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 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)