def main():
# steele_uniprot_codes = ['P07001', 'P0AB67', 'P27306', 'P0A7B3', 'P0ACS2', 'P0A9E2', 'P0A9B2', 'P0A6T1', 'P0AFG8', 'P06959', 'P0A9P0', 'P0AFG3', 'P0AFG6', 'P61889', 'P33940', 'P0AC53', 'P00350']
# # 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 = ['P0AB67', 'P27306', 'P0A7B3', 'P0A9E2', 'P0AFG8', 'P0AFG3', 'P0AFG6', 'P33940', 'P0AC53', 'H6N162']
genbank_ids = ['81171066', '11182439', '67470903', '71162387', '84027826', '84027822', '84027824', '2506692', '81175321', '170180374']
pdb_codes = ['1W36DBCY', '2ZHG']
pops_issue = []
pocket_finder_issue = []
ligand_issue = []
cleaned_file_mapping = {'1W36' : '1W36DBCY', '4B2N' : '4B2NA', '1U60' : '1U60AB', '2XUV' : '2XUVABCD', '1Y00' : '1Y00AB'}
done = ['1X15', '4N72', '4JDR', '2CMD', '2ZYA', '3NBU', '4TWZ', '1SRU', '1S7C', '4B2NA', '2J1N', '1U60AB', '1YAC', '2XUVABCD', '1Y00AB']
# 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
# pdb_getter = PDBFromUniprot()
# pdb_getter.fetch_pdb(pdb_code)
pdb_editor = EditPDB(pdb_code)
#cif_getter = CIFFromUniprot()
#cif_getter.fetch_mmCIF()
#
## Structural pipeline:
#
## # Get surface residues
## # THIS WORKS. DO NOT CHANGE
sr_getter = SurfaceResidues(pdb_code)
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()
#
#
## How many pdbs are there for each uniprot id? What is the difference between these sequences
## What ligand is bound? Extract out all residues within 5
#
# # Get ligand
# # THIS WORKS. DO NOT CHANGE
ligand = LigandBindingSite(pdb_code)
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()
#
#
## # Make 'mutants_list' file for ddg_monomer
## # THIS WORKS. DO NOT CHANGE
ListMaker = MutantListMaker(pdb_code)
# ListMaker.generate_mutant_list(pocketres=True, lpocket=True, SurfRes=True)
ListMaker.generate_mutant_list(pocketres=True, lpocket=True)
#
ddgMonomer = DDGMonomer(pdb_code)
ddgMonomer.get_targets(5.5)
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 main():
# # Get uniprot_id for target in database. Only one uniprot_id for each target.
# # This needs to be changed for postgress
# genbank_ids = []
# uniprot_ids = []
#
# Data = open('/Users/Andrea/repositories/design_pipeline/src/database/database.csv')
# data = Data.read().split('\r')
# Data.close
# for line in data:
# if line.startswith("#"):
# pass
# else:
# genbank_id, uniprot_id = line.split(',')[1], line.split(',')[2]
# genbank_ids.append(genbank_id)
# uniprot_ids.append(uniprot_id)
# # Get pdb_id for each structure in PDB with respective uniprot_id. Can be many pdb's per target.
# # THIS WORKS. DO NOT CHANGE.
# 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()
# steele_uniprot_codes = ['P07001', 'P0AB67', 'P27306', 'P0A7B3', 'P0ACS2', 'P0A9E2', 'P0A9B2', 'P0A6T1', 'P0AFG8', 'P06959', 'P0A9P0', 'P0AFG3', 'P0AFG6', 'P61889', 'P33940', 'P0AC53', 'P00350']
# steele_pdb_codes = ['1X15', '2ZHG', '1S7C', '3NBU', '4N72', '4JDR', '2CMD', '2ZYA']
# pdb_codes = pdb_from_uniprot.get_pdb_id(queryText)
# print pdb_codes
# # Download .pdb using pdb_id
# # THIS WORKS. DO NOT CHANGE
# pdb_getter = PDBFromUniprot()
# pdb_code = '4PDJ'
#pdb_code = '2XGE'
# pdb_getter.fetch_pdb(pdb_code)
# cif_getter = CIFFromUniprot()
# cif_getter.fetch_mmCIF(pdb_code, pdb_dir)
# Structural pipeline:
# How many pdbs are there for each uniprot id? What is the difference between these sequences
# What ligand is bound? Extract out all residues within 5
# # Get ligand
# # THIS WORKS. DO NOT CHANGE
ligand = LigandBindingSite('4PDJ')
ligand.get_residues_within_5A()
ligand.write_residue_output()
# # Get surface residues
# # THIS WORKS. DO NOT CHANGE
sr_getter = SurfaceResidues('4PDJ')
sr_getter.write_resi_sasa_output()
sr_getter.write_surface_resi_output(0.3)
# sr_getter.write_frac_sasa_output()
# # Find pockets
# # THIS WORKS. DO NOT CHANGE
rosetta = Rosetta('4PDJ')
rosetta.find_pockets()
# # Edit the B-factor column of a pdb
# # THIS WORKS. Needs improvement with file handling
pdb_editor = EditPDB('4PDJ')
pdb_editor.edit_bfactor_sasa()
pdb_editor.edit_bfactor_ligand_binding_pocket()
pdb_editor.edit_bfactor_surface_residues()
# pdb_editor.edit_bfactor_pockets()
pdb_editor.edit_bfactor_pocket_residues()
# pdb_editor.write_bfactor()
# # Make 'mutants_list' file for ddg_monomer
# # THIS WORKS. DO NOT CHANGE
ListMaker = MutantListMaker('4PDJ')
ListMaker.generate_mutant_list()
ddgMonomer = DDGMonomer('4PDJ')
ddgMonomer.get_targets(5.5)
def main():
