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')
