diff --git a/app.py b/app.py
index bbca4dc01b26593a7441f38f9fd7dbf7523f102f..0a67a46d72bed22e14a42d1ee40d67fc8ace0707 100644
--- a/app.py
+++ b/app.py
@@ -15,6 +15,10 @@ from rdkit import RDLogger
from rdkit.Chem import MolFromSmiles, AddHs
from torch_geometric.loader import DataLoader
import yaml
+import sys
+import csv
+
+csv.field_size_limit(sys.maxsize)
print(torch.__version__)
os.makedirs("data/esm2_output", exist_ok=True)
@@ -41,6 +45,8 @@ with open(f"workdir/paper_score_model/model_parameters.yml") as f:
with open(f"workdir/paper_confidence_model/model_parameters.yml") as f:
confidence_args = Namespace(**yaml.full_load(f))
+import shutil
+
t_to_sigma = partial(t_to_sigma_compl, args=score_model_args)
model = get_model(score_model_args, device, t_to_sigma=t_to_sigma, no_parallel=True)
@@ -66,30 +72,17 @@ state_dict = torch.load(
confidence_model.load_state_dict(state_dict, strict=True)
confidence_model = confidence_model.to(device)
confidence_model.eval()
-tr_schedule = get_t_schedule(inference_steps=10)
-rot_schedule = tr_schedule
-tor_schedule = tr_schedule
-print("common t schedule", tr_schedule)
-failures, skipped, confidences_list, names_list, run_times, min_self_distances_list = (
- 0,
- 0,
- [],
- [],
- [],
- [],
-)
-N = 10
def get_pdb(pdb_code="", filepath=""):
- if pdb_code is None or pdb_code == "":
- try:
- return filepath.name
- except AttributeError as e:
+ try:
+ return filepath.name
+ except AttributeError as e:
+ if pdb_code is None or pdb_code == "":
return None
- else:
- os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
- return f"{pdb_code}.pdb"
+ else:
+ os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
+ return f"{pdb_code}.pdb"
def get_ligand(smiles="", filepath=""):
@@ -111,11 +104,23 @@ def read_mol(molpath):
return mol
-def molecule(input_pdb, ligand_pdb):
+def molecule(input_pdb, ligand_pdb, original_ligand):
structure = read_mol(input_pdb)
mol = read_mol(ligand_pdb)
+ try:
+ ligand = read_mol(original_ligand.name)
+ _, ext = os.path.splitext(original_ligand.name)
+ lig_str_1 = """let original_ligand = `""" + ligand + """`"""
+ lig_str_2 = f"""
+ viewer.addModel( original_ligand, "{ext[1:]}" );
+ viewer.getModel(2).setStyle({{stick:{{colorscheme:"greenCarbon"}}}});"""
+ except AttributeError as e:
+ ligand = None
+ lig_str_1 = ""
+ lig_str_2 = ""
+
x = (
"""
@@ -134,11 +139,27 @@ def molecule(input_pdb, ligand_pdb):
.mol-container select{
background-image:None;
}
+ .green{
+ width:20px;
+ height:20px;
+ background-color:#33ff45;
+ display:inline-block;
+ }
+ .magenta{
+ width:20px;
+ height:20px;
+ background-color:magenta;
+ display:inline-block;
+ }
-
+
+
+ Uploaded ligand position
+ Predicted ligand position
+