def analyze_construct(self, filenames=None):
self.logger.info("ANALYZING CONSTRUCT STRUCTURES")
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in filenames:
if filename[-3:] != 'pdb' and filename[-3:] != 'ent':
continue
root, ext = os.path.splitext(os.path.basename(filename))
print(filename)
print(root)
filepath = os.sep.join([self.construct_data_dir, filename])
self.logger.info("Working on a file: {}".format(filename))
header = parse_pdb_header(filepath)
parser = SequenceParser(filepath)
json_data = OrderedDict()
json_data["header"] = header
json_data.update(parser.get_fusions())
json_data.update(parser.get_mutations())
json_data.update(parser.get_deletions())
json.dump(json_data,
open(
os.sep.join(
[settings.DATA_DIR,
"{}_auto.json".format(root)]), 'w'),
indent=4,
separators=(',', ': '))
def analyze_construct(self, filenames=None):
self.logger.info("ANALYZING CONSTRUCT STRUCTURES")
# read source files
if not filenames:
filenames = os.listdir(self.construct_data_dir)
for filename in filenames:
if filename[-3:]!='pdb' and filename[-3:]!='ent':
continue
root, ext = os.path.splitext(os.path.basename(filename))
print(filename)
print(root)
filepath = os.sep.join([self.construct_data_dir, filename])
self.logger.info("Working on a file: {}".format(filename))
header = parse_pdb_header(filepath)
parser = SequenceParser(filepath)
json_data = OrderedDict()
json_data["header"] = header
json_data.update(parser.get_fusions())
json_data.update(parser.get_mutations())
json_data.update(parser.get_deletions())
json.dump(json_data, open(os.sep.join([settings.DATA_DIR, "{}_auto.json".format(root)]), 'w'), indent=4, separators=(',', ': '))
def handle(self, *args, **options):
q = QueryPDB()
q.list_xtals(verbose=False)
for record in q.new_structures:
pdb_code = record[0]
wt_id = Protein.objects.get(entry_name=record[1]).id
if not os.path.exists(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)])):
self.download_pdb(pdb_code)
self.parser = SequenceParser(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]), wt_protein_id=wt_id)
header = parse_pdb_header(os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
self.create_yaml(pdb_code, record[1], header)
def handle(self, *args, **options):
print("Working on file {}".format(options['pdb_file']))
header = parse_pdb_header(options['pdb_file'])
print(header['compound'])
sp = SequenceParser(options['pdb_file'])
c = list(sp.mapping.keys())[0]
poly = sp.get_chain_peptides(c)
for peptide in poly:
print("Start: {} Stop: {} Len: {}".format(peptide[0].id[1], peptide[-1].id[1], len(peptide)))
sp.map_to_wt_blast(c, peptide, None, int(peptide[0].id[1]))
sp.map_seqres()
sp.save_excel_report("test.xlsx")
#sp.get_report()
def post(self, request):
# root, ext = os.path.splitext(request._request.FILES['pdb_file'].name)
pdb_file = StringIO(
request._request.FILES['pdb_file'].file.read().decode(
'UTF-8', "ignore"))
header = parse_pdb_header(pdb_file)
parser = SequenceParser(pdb_file)
json_data = OrderedDict()
json_data["header"] = header
json_data.update(parser.get_fusions())
json_data.update(parser.get_mutations())
json_data.update(parser.get_deletions())
return Response(json_data)
def handle(self, *args, **options):
root, ext = os.path.splitext(os.path.basename(options['pdb_file']))
print("Working on file {}".format(options['pdb_file']))
header = parse_pdb_header(options['pdb_file'])
sp = SequenceParser(options['pdb_file'])
print(sp.get_fusions())
print(sp.get_mutations())
print(sp.get_deletions())
json_data = {}
json_data["header"] = header
json_data.update(sp.get_fusions())
json_data.update(sp.get_mutations())
json_data.update(sp.get_deletions())
json.dump(json_data, open(os.sep.join([settings.DATA_DIR, "{}_auto.json".format(root)]), 'w'), indent=4, separators=(',', ': '))
#json.dump(json_data, open("test.json", 'w'), indent=4, separators=(',', ': '))
def Header_Data(AAAB14, pdbloc, ion_name):
""" Returns crucial Header Data for a specific pdbid.
