class RexgenForwardSynthesizer:
def __init__(self):
# load trained model
self.directcorefinder = DirectCoreFinder()
self.directcorefinder.load_model()
self.directcandranker = DirectCandRanker()
self.directcandranker.load_model()
def predict_outcome(self, list_of_mols, k=1):
"""
Using a predictor, produce top-k most likely reactions
Params:
:list_of_mols: list of reactants and reagents (both of class Molecule)
(former contribute atoms, latter don't)
"""
react = ".".join([m.smiles for m in list_of_mols])
(react, bond_preds, bond_scores,
cur_att_score) = self.directcorefinder.predict(react)
#---> TODO: add input check here: some molecules seem to be 'unparseable' <---#
# this might be a problem of Rexgen, though
outcomes = self.directcandranker.predict(react, bond_preds,
bond_scores)
res = []
for out in outcomes[:k]:
smiles = out["smiles"][0]
mol = Molecule(smiles)
mol.set_synthesis(list_of_mols)
res.append(mol)
return res
class RexgenForwardSynthesizer(ForwardSynthesizer):
def __init__(self):
# load trained model
self.directcorefinder = DirectCoreFinder()
self.directcorefinder.load_model()
self.directcandranker = DirectCandRanker()
self.directcandranker.load_model()
def predict_outcome(self, reaction, k=1):
"""
Using a predictor, produce top-k most likely reactions
Params:
reaction {Reaction}
k {int} - how many top predictions to set and return
Returns:
{list[Molecule]} - list of products of reaction
"""
react = reaction.get_input_str()
try:
(react, bond_preds, bond_scores,
cur_att_score) = self.directcorefinder.predict(react)
outcomes = self.directcandranker.predict(react, bond_preds,
bond_scores)
except RuntimeError as e:
logging.error(f"Error occured in DirectCandRanker.predict: {e}")
raise e
res = []
for out in outcomes:
if out["smiles"]: # may be empty for some reason?
smiles = out["smiles"][0]
mol = Molecule(smiles)
mol.set_synthesis(reaction.inputs)
res.append(mol)
else:
continue
# outcomes are sorted by probability in decreasing order
res = res[:k]
# setting predicted products, if not already set:
reaction.set_products(res)
return res
def __init__(self):
# load trained model
self.directcorefinder = DirectCoreFinder()
self.directcorefinder.load_model()
self.directcandranker = DirectCandRanker()
self.directcandranker.load_model()
return outcomes
if __name__ == '__main__':
sys.path.insert(
0,
os.path.dirname(
os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
print(sys.path)
from rexgen_direct.core_wln_global.directcorefinder import DirectCoreFinder
from rexgen_direct.scripts.eval_by_smiles import edit_mol
directcorefinder = DirectCoreFinder()
directcorefinder.load_model()
if len(sys.argv) < 2:
print('Using example reaction')
react = '[CH3:26][c:27]1[cH:28][cH:29][cH:30][cH:31][cH:32]1.[Cl:18][C:19](=[O:20])[O:21][C:22]([Cl:23])([Cl:24])[Cl:25].[NH2:1][c:2]1[cH:3][cH:4][c:5]([Br:17])[c:6]2[c:10]1[O:9][C:8]([CH3:11])([C:12](=[O:13])[O:14][CH2:15][CH3:16])[CH2:7]2'
print(react)
else:
react = str(sys.argv[1])
(react, bond_preds, bond_scores,
cur_att_score) = directcorefinder.predict(react)
directcandranker = DirectCandRanker()
directcandranker.load_model()
#outcomes = directcandranker.predict(react, bond_preds, bond_scores)
outcomes = directcandranker.predict(react, bond_preds, bond_scores)
return outcomes
if __name__ == '__main__':
sys.path.insert(
0,
os.path.dirname(
os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
print(sys.path)
from rexgen_direct.core_wln_global.directcorefinder import DirectCoreFinder
from rexgen_direct.scripts.eval_by_smiles import edit_mol
directcorefinder = DirectCoreFinder()
directcorefinder.restore()
if len(sys.argv) < 2:
print('Using example reaction')
react = '[CH3:26][c:27]1[cH:28][cH:29][cH:30][cH:31][cH:32]1.[Cl:18][C:19](=[O:20])[O:21][C:22]([Cl:23])([Cl:24])[Cl:25].[NH2:1][c:2]1[cH:3][cH:4][c:5]([Br:17])[c:6]2[c:10]1[O:9][C:8]([CH3:11])([C:12](=[O:13])[O:14][CH2:15][CH3:16])[CH2:7]2'
print(react)
else:
react = str(sys.argv[1])
(react, bond_preds, bond_scores,
cur_att_score) = directcorefinder.predict(react)
directcandranker = DirectCandRanker()
directcandranker.restore()
#outcomes = directcandranker.predict(react, bond_preds, bond_scores)
outcomes = directcandranker.predict_smiles(react, bond_preds, bond_scores)
import rdkit.Chem.AllChem as AllChem
from PIL import Image, ImageOps
import rdkit.Chem.Draw as Draw
from IPython.display import SVG, display, clear_output
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
import sys
print(sys.path)
sys.path += [os.path.dirname(rexgen_direct_root)
] # need to be able to import directcorefinder
from rexgen_direct.core_wln_global.directcorefinder import DirectCoreFinder
directcorefinder = DirectCoreFinder()
directcorefinder.restore()
def arrow():
subImgSize = (115, 115)
img, canvas = Draw._createCanvas(subImgSize)
p0 = (10, subImgSize[1] // 2)
p1 = (subImgSize[0] - 10, subImgSize[1] // 2)
p3 = (subImgSize[0] - 20, subImgSize[1] // 2 - 10)
p4 = (subImgSize[0] - 20, subImgSize[1] // 2 + 10)
def drawthick(pa, pb, d=1):
canvas.addCanvasLine(pa, pb, color=(0, 0, 0))
pa = (pa[0], pa[1] + d)
pb = (pb[0], pb[1] + d)
from rdkit.Chem.Draw import IPythonConsole, ReactionToImage, MolToImage, MolsToGridImage
import rdkit.Chem.AllChem as AllChem
from PIL import Image, ImageOps
import rdkit.Chem.Draw as Draw
from IPython.display import SVG, display, clear_output
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
import sys
print(sys.path)
sys.path += [os.path.dirname(rexgen_direct_root)] # need to be able to import directcorefinder
from rexgen_direct.core_wln_global.directcorefinder import DirectCoreFinder
directcorefinder = DirectCoreFinder()
directcorefinder.load_model()
def arrow():
subImgSize = (115, 115)
img, canvas = Draw._createCanvas(subImgSize)
p0 = (10, subImgSize[1]//2)
p1 = (subImgSize[0]-10, subImgSize[1]//2)
p3 = (subImgSize[0]-20, subImgSize[1]//2-10)
p4 = (subImgSize[0]-20, subImgSize[1]//2+10)
def drawthick(pa, pb, d=1):
canvas.addCanvasLine(pa, pb, color=(0, 0, 0))
pa = (pa[0], pa[1]+d)
pb = (pb[0], pb[1]+d)