Update app.py

app.py

@@ -1,4 +1,3 @@
-import concurrent.futures
 import glob
 import smtplib
 from datetime import datetime, timedelta
@@ -7,6 +6,7 @@ import textwrap
 from email.mime.multipart import MIMEMultipart
 from email.mime.text import MIMEText
 from email.utils import formatdate, make_msgid
+from functools import cache
 from math import pi
 from time import sleep, time
 from uuid import uuid4
@@ -428,12 +428,45 @@ def rule_of_three(mol):
         return True
 
 
-# def smarts_filter():
-#     alerts = Chem.MolFromSmarts("enter one smart here")
-#     detected_alerts = []
-#     for smiles in data['X1']:
-#         mol = Chem.MolFromSmiles(smiles)
-#         detected_alerts.append(mol.HasSubstructMatch(alerts))
+@cache
+def load_smarts_patterns(smarts_path):
+    # Load the CSV file containing SMARTS patterns
+    smarts_df = pd.read_csv(Path(smarts_path))
+    # Convert all SMARTS patterns to molecules
+    smarts_mols = [Chem.MolFromSmarts(smarts) for smarts in smarts_df['smarts']]
+    return smarts_mols
+
+
+def smarts_filter(mol, smarts_mols):
+    for smarts_mol in smarts_mols:
+        if smarts_mol is not None and mol.HasSubstructMatch(smarts_mol):
+            return False
+    return True
+
+
+def pains(mol):
+    smarts_mols = load_smarts_patterns("data/filters/pains.csv")
+    return smarts_filter(mol, smarts_mols)
+
+
+def mlsmr(mol):
+    smarts_mols = load_smarts_patterns("data/filters/mlsmr.csv")
+    return smarts_filter(mol, smarts_mols)
+
+
+def dundee(mol):
+    smarts_mols = load_smarts_patterns("data/filters/dundee.csv")
+    return smarts_filter(mol, smarts_mols)
+
+
+def glaxo(mol):
+    smarts_mols = load_smarts_patterns("data/filters/glaxo.csv")
+    return smarts_filter(mol, smarts_mols)
+
+
+def bms(mol):
+    smarts_mols = load_smarts_patterns("data/filters/bms.csv")
+    return smarts_filter(mol, smarts_mols)
 
 
 SCORE_MAP = {
@@ -455,7 +488,11 @@ FILTER_MAP = {
     'Ghose': ghose,
     'Rule of Three': rule_of_three,
     'Veber': veber,
-    # 'PAINS': pains,
+    'PAINS': pains,
+    'MLSMR': mlsmr,
+    'Dundee': dundee,
+    'Glaxo': glaxo,
+    'BMS': bms,
 }
 
 
@@ -876,7 +913,7 @@ def create_html_report(df, file=None, task=None, progress=gr.Progress(track_tqdm
         if any(df_html.columns.isin(bool_cols)):
             styled_df.applymap(lambda val: f'background-color: {bool_col_colors[val]}', subset=bool_cols)
 
-        table_html = styled_df.to_html()
+        table_html = styled_df.to_html(na_rep='')
         unique_html = ''
         if unique_df is not None:
             if 'Target FASTA' in unique_df.columns:
@@ -885,7 +922,7 @@ def create_html_report(df, file=None, task=None, progress=gr.Progress(track_tqdm
                 unique_df = unique_df.style.applymap(
                     lambda val: f"background-color: {bool_col_colors[val]}", subset=bool_cols)
             unique_html = (f'<div style="font-family: Courier !important;">'
-                           f'{unique_df.to_html(escape=False, index=False)}</div>')
+                           f'{unique_df.to_html(escape=False, index=False, na_rep="")}</div>')
 
         return (f'<div style="font-size: 16px; font-weight: bold;">{job} Report Preview (Top 30 Records)</div>'
                 f'<div style="overflow-x:auto; font-family: Courier !important;">{unique_html}</div>'
@@ -1701,13 +1738,19 @@ with gr.Blocks(theme=theme, title='DeepSEQreen', css=CSS, delete_cache=(3600, 48
             fasta = fasta_upload.decode()
         except Exception as e:
             gr.Warning(f"Please upload a valid FASTA file. Error: {str(e)}")
-            return fasta
+        return fasta
 
 
-    target_upload_btn.upload(fn=process_fasta_upload, inputs=target_upload_btn, outputs=target_fasta)
-    target_query_btn.click(uniprot_query,
-                           inputs=[target_input_type, target_id, target_gene, target_organism],
-                           outputs=target_fasta)
+    target_upload_btn.upload(
+        fn=process_fasta_upload, inputs=target_upload_btn, outputs=target_fasta
+    ).then(
+        fn=wrap_text, inputs=target_fasta, outputs=target_fasta, show_progress='hidden'
+    )
+    target_query_btn.click(
+        fn=uniprot_query, inputs=[target_input_type, target_id, target_gene, target_organism], outputs=target_fasta
+    ).then(
+        fn=wrap_text, inputs=target_fasta, outputs=target_fasta, show_progress='hidden'
+    )
 
 
     def target_family_detect(fasta, progress=gr.Progress(track_tqdm=True)):
@@ -2080,6 +2123,7 @@ QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
         else:
             raise gr.Error('System failed to create temporary files. Please try again later.')
 
+
     def fill_job_id(job_info):
         try:
             return job_info['id']
@@ -2261,7 +2305,7 @@ QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
         try:
             now = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
             filename = f"/data/{Path(file_report.name).stem}_DeepSEQreen_report_{now}.csv"
-            df.drop(labels=['Compound', 'Scaffold'], axis=1).to_csv(filename, index=False)
+            df.drop(labels=['Compound', 'Scaffold'], axis=1).to_csv(filename, index=True, na_rep='')
 
             return gr.File(filename)
         except Exception as e: