def post(self, request, *args, **kwargs):
form_class = self.get_form_class()
form = self.get_form(form_class)
if form.is_valid():
query_text = request.POST["pdb_code"]
print query_text
pdb_status_getter = PDBstatusGetter(query_text)
pdb_status = pdb_status_getter.get_status()
status_text = str(pdb_status)
if status_text == 'False':
pdb_info_getter = PDBinfoGetter(query_text)
pdb_map = pdb_info_getter.main()
print pdb_map
return render(request, self.template_name,
{'pdb_map': pdb_map,
'code': query_text,
'pdb_status': pdb_status,
'msg': self.msg,
'spt_ref_file': self.spt_ref_file,
'uniprot_id': self.uniprot_id,
'genbank': self.genbank,
'title': self.title,
'target_residue_files':
self.target_residue_files,
'sequence_annotations':
self.sequence_annotations,
'length_sa': self.length_sa})
elif status_text == 'True':
pdb_code = query_text.upper()
# Check if the pdb and ciff files have been downloaded. If not,
# then fetch them.
preprocessor = PDBPreProcessor(pdb_code)
preprocessor.preprocess_check()
number_of_structures, chains_in_asymmetric_unit = \
preprocessor.count_structures_in_asymmetric_unit()
experiment = preprocessor.get_experiment_type()
resolution = preprocessor.get_diffraction_resolution()
# Get organism ID, gene names, pdb_sequences, and paper
# metadata from .ciff file
cif_parser = CIFFParser(pdb_code)
chains, genes, organisms, pdb_sequences, title, authors = \
cif_parser.get_gene_annotations()
sequence_annotations = \
cif_parser.collate_sequence_annotations()
cif_parser.write_fasta(sequence_annotations)
gene_info = cif_parser.get_gene_info_from_genbank()
spt_writer = JmolSPTWriter(pdb_code)
spt_writer.write_spt()
spt_ref_file = 'jmol_script_' + pdb_code + '.spt'
if sequence_annotations != []:
for gene in gene_info:
gene_name = gene_info[gene]['GENE'][0]
product = gene_info[gene]['PRODUCT']
function = gene_info[gene]['FUNCTION']
ref_seq = gene_info[gene]['PROTEIN_ID']
for information in sequence_annotations:
if gene_name.upper() == information[1]:
information[1] = gene_name
chain = information[0]
organism = information[2]
aa_sequence = information[3]
# Add data to database
created, msg = \
set_pdb_information(
pdb_code, title, authors, genes,
organism, number_of_structures, chain,
chains_in_asymmetric_unit, ref_seq,
product, function, gene_name,
spt_ref_file, aa_sequence)
print msg
colors = ['yellow', 'green', 'red', 'blue', 'orange',
'purple', 'grey']
recorded_info = {}
for entry in sequence_annotations:
if entry[1].upper() in gene_info:
recorded_info[entry[1].upper()] = \
gene_info[entry[1].upper()]
recorded_info[entry[1].upper()]['SEQUENCE'] = \
entry[3]
recorded_info[entry[1].upper()]['CHAIN'] = \
entry[0]
recorded_info[entry[1].upper()]['ORGANISM'] = \
entry[2]
library_calculator = \
LibraryCalculator(aa_sequence=entry[3])
saturated_library_size = \
library_calculator.calculate_library_size(
full_saturation=True)
recorded_info[entry[1].upper()]['LIBRARY_SIZE'] = \
saturated_library_size
recorded_info[entry[1].upper()]['COLOR'] = \
colors[sequence_annotations.index(entry)]
tot_library_size = 0
for key in recorded_info:
tot_library_size += \
recorded_info[key]['LIBRARY_SIZE']
print "recorded_info:", recorded_info
print "sequence annotations:", sequence_annotations
print "gene info:", gene_info
return render(request, self.template_name,
{'tot_library_size': tot_library_size,
'recorded_info': recorded_info,
'resolution': resolution,
'experiment': experiment,
'colors': colors,
'msg': self.msg,
'target_residue_files':
self.target_residue_files,
'number_of_structures': number_of_structures,
'str_chains': chains_in_asymmetric_unit,
'title': title,
'authors': authors,
'gene_info': gene_info,
'spt_ref_file': spt_ref_file,
'code': pdb_code,
'chains': chains,
'genes': genes,
'organisms': organisms,
'pdb_sequences': pdb_sequences,
'sequence_annotations': sequence_annotations})
else:
return render(request, self.template_name,
{'code': query_text,
'pdb_status': pdb_status,
'msg': self.msg,
'spt_ref_file': self.spt_ref_file,
'uniprot_id': self.uniprot_id,
'genbank': self.genbank,
'title': self.title,
'target_residue_files':
self.target_residue_files,
'sequence_annotations':
self.sequence_annotations,
'length_sa': self.length_sa})
