][1] = pdb_wt_dict[chain[
r[0].get_id()[1] - 1]]
# Adjust for shifted residue when residue is mutated and it's logged in SEQADV
if r[0].get_id()[1] in shifted_mutations:
pdb_num_dict[r[0].get_id()[1]][1] = resis.get(
sequence_number=shifted_mutations[
r[0].get_id()[1]][2])
# Adjust for shift
else:
pdb_num_dict[r[0].get_id()[1]][1] = pdb_wt_dict[
r[0]]
bulked_residues = []
for key, val in pdb_num_dict.items():
# print(key, val) # sanity check
res_obj = Residue()
res_obj.sequence_number = val[0].get_id()[1]
res_obj.amino_acid = AA[val[0].get_resname()]
res_obj.display_generic_number = val[
1].display_generic_number
res_obj.generic_number = val[1].generic_number
res_obj.protein_conformation = alpha_protconf
res_obj.protein_segment = val[1].protein_segment
bulked_residues.append(res_obj)
Residue.objects.bulk_create(bulked_residues)
self.logger.info(
'Protein, ProteinConformation and Residue build for alpha subunit of {} is finished'
.format(sc))
except Exception as msg:
print(
'Protein, ProteinConformation and Residue build for alpha subunit of {} has failed'
.format(sc))
print(msg)
self.logger.info(
'Protein, ProteinConformation and Residue build for alpha subunit of {} has failed'
.format(sc))
def create_constructs(self, filenames):
self.logger.info('CREATING CONSTRUCTS')
# what files should be parsed?
if not filenames:
filenames = os.listdir(self.construct_data_dir)
# parse files
for source_file in filenames:
source_file_path = os.sep.join([self.construct_data_dir, source_file])
if os.path.isfile(source_file_path) and source_file[0] != '.':
self.logger.info('Reading file {}'.format(source_file_path))
# read the yaml file
with open(source_file_path, 'r') as f:
sd = yaml.load(f)
# is a protein specified?
if 'protein' not in sd:
self.logger.error('Protein not specified for construct, skipping')
continue
# fetch the parent protein
try:
ppc = ProteinConformation.objects.select_related('protein__family', 'protein__species',
'protein__residue_numbering_scheme').get(protein__entry_name=sd['protein'],
state__slug=settings.DEFAULT_PROTEIN_STATE)
except ProteinConformation.DoesNotExist:
# abort if parent protein is not found
self.logger.error('Parent protein {} for construct {} not found, aborting!'.format(
sd['protein'], sd['name']))
continue
# create a protein record
p = Protein()
p.parent = ppc.protein
p.family = ppc.protein.family
p.species = ppc.protein.species
p.residue_numbering_scheme = ppc.protein.residue_numbering_scheme
p.sequence_type, created = ProteinSequenceType.objects.get_or_create(slug='mod',
defaults={'name': 'Modified'})
p.source, created = ProteinSource.objects.get_or_create(name='OTHER')
p.entry_name = slugify(strip_tags(sd['name']))
p.name = sd['name']
p.sequence = ppc.protein.sequence
# save protein (construct)
try:
p.save()
self.logger.info('Created construct {} with parent protein {}'.format(p.name,
ppc.protein.entry_name))
except Exception as e:
print(e)
self.logger.error('Failed creating construct {} with parent protein {}'.format(p.name,
ppc.protein.entry_name))
continue
# create protein conformation record
pc = ProteinConformation()
pc.protein = p
pc.state = ProteinState.objects.get(slug=settings.DEFAULT_PROTEIN_STATE)
try:
pc.save()
self.logger.info('Created conformation {} of protein {}'.format(pc.state.name, p.name))
except:
self.logger.error('Failed creating conformation {} of protein {}'.format(pc.state.name,
p.entry_name))
# create residue records
deletions = []
deletions_list = []
if 'deletions' in sd and sd['deletions']:
for t in sd['deletions']:
deletions += list(range(t[0],t[1]+1))
deletions_list.append(str(t[0])+'-'+str(t[1]))
s = ","
deletion_string = s.join(deletions_list)
mutations = {}
if 'mutations' in sd and sd['mutations']:
for m in sd['mutations']:
res_num = m[1:-1]
mutations[res_num] = {
'wt_res': m[0],
'mut_res': m[-1],
'full': m,
}
# Create construct record
c = Construct()
c.protein_conformation = pc
c.deletions = deletion_string
c.save()
# Create Auxiliary proteins
# if 'auxiliary_proteins' in sd and sd['auxiliary_proteins']:
# ap = AuxProtein()
# ap.construct = c
# apct = AuxProteinType.objects.create()
# ap.protein_type = apct
# apct.save()
# if 'remarks' in sd['auxiliary_proteins']:
# ap.remarks = sd['auxiliary_proteins']['remarks']
# ap.save()
# for step in sd['auxiliary_proteins']:
# if 'type' in step and 'name' in step and'sequence' in step:
# ap.protein_type = apct
# ap.protein_type, created = AuxProteinType.objects.get_or_create()
# ap.name = sd['auxiliary_proteins']['name']
# ap.uniprot_id = sd['auxiliary_proteins']['uniprot_id']
# ap.sequence = sd['auxiliary_proteins']['sequence']
#mutations if any to be included from mutation model along with reason of mutation
# ap.position = sd['auxiliary_proteins']['position']
# ap.deletions = sd['auxiliary_proteins']['deletions']
# else:
# self.logger.error('Auxiliary protein step incorrectly defined for {}'.format(p))
# create expression records
if 'expression_sys' in sd and sd['expression_sys']:
ce = ConstructExpression()
ce.construct = c
ce.expression_system, created = ConstructExpressionSystem.objects.get_or_create(expression_method = sd['expression_sys']['expression_method'], host_cell_type = sd['expression_sys']['host_cell_type'], host_cell = sd['expression_sys']['host_cell'])
if 'remarks' in sd:
ce.remarks = sd['expression_sys']['remarks']
ce.save()
# create solubilization records
if 'solubilization' in sd and sd['solubilization'] and 'steps' in sd['solubilization'] and sd['solubilization']['steps']:
so = ConstructSolubilization()
so.construct = c
cl = ChemicalList.objects.create()
so.chemical_list = cl
for step in sd['solubilization']['steps']:
if 'type' in step and 'item' in step and'concentration' in step:
chem = Chemical()
chem.chemical_type, created = ChemicalType.objects.get_or_create(name = step['type'])
chem.name = step['item']
chem.save()
cc = ChemicalConc()
cc.concentration = step['concentration']
cc.chemical = chem # since ChemicalConc has a ForeignKey to Chemical
cc.save()
cl.chemicals.add(cc)
else:
self.logger.error('Solubilization step incorrectly defined for {}'.format(p))
if 'remarks' in sd['solubilization']:
so.remarks = sd['solubilization']['remarks']
so.save()
# create purification records
if 'purification' in sd and sd['purification'] and sd['purification']['steps']:
pu = ConstructPurification()
pu.construct = c
if 'remarks' in sd['purification']:
pu.remarks = sd['purification']['remarks']
pu.save()
for step in sd['purification']['steps']:
if 'type' in step and 'description' in step:
pust = PurificationStep()
pust.description = step['description']
pust.purification = pu
pust.purification_type, created = PurificationStepType.objects.get_or_create(name = step['type'] ) # 2 values returned by get_or_create
if created:
self.logger.info('Created purification step type {}'.format(pust.purification_type))
pust.save()
else:
self.logger.error('Purification step incorrectly defined for {}'.format(p))
# create crystallization records
if 'crystallization' in sd and sd['crystallization']:
cy = ConstructCrystallization()
cy.construct = c
cyt = CrystallizationMethodTypes.objects.create()
cy.crystal_type = cyt
cy.method = sd['crystallization']['method']
cy.settings = sd['crystallization']['settings']
cy.protein_conc = sd['crystallization']['protein_conc']
cl = ChemicalList.objects.create()
cy.chemical_list = cl
for step in sd['crystallization']['chemicallist']:
if 'type' in step and 'item' in step and'concentration' in step:
chem = Chemical()
chem.chemical_type, created = ChemicalType.objects.get_or_create(name = step['type'])
chem.name = step['item']
chem.save()
cc = ChemicalConc()
cc.concentration = step['concentration']
cc.chemical = chem # since ChemicalConc has a ForeignKey to Chemical
cc.save()
cl.chemicals.add(cc)
else:
self.logger.error('Crystallization step incorrectly defined for {}'.format(p))
cy.aqueous_solution_lipid_ratio = sd['crystallization']['aqueous_solution_lipid_ratio_LCP']
cy.lcp_bolus_volume = sd['crystallization']['LCP_bolus_volume']
cy.precipitant_solution_volume = sd['crystallization']['precipitant_solution_volume']
cy.temp = sd['crystallization']['temperature']
cy.ph = sd['crystallization']['ph']
if 'remarks' in sd['crystallization']:
cy.remarks = sd['crystallization']['remarks']
cy.save()
# fusion proteins
split_segments = {}
if 'fusion_proteins' in sd and sd['fusion_proteins']:
for fp in sd['fusion_proteins']:
fp_start = Residue.objects.get(protein_conformation=ppc,
sequence_number=fp['positions'][0])
fp_end = Residue.objects.get(protein_conformation=ppc, sequence_number=fp['positions'][1])
# if the fusion protein is inserted within only one segment (the usual case), split that
# segment into two segments
if fp_start and fp_start.protein_segment == fp_end.protein_segment:
# get/create split protein segments
segment_before, created = ProteinSegment.objects.get_or_create(
slug=fp_start.protein_segment.slug+"_1", defaults={
'name': fp_start.protein_segment.name,
'category': fp_start.protein_segment.category,
'partial': True})
