Merge branch 'dev'

synrbl/SynCmd/cmd_benchmark.py

@@ -1,6 +1,7 @@
 import argparse
 import logging
 import pandas as pd
+import rdkit.Chem.rdChemReactions as rdChemReactions
 
 from synrbl import Balancer
 from synrbl.SynUtils import normalize_smiles, wc_similarity
@@ -50,29 +51,55 @@ def _sr(v, c):
     )
 
 
-def check_columns(reactions, reaction_col, result_col):
+def check_columns(reactions, reaction_col, result_col, passthrouh_columns):
     if len(reactions) == 0:
         raise ValueError("No reactions found in input.")
     cols = reactions[0].keys()
     if reaction_col not in cols:
         raise KeyError("No column '{}' found in input.".format(reaction_col))
+    if not isinstance(reactions[0][reaction_col], str):
+        raise TypeError(
+            "Reaction column '{}' must be of type string not '{}'.".format(
+                reaction_col, type(reactions[0][reaction_col])
+            )
+        )
+    mol = None
+    try:
+        mol = rdChemReactions.ReactionFromSmarts(
+            reactions[0][reaction_col], useSmiles=True
+        )
+    except Exception:
+        pass
+    if mol is None:
+        raise ValueError(
+            "Value '{}...' in reaction column '{}' is not a valid SMILES.".format(
+                reactions[0][reaction_col][0:30], reaction_col
+            )
+        )
     if result_col not in cols:
         raise KeyError("No column '{}' found in input.".format(result_col))
+    for c in passthrouh_columns:
+        if c not in reactions[0].keys():
+            raise KeyError("Column '{}' not found.".format(c))
 
 
 def run(args):
+    columns = args.columns if isinstance(args.columns, list) else [args.columns]
+    synrbl_cols = [c for c in columns if c in ["mcs"]]
+    passthrough_cols = [c for c in columns if c not in synrbl_cols]
     input_reactions = pd.read_csv(args.inputfile).to_dict("records")
     logger.info(
         "Run benchmark on {} containing {} reactions.".format(
             args.inputfile, len(input_reactions)
         )
     )
-    check_columns(input_reactions, args.col, args.result_col)
+    check_columns(input_reactions, args.col, args.result_col, passthrough_cols)
 
     stats = {}
     synrbl = Balancer(
         reaction_col=args.col, confidence_threshold=args.min_confidence, n_jobs=args.p
     )
+    synrbl.columns.extend(synrbl_cols)
     rbl_reactions = synrbl.rebalance(input_reactions, output_dict=True, stats=stats)
 
     rb_correct = 0
@@ -100,7 +127,9 @@ def run(args):
 
     if args.o is not None:
         for in_r, out_r in zip(input_reactions, rbl_reactions):
-            out_r[args.result_col] = in_r[args.result_col]
+            for c in columns + [args.result_col]:
+                if c in in_r.keys():
+                    out_r[c] = in_r[c]
         df = pd.DataFrame(rbl_reactions)
         df.to_csv(args.o)
 
@@ -117,9 +146,13 @@ def __str__(self):
         return "[{}, {}]".format(self.start, self.end)
 
 
+def list_of_strings(arg):
+    return arg.split(",")
+
+
 def configure_argparser(argparser: argparse._SubParsersAction):
     default_similarity_method = "pathway"
-    default_similarity_threshold = 0.85
+    default_similarity_threshold = 1 
     default_p = -1
     default_col = "reaction"
     default_result_col = "expected_reaction"
@@ -156,6 +189,13 @@ def configure_argparser(argparser: argparse._SubParsersAction):
         help="The reactions column name for in the expected output. "
         + "(Default: {})".format(default_result_col),
     )
+    test_parser.add_argument(
+        "--columns",
+        default=[],
+        type=list_of_strings,
+        help="A comma separated list of columns from the input that should "
+        + "be added to the output. (e.g.: col1,col2,col3)",
+    )
     test_parser.add_argument(
         "--min-confidence",
         type=float,

synrbl/SynMCSImputer/SubStructure/mcs_graph_detector.py

@@ -201,7 +201,7 @@ def fit(
 
         if method == "MCIS":
             params = rdFMCS.MCSParameters()
-            params.Timeout = Timeout
+            params.Timeout = 1 # Timeout
             params.BondCompareParameters.RingMatchesRingOnly = RingMatchesRingOnly
             params.BondCompareParameters.CompleteRingsOnly = CompleteRingsOnly
             if ignore_bond_order:
@@ -213,7 +213,7 @@ def fit(
             params = rdRascalMCES.RascalOptions()
             params.singleLargestFrag = False
             params.returnEmptyMCES = True
-            params.timeout = Timeout
+            params.timeout = 1 # Timeout
             params.similarityThreshold = similarityThreshold
 
         else: