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protein.py
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protein.py
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import logging as log
import os
from base64 import b64decode
from io import StringIO
from Bio.PDB import PDBParser
from Bio.SeqUtils import molecular_weight, seq1
from ..db import Database, bytea_to_str, str_to_bytea
from fastapi.exceptions import HTTPException
from ..api_types import ProteinEntry, UploadBody, UploadError, EditBody, CamelModel
from ..tmalign import tm_align_return
from ..auth import requires_authentication
from io import BytesIO
from fastapi import APIRouter
from fastapi.responses import FileResponse, StreamingResponse
from fastapi.requests import Request
import re
router = APIRouter()
class PDB:
def __init__(self, file_contents, name=""):
self.name = name
self.file_contents = file_contents
try:
self.parser = PDBParser()
self.structure = self.parser.get_structure(
id=name, file=StringIO(file_contents)
)
except Exception as e:
raise e # raise to the user who calls this PDB class
@property
def num_amino_acids(self) -> int:
return len(self.amino_acids())
@property
def mass_daltons(self):
return molecular_weight(seq="".join(self.amino_acids()), seq_type="protein")
def amino_acids(self, one_letter_code=True):
return [
seq1(residue.resname) if one_letter_code else residue.resname
for residue in self.structure.get_residues()
]
def decode_base64(b64_header_and_data: str):
"""Converts a base64 string to bytes"""
# only decode after the header (data:application/octet-stream;base64,)
end_of_header = b64_header_and_data.index(",")
b64_data_only = b64_header_and_data[end_of_header:]
return b64decode(b64_data_only).decode("utf-8")
def stored_pdb_file_name(protein_name: str):
return os.path.join("src/data/stored_proteins", protein_name) + ".pdb"
def parse_protein_pdb(name: str, file_contents: str = "", encoding="str"):
if encoding == "str":
return PDB(file_contents, name)
elif encoding == "b64":
return PDB(decode_base64(file_contents), name)
elif encoding == "file":
return PDB(open(stored_pdb_file_name(name), "r").read(), name)
else:
raise ValueError(f"Invalid encoding: {encoding}")
def format_protein_name(name: str):
name = name.replace(" ", "_")
return name
def protein_name_found(name: str):
"""Checks if a protein name already exists in the database
Returns: True if exists | False if not exists
"""
with Database() as db:
try:
entry_sql = db.execute_return(
"""SELECT name FROM proteins
WHERE name = %s""",
[name],
)
# if we got a result back
return entry_sql is not None and len(entry_sql) != 0
except Exception:
return False
def pdb_to_fasta(pdb: PDB):
return ">{}\n{}".format(pdb.name, "".join(pdb.amino_acids()))
def str_as_file_stream(input_str: str, filename_as: str) -> StreamingResponse:
return StreamingResponse(
BytesIO(input_str.encode()),
media_type="text/plain",
headers={"Content-Disposition": f"attachment; filename={filename_as}"},
)
def get_residue_bfactors(pdb: PDB):
chains = {}
for chain in pdb.structure.get_chains():
chains[chain.get_id()] = []
for r in chain.get_residues():
for a in r.get_atoms():
chains[chain.get_id()].append(a.bfactor)
break
return chains
"""
ENDPOINTS TODO: add the other protein types here instead of in api_types.py
"""
@router.get("/protein/pLDDT/{protein_name:str}", response_model=dict[str, list[float]])
def get_pLDDT_given_protein(protein_name: str):
if protein_name_found(protein_name):
pdb = parse_protein_pdb(protein_name, encoding="file")
return get_residue_bfactors(pdb)
return {}
class UploadPNGBody(CamelModel):
protein_name: str
base64_encoding: str
@router.get("/protein/pdb/{protein_name:str}")
def get_pdb_file(protein_name: str):
if protein_name_found(protein_name):
return FileResponse(
stored_pdb_file_name(protein_name), filename=protein_name + ".pdb"
)
@router.get("/protein/fasta/{protein_name:str}")
def get_fasta_file(protein_name: str):
if protein_name_found(protein_name):
pdb = parse_protein_pdb(protein_name, encoding="file")
fasta = pdb_to_fasta(pdb)
return StreamingResponse(
BytesIO(fasta.encode()),
media_type="text/plain",
headers={
"Content-Disposition": f"attachment; filename={protein_name}.fasta"
},
)
@router.get("/protein/entry/{protein_name:str}", response_model=ProteinEntry | None)
def get_protein_entry(protein_name: str):
"""Get a single protein entry by its id
Returns: ProteinEntry if found | None if not found
"""
with Database() as db:
try:
query = """SELECT proteins.name,
proteins.description,
proteins.length,
proteins.mass,
proteins.content,
proteins.refs,
species.name,
proteins.thumbnail,
proteins.date_published
FROM proteins
JOIN species ON species.id = proteins.species_id
WHERE proteins.name = %s;"""
entry_sql = db.execute_return(query, [protein_name])
# if we got a result back
if entry_sql is not None and len(entry_sql) != 0:
# return the only entry
only_returned_entry = entry_sql[0]