Somewhat non specific to Ion Environments project. """
Data = []
Head = AAAB14[0]
Tail = AAAB14[1:]
Head.insert(1, 'StructMethod')
Head.insert(1, 'Resolution')
Head.insert(len(Head), 'ECNum')
Head.insert(len(Head), 'Type')
Head.insert(len(Head), 'Ion')
Data.append(Head)
for item in Tail:
fname = item[0]
fname = fname.split('_')
pdbid = fname[0]
pdb = 'pdb' + pdbid + '.ent'
chain = fname[1]
handle = open(pdbloc + pdb, 'r')
header_dict = parse_pdb_header(handle)
handle.close()
name = header_dict['name']
head = header_dict['head']
method = header_dict['structure_method']
reso = header_dict['resolution']
Comp = header_dict['compound']
ec = FindEC(chain.lower(), 'ec_number', Comp)
if ec.startswith('1.'):
txt = 'Oxidoreductase'
elif ec.startswith('2.'):
txt = 'Transferase'
elif ec.startswith('3.'):
txt = 'Hydrolase'
elif ec.startswith('4.'):
txt = 'Lyase'
elif ec.startswith('5.'):
txt = 'Isomerase'
elif ec.startswith('6.'):
txt = 'Ligase'
else:
txt = 'Non_Enzyme'
item.insert(1, method)
item.insert(1, reso)
item.insert(len(item), ec)
item.insert(len(item), txt)
item.insert(len(item), ion_name)
Data.append(item)
return Data
def get_pdb(pss_result,
if_full_match=True,
if_best_resolution=True,
if_download=True):
outdir_pdb = './pdb_download'
if not path.exists(outdir_pdb):
makedirs(outdir_pdb)
pdb_reso = []
for r in pss_result:
pdb_id = None
pdb_full = None
# fully matched or not
if if_full_match:
info = r['services'][0]['nodes'][0]['match_context'][0]
if info['mismatches'] == 0 \
and info['gaps_opened'] == 0 \
and info['query_length'] == info['subject_length']:
pdb_full = r['identifier']
pdb_id = pdb_full.split('_')[0]
else:
pdb_full = r['identifier']
pdb_id = pdb_full.split('_')[0]
# if match, download pdb file
if pdb_id and pdb_full:
outfile = path.join(outdir_pdb,
str(pdb_id) +
'.pdb') if if_download else path.join(
outdir_pdb, 'tmp.pdb')
if download_pdb(pdb_id, outfile):
structure = parse_pdb_header(outfile)
pdb_reso.append((pdb_full, structure['resolution']))
if if_best_resolution:
# find the pdb with best resolution
tmp_dict = {r: p for p, r in pdb_reso}
best_pdb_id = tmp_dict[max(tmp_dict.keys())]
return [(best_pdb_id, tmp_dict[best_pdb_id])]
# write to file
# with open('./dataset_pos.csv', 'a') as f:
# f.write("{}, {}, {}\n".format(best_pdb_id, seq, pdb_reso))
# print("{} - {}".format(i, pdb_reso))
return pdb_reso
def handle(self, *args, **options):
q = QueryPDB()
q.list_xtals(verbose=False)
for record in q.new_structures:
pdb_code = record[0]
wt_id = Protein.objects.get(entry_name=record[1]).id
if not os.path.exists(
os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)
])):
self.download_pdb(pdb_code)
self.parser = SequenceParser(os.sep.join(
[self.pdb_data_dir, "{}.pdb".format(pdb_code)]),
wt_protein_id=wt_id)
header = parse_pdb_header(
os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
self.create_yaml(pdb_code, record[1], header)
def handle(self, *args, **options):
root, ext = os.path.splitext(os.path.basename(options['pdb_file']))
print("Working on file {}".format(options['pdb_file']))
header = parse_pdb_header(options['pdb_file'])
sp = SequenceParser(options['pdb_file'])
print(sp.get_fusions())
print(sp.get_mutations())
print(sp.get_deletions())
json_data = {}
json_data["header"] = header
json_data.update(sp.get_fusions())
json_data.update(sp.get_mutations())
json_data.update(sp.get_deletions())
json.dump(
json_data,
open(os.sep.join([settings.DATA_DIR, "{}_auto.json".format(root)]),
'w'),
indent=4,
separators=(',', ': '))
from Bio.PDB.PDBParser import PDBParser
parser = PDBParser(PERMISSIVE=1)
structure_id = "2b10"
filename = "/home/koreanraichu/2b10.pdb"
structure = parser.get_structure(structure_id, filename)
print(structure)