segment_after, created = ProteinSegment.objects.get_or_create(
slug=fp_start.protein_segment.slug+"_2", defaults={
'name': fp_start.protein_segment.name,
'category': fp_start.protein_segment.category,
'partial': True})
# keep track of information about split segments
split_segments[fp_start.protein_segment.slug] = {
'start': {
'sequence_number': fp['positions'][0],
'segment': segment_before,
},
'end': {
'sequence_number': fp['positions'][1],
'segment': segment_after,
},
}
# get/insert fusion protein
fusion, create = ProteinFusion.objects.get_or_create(name=fp['name'], defaults={
'sequence': fp['sequence']})
# create relationship with protein
ProteinFusionProtein.objects.create(protein=p, protein_fusion=fusion,
segment_before=segment_before, segment_after=segment_after)
prs = Residue.objects.filter(protein_conformation=ppc).prefetch_related(
'protein_conformation__protein', 'protein_segment', 'generic_number',
'display_generic_number__scheme', 'alternative_generic_numbers__scheme')
updated_sequence = ''
for pr in prs:
if pr.sequence_number not in deletions:
r = Residue()
r.protein_conformation = pc
r.generic_number = pr.generic_number
r.display_generic_number = pr.display_generic_number
r.sequence_number = pr.sequence_number
# check for split segments
if pr.protein_segment.slug in split_segments:
rsns = split_segments[pr.protein_segment.slug]['start']['sequence_number']
rsne = split_segments[pr.protein_segment.slug]['end']['sequence_number']
if r.sequence_number <= rsns:
r.protein_segment = split_segments[pr.protein_segment.slug]['start']['segment']
elif r.sequence_number >= rsne:
r.protein_segment = split_segments[pr.protein_segment.slug]['end']['segment']
else:
r.protein_segment = pr.protein_segment
# amino acid, check for mutations
if r.sequence_number in mutations:
if mutations[r.sequence_number]['wt_res'] == pr.amino_acid:
r.amino_acid = mutations[r.sequence_number]['mut_res']
else:
self.logger.error('Mutation {} in construct {} does not match wild-type sequence' \
+ ' of {}'.format(mutations[r.sequence_number]['full'], pc.protein.name,
ppc.protein.entry_name))
else:
r.amino_acid = pr.amino_acid
# save amino acid to updated sequence
updated_sequence += r.amino_acid
# save residue before populating M2M relations
r.save()
# alternative generic numbers
agns = pr.alternative_generic_numbers.all()
for agn in agns:
r.alternative_generic_numbers.add(agn)
# update sequence
p.sequence = updated_sequence
p.save()
self.logger.info('COMPLETED CREATING CONSTRUCTS')
def handle(self, *args, **options):
self.options = options
if self.options['purge']:
Residue.objects.filter(
protein_conformation__protein__entry_name__endswith='_a',
protein_conformation__protein__family__parent__parent__name=
'Alpha').delete()
ProteinConformation.objects.filter(
protein__entry_name__endswith='_a',
protein__family__parent__parent__name='Alpha').delete()
Protein.objects.filter(
entry_name__endswith='_a',
family__parent__parent__name='Alpha').delete()
SignprotStructureExtraProteins.objects.all().delete()
SignprotStructure.objects.all().delete()
if not options['only_signprot_structures']:
# Building protein and protconf objects for g protein structure in complex
scs = SignprotComplex.objects.all()
for sc in scs:
self.logger.info(
'Protein, ProteinConformation and Residue build for alpha subunit of {} is building'
.format(sc))
try:
# Alpha subunit
try:
alpha_protein = Protein.objects.get(
entry_name=sc.structure.pdb_code.index.lower() +
'_a')
except:
alpha_protein = Protein()
alpha_protein.entry_name = sc.structure.pdb_code.index.lower(
) + '_a'
alpha_protein.accession = None
alpha_protein.name = sc.structure.pdb_code.index.lower(
) + '_a'
alpha_protein.sequence = sc.protein.sequence
alpha_protein.family = sc.protein.family
alpha_protein.parent = sc.protein
alpha_protein.residue_numbering_scheme = sc.protein.residue_numbering_scheme
alpha_protein.sequence_type = ProteinSequenceType.objects.get(
slug='mod')
alpha_protein.source = ProteinSource.objects.get(
name='OTHER')
alpha_protein.species = sc.protein.species
alpha_protein.save()
try:
alpha_protconf = ProteinConformation.objects.get(
protein__entry_name=sc.structure.pdb_code.index.
lower() + '_a')
except:
alpha_protconf = ProteinConformation()
alpha_protconf.protein = alpha_protein
alpha_protconf.state = ProteinState.objects.get(
slug='active')
alpha_protconf.save()
pdbp = PDBParser(PERMISSIVE=True, QUIET=True)
s = pdbp.get_structure('struct',
StringIO(sc.structure.pdb_data.pdb))
chain = s[0][sc.alpha]
nums = []
for res in chain:
try:
res['CA']
nums.append(res.get_id()[1])
except:
pass
resis = Residue.objects.filter(
protein_conformation__protein=sc.protein)
num_i = 0
temp_seq2 = ''
pdb_num_dict = OrderedDict()
# Create first alignment based on sequence numbers
for n in nums:
if sc.structure.pdb_code.index == '6OIJ' and n < 30:
nr = n + 6
else:
nr = n
pdb_num_dict[n] = [
chain[n], resis.get(sequence_number=nr)
]
# Find mismatches
mismatches = []
for n, res in pdb_num_dict.items():
if AA[res[0].get_resname()] != res[1].amino_acid:
mismatches.append(res)
pdb_lines = sc.structure.pdb_data.pdb.split('\n')
seqadv = []
for l in pdb_lines:
if l.startswith('SEQADV'):
seqadv.append(l)
mutations, shifted_mutations = OrderedDict(), OrderedDict()
# Search for annotated engineered mutations in pdb SEQADV
for s in seqadv:
line_search = re.search(
'SEQADV\s{1}[A-Z\s\d]{4}\s{1}([A-Z]{3})\s{1}([A-Z]{1})\s+(\d+)[\s\S\d]{5}([\s\S\d]{12})([A-Z]{3})\s+(\d+)(\s\S+)',
s)
if line_search != None:
if line_search.group(2) == sc.alpha:
if line_search.group(
4).strip() == sc.protein.accession:
if line_search.group(
3) == line_search.group(6):
mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
else:
shifted_mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5),
int(line_search.group(6))
]
else:
# Exception for 6G79
if line_search.group(
3
) != line_search.group(
6
) and 'CONFLICT' in line_search.group(7):
mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
# Exception for 5G53
if line_search.group(
4).strip() != sc.protein.accession:
mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
remaining_mismatches = []
# Check and clear mismatches that are registered in pdb SEQADV as engineered mutation
for m in mismatches:
num = m[0].get_id()[1]
if num in mutations:
if m[0].get_resname() != mutations[num][0] and m[
1].amino_acid != AA[mutations[num][1]]:
remaining_mismatches.append(m)
elif num in shifted_mutations:
remaining_mismatches.append(m)
else:
remaining_mismatches.append(m)
### sanity check
# print(sc)
# print(mutations)
# print(shifted_mutations)
# print(mismatches)
# print('======')
# print(remaining_mismatches)
# pprint.pprint(pdb_num_dict)
# Mismatches remained possibly to seqnumber shift, making pairwise alignment to try and fix alignment
if len(remaining_mismatches
) > 0 and sc.structure.pdb_code.index not in [
'6OIJ', '6OY9', '6OYA', '6LPB', '6WHA'
]:
ppb = PPBuilder()
seq = ''
for pp in ppb.build_peptides(chain, aa_only=False):
seq += str(pp.get_sequence())
pw2 = pairwise2.align.localms(sc.protein.sequence, seq,
2, -1, -.5, -.1)
ref_seq, temp_seq = str(pw2[0][0]), str(pw2[0][1])
wt_pdb_dict = OrderedDict()
pdb_wt_dict = OrderedDict()
j, k = 0, 0
for i, ref, temp in zip(range(0, len(ref_seq)),
ref_seq, temp_seq):
# print(i, ref, temp) # alignment check
if ref != '-' and temp != '-':
wt_pdb_dict[resis[j]] = pdb_num_dict[nums[k]]
pdb_wt_dict[pdb_num_dict[nums[k]]
[0]] = resis[j]
j += 1
k += 1
elif ref == '-':
wt_pdb_dict[i] = pdb_num_dict[nums[k]]
pdb_wt_dict[pdb_num_dict[nums[k]][0]] = i
k += 1
elif temp == '-':
wt_pdb_dict[resis[j]] = i
pdb_wt_dict[i] = resis[j]
j += 1
for i, r in enumerate(remaining_mismatches):
# Adjust for shifted residue when residue is a match
if r[0].get_id()[1] - remaining_mismatches[
i - 1][0].get_id()[1] > 1:
pdb_num_dict[r[0].get_id()[1] -
1][1] = pdb_wt_dict[chain[
r[0].get_id()[1] - 1]]
# Adjust for shifted residue when residue is mutated and it's logged in SEQADV
if r[0].get_id()[1] in shifted_mutations:
pdb_num_dict[r[0].get_id()[1]][1] = resis.get(
sequence_number=shifted_mutations[
r[0].get_id()[1]][2])
# Adjust for shift
else:
pdb_num_dict[r[0].get_id()
[1]][1] = pdb_wt_dict[r[0]]
# Custom alignment fix for 6WHA mini-Gq/Gi2/Gs chimera
# elif sc.structure.pdb_code.index=='6WHA':
# ref_seq = 'MTLESIMACCLSEEAKEARRINDEIERQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGSGYSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENPYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPTTGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMY--SHLVDYFPEYDGP----QRDAQAAREFILKMFVDL---NPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV'
# temp_seq = '----------VSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVK----------------------------------------------------------------------------------------------------------------------------------GIFETKFQVDKVNFHMFDVG-----RRKWIQCFNDVTAIIFVVDSSDYNR----------LQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPDPRVTRAKY-FIRKEFVDISTASGDGRHICYPHFTC-VDTENARRIFNDCKDIILQMNLREYNLV'
# for i, ref, temp in zip(range(0,len(ref_seq)), ref_seq, temp_seq):
# print(i, ref, temp)
# pprint.pprint(pdb_num_dict)
bulked_residues = []
