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BonDNet tweaks on Zoom w/ guys #14

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Nov 9, 2023
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BonDNet tweaks on Zoom w/ guys #14

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8 changes: 2 additions & 6 deletions HiPRGen/reaction_filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -240,7 +240,9 @@ def dispatcher(
reaction['is_redox']
))

# Create reaction graph + add to LMDB
rxn_networks_g.create_rxn_networks_graph(reaction, reaction_index)

reaction_index += 1
if reaction_index % dispatcher_payload.commit_frequency == 0:
rn_con.commit()
Expand Down Expand Up @@ -350,12 +352,6 @@ def worker(
dest=DISPATCHER_RANK,
tag=NEW_REACTION_DB)

# rxn_networks_g.create_rxn_networks_graph(reaction, reaction_index)
# reaction_index += 1
# if reaction_index % dispatcher_payload.commit_frequency == 0:
# rn_con.commit()




if run_decision_tree(reaction,
Expand Down
54 changes: 29 additions & 25 deletions HiPRGen/rxn_networks_graph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import copy
from collections import defaultdict
from monty.serialization import dumpfn
from bondnet.data.utils import create_rxn_graph
from bondnet.data.utils import construct_rxn_graph_empty
from HiPRGen.lmdb_dataset import LmdbDataset
import lmdb
import tqdm
Expand Down Expand Up @@ -229,36 +229,40 @@ def find_total_bonds(rxn, species, reactants, products):
# print(f"has_bonds: {has_bonds}")
# print(f"mappings: {mappings}")

# step 5: Create a reaction graphs and features
rxn_graph, features = create_rxn_graph(
reactants = reactants_dgl_graphs,
products = products_dgl_graphs,
mappings = mappings,
has_bonds = has_bonds,
device = None,
ntypes=("global", "atom", "bond"),
ft_name="feat",
reverse=False,
)

# print(f"rxn_graph: {rxn_graph}")
if rxn['is_redox']:
print(f"mappings: {mappings}")
print(f"features: {features}")
print(f"transformed_atom_map: {transformed_atom_map}")
print(f"atom_map: {atom_map}")
# # step 5: Create a reaction graphs and features
# rxn_graph, features = create_rxn_graph(
# reactants = reactants_dgl_graphs,
# products = products_dgl_graphs,
# mappings = mappings,
# has_bonds = has_bonds,
# device = None,
# ntypes=("global", "atom", "bond"),
# ft_name="feat",
# reverse=False,
# zero_fts=True,
# )

# # print(f"rxn_graph: {rxn_graph}")
# if rxn['is_redox']:
# print(f"mappings: {mappings}")
# print(f"features: {features}")
# print(f"transformed_atom_map: {transformed_atom_map}")
# print(f"atom_map: {atom_map}")

# # step 5: update reaction features to the reaction graph
# for nt, ft in features.items():
# # print(f"nt: {nt}")
# # print(f"ft: {ft}")
# rxn_graph.nodes[nt].data.update({'ft': ft})

# step 5: update reaction features to the reaction graph
for nt, ft in features.items():
# print(f"nt: {nt}")
# print(f"ft: {ft}")
rxn_graph.nodes[nt].data.update({'ft': ft})
rxn_graph = construct_rxn_graph_empty(mappings)

# step 6: save a reaction graph and dG
self.data[rxn_id] = {} # {'id': {}}
self.data[rxn_id]['rxn_graph'] = rxn_graph
self.data[rxn_id]['value'] = rxn['dG'] #torch.tensor([rxn['dG']])
self.data[rxn_id]['reaction_features'] = features
self.data[rxn_id]['mappings'] = mappings
# self.data[rxn_id]['reaction_features'] = features


#### Write LMDB ####
Expand Down
3 changes: 3 additions & 0 deletions HiPRGen/species_filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,6 +305,9 @@ def collapse_isomorphism_group(g):
#print(dgl_molecules_dict)


#ADD WRITING MOLECULE LMDB HERE!!!


log_message("creating molecule entry pickle")
# ideally we would serialize mol_entries to a json
# some of the auxilary_data we compute
Expand Down
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