# 이거 PC에 있는 파일 가져오는건가?
# FileNotFoundError: [Errno 2] No such file or directory: 'pdb1fat.ent'
from Bio.PDB import parse_pdb_header
with open(filename, "r") as handle:
header_dict = parse_pdb_header(handle)
print(header_dict)
def main_func(self, positions, iteration):
# filenames
if not positions[1]:
filenames = self.filenames[positions[0]:]
else:
filenames = self.filenames[positions[0]:positions[1]]
for source_file in filenames:
source_file_path = os.sep.join([self.structure_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 this a representative structure (will be used to guide structure-based alignments)?
representative = False
if 'representative' in sd and sd['representative']:
representative = True
# only process representative structures on first iteration
if not representative and iteration == 1:
continue
# skip representative structures on second iteration
if representative and iteration == 2:
continue
# is there a construct?
if 'construct' not in sd:
self.logger.error('No construct specified, skipping!')
continue
# does the construct exists?
try:
con = Protein.objects.get(entry_name=sd['construct'])
except Protein.DoesNotExist:
self.logger.error('Construct {} does not exists, skipping!'.format(sd['construct']))
continue
# create a structure record
try:
s = Structure.objects.get(protein_conformation__protein=con)
except Structure.DoesNotExist:
s = Structure()
s.representative = representative
# protein state
if 'state' not in sd:
self.logger.warning('State not defined, using default state {}'.format(
settings.DEFAULT_PROTEIN_STATE))
state = settings.DEFAULT_STATE.title()
else:
state = sd['state']
state_slug = slugify(state)
try:
ps, created = ProteinState.objects.get_or_create(slug=state_slug, defaults={'name': state})
if created:
self.logger.info('Created protein state {}'.format(ps.name))
except IntegrityError:
ps = ProteinState.objects.get(slug=state_slug)
s.state = ps
# protein conformation
try:
s.protein_conformation = ProteinConformation.objects.get(protein=con)
except ProteinConformation.DoesNotExist:
self.logger.error('Protein conformation for construct {} does not exists'.format(con))
continue
if s.protein_conformation.state is not state:
ProteinConformation.objects.filter(protein=con).update(state=ps)
# get the PDB file and save to DB
sd['pdb'] = sd['pdb'].upper()
if not os.path.exists(self.pdb_data_dir):
os.makedirs(self.pdb_data_dir)
pdb_path = os.sep.join([self.pdb_data_dir, sd['pdb'] + '.pdb'])
if not os.path.isfile(pdb_path):
self.logger.info('Fetching PDB file {}'.format(sd['pdb']))
url = 'http://www.rcsb.org/pdb/files/%s.pdb' % sd['pdb']
pdbdata_raw = urlopen(url).read().decode('utf-8')
with open(pdb_path, 'w') as f:
f.write(pdbdata_raw)
else:
with open(pdb_path, 'r') as pdb_file:
pdbdata_raw = pdb_file.read()
pdbdata, created = PdbData.objects.get_or_create(pdb=pdbdata_raw)
s.pdb_data = pdbdata
# UPDATE HETSYN with its PDB reference instead + GRAB PUB DATE, PMID, DOI AND RESOLUTION
hetsyn = {}
hetsyn_reverse = {}
for line in pdbdata_raw.splitlines():
if line.startswith('HETSYN'):
m = re.match("HETSYN[\s]+([\w]{3})[\s]+(.+)",line) ### need to fix bad PDB formatting where col4 and col5 are put together for some reason -- usually seen when the id is +1000
if (m):
hetsyn[m.group(2).strip()] = m.group(1).upper()
hetsyn_reverse[m.group(1)] = m.group(2).strip().upper()
if line.startswith('HETNAM'):
m = re.match("HETNAM[\s]+([\w]{3})[\s]+(.+)",line) ### need to fix bad PDB formatting where col4 and col5 are put together for some reason -- usually seen when the id is +1000
if (m):
hetsyn[m.group(2).strip()] = m.group(1).upper()
hetsyn_reverse[m.group(1)] = m.group(2).strip().upper()
if line.startswith('REVDAT 1'):