for key, val in pdb_num_dict.items():
# print(key, val) # sanity check
if not isinstance(val[1], int):
res_obj = Residue()
res_obj.sequence_number = val[0].get_id()[1]
res_obj.amino_acid = AA[val[0].get_resname()]
res_obj.display_generic_number = val[
1].display_generic_number
res_obj.generic_number = val[1].generic_number
res_obj.protein_conformation = alpha_protconf
res_obj.protein_segment = val[1].protein_segment
bulked_residues.append(res_obj)
else:
self.logger.info(
'Skipped {} as no annotation was present, while building for alpha subunit of {}'
.format(val[1], sc))
Residue.objects.bulk_create(bulked_residues)
self.logger.info(
'Protein, ProteinConformation and Residue build for alpha subunit of {} is finished'
.format(sc))
except Exception as msg:
#print('Protein, ProteinConformation and Residue build for alpha subunit of {} has failed'.format(sc))
#print(msg)
#print(traceback.format_exc())
#exit(0)
self.logger.info(
'Protein, ProteinConformation and Residue build for alpha subunit of {} has failed'
.format(sc))
### Build SignprotStructure objects from non-complex signprots
g_prot_alphas = Protein.objects.filter(
family__slug__startswith='100_001',
accession__isnull=False) #.filter(entry_name='gnai1_human')
complex_structures = SignprotComplex.objects.all().values_list(
'structure__pdb_code__index', flat=True)
for a in g_prot_alphas:
pdb_list = get_pdb_ids(a.accession)
for pdb in pdb_list:
if pdb not in complex_structures:
try:
data = self.fetch_gprot_data(pdb, a)
if data:
self.build_g_prot_struct(a, pdb, data)
except Exception as msg:
self.logger.error(
'SignprotStructure of {} {} failed\n{}: {}'.format(
a.entry_name, pdb, type(msg), msg))
def create_residues(self, args):
schemes = {
'gpcrdb': {'type': False},
'gpcrdba': {
'type': 'structure',
'seq_based': 'bw',
},
'gpcrdbb': {
'type': 'structure',
'seq_based': 'woot',
},
'gpcrdbc': {
'type': 'structure',
'seq_based': 'pin',
},
'gpcrdbf': {
'type': 'structure',
'seq_based': 'wang',
},
'bw': {'type': 'sequence'},
'woot': {'type': 'sequence'},
'pin': {'type': 'sequence'},
'wang': {'type': 'sequence'},
}
for scheme_name, scheme in schemes.items():
schemes[scheme_name]['obj'] = ResidueNumberingScheme.objects.get(slug=scheme_name)
mapping_file = os.sep.join([self.generic_numbers_source_dir, 'mapping_' + scheme_name + '.txt'])
if os.path.isfile(mapping_file):
with open(mapping_file, "r", encoding='UTF-8') as scheme_table_file:
schemes[scheme_name]['table'] = {}
for row in scheme_table_file:
split_row = shlex.split(row)
schemes[scheme_name]['table'][split_row[0]] = split_row[1]
missing_proteins = []
self.logger.info('CREATING RESIDUES')
for arg in args:
if os.path.exists(os.sep.join([self.dump_source_dir, arg])):
residue_data_fh = open(os.sep.join([self.dump_source_dir, arg]), 'r')
self.logger.info('Parsing residue data from {}'.format(arg))
else:
print("Failed to open file {!s}".format(os.sep.join([self.dump_source_dir, arg])))
self.logger.error("Failed to open file {!s}".format(os.sep.join([self.dump_source_dir, arg])))
continue
for line in residue_data_fh:
id,res_num,res_name,oli,gpcrdb,bw,bw2,bs,prot_name,sec_str_name = [x.strip().strip('"') for x in line.split(',')] #double strip due to some weird bug...
if prot_name in missing_proteins:
continue
# fetch schemes and conversion tables
#Checking if the protein exists in the db
try:
pconf = ProteinConformation.objects.get(protein__entry_name=prot_name,
state__slug=settings.DEFAULT_PROTEIN_STATE)
except ProteinConformation.DoesNotExist as e:
missing_proteins.append(prot_name)
continue
#Checking if given residue already exists in the db
try:
Residue.objects.get(protein_conformation=pconf.id, sequence_number=res_num)
continue
except Residue.DoesNotExist as e:
pass
r = Residue()
r.protein_conformation = pconf
r.sequence_number = int(res_num)
r.amino_acid = polypeptide.three_to_one(res_name.upper())
generic_numbers = []
try:
r.save()
self.logger.info('Created residue {:n}{!s} for protein {!s}'.format(r.sequence_number,
r.amino_acid, pconf.protein.entry_name))
except Exception as msg:
print(msg)
self.logger.error('Failed to create residue {:n}{!s} for protein {!s}'.format(
r.sequence_number, r.amino_acid, pconf.protein.entry_name))
continue
# residue segment
dump_segment = sec_str_name
try:
r.protein_segment = ProteinSegment.objects.get(slug=dump_segment)
except:
self.logger.error('Failed to fetch protein segment {}'.format(dump_segment))
# generic number
if (str(oli) != '0' and gpcrdb != 'None' and bw != 'None'):
# separate bulge number (1241 - > 124 + 1)
bulge_prime = ''
dump_oliveira = str(oli)
if len(dump_oliveira) == 4:
bulge_prime = dump_oliveira[3]
dump_oliveira = dump_oliveira[:3]
dump_gpcrdb = gpcrdb[:4]
dump_seq_based = bw
# default gpcrdb number
def_gpcrdb = False
if dump_oliveira in schemes[settings.DEFAULT_NUMBERING_SCHEME]['table']:
default_label = (schemes[settings.DEFAULT_NUMBERING_SCHEME]['table'][dump_oliveira] +
bulge_prime)
try:
def_gpcrdb = ResidueGenericNumber.objects.get(label=default_label,
scheme=schemes[settings.DEFAULT_NUMBERING_SCHEME]['obj'])
except ResidueGenericNumber.DoesNotExist as e:
def_gpcrdb = ResidueGenericNumber()
def_gpcrdb.label = default_label
def_gpcrdb.scheme = schemes[settings.DEFAULT_NUMBERING_SCHEME]['obj']
def_gpcrdb.protein_segment = r.protein_segment
def_gpcrdb.save()
self.logger.info('Created generic number {:s} in numbering scheme {:s}'
.format(default_label,
schemes[settings.DEFAULT_NUMBERING_SCHEME]['obj'].short_name))
# if default number was found/added successfully, process the alternative numbers
if def_gpcrdb:
# add default generic number to residue record
r.generic_number = def_gpcrdb
# dict of sequence-based numbers, for use in structure-based numbers (5.46x461)
seq_based_labels = {}
# sequence-based schemes first (the sequence-based numbers are needed for the
# structure based schemes)
for scheme_name, scheme in schemes.items():
if scheme['type'] == 'sequence':
# is this number in the scheme defined for this protein?
if scheme_name == schemes[pconf.protein.residue_numbering_scheme.slug]['seq_based']:
seq_based_label = dump_seq_based
# if not convert the number to the correct scheme
else:
slug = pconf.protein.residue_numbering_scheme.slug
for d, c in schemes[schemes[slug]['seq_based']]['table'].items():
if c == dump_seq_based:
seq_based_label = scheme['table'][d]
break
# fetch/insert the number
try:
seq_based = ResidueGenericNumber.objects.get(label=seq_based_label,
scheme=scheme['obj'])
except ResidueGenericNumber.DoesNotExist as e:
seq_based = ResidueGenericNumber()
seq_based.label = seq_based_label
seq_based.scheme = scheme['obj']
seq_based.protein_segment = r.protein_segment
seq_based.save()
r.alternative_generic_numbers.add(seq_based)
# add added number to the dict for later use
seq_based_labels[scheme_name] = seq_based_label
# structure-based numbers
for scheme_name, scheme in schemes.items():
if scheme['type'] == 'structure':
# is this number in the scheme defined for this protein?
if scheme_name == pconf.protein.residue_numbering_scheme.slug:
struct_based_label = dump_gpcrdb + bulge_prime
# if not convert the number to the correct scheme
else:
for d, c in schemes[pconf.protein.residue_numbering_scheme.slug]['table'].items():
if c == dump_gpcrdb:
struct_based_label = scheme['table'][d] + bulge_prime
break
# add the sequence-based label (5x461 -> 5.46x461)
split_struct_based_label = struct_based_label.split('x')
struct_based_label = (seq_based_labels[scheme['seq_based']] + 'x' +
split_struct_based_label[1])
# fetch/insert the number
try:
struct_based = ResidueGenericNumber.objects.get(
label=struct_based_label, scheme=scheme['obj'])
except ResidueGenericNumber.DoesNotExist as e:
struct_based = ResidueGenericNumber()
struct_based.label = struct_based_label
struct_based.scheme = scheme['obj']
struct_based.protein_segment = r.protein_segment
struct_based.save()
# add to residue as a display number or alternative number?
if scheme_name == pconf.protein.residue_numbering_scheme.slug:
r.display_generic_number = struct_based
else:
r.alternative_generic_numbers.add(struct_based)
try:
r.save()
self.logger.info('Added generic numbers for residue {}{!s} for protein {!s}'.format(res_num,
res_name, pconf.protein.entry_name))
except Exception as msg:
print(msg)
self.logger.error(
'Failed to create generic numbers for residue {}{!s} for protein {!s}'.format(res_num,
res_name, pconf.protein.entry_name))
self.logger.info('COMPLETED CREATING RESIDUES')
def main_func(self, positions, iteration):
# filenames
if not positions[1]:
filenames = self.filenames[positions[0]:]
else:
filenames = self.filenames[positions[0]:positions[1]]
# parse files
for source_file in filenames:
source_file_path = os.sep.join([self.construct_data_dir, source_file])
if os.path.isfile(source_file_path) and source_file[0] != '.':
self.logger.info('Reading file {}'.format(source_file_path))
# read the yaml file
with open(source_file_path, 'r') as f:
sd = yaml.load(f)
