コード例 #1
0
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)
コード例 #2
0
ファイル: views.py プロジェクト: kata9238/bioverse
    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})