class Command(BaseCommand):
logger = logging.getLogger(__name__)
# source file directory
structure_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data', 'structures'])
structure_build_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data'])
pdb_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data', 'pdbs'])
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 download_pdb(self, pdb_code):
url = "http://www.rcsb.org/pdb/files/{}.pdb".format(pdb_code)
urllib.request.urlretrieve(url, os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
def create_yaml(self, pdb_code, prot_name, data):
yaml_pdb_data = {
'pdb' : pdb_code,
'resolution' : data['resolution'],
'publication_date' : data['release_date'][:10],
#PDB header contains full citation
#'pubmed_id' : data['journal_reference'],
}
yaml_struct_annotations = {
'fusion_proteins' : { x : [y[0], y[1]] for x,y in enumerate(self.parser.fusions) }
}
yaml_other_data = {
'construct' : pdb_code.lower(),
'segments' : self.get_segments_data(prot_name),
'segments_in_structure' : self.parser.get_segments(),
}
out_fh = open('{}.yaml'.format(os.sep.join([self.structure_build_data_dir, 'structures', pdb_code])), 'w')
out_fh.write('# PDB data\n\n')
yaml.dump(yaml_pdb_data, out_fh, default_flow_style=False)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_struct_annotations, out_fh)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_other_data, out_fh)
out_fh.close()
yaml_construct = {
'name' : pdb_code.lower(),
'protein' : prot_name,
}
construct_fh = open('auto_{}.yaml'.format(os.sep.join([self.structure_build_data_dir, 'constructs', pdb_code])), 'w')
yaml.dump(yaml_construct, construct_fh, indent=4)
construct_fh.close()
def get_segments_data(self, prot_entry_name):
output = {}
segments = ProteinSegment.objects.all()
for segment in segments:
resi = list(Residue.objects.filter(protein_segment = segment,
protein_conformation__protein__entry_name = prot_entry_name).order_by('sequence_number'))
try:
if resi:
output[segment.slug] = [resi[0].sequence_number, resi[-1].sequence_number]
except Exception as e:
output[segment.slug] = ['-,-']
return output
class Command(BaseCommand):
logger = logging.getLogger(__name__)
# source file directory
structure_data_dir = os.sep.join(
[settings.DATA_DIR, 'structure_data', 'structures'])
structure_build_data_dir = os.sep.join(
[settings.DATA_DIR, 'structure_data'])
pdb_data_dir = os.sep.join([settings.DATA_DIR, 'structure_data', 'pdbs'])
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 download_pdb(self, pdb_code):
url = "https://www.rcsb.org/pdb/files/{}.pdb".format(pdb_code)
urllib.request.urlretrieve(
url, os.sep.join([self.pdb_data_dir, "{}.pdb".format(pdb_code)]))
def create_yaml(self, pdb_code, prot_name, data):
yaml_pdb_data = {
'pdb': pdb_code,
'resolution': data['resolution'],
'publication_date': data['release_date'][:10],
#PDB header contains full citation
#'pubmed_id' : data['journal_reference'],
}
yaml_struct_annotations = {
'fusion_proteins':
{x: [y[0], y[1]]
for x, y in enumerate(self.parser.fusions)}
}
yaml_other_data = {
'construct': pdb_code.lower(),
'segments': self.get_segments_data(prot_name),
'segments_in_structure': self.parser.get_segments(),
}
out_fh = open(
'{}.yaml'.format(
os.sep.join(
[self.structure_build_data_dir, 'structures', pdb_code])),
'w')
out_fh.write('# PDB data\n\n')
yaml.dump(yaml_pdb_data, out_fh, default_flow_style=False)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_struct_annotations, out_fh)
out_fh.write('\n# Structure annotations\n\n')
yaml.dump(yaml_other_data, out_fh)
out_fh.close()
yaml_construct = {
'name': pdb_code.lower(),
'protein': prot_name,
}
construct_fh = open(
'auto_{}.yaml'.format(
os.sep.join(
[self.structure_build_data_dir, 'constructs', pdb_code])),
'w')
yaml.dump(yaml_construct, construct_fh, indent=4)
construct_fh.close()
def get_segments_data(self, prot_entry_name):
output = {}
segments = ProteinSegment.objects.all()
for segment in segments:
resi = list(
Residue.objects.filter(
protein_segment=segment,
protein_conformation__protein__entry_name=prot_entry_name).
order_by('sequence_number'))
try:
if resi:
output[segment.slug] = [
resi[0].sequence_number, resi[-1].sequence_number
]
except Exception as e:
output[segment.slug] = ['-,-']
return output
