diff sdf_to_tab.py @ 0:55a2082540a9 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sdf_to_tab.py	Sat Dec 04 16:36:56 2021 +0000
@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+import argparse
+
+import pandas as pd
+from rdkit import Chem
+
+
+def sdf_to_tab(vars):
+    mols = Chem.SDMolSupplier(vars.inp, sanitize=False)
+    df = pd.DataFrame()  # for output
+
+    for n in range(len(mols)):
+        if mols[n]:
+            d = mols[n].GetPropsAsDict()
+            # filter dict for desired props
+            if vars.props.strip() == "":  # none specified, return all
+                d = {
+                    prop: val
+                    for (prop, val) in d.items()
+                    if not any(x in str(val) for x in ["\n", "\t"])
+                }  # remove items containing newlines or tabs
+            else:
+                d = {
+                    prop: val
+                    for (prop, val) in d.items()
+                    if prop in vars.props.replace(" ", "").split(",")
+                }  # remove items not requested via CLI
+            if vars.name:
+                d["SDFMoleculeName"] = mols[n].GetProp("_Name")
+            if vars.smiles:
+                d["SMILES"] = Chem.MolToSmiles(mols[n], isomericSmiles=False)
+            d["Index"] = int(n)
+
+            df = df.append(d, ignore_index=True)
+        else:
+            print("Molecule could not be read - skipped.")
+
+    df = df.astype({"Index": int}).set_index("Index")
+    sorted_cols = sorted(df.columns.values.tolist())
+    df.to_csv(vars.out, sep="\t", header=vars.header, columns=sorted_cols)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Convert SDF to tabular")
+    parser.add_argument("--inp", "-i", help="The input file", required=True)
+    parser.add_argument("--out", "-o", help="The output file", required=True)
+    parser.add_argument(
+        "--props",
+        "-p",
+        help="Properties to filter (leave blank for all)",
+        required=True,
+    )
+    parser.add_argument(
+        "--header",
+        "-t",
+        action="store_true",
+        help="Write property name as the first row.",
+    )
+    parser.add_argument(
+        "--smiles", "-s", action="store_true", help="Include SMILES in output."
+    )
+    parser.add_argument(
+        "--name", "-n", action="store_true", help="Include molecule name in output."
+    )
+    sdf_to_tab(parser.parse_args())
+
+
+if __name__ == "__main__":
+    main()