sd['publication_date'] = line[13:22]
if line.startswith('JRNL PMID'):
sd['pubmed_id'] = line[19:].strip()
if line.startswith('JRNL DOI'):
sd['doi_id'] = line[19:].strip()
if len(hetsyn) == 0:
self.logger.info("PDB file contained NO hetsyn")
with open(pdb_path,'r') as header:
header_dict = parse_pdb_header(header)
sd['publication_date'] = header_dict['release_date']
sd['resolution'] = str(header_dict['resolution']).strip()
sd['structure_method'] = header_dict['structure_method']
# structure type
if 'structure_method' in sd and sd['structure_method']:
structure_type = sd['structure_method'].capitalize()
structure_type_slug = slugify(sd['structure_method'])
try:
st, created = StructureType.objects.get_or_create(slug=structure_type_slug,
defaults={'name': structure_type})
if created:
self.logger.info('Created structure type {}'.format(st))
except IntegrityError:
st = StructureType.objects.get(slug=structure_type_slug)
s.structure_type = st
else:
self.logger.warning('No structure type specified in PDB file {}'.format(sd['pdb']))
matched = 0
if 'ligand' in sd and sd['ligand']:
if isinstance(sd['ligand'], list):
ligands = sd['ligand']
else:
ligands = [sd['ligand']]
for ligand in ligands:
if 'name' in ligand:
if ligand['name'].upper() in hetsyn:
self.logger.info('Ligand {} matched to PDB records'.format(ligand['name']))
matched = 1
ligand['name'] = hetsyn[ligand['name'].upper()]
elif ligand['name'].upper() in hetsyn_reverse:
matched = 1
if matched==0 and len(hetsyn)>0:
self.logger.info('No ligand names found in HET in structure {}'.format(sd['pdb']))
# REMOVE? can be used to dump structure files with updated ligands
# yaml.dump(sd, open(source_file_path, 'w'), indent=4)
# pdb code
if 'pdb' in sd:
try:
web_resource = WebResource.objects.get(slug='pdb')
except:
# abort if pdb resource is not found
raise Exception('PDB resource not found, aborting!')
s.pdb_code, created = WebLink.objects.get_or_create(index=sd['pdb'],
web_resource=web_resource)
else:
self.logger.error('PDB code not specified for structure {}, skipping!'.format(sd['pdb']))
continue
# insert into plain text fields
if 'preferred_chain' in sd:
s.preferred_chain = sd['preferred_chain']
else:
self.logger.warning('Preferred chain not specified for structure {}'.format(sd['pdb']))
if 'resolution' in sd:
s.resolution = float(sd['resolution'])
else:
self.logger.warning('Resolution not specified for structure {}'.format(sd['pdb']))
if 'publication_date' in sd:
s.publication_date = sd['publication_date']
else:
self.logger.warning('Publication date not specified for structure {}'.format(sd['pdb']))
# publication
try:
if 'doi_id' in sd:
try:
s.publication = Publication.objects.get(web_link__index=sd['doi_id'])
except Publication.DoesNotExist as e:
p = Publication()
try:
p.web_link = WebLink.objects.get(index=sd['doi_id'], web_resource__slug='doi')
except WebLink.DoesNotExist:
wl = WebLink.objects.create(index=sd['doi_id'],
web_resource = WebResource.objects.get(slug='doi'))
p.web_link = wl
p.update_from_doi(doi=sd['doi_id'])
p.save()
s.publication = p
elif 'pubmed_id' in sd:
try:
s.publication = Publication.objects.get(web_link__index=sd['pubmed_id'])
except Publication.DoesNotExist as e:
p = Publication()
try:
p.web_link = WebLink.objects.get(index=sd['pubmed_id'],
web_resource__slug='pubmed')
except WebLink.DoesNotExist:
wl = WebLink.objects.create(index=sd['pubmed_id'],
web_resource = WebResource.objects.get(slug='pubmed'))
p.web_link = wl
p.update_from_pubmed_data(index=sd['pubmed_id'])
p.save()
s.publication = p
except:
self.logger.error('Error saving publication'.format(ps.name))
# save structure before adding M2M relations
s.save()
#Delete previous interaction data to prevent errors.
