from klab.bio.basics import ChainMutation
from klab.fs.fsio import read_file, write_temp_file, open_temp_file, write_file
from klab.bio.pfam import Pfam
from klab.bio.dssp import MonomerDSSP, ComplexDSSP, MissingAtomException
from klab.bio.ligand import Ligand, PDBLigand
from klab.bio.pdbtm import PDBTM
from klab.db.sqlalchemy_interface import get_single_record_from_query, get_or_create_in_transaction
from kddg.api.schema import test_schema_against_database_instance
from kddg.api.schema import PDBFile, PDBChain, PDBMolecule, PDBMoleculeChain, PDBResidue, LigandDescriptor, LigandIdentifier, LigandSynonym, PDBLigand
from kddg.api.schema import Ligand as DBLigand
#from kddg.api.schema import Publication, PublicationAuthor, PublicationIdentifier
from kddg.api.layers import *
from kddg.api.db import ddG, PartialDataException, SanityCheckException
import kddg.api.dbi as dbi
rosetta_scripts_path = '/home/oconchus/t14benchmarking/r57934/main/source/bin/rosetta_scripts.linuxgccrelease'
rosetta_database_path = '/home/oconchus/t14benchmarking/r57934/main/database'
p = PDB(read_file('/kortemmelab/data/kyleb/ddg_numbering_for_shane/24548-data/1CBW_FGHI.pdb'))
#p.construct_pdb_to_rosetta_residue_map(rosetta_scripts_path, rosetta_database_path)
p.construct_pdb_to_rosetta_residue_map(rosetta_scripts_path, rosetta_database_path, extra_command_flags = '-ignore_zero_occupancy false -ignore_unrecognized_res')
pprint.pprint(p.get_atom_sequence_to_rosetta_map())
pprint.pprint(p.rosetta_sequences)
from kddg.api.ppi import get_interface as get_ppi_interface
ppi_api = get_ppi_interface(read_file('../misc/ddgdb.pw'),
rosetta_scripts_path = '/home/oconchus/t14benchmarking/r57934/main/source/bin/rosetta_scripts.linuxgccrelease',
rosetta_database_path = '/home/oconchus/t14benchmarking/r57934/main/database')
content = ppi_api.DDG_db.execute_select('SELECT Content FROM PDBFile WHERE ID="1CBW"')[0]['Content']
print(content)
write_file('/tmp/ddginterface/1CBW_FGHI_db.pdb', content)
