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api.py
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api.py
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import json
import networkx as nx
from os import environ
from dotenv import load_dotenv
from rdkit import Chem
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
bond_type = {
'single': Chem.rdchem.BondType.SINGLE,
'double': Chem.rdchem.BondType.DOUBLE,
'triple': Chem.rdchem.BondType.TRIPLE,
'single_up': Chem.rdchem.BondType.SINGLE,
'single_down': Chem.rdchem.BondType.SINGLE
}
def check_authorization(provided_key: str) -> bool:
allowed_key = environ.get('API_KEY')
if not allowed_key:
return False
return provided_key == allowed_key
def read_vec2(data) -> tuple[float, float]:
if isinstance(data, list):
return (data[0] / 100, data[1] / 100)
else:
return (data['x'] / 100, data['y'] / 100)
def json_to_graph(data) -> nx.Graph:
g = nx.Graph()
for v, atom in enumerate(data['atoms']):
g.add_node(v, **{
'symbol': atom['symbol'],
'position': read_vec2(atom['position']),
'formal_charge': atom.get('formal_charge', 0),
'non_bonded_ve': atom.get('non_bonded_ve', 0)
})
for bond in data['bonds']:
g.add_edge(bond['from'], bond['to'], type=bond['type'])
return g
def graph_to_mol(g: nx.Graph) -> Chem.rdchem.RWMol:
mol = Chem.rdchem.RWMol()
index = {}
for v in g.nodes:
a = Chem.rdchem.Atom(g.nodes[v]['symbol'])
a.SetFormalCharge(g.nodes[v]['formal_charge'])
index[v] = mol.AddAtom(a)
for u, v in g.edges:
mol.AddBond(index[u], index[v], bond_type[g.edges[(u,v)]['type']])
# Build 2D conformer.
conf = Chem.Conformer(mol.GetNumAtoms())
for v in g.nodes:
# Note that we add a Z-coordinate with value 0.
conf.SetAtomPosition(index[v], g.nodes[v]['position'] + (0,))
# Assign conformer and compute stereochemistry.
mol = mol.GetMol()
mol.AddConformer(conf)
Chem.AssignStereochemistryFrom3D(mol)
return mol
def json_to_mol(data) -> Chem.rdchem.RWMol:
return graph_to_mol(json_to_graph(data))
def _node_match(v1, v2):
props = ['symbol', 'formal_charge', 'non_bonded_ve']
return all(map(lambda p: v1[p] == v2[p], props))
def _edge_match(e1, e2):
return e1['type'] == e2['type']
def _graph_to_smiles(g: nx.Graph) -> str:
mol = graph_to_mol(g)
return Chem.rdmolfiles.MolToSmiles(mol, isomericSmiles=True)
def compare_components(g1: nx.Graph, g2: nx.Graph) -> bool:
return (
nx.is_isomorphic(g1, g2, _node_match, _edge_match) and
_graph_to_smiles(g1) == _graph_to_smiles(g2))
def compare(diagram1, diagram2) -> bool:
g1 = json_to_graph(diagram1)
g2 = json_to_graph(diagram2)
cs1 = list(map(lambda c: g1.subgraph(c), nx.connected_components(g1)))
cs2 = list(map(lambda c: g2.subgraph(c), nx.connected_components(g2)))
# Check if every component in g1 matches a unique component in g2.
for c1 in cs1:
match = (i for i, c2 in enumerate(cs2) if compare_components(c1, c2))
index = next(match, None)
if index is None:
return False
else:
# Every component can only be matched once.
cs2.pop(index)
return len(cs2) == 0
def validate(diagram) -> bool:
mol = json_to_mol(diagram)
try:
Chem.SanitizeMol(mol)
return True
except ValueError:
return False
def handle_validate(body):
return {
'valid': validate(body['diagram'])
}
def handle_compare(body):
return {
'equal': compare(
body['reference_diagram'],
body['student_diagram'])
}
def handler(event, context):
try:
load_dotenv()
headers = event.get('headers', {})
auth_header: str = headers.get('Authorization') or headers.get('authorization')
if not auth_header:
return {
'body': json.dumps({'err': 'Authorization Required'}),
'headers': {
'Content-Type': 'application/json'
},
'statusCode': 401,
}
auth_header = auth_header.replace('Bearer ', '')
if not check_authorization(auth_header):
return {
'body': json.dumps({'err': 'Invalid authorization token'}),
'headers': {
'Content-Type': 'application/json'
},
'statusCode': 401,
}
request_path_raw: str = event.get('requestContext', {}).get('path', '')
request_path = request_path_raw.replace('/api/v1/', '')
request_body = json.loads(event['body'])
match request_path:
case 'compare':
response_body = handle_compare(request_body)
case 'validate':
response_body = handle_validate(request_body)
case _:
response_body = {'err': 'Invalid request'}
return {
'body': json.dumps(response_body),
'headers': {
'Content-Type': 'application/json'
},
'statusCode': 200,
}
except Exception as e:
print(e)
return {
'body': json.dumps({'err': 'Unable to parse diagrams or an internal error occurred.'}),
'headers': {
'Content-Type': 'application/json'
},
'statusCode': 400,
}