ResidueFragmentInteraction.objects.filter(structure_ligand_pair__structure=s).delete()
StructureLigandInteraction.objects.filter(structure=s).delete()
#Remove previous Rotamers/Residues to prepare repopulate
Fragment.objects.filter(structure=s).delete()
Rotamer.objects.filter(structure=s).all().delete()
Residue.objects.filter(protein_conformation=s.protein_conformation).all().delete()
# endogenous ligand(s)
default_ligand_type = 'Small molecule'
if representative and 'endogenous_ligand' in sd and sd['endogenous_ligand']:
if isinstance(sd['endogenous_ligand'], list):
endogenous_ligands = sd['endogenous_ligand']
else:
endogenous_ligands = [sd['endogenous_ligand']]
for endogenous_ligand in endogenous_ligands:
if endogenous_ligand['type']:
lt, created = LigandType.objects.get_or_create(slug=slugify(endogenous_ligand['type']),
defaults={'name': endogenous_ligand['type']})
else:
lt, created = LigandType.objects.get_or_create(slug=slugify(default_ligand_type),
defaults={'name': default_ligand_type})
ligand = Ligand()
if 'iupharId' not in endogenous_ligand:
endogenous_ligand['iupharId'] = 0
ligand = ligand.load_by_gtop_id(endogenous_ligand['name'], endogenous_ligand['iupharId'],
lt)
try:
s.protein_conformation.protein.parent.endogenous_ligands.add(ligand)
except IntegrityError:
self.logger.info('Endogenous ligand for protein {}, already added. Skipping.'.format(
s.protein_conformation.protein.parent))
# ligands
if 'ligand' in sd and sd['ligand']:
if isinstance(sd['ligand'], list):
ligands = sd['ligand']
else:
ligands = [sd['ligand']]
for ligand in ligands:
l = False
peptide_chain = ""
if 'chain' in ligand:
peptide_chain = ligand['chain']
ligand['name'] = 'pep'
if ligand['name'] and ligand['name'] != 'None': # some inserted as none.
# use annoted ligand type or default type
if ligand['type']:
lt, created = LigandType.objects.get_or_create(slug=slugify(ligand['type']),
defaults={'name': ligand['type']})
else:
lt, created = LigandType.objects.get_or_create(
slug=slugify(default_ligand_type), defaults={'name': default_ligand_type})
# set pdb reference for structure-ligand interaction
pdb_reference = ligand['name']
# use pubchem_id
if 'pubchemId' in ligand and ligand['pubchemId'] and ligand['pubchemId'] != 'None':
# create ligand
l = Ligand()
# update ligand by pubchem id
ligand_title = False
if 'title' in ligand and ligand['title']:
ligand_title = ligand['title']
l = l.load_from_pubchem('cid', ligand['pubchemId'], lt, ligand_title)
# if no pubchem id is specified, use name
else:
# use ligand title, if specified
if 'title' in ligand and ligand['title']:
ligand['name'] = ligand['title']
# create empty properties
lp = LigandProperities.objects.create()
# create the ligand
try:
l, created = Ligand.objects.get_or_create(name=ligand['name'], canonical=True,
defaults={'properities': lp, 'ambigious_alias': False})
if created:
self.logger.info('Created ligand {}'.format(ligand['name']))
else:
pass
except IntegrityError:
l = Ligand.objects.get(name=ligand['name'], canonical=True)
# save ligand
l.save()
else:
continue
# structure-ligand interaction
if l and ligand['role']:
role_slug = slugify(ligand['role'])
try:
lr, created = LigandRole.objects.get_or_create(slug=role_slug,
defaults={'name': ligand['role']})
if created:
self.logger.info('Created ligand role {}'.format(ligand['role']))
except IntegrityError:
lr = LigandRole.objects.get(slug=role_slug)
i, created = StructureLigandInteraction.objects.get_or_create(structure=s,
ligand=l, ligand_role=lr, annotated=True,
defaults={'pdb_reference': pdb_reference})
if i.pdb_reference != pdb_reference:
i.pdb_reference = pdb_reference
i.save()
# structure segments
if 'segments' in sd and sd['segments']:
for segment, positions in sd['segments'].items():
# fetch (create if needed) sequence segment
try:
protein_segment = ProteinSegment.objects.get(slug=segment)
except ProteinSegment.DoesNotExist:
self.logger.error('Segment {} not found'.format(segment))
continue
struct_seg, created = StructureSegment.objects.update_or_create(structure=s,
protein_segment=protein_segment, defaults={'start': positions[0], 'end': positions[1]})
# all representive structures should have defined segments
elif representative:
self.logger.warning('Segments not defined for representative structure {}'.format(sd['pdb']))
# structure segments for modeling
if 'segments_in_structure' in sd and sd['segments_in_structure']:
for segment, positions in sd['segments_in_structure'].items():
# fetch (create if needed) sequence segment
try:
protein_segment = ProteinSegment.objects.get(slug=segment)
except ProteinSegment.DoesNotExist:
self.logger.error('Segment {} not found'.format(segment))
continue
struct_seg_mod, created = StructureSegmentModeling.objects.update_or_create(structure=s,
protein_segment=protein_segment, defaults={'start': positions[0], 'end': positions[1]})
# structure coordinates
if 'coordinates' in sd and sd['coordinates']:
for segment, coordinates in sd['coordinates'].items():
# fetch (create if needed) sequence segment
try:
protein_segment = ProteinSegment.objects.get(slug=segment)
except ProteinSegment.DoesNotExist:
self.logger.error('Segment {} not found'.format(segment))
continue
# fetch (create if needed) coordinates description
try:
description, created = StructureCoordinatesDescription.objects.get_or_create(
text=coordinates)
if created:
self.logger.info('Created structure coordinate description {}'.format(coordinates))
except IntegrityError:
description = StructureCoordinatesDescription.objects.get(text=coordinates)
sc = StructureCoordinates()
sc.structure = s
sc.protein_segment = protein_segment
sc.description = description
sc.save()
# structure engineering
if 'engineering' in sd and sd['engineering']:
for segment, engineering in sd['engineering'].items():
# fetch (create if needed) sequence segment
try:
protein_segment = ProteinSegment.objects.get(slug=segment)
except ProteinSegment.DoesNotExist:
self.logger.error('Segment {} not found'.format(segment))
continue
# fetch (create if needed) engineering description
try:
description, created = StructureEngineeringDescription.objects.get_or_create(
text=engineering)
if created:
self.logger.info('Created structure coordinate description {}'.format(engineering))
except IntegrityError:
description = StructureEngineeringDescription.objects.get(text=engineering)
se = StructureEngineering()
se.structure = s
se.protein_segment = protein_segment
se.description = description
se.save()
# protein anomalies
scheme = s.protein_conformation.protein.residue_numbering_scheme
if 'bulges' in sd and sd['bulges']:
pa_slug = 'bulge'
try:
pab, created = ProteinAnomalyType.objects.get_or_create(slug=pa_slug, defaults={
'name': 'Bulge'})
if created:
self.logger.info('Created protein anomaly type {}'.format(pab))
except IntegrityError:
pab = ProteinAnomalyType.objects.get(slug=pa_slug)
for segment, bulges in sd['bulges'].items():
for bulge in bulges:
try:
gn, created = ResidueGenericNumber.objects.get_or_create(label=bulge,
scheme=scheme, defaults={'protein_segment': ProteinSegment.objects.get(
slug=segment)})
if created:
self.logger.info('Created generic number {}'.format(gn))
except IntegrityError:
gn = ResidueGenericNumber.objects.get(label=bulge, scheme=scheme)
try:
pa, created = ProteinAnomaly.objects.get_or_create(anomaly_type=pab,
generic_number=gn)
if created:
self.logger.info('Created protein anomaly {}'.format(pa))
except IntegrityError:
pa, created = ProteinAnomaly.objects.get(anomaly_type=pab, generic_number=gn)
s.protein_anomalies.add(pa)
if 'constrictions' in sd and sd['constrictions']:
pa_slug = 'constriction'
try:
pac, created = ProteinAnomalyType.objects.get_or_create(slug=pa_slug, defaults={
'name': 'Constriction'})
if created:
self.logger.info('Created protein anomaly type {}'.format(pac))
except IntegrityError:
pac = ProteinAnomalyType.objects.get(slug=pa_slug)
for segment, constrictions in sd['constrictions'].items():
for constriction in constrictions:
try:
gn, created = ResidueGenericNumber.objects.get_or_create(label=constriction,
scheme=scheme, defaults={'protein_segment': ProteinSegment.objects.get(
slug=segment)})
if created:
self.logger.info('Created generic number {}'.format(gn))
except IntegrityError:
gn = ResidueGenericNumber.objects.get(label=constriction, scheme=scheme)
try:
pa, created = ProteinAnomaly.objects.get_or_create(anomaly_type=pac,
generic_number=gn)
if created:
self.logger.info('Created protein anomaly {}'.format(pa))
except IntegrityError:
pa, created = ProteinAnomaly.objects.get(anomaly_type=pac, generic_number=gn)
s.protein_anomalies.add(pa)