# is a protein specified?
if 'protein' not in sd:
self.logger.error('Protein not specified for construct, skipping')
continue
# fetch the parent protein
try:
ppc = ProteinConformation.objects.prefetch_related('protein__family', 'protein__species',
'protein__residue_numbering_scheme').get(protein__entry_name=sd['protein'],
state__slug=settings.DEFAULT_PROTEIN_STATE)
except ProteinConformation.DoesNotExist:
# abort if parent protein is not found
self.logger.error('Parent protein {} for construct {} not found, aborting!'.format(
sd['protein'], sd['name']))
continue
# sequence type
try:
sequence_type, created = ProteinSequenceType.objects.get_or_create(slug='mod',
defaults={'name': 'Modified'})
if created:
self.logger.info('Created sequence type {}'.format(sequence_type))
except IntegrityError:
sequence_type = ProteinSequenceType.objects.get(slug='mod')
# protein source
try:
protein_source, created = ProteinSource.objects.get_or_create(name='OTHER')
if created:
self.logger.info('Created protein source {}'.format(protein_source))
except IntegrityError:
protein_source = ProteinSource.objects.get(name='OTHER')
# create a protein record
p = Protein()
p.parent = ppc.protein
p.family = ppc.protein.family
p.species = ppc.protein.species
p.residue_numbering_scheme = ppc.protein.residue_numbering_scheme
p.sequence_type= sequence_type
p.source = protein_source
p.entry_name = slugify(strip_tags(sd['name']))
p.name = sd['name']
p.sequence = ppc.protein.sequence
# save protein (construct)
try:
p.save()
self.logger.info('Created construct {} with parent protein {}'.format(p.name,
ppc.protein.entry_name))
except:
self.logger.error('Failed creating construct {} with parent protein {}'.format(p.name,
ppc.protein.entry_name))
continue
# create protein conformation record
pc = ProteinConformation()
pc.protein = p
pc.state = ProteinState.objects.get(slug=settings.DEFAULT_PROTEIN_STATE)
try:
pc.save()
self.logger.info('Created conformation {} of protein {}'.format(pc.state.name, p.name))
except:
self.logger.error('Failed creating conformation {} of protein {}'.format(pc.state.name,
p.entry_name))
# process deletions (save in db, and for sequence processing)
deletions = []
if 'deletions' in sd and sd['deletions']:
for t in sd['deletions']:
deletions += list(range(t[0],t[1]+1))
deletion = ConstructDeletion.objects.create(construct=pc, start=t[0], end=t[1])
if created:
self.logger.info('Created deletion {}-{} for {}'.format(t[0], t[1],
pc.protein.entry_name))
# process mutations (save in db, and for sequence processing)
mutations = {}
if 'mutations' in sd and sd['mutations']:
for m in sd['mutations']:
res_num = int(m[1:-1])
mutations[res_num] = {
'wt_res': m[0],
'mut_res': m[-1],
'full': m,
}
mutation = ConstructMutation.objects.get_or_create(
construct=pc,
sequence_number=res_num,
wild_type_amino_acid=m[0],
mutated_amino_acid=m[-1],
)
# insertions
split_segments = {}
if 'insertions' in sd and sd['insertions']:
for ins in sd['insertions']:
ins_start = Residue.objects.get(protein_conformation=ppc,
sequence_number=ins['positions'][0])
ins_end = Residue.objects.get(protein_conformation=ppc,
sequence_number=ins['positions'][1])
# if the insertion is within only one segment (the usual case), split that
# segment into two segments
if ins_start and ins_start.protein_segment == ins_end.protein_segment:
# get/create split protein segments
slug_1 = ins_start.protein_segment.slug + "_1"
try:
segment_before, created = ProteinSegment.objects.get_or_create(slug=slug_1,
defaults={'name': ins_start.protein_segment.name,
'category': ins_start.protein_segment.category, 'partial': True})
if created:
self.logger.info('Created protein segment {}'.format(segment_before))
except IntegrityError:
segment_before = ProteinSegment.objects.get(slug=slug_1)
slug_2 = ins_start.protein_segment.slug + "_2"
try:
segment_after, created = ProteinSegment.objects.get_or_create(slug=slug_2,
defaults={'name': ins_start.protein_segment.name,
'category': ins_start.protein_segment.category, 'partial': True})
if created:
self.logger.info('Created protein segment {}'.format(segment_after))
except IntegrityError:
segment_after = ProteinSegment.objects.get(slug=slug_2)
# keep track of information about split segments
split_segments[ins_start.protein_segment.slug] = {
'start': {
'sequence_number': ins['positions'][0],
'segment': segment_before,
},
'end': {
'sequence_number': ins['positions'][1],
'segment': segment_after,
},
}
# if the insertion covers two segments, use those two as the segments before and after
elif ins_start:
segment_before = ins_start.protein_segment
segment_after = ins_end.protein_segment
# if the insertion replaces a part of the sequence, add that range as a deletion
if ins['positions'][1] > (ins['positions'][0] + 1):
deletions += list(range((ins['positions'][0] + 1), ins['positions'][1]))
# get/insert fusion protein
fusion, create = ProteinFusion.objects.get_or_create(name=ins['name'], defaults={
'sequence': ins['sequence']})
# create relationship with protein
ProteinFusionProtein.objects.create(protein=p, protein_fusion=fusion,
segment_before=segment_before, segment_after=segment_after)
# create expression records
if 'expression_sys' in sd and sd['expression_sys']:
ce = Expression()
ce.construct = pc
ce.expression_system, created = ExpressionSystem.objects.get_or_create(
expression_method = sd['expression_sys']['expression_method'],
host_cell_type = sd['expression_sys']['host_cell_type'],
host_cell = sd['expression_sys']['host_cell'])
if 'remarks' in sd:
ce.remarks = sd['expression_sys']['remarks']
ce.save()
# create solubilization records
if ('solubilization' in sd and sd['solubilization'] and 'steps' in sd['solubilization']
and sd['solubilization']['steps']):
so = Solubilization()
so.construct = pc
cl = ChemicalList.objects.create()
so.chemical_list = cl
for step in sd['solubilization']['steps']:
if 'type' in step and 'item' in step and'concentration' in step:
chem = Chemical()
chem.chemical_type, created = ChemicalType.objects.get_or_create(name = step['type'])
chem.name = step['item']
chem.save()
cc = ChemicalConc()
cc.concentration = step['concentration']
cc.chemical = chem # since ChemicalConc has a ForeignKey to Chemical
cc.save()
cl.chemicals.add(cc)
else:
self.logger.error('Solubilization step incorrectly defined for {}'.format(p))
if 'remarks' in sd['solubilization']:
so.remarks = sd['solubilization']['remarks']
so.save()
# create purification records
if 'purification' in sd and sd['purification'] and sd['purification']['steps']:
pu = Purification()
pu.construct = pc
if 'remarks' in sd['purification']:
pu.remarks = sd['purification']['remarks']
pu.save()
for step in sd['purification']['steps']:
if 'type' in step and 'description' in step:
pust = PurificationStep()
pust.description = step['description']
pust.purification = pu
pust.purification_type, created = PurificationStepType.objects.get_or_create(
name = step['type'] ) # 2 values returned by get_or_create
if created:
self.logger.info('Created purification step type {}'.format(
pust.purification_type))
pust.save()
else:
self.logger.error('Purification step incorrectly defined for {}'.format(p))
# create crystallization records
if 'crystallization' in sd and sd['crystallization']:
cy = Crystallization()
cy.construct = pc
cyt = CrystallizationMethodTypes.objects.create()
cy.crystal_type = cyt
cy.method = sd['crystallization']['method']
cy.settings = sd['crystallization']['settings']
cy.protein_conc = sd['crystallization']['protein_conc']
cl = ChemicalList.objects.create()
cy.chemical_list = cl
for step in sd['crystallization']['chemicallist']:
if 'type' in step and 'item' in step and'concentration' in step:
chem = Chemical()
chem.chemical_type, created = ChemicalType.objects.get_or_create(name = step['type'])
chem.name = step['item']
chem.save()
cc = ChemicalConc()
cc.concentration = step['concentration']
cc.chemical = chem # since ChemicalConc has a ForeignKey to Chemical
cc.save()
cl.chemicals.add(cc)
else:
self.logger.error('Crystallization step incorrectly defined for {}'.format(p))
cy.aqueous_solution_lipid_ratio = sd['crystallization']['aqueous_solution_lipid_ratio_LCP']
cy.lcp_bolus_volume = sd['crystallization']['LCP_bolus_volume']
cy.precipitant_solution_volume = sd['crystallization']['precipitant_solution_volume']
cy.temp = sd['crystallization']['temperature']
cy.ph = sd['crystallization']['ph']
if 'remarks' in sd['crystallization']:
cy.remarks = sd['crystallization']['remarks']
cy.save()
# create residues
prs = Residue.objects.filter(protein_conformation=ppc).prefetch_related(
'protein_conformation__protein', 'protein_segment', 'generic_number',
'display_generic_number__scheme', 'alternative_generic_numbers__scheme')
updated_sequence = ''
for pr in prs:
if pr.sequence_number not in deletions:
r = Residue()
r.protein_conformation = pc
r.generic_number = pr.generic_number
r.display_generic_number = pr.display_generic_number
r.sequence_number = pr.sequence_number
# check for split segments
if pr.protein_segment.slug in split_segments:
rsns = split_segments[pr.protein_segment.slug]['start']['sequence_number']
rsne = split_segments[pr.protein_segment.slug]['end']['sequence_number']
if r.sequence_number <= rsns:
r.protein_segment = split_segments[pr.protein_segment.slug]['start']['segment']
elif r.sequence_number >= rsne:
r.protein_segment = split_segments[pr.protein_segment.slug]['end']['segment']