# # Get uniprot_id for target in database. Only one uniprot_id for each target.
# # This needs to be changed for postgress
# genbank_ids = []
# uniprot_ids = []
#
# Data = open('/Users/Andrea/repositories/design_pipeline/src/database/database.csv')
# data = Data.read().split('\r')
# Data.close
# for line in data:
# if line.startswith("#"):
# pass
# else:
# genbank_id, uniprot_id = line.split(',')[1], line.split(',')[2]
# genbank_ids.append(genbank_id)
# uniprot_ids.append(uniprot_id)
# # Get pdb_id for each structure in PDB with respective uniprot_id. Can be many pdb's per target.
# # THIS WORKS. DO NOT CHANGE.
# 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()
# pdb_codes = pdb_from_uniprot.get_pdb_id(queryText)
# print pdb_codes
# # Download .pdb using pdb_id
# # THIS WORKS. DO NOT CHANGE
# pdb_getter = PDBFromUniprot()
# pdb_code = '4PDJ'
# pdb_getter.fetch_pdb(pdb_code)
# cif_getter = CIFFromUniprot()
# cif_getter.fetch_mmCIF(pdb_code, pdb_dir)
# Structural pipeline:
# How many pdbs are there for each uniprot id? What is the difference between these sequences
# What ligand is bound? Extract out all residues within 5
# # Get ligand
# # THIS WORKS. DO NOT CHANGE
# ligand = LigandBindingSite('4PDJ')
# ligand.get_residues_within_5A()
# ligand.write_residue_output()
# # Get surface residues
# # THIS WORKS. DO NOT CHANGE
sr_getter = SurfaceResidues('4PDJ')
# sr_getter.write_resi_sasa_output()
# sr_getter.write_surface_resi_output(0.3)
sr_getter.write_frac_sasa_output()
# # Edit the B-factor column of a pdb
# # Currently this requires a .txt file in the /pdb directory for the editing... needs work
pdb_editor = EditPDB('test')
# pdb_editor.edit_bfactor_sasa()
# pdb_editor.edit_bfactor_ligand_binding_pocket()
# pdb_editor.edit_bfactor_surface_residues()
pdb_editor.write_bfactor()
# # Linear regression
correlation = Correlation()
correlation.linregress('4PDJ_fracsasa.txt', 'test_pulled_bfactors.txt')
def main():
# # Get uniprot_id for target in database. Only one uniprot_id for each target.
# # This needs to be changed for postgress
# genbank_ids = []
# uniprot_ids = []
#
# Data = open('/Users/Andrea/repositories/design_pipeline/src/database/database.csv')
# data = Data.read().split('\r')
# Data.close
# for line in data:
# if line.startswith("#"):
# pass
# else:
# genbank_id, uniprot_id = line.split(',')[1], line.split(',')[2]
# genbank_ids.append(genbank_id)
# uniprot_ids.append(uniprot_id)
# # Get pdb_id for each structure in PDB with respective uniprot_id. Can be many pdb's per target.
# # THIS WORKS. DO NOT CHANGE.
# 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()
# pdb_codes = pdb_from_uniprot.get_pdb_id(queryText)
# print pdb_codes
# # Download .pdb using pdb_id
# # THIS WORKS. DO NOT CHANGE
# pdb_getter = PDBFromUniprot()
# pdb_code = '4PDJ'
# pdb_getter.fetch_pdb(pdb_code)
# cif_getter = CIFFromUniprot()
# cif_getter.fetch_mmCIF(pdb_code, pdb_dir)
# Structural pipeline:
# How many pdbs are there for each uniprot id? What is the difference between these sequences
# What ligand is bound? Extract out all residues within 5
# # Get ligand
# # THIS WORKS. DO NOT CHANGE
# ligand = LigandBindingSite('4PDJ')
# ligand.get_residues_within_5A()
# ligand.write_residue_output()
# # Get surface residues
# # THIS WORKS. DO NOT CHANGE
sr_getter = SurfaceResidues('4PDJ')
# sr_getter.write_resi_sasa_output()
# sr_getter.write_surface_resi_output(0.3)
sr_getter.write_frac_sasa_output()
# # Edit the B-factor column of a pdb
# # Currently this requires a .txt file in the /pdb directory for the editing... needs work
pdb_editor = EditPDB('test')
# pdb_editor.edit_bfactor_sasa()
# pdb_editor.edit_bfactor_ligand_binding_pocket()
# pdb_editor.edit_bfactor_surface_residues()
pdb_editor.write_bfactor()
# # Linear regression
correlation = Correlation()
correlation.linregress('4PDJ_fracsasa.txt', 'test_pulled_bfactors.txt')