# stabilizing agents, FIXME - redesign this!
# fusion proteins moved to constructs, use this for G-proteins and other agents?
aux_proteins = []
if 'signaling_protein' in sd and sd['signaling_protein'] and sd['signaling_protein'] != 'None':
aux_proteins.append('signaling_protein')
if 'auxiliary_protein' in sd and sd['auxiliary_protein'] and sd['auxiliary_protein'] != 'None':
aux_proteins.append('auxiliary_protein')
for index in aux_proteins:
if isinstance(sd[index], list):
aps = sd[index]
else:
aps = [sd[index]]
for aux_protein in aps:
aux_protein_slug = slugify(aux_protein)[:50]
try:
sa, created = StructureStabilizingAgent.objects.get_or_create(
slug=aux_protein_slug, defaults={'name': aux_protein})
except IntegrityError:
sa = StructureStabilizingAgent.objects.get(slug=aux_protein_slug)
s.stabilizing_agents.add(sa)
# save structure
s.save()
self.logger.info('Calculate rotamers / residues')
self.create_rotamers(s,pdb_path)
self.logger.info('Calculate interactions') #Should not error anymore. If it does, fix.
runcalculation(sd['pdb'],peptide_chain)
parsecalculation(sd['pdb'],False)
from Bio.PDB import *
from Bio.PDB import parse_pdb_header
from numpy import loadtxt
import numpy as np
from Bio.PDB import PDBList
from Bio.PDB.Entity import Entity
from Bio.PDB.Residue import Residue
parser = PDBParser()
#taking a pdb file of choice from the user
# the strip() is to strip spaces in the input of the user so there is less error
# the lower() is to take all the input of the user in small letter to reduce the error rate as most pdb files are saved in lower case letters
pdb_file = input("Select a pdb file of your choice?").strip().lower()
# decided to use with open because i wanted to be able to use dictionary and also run a for loop if i wanted
with open(pdb_file, "r") as file:
dict_file = parse_pdb_header(file)
structure = parser.get_structure(file, file)
for key in dict_file:
if key == "idcode":
id = dict_file[key]
#print(id)
#calling a class in biopython
ppb = PPBuilder()
# using the functions of the class to get the sequence of the protein (pdb file)
for pp in ppb.build_peptides(structure):
seq1 = pp.get_sequence()
print("The sequence of the structure is : " + seq1)
# storing the model of the structure of the first pdb file
model = structure[0]
# asking the user for the second file
'query_length'] == info['subject_length']:
pdb_id = r['identifier'].split('_')[0]
pdb_full = r['identifier']
# if match, download pdb file
if pdb_id and pdb_full:
page = 'http://files.rcsb.org/view/{}.pdb'.format(pdb_id)
req = requests.get(page)
if req.status_code == 200:
response = req.text
outfile = 'tmp.pdb'
if outfile:
with open(outfile, 'w') as f:
f.write(response)
# parse to get the resolution
structure = parse_pdb_header(outfile)
pdb_reso.append((pdb_full, structure['resolution']))
# append to dataset file
if pdb_reso:
# find the pdb with best resolution
tmp_dict = {r: p for p, r in pdb_reso}
best_pdb_id = tmp_dict[max(tmp_dict.keys())]
# write to file
with open('./all_targets.csv', 'a') as f:
f.write("{}, {}, {}, {}\n".format(best_pdb_id, pdb_reso,
records_all[i].description,
seq))
print("{} - {}".format(i, pdb_reso))
except:
pass