else:
r.protein_segment = pr.protein_segment
# amino acid, check for mutations
if r.sequence_number in mutations:
if mutations[r.sequence_number]['wt_res'] == pr.amino_acid:
r.amino_acid = mutations[r.sequence_number]['mut_res']
else:
self.logger.error('Mutation {} in construct {} does not match wild-type sequence' \
+ ' of {}'.format(mutations[r.sequence_number]['full'], pc.protein.name,
ppc.protein.entry_name))
else:
r.amino_acid = pr.amino_acid
# save amino acid to updated sequence
updated_sequence += r.amino_acid
# save residue before populating M2M relations
r.save()
# alternative generic numbers
agns = pr.alternative_generic_numbers.all()
for agn in agns:
r.alternative_generic_numbers.add(agn)
# update sequence
p.sequence = updated_sequence
p.save()
def create_rotamers(self, structure, pdb_path):
wt_lookup = {} #used to match WT seq_number to WT residue record
pdbseq = {} #used to keep track of pdbseq residue positions vs index in seq
ref_positions = {} #WT postions in alignment
mapped_seq = {} # index in contruct, tuple of AA and WT [position,AA]
preferred_chain = structure.preferred_chain
if len(preferred_chain.split(','))>1: #if A,B
preferred_chain = preferred_chain.split(',')[0]
AA = {'ALA':'A', 'ARG':'R', 'ASN':'N', 'ASP':'D',
'CYS':'C', 'GLN':'Q', 'GLU':'E', 'GLY':'G',
'HIS':'H', 'ILE':'I', 'LEU':'L', 'LYS':'K',
'MET':'M', 'PHE':'F', 'PRO':'P', 'SER':'S',
'THR':'T', 'TRP':'W', 'TYR':'Y', 'VAL':'V'}
s = PDBParser(PERMISSIVE=True, QUIET=True).get_structure('ref', pdb_path)[0]
chain = s[preferred_chain] #select only one chain (avoid n-mer receptors)
ppb=PPBuilder()
seq = ''
i = 1
check_1000 = 0
for pp in ppb.build_peptides(chain): #remove >1000 pos (fusion protein / gprotein)
for res in pp:
id = res.id
if id[1]<600:
check_1000 += 1
#need check_1000 to catch structures where they lie in 1000s (4LDE, 4LDL, 4LDO, 4N4W, 4QKX)
if id[1]>1000 and check_1000>200:
chain.detach_child(id)
for pp in ppb.build_peptides(chain):
seq += str(pp.get_sequence()) #get seq from fasta (only chain A)
for residue in pp:
residue_id = residue.get_full_id()
chain = residue_id[2]
if chain not in pdbseq:
pdbseq[chain] = {}
pos = residue_id[3][1]
pdbseq[chain][pos] = [i,AA[residue.resname]]
i += 1
parent_seq = str(structure.protein_conformation.protein.parent.sequence)
rs = Residue.objects.filter(protein_conformation__protein=structure.protein_conformation.protein.parent).prefetch_related('display_generic_number','generic_number','protein_segment')
for r in rs: #required to match WT position to a record (for duplication of GN values)
wt_lookup[r.sequence_number] = r
#align WT with structure seq -- make gaps penalties big, so to avoid too much overfitting
pw2 = pairwise2.align.localms(parent_seq, seq, 2, -4, -4, -.1)
gaps = 0
unmapped_ref = {}
for i, r in enumerate(pw2[0][0], 1): #loop over alignment to create lookups (track pos)
#print(i,r,pw2[0][1][i-1]) #print alignment for sanity check
if r == "-":
gaps += 1
if r != "-":
ref_positions[i] = [i-gaps,r]
elif r == "-":
ref_positions[i] = [None,'-']
if pw2[0][1][i-1]=='-':
unmapped_ref[i-gaps] = '-'
gaps = 0
for i, r in enumerate(pw2[0][1], 1): #make second lookup
if r == "-":
gaps += 1
if r != "-":
mapped_seq[i-gaps] = [r,ref_positions[i]]
pdb = structure.pdb_data.pdb
protein_conformation=structure.protein_conformation
temp = ''
check = 0
errors = 0
mismatch_seq = 0
match_seq = 0
not_matched = 0
matched_by_pos = 0
aa_mismatch = 0
pdblines_temp = pdb.splitlines()
pdblines = []
for line in pdblines_temp: #Get rid of all odd records
if line.startswith('ATOM'):
pdblines.append(line)
pdblines.append('') #add a line to not "run out"
for i,line in enumerate(pdblines):
if line.startswith('ATOM'):
chain = line[21]
if preferred_chain and chain!=preferred_chain: #If perferred is defined and is not the same as the current line, then skip
pass
else:
nextline = pdblines[i+1]
residue_number = line[22:26].strip()
if (check==0 or nextline[22:26].strip()==check) and nextline.startswith('TER')==False and nextline.startswith('ATOM')==True: #If this is either the begining or the same as previous line add to current rotamer
temp += line + "\n"
#print('same res',pdb.splitlines()[i+1])
else: #if this is a new residue
#print(pdb.splitlines()[i+1][22:26].strip(),check)
temp += line + "\n"
if int(check.strip())<2000:
residue = Residue()
residue.sequence_number = int(check.strip())
residue.amino_acid = AA[residue_name.upper()]
residue.protein_conformation = protein_conformation
#print(residue.sequence_number,residue.amino_acid) #sanity check
try:
seq_num_pos = pdbseq[chain][residue.sequence_number][0]
except:
#print('failed residue',pdb_path,residue.sequence_number)
temp = "" #start new line for rotamer
check = pdblines[i+1][22:26].strip()
continue
if seq_num_pos in mapped_seq:
if mapped_seq[seq_num_pos][1][0]==None:
#print('no match found') #sanity check
#print(residue.sequence_number,residue.amino_acid) #sanity check
residue.display_generic_number = None
residue.generic_number = None
residue.protein_segment = None
not_matched +=1
else:
wt_r = wt_lookup[mapped_seq[seq_num_pos][1][0]]
if residue.sequence_number!=wt_r.sequence_number and residue.amino_acid!=wt_r.amino_acid and residue.sequence_number in wt_lookup: #if pos numbers not work -- see if the pos number might be in WT and unmapped
if wt_lookup[residue.sequence_number].amino_acid==residue.amino_acid:
if residue.sequence_number in unmapped_ref: #WT was not mapped, so could be it
# print(residue.sequence_number,residue.amino_acid) #sanity check
#print('wrongly matched, better match on pos+aa',residue.sequence_number,residue.amino_acid,wt_r.sequence_number,wt_r.amino_acid)
wt_r = wt_lookup[residue.sequence_number]
matched_by_pos +=1
match_seq += 1
else:
mismatch_seq += 1
#print('could have been matched, but already aligned to another position',residue.sequence_number,residue.amino_acid,wt_r.sequence_number,wt_r.amino_acid)
else:
#print('WT pos not same AA, mismatch',residue.sequence_number,residue.amino_acid,wt_r.sequence_number,wt_r.amino_acid)
mismatch_seq += 1
elif residue.sequence_number!=wt_r.sequence_number:
#print('WT pos not same pos, mismatch',residue.sequence_number,residue.amino_acid,wt_r.sequence_number,wt_r.amino_acid)
mismatch_seq += 1
elif residue.amino_acid!=wt_r.amino_acid:
#print('aa mismatch',residue.sequence_number,residue.amino_acid,wt_r.sequence_number,wt_r.amino_acid)
aa_mismatch += 1
else:
match_seq += 1
if wt_r.generic_number is not None:
residue.display_generic_number = wt_r.display_generic_number
residue.generic_number = wt_r.generic_number
else:
residue.display_generic_number = None
residue.generic_number = None
#print('no GN')
residue.protein_segment = wt_r.protein_segment
else:
#print('wierd error') #sanity check
residue.display_generic_number = None
residue.generic_number = None
residue.protein_segment = None
#print('inserted',residue.sequence_number) #sanity check
residue.save()
rotamer_data, created = PdbData.objects.get_or_create(pdb=temp)
rotamer, created = Rotamer.objects.get_or_create(residue=residue, structure=structure, pdbdata=rotamer_data)
temp = "" #start new line for rotamer
check = pdblines[i+1][22:26].strip()
check = pdblines[i+1][22:26].strip()
chain = line[21]
residue_name = line[17:20].title() #use title to get GLY to Gly so it matches
#print(structure.pdb_code.index,'length',len(seq),len(mapped_seq),'mapped res',str(mismatch_seq+match_seq+aa_mismatch),'pos mismatch',mismatch_seq,'aa mismatch',aa_mismatch,'not mapped',not_matched,' mapping off, matched on pos,aa',matched_by_pos)
return None
def handle(self, *args, **options):
startTime = datetime.datetime.now()
self.options = options
if self.options["purge"]:
Residue.objects.filter(
protein_conformation__protein__entry_name__endswith="_a",
protein_conformation__protein__family__parent__parent__name=
"Alpha").delete()
ProteinConformation.objects.filter(
protein__entry_name__endswith="_a",
protein__family__parent__parent__name="Alpha").delete()
Protein.objects.filter(
entry_name__endswith="_a",
family__parent__parent__name="Alpha").delete()
SignprotStructureExtraProteins.objects.all().delete()
SignprotStructure.objects.all().delete()
if not options["only_signprot_structures"]:
# Building protein and protconf objects for g protein structure in complex
if options["s"]:
scs = SignprotComplex.objects.filter(
structure__pdb_code__index__in=[
i.upper() for i in options["s"]
])
else:
scs = SignprotComplex.objects.all()
for sc in scs:
self.logger.info(
"Protein, ProteinConformation and Residue build for alpha subunit of {} is building"
.format(sc))
try:
# Alpha subunit
try:
alpha_protein = Protein.objects.get(
entry_name=sc.structure.pdb_code.index.lower() +
"_a")
except:
alpha_protein = Protein()
alpha_protein.entry_name = sc.structure.pdb_code.index.lower(
) + "_a"
alpha_protein.accession = None
alpha_protein.name = sc.structure.pdb_code.index.lower(
) + "_a"
alpha_protein.sequence = sc.protein.sequence
alpha_protein.family = sc.protein.family
alpha_protein.parent = sc.protein
alpha_protein.residue_numbering_scheme = sc.protein.residue_numbering_scheme
alpha_protein.sequence_type = ProteinSequenceType.objects.get(
slug="mod")
alpha_protein.source = ProteinSource.objects.get(
name="OTHER")
alpha_protein.species = sc.protein.species
alpha_protein.save()
try:
alpha_protconf = ProteinConformation.objects.get(
protein__entry_name=sc.structure.pdb_code.index.
