def main():
# # Get pdb_id for each structure in PDB with respective uniprot_id. Can be many pdb's per target.
# # THIS WORKS. DO NOT CHANGE.
# Ignore this for now. Need to build tool that allows selection of a pdb based on header file information.
# Need to build capability for psiBLAST.
# pdb_from_uniprot = PDBFromUniprot()
# pdb_getter = PDBFromUniprot()
# uniprot_pdb_mapping = {}
# for uniprot_id in steele_uniprot_codes:
# uniprot_pdb_mapping[uniprot_id] = []
# pdb_codes = pdb_from_uniprot.get_pdb_id(queryText)
# if pdb_codes != []:
# for pdb_id in pdb_codes:
# uniprot_pdb_mapping[uniprot_id].append(pdb_id)
# else:
# print "%s returned no pdb codes" % uniprot_id
# print "steele's mapping: ", uniprot_pdb_mapping
# uniprot_id = 'P0A9Q1'
# queryText = ("<orgPdbQuery>" +
# "<queryType>org.pdb.query.simple.UpAccessionIdQuery</queryType>" +
# "<description>Simple query for a list of Uniprot Accession IDs: " + uniprot_id + " </description>" +
# "<accessionIdList>" + uniprot_id + "</accessionIdList>" +
# "</orgPdbQuery>")
# pdb_from_uniprot = PDBFromUniprot()
# proteins with no E. coli structures
uniprot_ids = ['P07001', 'P0AB67', 'P27306', 'P0A7B3', 'P0ACS2', 'P0A9E2', 'P0A9B2', 'P0A6T1', 'P0AFG8', 'P06959', 'P0A9P0', 'P0AFG3', 'P0AFG6', 'P61889', 'P33940', 'P0AC53', 'P00350', 'P0AB67', 'P27306', 'P0A7B3', 'P0A9E2', 'P0AFG8', 'P0AFG3', 'P0AFG6', 'P33940', 'P0AC53', 'H6N162']
genbank_ids = ['81171066', '11182439', '67470903', '71162387', '84027826', '84027822', '84027824', '2506692', '81175321', '170180374']
ronming = ['3TCF', '3TCG', '3TCH']
gene_names = ['pntA']
pdb_codes = ['2BHS']
queue = ['...', '3BP8', '1LB2', '1DPS', '1BG8', '2XUV', '3UCS']
#pdb_codes = ['2ZHG', '2CGP', '2H27']
rerun = ['4JDR', '3NBU', '2CMD', '2ZYA', '4TWZ', '1SRU', '1JTS']
#pdb_codes = ['1X15', '4N72', '4JDR', '2CMD', '2ZYA', '3NBU', '4TWZ', '1SRU', '1W36']
dna_bound = ['3JRG', '3JRH', '2ZHG', '2CGP', '2H27']
key_error = ['1XGE'] # line 1433 in _edit_bfactor KeyErro 103
list_index_out_of_range = ['4TWZ', '2BUI', '2BHS'] # list index out of range line 1395
ligan_is_on_chain_B = ['1X15']
homodimer_is_inverted = ['3PFL', '2ZYA', '1NYT', '2EFT', '1DFG'] # targeted residues are on wrong chain or both chains. need to get residues for both chains (copy B to A)
hold = ['4OX6']
two_chains = ['1NYE', '3UCS', '2O97']
gaps_in_structure = ['2G67'] # need to fix write_csv_output to be robust to gaps in seq. currently just subtracting the first aln_diff
pops_issue = []
pocket_finder_issue = ['1IHF', '1OR7', '1SRU']
ligand_issue = ['2ZHG', '1IHF']
cleaned_file_mapping = {'1W36' : '1W36DBCY', '1W36': '1W36D', '1W36': '1W36B', '1W36': '1W36C', '4B2N' : '4B2NA', '1U60' : '1U60AB', '2XUV' : '2XUVABCD', '1Y00' : '1Y00AB'}
done = ['1X15', '4N72', '4JDR', '2CMD', '2ZYA', '3NBU', '4TWZ', '1SRU', '1S7C', '4B2NA', '2J1N', '1U60AB', '1YAC', '2XUVABCD', '1Y00AB', '1W36D', '1W36B', '1W36C', '3NR7', '2L15', '1A04', '2GQQ', '1LB2', '3I2Z', '3TCH', '3TCH', '1H16', '3TCH']
preliminary = []
final = ['4N72', '3NBU', '3TCH', '1DPS', '1NYE', '3NR7', '2GQQ', '3I2Z', '1BG8', '1YAC', '2CMD', '1GS5', '3N1C', '2R97', '4LFU', '4JDR', '3PFL', '1S7C', '2GFY', '2GFW']
# Download .pdb using pdb_id
# THIS WORKS. DO NOT CHANGE
# pdb_getter = PDBFromUniprot()
print "===================================================================="
print "Entering bioverse Design Pipeline"
print "===================================================================="
