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')