lower() + "_a")
except:
alpha_protconf = ProteinConformation()
alpha_protconf.protein = alpha_protein
alpha_protconf.state = ProteinState.objects.get(
slug="active")
alpha_protconf.save()
pdbp = PDBParser(PERMISSIVE=True, QUIET=True)
s = pdbp.get_structure("struct",
StringIO(sc.structure.pdb_data.pdb))
chain = s[0][sc.alpha]
nums = []
for res in chain:
if "CA" in res and res.id[0] == " ":
nums.append(res.get_id()[1])
resis = Residue.objects.filter(
protein_conformation__protein=sc.protein)
num_i = 0
temp_seq2 = ""
pdb_num_dict = OrderedDict()
# Create first alignment based on sequence numbers
for n in nums:
if sc.structure.pdb_code.index == "6OIJ" and n < 30:
nr = n + 6
else:
nr = n
pdb_num_dict[n] = [
chain[n], resis.get(sequence_number=nr)
]
# Find mismatches
mismatches = []
for n, res in pdb_num_dict.items():
if AA[res[0].get_resname()] != res[1].amino_acid:
mismatches.append(res)
pdb_lines = sc.structure.pdb_data.pdb.split("\n")
seqadv = []
for l in pdb_lines:
if l.startswith("SEQADV"):
seqadv.append(l)
mutations, shifted_mutations = OrderedDict(), OrderedDict()
# Search for annotated engineered mutations in pdb SEQADV
for s in seqadv:
line_search = re.search(
"SEQADV\s{1}[A-Z\s\d]{4}\s{1}([A-Z]{3})\s{1}([A-Z]{1})\s+(\d+)[\s\S\d]{5}([\s\S\d]{12})([A-Z]{3})\s+(\d+)(\s\S+)",
s)
if line_search != None:
if line_search.group(2) == sc.alpha:
if line_search.group(
4).strip() == sc.protein.accession:
if line_search.group(
3) == line_search.group(6):
mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
else:
shifted_mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5),
int(line_search.group(6))
]
else:
# Exception for 6G79
if line_search.group(
3
) != line_search.group(
6
) and "CONFLICT" in line_search.group(7):
mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
# Exception for 5G53
if line_search.group(
4).strip() != sc.protein.accession:
mutations[int(
line_search.group(3))] = [
line_search.group(1),
line_search.group(5)
]
remaining_mismatches = []
# Check and clear mismatches that are registered in pdb SEQADV as engineered mutation
for m in mismatches:
num = m[0].get_id()[1]
if num in mutations:
if m[0].get_resname() != mutations[num][0] and m[
1].amino_acid != AA[mutations[num][1]]:
remaining_mismatches.append(m)
elif num in shifted_mutations:
remaining_mismatches.append(m)
else:
remaining_mismatches.append(m)
if options["debug"]:
print(sc)
print(mutations)
print(shifted_mutations)
print(mismatches)
print("======")
print(remaining_mismatches)
pprint.pprint(pdb_num_dict)
no_seqnum_shift = [
'6OY9', '6OYA', '6LPB', '6WHA', '7D77', '6XOX', '7L1U',
'7L1V'
]
# Check if HN is mutated to GNAI1 for the scFv16 stabilizer
if sc.protein.entry_name != 'gnai1_human' and len(
remaining_mismatches) > 0:
target_HN = resis.filter(protein_segment__slug='HN')
gnai1_HN = Residue.objects.filter(
protein_conformation__protein__entry_name=
'gnai1_human',
protein_segment__slug='HN')
pdb_HN_seq = ''
for num, val in pdb_num_dict.items():
if num <= target_HN.reverse()[0].sequence_number:
pdb_HN_seq += Polypeptide.three_to_one(
val[0].get_resname())
if options['debug']:
print('Checking if HN is gnai1_human')
print(pdb_HN_seq)
print(''.join(
gnai1_HN.values_list('amino_acid', flat=True)))
gnai1_HN_seq = ''.join(
gnai1_HN.values_list('amino_acid', flat=True))
pw2 = pairwise2.align.localms(gnai1_HN_seq, pdb_HN_seq,
3, -4, -3, -1)
ref_seq, temp_seq = str(pw2[0][0]), str(pw2[0][1])
length, match = 0, 0
for r, t in zip(ref_seq, temp_seq):
if options['debug']:
print(r, t)
if t != '-':
if r == t:
match += 1
length += 1
identity = match / length * 100
if options['debug']:
print(identity)
if identity > 85:
if sc.structure.pdb_code.index not in ['7DFL']:
no_seqnum_shift.append(
sc.structure.pdb_code.index)
if options['debug']:
print(
'INFO: HN has {}% with gnai1_human HN, skipping seqnum shift correction'
.format(round(identity)))
# Mismatches remained possibly to seqnumber shift, making pairwise alignment to try and fix alignment
if len(
remaining_mismatches
) > 0 and sc.structure.pdb_code.index not in no_seqnum_shift:
ppb = PPBuilder()
seq = ""
for pp in ppb.build_peptides(chain, aa_only=False):
seq += str(pp.get_sequence())
if sc.structure.pdb_code.index in [
'7JVQ', '7L1U', '7L1V'
]:
pw2 = pairwise2.align.localms(
sc.protein.sequence, seq, 3, -4, -3, -1)
else:
pw2 = pairwise2.align.localms(
sc.protein.sequence, seq, 2, -1, -.5, -.1)
ref_seq, temp_seq = str(pw2[0][0]), str(pw2[0][1])
# Custom fix for A->G mutation at pos 18
if sc.structure.pdb_code.index == '7JJO':
ref_seq = ref_seq[:18] + ref_seq[19:]
temp_seq = temp_seq[:17] + temp_seq[18:]
# Custom alignment fixes
elif sc.structure.pdb_code.index == '7DFL':
ref_seq = 'MTLESIMACCLSEEAKEARRINDEIERQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGSGYSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENPYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPTTGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV'
temp_seq = '--------CTLSAEDKAAVERSKMIDRNLREDGEKARRELKLLLLGTGESGKSTFIKQMRIIHG--------------------------------------------------------------------------------------------------------------------------TGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQV----DNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILKMFVDLNPDSDKILYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV'
elif sc.structure.pdb_code.index == '7JOZ':
temp_seq = temp_seq[:67] + (
'-' * 14) + 'FNGDS' + temp_seq[86:]
elif sc.structure.pdb_code.index == '7AUE':
ref_seq = ref_seq[:31].replace('-',
'') + ref_seq[31:]
temp_seq = (
9 *
'-') + temp_seq[2:5] + temp_seq[5:54].replace(
'-', '') + temp_seq[54:]
wt_pdb_dict = OrderedDict()
pdb_wt_dict = OrderedDict()
j, k = 0, 0
for i, ref, temp in zip(range(0, len(ref_seq)),
ref_seq, temp_seq):
if options["debug"]:
print(i, ref, temp) # alignment check
if ref != "-" and temp != "-":
wt_pdb_dict[resis[j]] = pdb_num_dict[nums[k]]
pdb_wt_dict[pdb_num_dict[nums[k]]
[0]] = resis[j]
j += 1
k += 1
elif ref == "-":
wt_pdb_dict[i] = pdb_num_dict[nums[k]]
pdb_wt_dict[pdb_num_dict[nums[k]][0]] = i
k += 1
elif temp == "-":
wt_pdb_dict[resis[j]] = i
pdb_wt_dict[i] = resis[j]
j += 1
# Custom fix for 7JJO isoform difference
if sc.structure.pdb_code.index in [
'7JJO', '7JOZ', '7AUE'
]:
pdb_num_dict = OrderedDict()
for wt_res, st_res in wt_pdb_dict.items():
if type(st_res) == type([]):
pdb_num_dict[wt_res.sequence_number] = [
st_res[0], wt_res
]
else:
for i, r in enumerate(remaining_mismatches):
# Adjust for shifted residue when residue is a match
if r[0].get_id()[1] - remaining_mismatches[
i - 1][0].get_id()[1] > 1:
pdb_num_dict[r[0].get_id()[1] -
1][1] = pdb_wt_dict[chain[
r[0].get_id()[1] - 1]]
# Adjust for shifted residue when residue is mutated and it's logged in SEQADV
if r[0].get_id()[1] in shifted_mutations:
pdb_num_dict[
r[0].get_id()[1]][1] = resis.get(
sequence_number=shifted_mutations[
r[0].get_id()[1]][2])
# Adjust for shift
else:
pdb_num_dict[r[0].get_id()
[1]][1] = pdb_wt_dict[r[0]]
if sc.structure.pdb_code.index == '7JVQ':
pdb_num_dict[198][1] = Residue.objects.get(
protein_conformation__protein=sc.protein,
sequence_number=346)
pdb_num_dict[235][1] = Residue.objects.get(
protein_conformation__protein=sc.protein,
sequence_number=383)
elif sc.structure.pdb_code.index == '6PB0':
pdb_num_dict[205][1] = Residue.objects.get(
protein_conformation__protein=sc.protein,
sequence_number=205)
### Custom alignment fix for 6WHA mini-Gq/Gi2/Gs chimera
elif sc.structure.pdb_code.index == "6WHA":
ref_seq = "MTLESIMACCLSEEAKEARRINDEIERQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGSGYSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENPYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPTTGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIM--YSHLVDYFPEYDGP----QRDAQAAREFILKMFVDL---NPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV"
temp_seq = "----------VSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVK----------------------------------------------------------------------------------------------------------------------------------GIFETKFQVDKVNFHMFDVG-----RRKWIQCFNDVTAIIFVVDSSDYNR----------LQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPDPRVTRAKY-FIRKEFVDISTASGDGRHICYPHFTC-VDTENARRIFNDCKDIILQMNLREYNLV"
pdb_num_dict = OrderedDict()
temp_resis = [res for res in chain]
temp_i = 0
mapped_cgns = []
for i, aa in enumerate(temp_seq):
if aa != "-":
ref_split_on_gaps = ref_seq[:i + 1].split("-")
ref_seqnum = i - (len(ref_split_on_gaps) -
1) + 1
res = resis.get(sequence_number=ref_seqnum)
if res.display_generic_number.label in mapped_cgns:
next_presumed_cgn = self.get_next_presumed_cgn(
res)
if next_presumed_cgn:
res = next_presumed_cgn
while res and res.display_generic_number.label in mapped_cgns:
res = self.get_next_presumed_cgn(
res)
else:
print(
"Error: {} CGN does not exist. Incorrect mapping of {} in {}"
.format(next_presumed_cgn,
chain[nums[temp_i]],
sc.structure))
mapped_cgns.append(
res.display_generic_number.label)
pdb_num_dict[nums[temp_i]] = [
chain[nums[temp_i]], res
]
temp_i += 1
bulked_rotamers = []
for key, val in pdb_num_dict.items():
# print(key, val) # sanity check
if not isinstance(val[1], int):
res_obj = Residue()
res_obj.sequence_number = val[0].get_id()[1]
res_obj.amino_acid = AA[val[0].get_resname()]
res_obj.display_generic_number = val[
1].display_generic_number
res_obj.generic_number = val[1].generic_number
res_obj.protein_conformation = alpha_protconf
res_obj.protein_segment = val[1].protein_segment
res_obj.save()
rot = self.create_structure_rotamer(
val[0], res_obj, sc.structure)
bulked_rotamers.append(rot)
else:
self.logger.info(
"Skipped {} as no annotation was present, while building for alpha subunit of {}"
.format(val[1], sc))
if options["debug"]:
pprint.pprint(pdb_num_dict)
Rotamer.objects.bulk_create(bulked_rotamers)
self.logger.info(
"Protein, ProteinConformation and Residue build for alpha subunit of {} is finished"
.format(sc))
except Exception as msg:
if options["debug"]:
print("Error: ", sc, msg)
self.logger.info(
"Protein, ProteinConformation and Residue build for alpha subunit of {} has failed"
.format(sc))
if not options["s"]:
### Build SignprotStructure objects from non-complex signprots
g_prot_alphas = Protein.objects.filter(
family__slug__startswith="100_001",
accession__isnull=False) #.filter(entry_name="gnai1_human")
complex_structures = SignprotComplex.objects.all().values_list(
"structure__pdb_code__index", flat=True)
for a in g_prot_alphas:
pdb_list = get_pdb_ids(a.accession)
for pdb in pdb_list:
if pdb not in complex_structures:
try:
data = self.fetch_gprot_data(pdb, a)
if data:
self.build_g_prot_struct(a, pdb, data)
except Exception as msg:
self.logger.error(
"SignprotStructure of {} {} failed\n{}: {}".
