Sprint 14 : Prioritization of quinolones

synthetic-enumeration/sprint-14-quinolones/01-aggregate-compounds.py

@@ -0,0 +1,105 @@
+from openeye import oechem
+from rich.progress import track
+
+"""
+Prepare list of annotated compounds for docking
+
+* Aggregate all compound designs
+* Annotate by intermediate
+* Sort compounds by size
+* Interleave compounds by intermediate
+
+"""
+
+mols = list()
+
+# TODO: Auto-download and timestamp
+submissions_csv_filename = 'submissions/submissions-2022-02-24.csv.bz2'
+
+# Read all submitted designs: Compounds with the key substructure will be retained
+print('Reading submitted designs...')
+# Drop columns that cause trouble for OpenEye
+import pandas as pd
+drop_columns = ['Submission Rationale', 'Submission Notes']
+df = pd.read_csv(submissions_csv_filename, dtype=str)
+df.drop(columns=drop_columns, inplace=True)
+print(f'{len(df)} records read')
+import tempfile
+with tempfile.NamedTemporaryFile(suffix='.csv') as csv_file:
+    df.to_csv(csv_file.name, header=True, index=False)
+    # Read file
+    with oechem.oemolistream(csv_file.name) as ifs:
+        mol = oechem.OEGraphMol()
+        while oechem.OEReadMolecule(ifs, mol):
+            # Clear SD tags
+            oechem.OEClearSDData(mol)
+            # Store the molecule
+            mols.append(mol.CreateCopy())
+print(f'{len(mols)} molecules read')
+
+# Aggregate all compound designs
+print('reading compound designs...')
+source_filenames = [
+    # Filtered synthetic designs
+    'virtual-libraries/amidation-renamed.csv',
+    'virtual-libraries/mitsunobu-renamed.csv',
+    'virtual-libraries/red_ami-renamed.csv',
+    'virtual-libraries/red_amination_1-renamed.csv',
+    'virtual-libraries/williamson_ether-renamed.csv',
+]
+for source_filename in source_filenames:
+    print(source_filename)
+    with oechem.oemolistream(source_filename) as ifs:
+        mol = oechem.OEGraphMol()
+        while oechem.OEReadMolecule(ifs, mol):
+            # Clear SD tags
+            oechem.OEClearSDData(mol)
+            # Store the molecule
+            mols.append(mol.CreateCopy())
+print(f'{len(mols)} molecules read')
+
+# Annotate molecules with SMARTS labels
+print('Annotating SMARTS labels...')
+import csv
+labels_filename = 'annotations/annotations.csv' # list of labels for various SMARTS patterns
+smarts_labels = dict()
+with open(labels_filename, 'r') as csvfile:
+    csvreader = csv.reader(csvfile, delimiter=',')
+    for row in csvreader:
+        smarts = row[0]
+        label = row[1]
+        if smarts[0] != '#': # allow comments
+            smarts_labels[smarts] = label
+# Label the molecules
+for smarts, label in smarts_labels.items():
+    ss = oechem.OESubSearch(smarts)
+    for mol in track(mols, description=label):
+        oechem.OEPrepareSearch(mol, ss)
+        if ss.SingleMatch(mol):
+            oechem.OESetSDData(mol, 'scaffold', label)
+# Discard molecules without labels
+mols = [ mol for mol in mols if oechem.OEHasSDData(mol, 'scaffold') ]
+print(f'{len(mols)} molecules remain after discarding molecules that do not match scaffold')
+
+# Sort based on molecular weight
+print(f'Sorting molecules by number of atoms...')
+mols.sort(key=lambda mol : mol.NumAtoms())
+
+# Filter the number of heavy atoms
+#n_heavy_max = 35
+n_heavy_max = 50
+mols = [ mol for mol in mols if oechem.OECount(mol, oechem.OEIsHeavy()) <= n_heavy_max ]
+print(f'{len(mols)} molecule remain after filtering atoms with more than {n_heavy_max} heavy atoms')
+
+# Write molecules
+output_filename = 'sorted/sprint-14.csv'
+with oechem.oemolostream(output_filename) as ofs:
+    for mol in track(mols, description='Writing molecules...'):
+        oechem.OEWriteMolecule(ofs, mol)
+
+# Generate PDF
+pdf_filename = output_filename.replace('.csv', '.pdf')
+print(f'Generating PDF as {pdf_filename}')
+cmd = f"mols2pdf.py -in {output_filename} -out {pdf_filename}"
+import os
+os.system(cmd)