#
for pdb_code in pdb_codes:
# print "\n\nIdentifying residues of interest for %s" % pdb_code
# Download .pdb using pdb_id
# THIS WORKS. DO NOT CHANGE
preprocessor = PDBPreProcessor(pdb_code)
preprocessor.preprocess_check()
#pdb_getter = PDBFromUniprot()
#pdb_getter.fetch_pdb(pdb_code)
#cif_getter = CIFFromUniprot(pdb_code)
#cif_getter.fetch_mmCIF()
#
## Structural pipeline:
## # Parse PDB header
## # THIS WORKS. DO NOT CHANGE
header_parser = HeaderParser(pdb_code)
header_parser.get_header_dict()
#
## # CIF parser
## # THIS WORKS. DO NOT CHANGE
cif_parser = CIFFParser(pdb_code)
chains, genes, organisms, pdb_sequences = cif_parser.get_gene_annotations()
sequence_annotations = cif_parser.collate_sequence_annotations()
print sequence_annotations
cif_parser.write_fasta(sequence_annotations)
# what is the gene_name on each chain and what is the sequence on each chain. then save each sequence to different fasta file
# ( chain, gene_name, sequence )
#
## # Sequence Analysis
## # THIS WORKS. DO NOT CHANGE
seq_getter = SequenceGetter(genes, organisms)
dna_sequences = seq_getter.get_DNA_sequence()
seq_getter.get_protein_sequence()
#
## # Preprocessing
## # THIS WORKS. DO NOT CHANGE
number_of_structures = preprocessor.process()
preprocessor.get_complex_info()
#
## # Find start site for structure
## # THIS WORKS. DO NOT CHANGE
local_blast = localBLAST(pdb_code, sequence_annotations)
aln_diff = local_blast.align_pdb_seqs()
print aln_diff
#
## # Instantiate PDBEditor
## # THIS WORKS. DO NOT CHANGE
pdb_editor = EditPDB(pdb_code, server_mode=False)
#
## # Get surface residues
## # THIS WORKS. DO NOT CHANGE
# sr_getter = SurfaceResidues(pdb_code, server_mode=False)
# sr_getter.write_resi_sasa_output()
# sr_getter.write_frac_sasa_output()
# pdb_editor.edit_bfactor_sasa()
# sr_getter.write_surface_resi_output(0.3)
# pdb_editor.edit_bfactor_surface_residues()
#
# # Get ligand
# # THIS WORKS. DO NOT CHANGE
# ligand = LigandBindingSite(pdb_code, chains)
# ligand.get_residues_within_5A()
# ligand.write_residue_output()
# pdb_editor.edit_bfactor_ligand_binding_pocket()
#
#
## # Find pockets
## # THIS WORKS. DO NOT CHANGE
# rosetta = Rosetta(pdb_code)
# rosetta.find_pockets()
pdb_editor.edit_bfactor_pocket_residues()
#
#
## # Create Rosetta minimized structure for non-redundant monomers in the structure
## # This will be used for ddG monomer
preprocessor = PDBPreProcessor(pdb_code, target_finder_mode=False)
preprocessor.process()
number_of_structures, chains, minimum_chains = preprocessor.count_structures_in_asymmetric_unit()
#
#
## # Make 'mutants_list' file for ddg_monomer
## # THIS WORKS. DO NOT CHANGE
ListMaker1 = MutantListMaker(pdb_code, chains)
# ListMaker.generate_mutant_list(lpocket=True, SurfRes=True)
ListMaker1.generate_mutant_list(pocketres=True, lpocket=True, SurfRes=True)
# ListMaker.generate_mutant_list(pocketres=True, lpocket=True)
ListMaker2 = MutantListMaker(pdb_code, minimum_chains, asymmetric_unit=True)
ListMaker2.filter_mutant_list(minimum_chains)
#
#
## # Calculate ddG
## # THIS WORKS. DO NOT CHANGE
ddgMonomer = DDGMonomer(pdb_code, minimum_chains)
ddgMonomer.get_targets(5.5)
#
## # Write output csv
## # THIS WORKS. DO NOT CHANGE
mutation_list_generator = MutationListGenerator(sequence_annotations, dna_sequences, aln_diff, pdb_code=pdb_code)
mutation_list_generator.write_csv_output(aln_diff)
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})