format(a.entry_name, pdb, type(msg), msg))
if options["debug"]:
print(datetime.datetime.now() - startTime)
def add_cgn_residues(self, gprotein_list):
#Parsing pdb uniprot file for residues
self.logger.info('Start parsing PDB_UNIPROT_ENSEMBLE_ALL')
self.logger.info('Parsing file ' + self.gprotein_data_file)
residue_data = pd.read_table(self.gprotein_data_file, sep="\t", low_memory=False)
residue_data = residue_data.loc[residue_data['Uniprot_ACC'].isin(gprotein_list)]
cgn_scheme = ResidueNumberingScheme.objects.get(slug='cgn')
# Temp files to speed things up
temp = {}
temp['proteins'] = {}
temp['rgn'] = {}
temp['segment'] = {}
temp['equivalent'] = {}
bulk = []
self.logger.info('Insert residues: {} rows'.format(len(residue_data)))
for index, row in residue_data.iterrows():
if row['Uniprot_ACC'] in temp['proteins']:
pr = temp['proteins'][row['Uniprot_ACC']][0]
pc = temp['proteins'][row['Uniprot_ACC']][1]
else:
#fetch protein for protein conformation
pr, c= Protein.objects.get_or_create(accession=row['Uniprot_ACC'])
#fetch protein conformation
pc, c= ProteinConformation.objects.get_or_create(protein_id=pr)
temp['proteins'][row['Uniprot_ACC']] = [pr,pc]
#fetch residue generic number
rgnsp=[]
if(int(row['CGN'].split('.')[2])<10):
rgnsp = row['CGN'].split('.')
rgn_new = rgnsp[0]+'.'+rgnsp[1]+'.0'+rgnsp[2]
if rgn_new in temp['rgn']:
rgn = temp['rgn'][rgn_new]
else:
rgn, c= ResidueGenericNumber.objects.get_or_create(label=rgn_new)
temp['rgn'][rgn_new] = rgn
else:
if row['CGN'] in temp['rgn']:
rgn = temp['rgn'][row['CGN']]
else:
rgn, c= ResidueGenericNumber.objects.get_or_create(label=row['CGN'])
temp['rgn'][row['CGN']] = rgn
#fetch protein segment id
if row['CGN'].split(".")[1] in temp['segment']:
ps = temp['segment'][row['CGN'].split(".")[1]]
else:
ps, c= ProteinSegment.objects.get_or_create(slug=row['CGN'].split(".")[1], proteinfamily='Gprotein')
temp['segment'][row['CGN'].split(".")[1]] = ps
try:
bulk_r = Residue(sequence_number=row['Position'], protein_conformation=pc, amino_acid=row['Residue'], generic_number=rgn, display_generic_number=rgn, protein_segment=ps)
# self.logger.info("Residues added to db")
bulk.append(bulk_r)
except:
self.logger.error("Failed to add residues")
if len(bulk) % 10000 == 0:
self.logger.info('Inserted bulk {} (Index:{})'.format(len(bulk),index))
# print(len(bulk),"inserts!",index)
Residue.objects.bulk_create(bulk)
# print('inserted!')
bulk = []
# Add also to the ResidueGenericNumberEquivalent table needed for single residue selection
try:
if rgn.label not in temp['equivalent']:
ResidueGenericNumberEquivalent.objects.get_or_create(label=rgn.label,default_generic_number=rgn, scheme=cgn_scheme)
temp['equivalent'][rgn.label] = 1
# self.logger.info("Residues added to ResidueGenericNumberEquivalent")
except:
self.logger.error("Failed to add residues to ResidueGenericNumberEquivalent")
self.logger.info('Inserted bulk {} (Index:{})'.format(len(bulk),index))
Residue.objects.bulk_create(bulk)
def main_func(self, positions, iteration):
# filenames
if not positions[1]:
filenames = self.filenames[positions[0]:]
else:
filenames = self.filenames[positions[0]:positions[1]]
# parse files
for source_file in filenames:
source_file_path = os.sep.join([self.construct_data_dir, source_file])
if os.path.isfile(source_file_path) and source_file[0] != '.':
self.logger.info('Reading file {}'.format(source_file_path))
# read the yaml file
with open(source_file_path, 'r') as f:
sd = yaml.load(f)
# is a protein specified?
if 'protein' not in sd:
self.logger.error('Protein not specified for construct, skipping')
continue
# fetch the parent protein
try:
ppc = ProteinConformation.objects.prefetch_related('protein__family', 'protein__species',
'protein__residue_numbering_scheme').get(protein__entry_name=sd['protein'],
state__slug=settings.DEFAULT_PROTEIN_STATE)
except ProteinConformation.DoesNotExist:
# abort if parent protein is not found
self.logger.error('Parent protein {} for construct {} not found, aborting!'.format(
sd['protein'], sd['name']))
continue
# sequence type
try:
sequence_type, created = ProteinSequenceType.objects.get_or_create(slug='mod',
defaults={'name': 'Modified'})
if created:
self.logger.info('Created sequence type {}'.format(sequence_type))
except IntegrityError:
sequence_type = ProteinSequenceType.objects.get(slug='mod')
# protein source
try:
protein_source, created = ProteinSource.objects.get_or_create(name='OTHER')
if created:
self.logger.info('Created protein source {}'.format(protein_source))
except IntegrityError:
protein_source = ProteinSource.objects.get(name='OTHER')
# create a protein record
p = Protein()
p.parent = ppc.protein
p.family = ppc.protein.family
p.species = ppc.protein.species
p.residue_numbering_scheme = ppc.protein.residue_numbering_scheme
p.sequence_type= sequence_type
p.source = protein_source
p.entry_name = slugify(strip_tags(sd['name']))
p.name = sd['name']
p.sequence = ppc.protein.sequence
# save protein (construct)
try:
p.save()
self.logger.info('Created construct {} with parent protein {}'.format(p.name,
ppc.protein.entry_name))
except:
self.logger.error('Failed creating construct {} with parent protein {}'.format(p.name,
ppc.protein.entry_name))
continue
# create protein conformation record
pc = ProteinConformation()
pc.protein = p
pc.state = ProteinState.objects.get(slug=settings.DEFAULT_PROTEIN_STATE)
try:
pc.save()
self.logger.info('Created conformation {} of protein {}'.format(pc.state.name, p.name))
except:
self.logger.error('Failed creating conformation {} of protein {}'.format(pc.state.name,
p.entry_name))
# create residue records
deletions = []
if 'deletions' in sd and sd['deletions']:
for t in sd['deletions']:
deletions += list(range(t[0],t[1]+1))
mutations = {}
if 'mutations' in sd and sd['mutations']:
for m in sd['mutations']:
res_num = int(m[1:-1])
mutations[res_num] = {
'wt_res': m[0],
'mut_res': m[-1],
'full': m,
}
# insertions
split_segments = {}
if 'insertions' in sd and sd['insertions']:
for ins in sd['insertions']:
ins_start = Residue.objects.get(protein_conformation=ppc,
sequence_number=ins['positions'][0])
ins_end = Residue.objects.get(protein_conformation=ppc,
sequence_number=ins['positions'][1])
# if the insertion is within only one segment (the usual case), split that
# segment into two segments
if ins_start and ins_start.protein_segment == ins_end.protein_segment:
# get/create split protein segments
slug_1 = ins_start.protein_segment.slug + "_1"
try:
segment_before, created = ProteinSegment.objects.get_or_create(slug=slug_1,
defaults={'name': ins_start.protein_segment.name,
'category': ins_start.protein_segment.category, 'partial': True})
if created:
self.logger.info('Created protein segment {}'.format(segment_before))
except IntegrityError:
segment_before = ProteinSegment.objects.get(slug=slug_1)
slug_2 = ins_start.protein_segment.slug + "_2"
try:
segment_after, created = ProteinSegment.objects.get_or_create(slug=slug_2,
defaults={'name': ins_start.protein_segment.name,
'category': ins_start.protein_segment.category, 'partial': True})
if created:
self.logger.info('Created protein segment {}'.format(segment_after))
except IntegrityError:
segment_after = ProteinSegment.objects.get(slug=slug_2)
# keep track of information about split segments
split_segments[ins_start.protein_segment.slug] = {
'start': {
'sequence_number': ins['positions'][0],
'segment': segment_before,
},
'end': {
'sequence_number': ins['positions'][1],
'segment': segment_after,
},
}
# if the insertion covers two segments, use those two as the segments before and after
elif ins_start:
segment_before = ins_start.protein_segment
segment_after = ins_end.protein_segment
# if the insertion replaces a part of the sequence, add that range as a deletion
if ins['positions'][1] > (ins['positions'][0] + 1):
deletions += list(range((ins['positions'][0] + 1), ins['positions'][1]))
# get/insert fusion protein
fusion, create = ProteinFusion.objects.get_or_create(name=ins['name'], defaults={
'sequence': ins['sequence']})
# create relationship with protein
ProteinFusionProtein.objects.create(protein=p, protein_fusion=fusion,
segment_before=segment_before, segment_after=segment_after)
prs = Residue.objects.filter(protein_conformation=ppc).prefetch_related(
'protein_conformation__protein', 'protein_segment', 'generic_number',
'display_generic_number__scheme', 'alternative_generic_numbers__scheme')
updated_sequence = ''
for pr in prs:
if pr.sequence_number not in deletions:
r = Residue()
r.protein_conformation = pc
r.generic_number = pr.generic_number
r.display_generic_number = pr.display_generic_number
r.sequence_number = pr.sequence_number
# check for split segments
if pr.protein_segment.slug in split_segments:
rsns = split_segments[pr.protein_segment.slug]['start']['sequence_number']
rsne = split_segments[pr.protein_segment.slug]['end']['sequence_number']
if r.sequence_number <= rsns:
r.protein_segment = split_segments[pr.protein_segment.slug]['start']['segment']
elif r.sequence_number >= rsne:
r.protein_segment = split_segments[pr.protein_segment.slug]['end']['segment']
else:
r.protein_segment = pr.protein_segment
# amino acid, check for mutations
if r.sequence_number in mutations:
if mutations[r.sequence_number]['wt_res'] == pr.amino_acid:
r.amino_acid = mutations[r.sequence_number]['mut_res']
else:
self.logger.error('Mutation {} in construct {} does not match wild-type sequence' \
+ ' of {}'.format(mutations[r.sequence_number]['full'], pc.protein.name,
ppc.protein.entry_name))
else:
r.amino_acid = pr.amino_acid
# save amino acid to updated sequence
updated_sequence += r.amino_acid
# save residue before populating M2M relations
r.save()
# alternative generic numbers
agns = pr.alternative_generic_numbers.all()
for agn in agns:
r.alternative_generic_numbers.add(agn)
# update sequence
p.sequence = updated_sequence
p.save()
def main_func(self, positions, iteration):
# filenames
if not positions[1]:
filenames = self.filenames[positions[0]:]
else:
filenames = self.filenames[positions[0]:positions[1]]
# parse files
for source_file in filenames:
source_file_path = os.sep.join(
[self.construct_data_dir, source_file])
if os.path.isfile(source_file_path) and source_file[0] != '.':
self.logger.info('Reading file {}'.format(source_file_path))
# read the yaml file
with open(source_file_path, 'r') as f:
sd = yaml.load(f)
# is a protein specified?
if 'protein' not in sd:
self.logger.error(
'Protein not specified for construct, skipping')
continue
# fetch the parent protein
try:
ppc = ProteinConformation.objects.prefetch_related(
'protein__family', 'protein__species',
'protein__residue_numbering_scheme').get(
protein__entry_name=sd['protein'],
state__slug=settings.DEFAULT_PROTEIN_STATE)
except ProteinConformation.DoesNotExist:
# abort if parent protein is not found
self.logger.error(
'Parent protein {} for construct {} not found, aborting!'
.format(sd['protein'], sd['name']))
continue
# sequence type
try:
sequence_type, created = ProteinSequenceType.objects.get_or_create(
slug='mod', defaults={'name': 'Modified'})
if created:
self.logger.info('Created sequence type {}'.format(
sequence_type))
except IntegrityError:
sequence_type = ProteinSequenceType.objects.get(
slug='mod')
# protein source
try:
protein_source, created = ProteinSource.objects.get_or_create(
name='OTHER')
if created:
self.logger.info(
'Created protein source {}'.format(
protein_source))
except IntegrityError:
protein_source = ProteinSource.objects.get(
name='OTHER')
# create a protein record
p = Protein()
p.parent = ppc.protein
p.family = ppc.protein.family
p.species = ppc.protein.species
p.residue_numbering_scheme = ppc.protein.residue_numbering_scheme
p.sequence_type = sequence_type
p.source = protein_source
p.entry_name = slugify(strip_tags(sd['name']))
p.name = sd['name']
p.sequence = ppc.protein.sequence
# save protein (construct)
try:
p.save()
self.logger.info(
'Created construct {} with parent protein {}'.
format(p.name, ppc.protein.entry_name))
except:
self.logger.error(
'Failed creating construct {} with parent protein {}'
.format(p.name, ppc.protein.entry_name))
continue
# create protein conformation record
pc = ProteinConformation()
pc.protein = p
pc.state = ProteinState.objects.get(
slug=settings.DEFAULT_PROTEIN_STATE)
try:
pc.save()
self.logger.info(
'Created conformation {} of protein {}'.format(
pc.state.name, p.name))
except:
self.logger.error(
'Failed creating conformation {} of protein {}'.
format(pc.state.name, p.entry_name))
# create residue records
deletions = []
if 'deletions' in sd and sd['deletions']:
for t in sd['deletions']:
deletions += list(range(t[0], t[1] + 1))
mutations = {}
if 'mutations' in sd and sd['mutations']:
for m in sd['mutations']:
res_num = int(m[1:-1])
mutations[res_num] = {
'wt_res': m[0],
'mut_res': m[-1],
'full': m,
}
# insertions
split_segments = {}
if 'insertions' in sd and sd['insertions']:
for ins in sd['insertions']:
ins_start = Residue.objects.get(
protein_conformation=ppc,
sequence_number=ins['positions'][0])
ins_end = Residue.objects.get(
protein_conformation=ppc,
sequence_number=ins['positions'][1])
# if the insertion is within only one segment (the usual case), split that
# segment into two segments
if ins_start and ins_start.protein_segment == ins_end.protein_segment:
# get/create split protein segments
slug_1 = ins_start.protein_segment.slug + "_1"
try:
segment_before, created = ProteinSegment.objects.get_or_create(
slug=slug_1,
defaults={
'name':
ins_start.protein_segment.name,
'category':
ins_start.protein_segment.category,
'partial': True
})
if created:
self.logger.info(
'Created protein segment {}'.
format(segment_before))
except IntegrityError:
segment_before = ProteinSegment.objects.get(
slug=slug_1)
slug_2 = ins_start.protein_segment.slug + "_2"
try:
segment_after, created = ProteinSegment.objects.get_or_create(
slug=slug_2,
defaults={
'name':
ins_start.protein_segment.name,
'category':
ins_start.protein_segment.category,
'partial': True
})
if created:
self.logger.info(
'Created protein segment {}'.
format(segment_after))
except IntegrityError:
segment_after = ProteinSegment.objects.get(
slug=slug_2)
# keep track of information about split segments
split_segments[
ins_start.protein_segment.slug] = {
'start': {
'sequence_number':
ins['positions'][0],
'segment': segment_before,
},
'end': {
'sequence_number':
ins['positions'][1],
'segment': segment_after,
},
}
# if the insertion covers two segments, use those two as the segments before and after
elif ins_start:
segment_before = ins_start.protein_segment
segment_after = ins_end.protein_segment
# if the insertion replaces a part of the sequence, add that range as a deletion
if ins['positions'][1] > (ins['positions'][0] + 1):
deletions += list(
range((ins['positions'][0] + 1),
ins['positions'][1]))
# get/insert fusion protein
fusion, create = ProteinFusion.objects.get_or_create(
name=ins['name'],
defaults={'sequence': ins['sequence']})
# create relationship with protein
ProteinFusionProtein.objects.create(
protein=p,
protein_fusion=fusion,
segment_before=segment_before,
segment_after=segment_after)
prs = Residue.objects.filter(
protein_conformation=ppc).prefetch_related(
'protein_conformation__protein', 'protein_segment',
'generic_number', 'display_generic_number__scheme',
'alternative_generic_numbers__scheme')
updated_sequence = ''
for pr in prs:
if pr.sequence_number not in deletions:
r = Residue()
r.protein_conformation = pc
r.generic_number = pr.generic_number
r.display_generic_number = pr.display_generic_number
r.sequence_number = pr.sequence_number
# check for split segments
if pr.protein_segment.slug in split_segments:
rsns = split_segments[pr.protein_segment.slug][
'start']['sequence_number']
rsne = split_segments[pr.protein_segment.slug][
'end']['sequence_number']
if r.sequence_number <= rsns:
r.protein_segment = split_segments[
pr.protein_segment.
slug]['start']['segment']
elif r.sequence_number >= rsne:
r.protein_segment = split_segments[
pr.protein_segment.
slug]['end']['segment']
else:
r.protein_segment = pr.protein_segment
# amino acid, check for mutations
if r.sequence_number in mutations:
if mutations[r.sequence_number][
'wt_res'] == pr.amino_acid:
r.amino_acid = mutations[
r.sequence_number]['mut_res']
else:
self.logger.error('Mutation {} in construct {} does not match wild-type sequence' \
+ ' of {}'.format(mutations[r.sequence_number]['full'], pc.protein.name,
ppc.protein.entry_name))
else:
r.amino_acid = pr.amino_acid
# save amino acid to updated sequence
updated_sequence += r.amino_acid
# save residue before populating M2M relations
r.save()
# alternative generic numbers
agns = pr.alternative_generic_numbers.all()
for agn in agns:
r.alternative_generic_numbers.add(agn)
# update sequence
p.sequence = updated_sequence
p.save()
