new file: bin/mols2html.py

bin/mols2html.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+# create an HTML table to view all molecules in a web browser
+
+import mols2grid, rdkit, sys
+from rdkit import Chem
+
+input_fn  = sys.argv[1]
+output_fn = sys.argv[2]
+
+def sdf_read_mols(fn):
+    suppl = Chem.SDMolSupplier(fn)
+    return [mol for mol in suppl]
+
+# in a proper .smi file: the first field is the SMILES string
+# what's left on the right of it is the molecule's name
+def mol_of_smi_line(line):
+    strip = line.strip()
+    words = strip.split()
+    smi = words[0]
+    return Chem.MolFromSmiles(smi)
+
+def smi_read_mols(fn):
+    lines = open(fn, 'r').readlines()
+    return [mol_of_smi_line(line) for line in lines]
+
+mols = []
+# ----- SDF -----
+if input_fn.endswith(".sdf"):
+    # with some CLI options, we could select a subset:
+    # top 50, i..j, last 50, etc.
+    mols = sdf_read_mols(input_fn)
+# ----- MOL2 -----
+elif input_fn.endswith(".mol2"):
+    print("MOL2 not supported by rdkit!", file=sys.stderr)
+    exit(1)
+# ----- SMILES -----
+elif input_fn.endswith(".smi"):
+    mols = smi_read_mols(input_fn)
+else:
+    print("unsupported file type: %s" % input_fn, file=sys.stderr)
+    exit(1)
+
+mols2grid.save(mols, output=output_fn, template="table", prerender=True)