(
name,
description,
length,
mass,
content,
refs,
species_name,
thumbnail,
date_published,
) = only_returned_entry
if thumbnail is not None:
# if byte arrays are present, decode them into a string
thumbnail = bytea_to_str(thumbnail)
if date_published is not None:
# forces the datetime object into a linux utc string
date_published = str(date_published)
return ProteinEntry(
name=name,
description=description,
length=length,
mass=mass,
content=content,
refs=refs,
species_name=species_name,
thumbnail=thumbnail,
date_published=date_published,
)
except Exception as e:
log.error(e)
# TODO: add permissions so only the creator can delete not just anyone
@router.delete("/protein/entry/{protein_name:str}", response_model=None)
def delete_protein_entry(protein_name: str, req: Request):
requires_authentication(req)
# Todo, have a meaningful error if the delete fails
with Database() as db:
# remove protein
try:
db.execute(
"""DELETE FROM proteins
WHERE name = %s""",
[protein_name],
)
# delete the file from the data/ folder
os.remove(stored_pdb_file_name(protein_name))
except Exception as e:
log.error(e)
@router.post("/protein/upload/png", response_model=None)
def upload_protein_png(body: UploadPNGBody, req: Request):
requires_authentication(req)
with Database() as db:
try:
query = """UPDATE proteins SET thumbnail = %s WHERE name = %s"""
db.execute(query, [str_to_bytea(body.base64_encoding), body.protein_name])
except Exception as e:
log.error(e)
# None return means success
@router.post("/protein/upload", response_model=UploadError | None)
def upload_protein_entry(body: UploadBody, req: Request):
requires_authentication(req)
body.name = format_protein_name(body.name)
# check that the name is not already taken in the DB
if protein_name_found(body.name):
return UploadError.NAME_NOT_UNIQUE
# if name is unique, save the pdb file and add the entry to the database
try:
# TODO: consider somehow sending the file as a stream instead of a b64 string or send as regular string
pdb = parse_protein_pdb(body.name, body.pdb_file_str)
except Exception:
return UploadError.PARSE_ERROR
try:
# write to file to data/ folder
with open(stored_pdb_file_name(pdb.name), "w") as f:
f.write(pdb.file_contents)
except Exception:
log.warn("Failed to write to file")
return UploadError.WRITE_ERROR
# save to db
with Database() as db:
try:
# first add the species if it doesn't exist
db.execute(
"""INSERT INTO species (name) VALUES (%s) ON CONFLICT DO NOTHING;""",
[body.species_name],
)
except Exception:
log.warn("Failed to insert into species table")
return UploadError.QUERY_ERROR
try:
# add the protein itself
query = """INSERT INTO proteins (name, description, length, mass, content, refs, species_id)
VALUES (%s, %s, %s, %s, %s, %s, (SELECT id FROM species WHERE name = %s));"""
db.execute(
query,
[
pdb.name,
body.description,
pdb.num_amino_acids,
pdb.mass_daltons,
body.content,
body.refs,
body.species_name,
],
)
except Exception:
log.warn("Failed to insert into proteins table")
return UploadError.QUERY_ERROR
class ProteinEditSuccess(CamelModel):
edited_name: str
@router.put("/protein/edit", response_model=ProteinEditSuccess)
def edit_protein_entry(body: EditBody, req: Request):
"""edit_protein_entry
Returns: On successful edit, will return an object with editedName
If not successful will through an HTTP status 500
"""
# check that the name is not already taken in the DB
# TODO: check if permission so we don't have people overriding other people's names
requires_authentication(req)
try:
# replace spaces in the name with underscores
body.old_name = format_protein_name(body.old_name)
body.new_name = format_protein_name(body.new_name)
if body.new_name != body.old_name:
os.rename(
stored_pdb_file_name(body.old_name), stored_pdb_file_name(body.new_name)
)
with Database() as db:
name_changed = False
if body.new_name != body.old_name:
db.execute(
"""UPDATE proteins SET name = %s WHERE name = %s""",
[
body.new_name,
body.old_name,
],
)
name_changed = True
if body.new_species_name != body.old_species_name:
db.execute(
"""UPDATE proteins SET species_id = (SELECT id FROM species WHERE name = %s) WHERE name = %s""",
[
body.new_species_name,
body.old_name if not name_changed else body.new_name,
],
)
if body.new_content is not None:
db.execute(
"""UPDATE proteins SET content = %s WHERE name = %s""",
[
body.new_content,
body.old_name if not name_changed else body.new_name,
],
)
if body.new_refs is not None:
db.execute(
"""UPDATE proteins SET refs = %s WHERE name = %s""",
[
body.new_refs,
body.old_name if not name_changed else body.new_name,
],
)
if body.new_description is not None:
db.execute(
"""UPDATE proteins SET description = %s WHERE name = %s""",
[
body.new_description,
body.old_name if not name_changed else body.new_name,
],
)
return ProteinEditSuccess(edited_name=body.new_name)
except Exception:
raise HTTPException(500, "Edit failed, git gud")
# /pdb with two attributes returns both PDBs, superimposed and with different colors.
@router.get("/protein/pdb/{proteinA:str}/{proteinB:str}", response_model=str)
def align_proteins(proteinA: str, proteinB: str):
if not protein_name_found(proteinA) or not protein_name_found(proteinB):
raise HTTPException(
status_code=404, detail="One of the proteins provided is not found in DB"
)
try:
filepath_pdbA = stored_pdb_file_name(proteinA)
filepath_pdbB = stored_pdb_file_name(proteinB)
superimposed_pdb = tm_align_return(filepath_pdbA, filepath_pdbB)
return str_as_file_stream(superimposed_pdb, f"{proteinA}_{proteinB}.pdb")
except Exception as e:
log.error(e)
raise HTTPException(status_code=500, detail=str(e))
class TMAlignInfo(CamelModel):
aligned_length: str | None
rmsd: str | None
seq_id: str | None
chain1_tm_score: str | None
chain2_tm_score: str | None
alignment_string: str
# Returns the alignment string info from TM Align's console log.
@router.get(
"/protein/tmalign/{proteinA:str}/{proteinB:str}", response_model=TMAlignInfo
)
def get_tm_info(proteinA: str, proteinB: str):
if not protein_name_found(proteinA) or not protein_name_found(proteinB):
raise HTTPException(
status_code=404, detail="One of the proteins provided is not found in DB"
)
try:
filepath_pdbA = stored_pdb_file_name(proteinA)
filepath_pdbB = stored_pdb_file_name(proteinB)
tmalign_output = tm_align_return(filepath_pdbA, filepath_pdbB, 1)
log.warn("TM Align Output follows:")
# Split TMAlign data into an array format
tmalign_output_list = tmalign_output.splitlines()
log.warn(tmalign_output)
# Grab aligned length, RMSD, and Seq ID
tmalign_tri = tmalign_output_list[12].split(", ")
# Note: \d+?.\d* means "match 1 or more numbers, 0 or 1 decimal points, and 0 or more numbers" in regex
aligned_length = re.search("\d+?.\d*", tmalign_tri[0]).group()
rmsd = re.search("\d+.?\d*", tmalign_tri[1]).group()
seq_id = re.search("\d+.?\d*", tmalign_tri[2]).group()
# Grabs both TM scores
# NOTE: This is ONLY grabbing the TM-Score from the file. It's leaving out the LN and d0 stats.
chain1_normalized_tm_score = re.search(
"\d+.?\d*", tmalign_output_list[13]
).group()
chain2_normalized_tm_score = re.search(
"\d+.?\d*", tmalign_output_list[14]
).group()
# Grabs TM Alignment String
tmalign_string = "\n".join(tmalign_output_list[18:21])
log.warn(tmalign_string)
return TMAlignInfo(
aligned_length=aligned_length,
rmsd=rmsd,
seq_id=seq_id,
chain1_tm_score=chain1_normalized_tm_score,
chain2_tm_score=chain2_normalized_tm_score,
alignment_string=tmalign_string,
)
except Exception as e:
log.error(e)
raise HTTPException(status_code=500, detail=str(e))
@router.get("/protein/random", response_model=ProteinEntry)
def get_random_protein():
with Database() as db:
try:
query = """SELECT
proteins.name,
proteins.length,
proteins.mass,
proteins.description,
species.name as species_name
FROM proteins TABLESAMPLE SYSTEM_ROWS(1)
JOIN species ON species.id = proteins.species_id;"""
res = db.execute_return(query)
if res is not None:
name, length, mass, description, species_name = res[0]
return ProteinEntry(
name=name,
length=length,
mass=mass,
description=description,
species_name=species_name,
)
else:
raise HTTPException(
status_code=501, detail="SQL query couldn't execute"
)
except Exception as e:
log.error(e)
raise HTTPException(status_code=500, detail=str(e))