update timeout arg

TieuLongPhan · Apr 29, 2024 · ac399ed · ac399ed
1 parent d78f1a1
commit ac399ed
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Showing 3 changed files with 7 additions and 10 deletions.
diff --git a/synrbl/SynMCSImputer/SubStructure/mcs_graph_detector.py b/synrbl/SynMCSImputer/SubStructure/mcs_graph_detector.py
@@ -174,7 +174,7 @@ def fit(
         reaction_dict,
         RingMatchesRingOnly=True,
         CompleteRingsOnly=True,
-        Timeout=60,
+        timeout=1,
         similarityThreshold=0.5,
         sort="MCIS",
         method="MCIS",
@@ -201,7 +201,7 @@ def fit(
 
         if method == "MCIS":
             params = rdFMCS.MCSParameters()
-            params.Timeout = 1  # Timeout
+            params.Timeout = 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 = 1  # Timeout
+            params.timeout = timeout
             params.similarityThreshold = similarityThreshold
 
         else:

diff --git a/synrbl/SynMCSImputer/SubStructure/mcs_process.py b/synrbl/SynMCSImputer/SubStructure/mcs_process.py
@@ -18,7 +18,7 @@ def single_mcs(
     issue_col="issue",
     RingMatchesRingOnly=True,
     CompleteRingsOnly=True,
-    Timeout=60,
+    timeout=1,
     sort="MCES",
     method="MCES",
     similarityThreshold=0.5,
@@ -52,7 +52,7 @@ def single_mcs(
             sort=sort,
             method=method,
             remove_substructure=remove_substructure,
-            Timeout=Timeout,
+            timeout=timeout,
             similarityThreshold=similarityThreshold,
             ignore_bond_order=ignore_bond_order,
         )
@@ -71,9 +71,7 @@ def single_mcs(
     return mcs_data
 
 
-def ensemble_mcs(
-    data, conditions, id_col="id", issue_col="issue", n_jobs=-1, Timeout=60
-):
+def ensemble_mcs(data, conditions, id_col="id", issue_col="issue", n_jobs=-1, timeout=1):
     condition_results = []
     start_time = time.time()
     last_tsmp = start_time
@@ -86,7 +84,7 @@ def ensemble_mcs(
                 id_col=id_col,
                 issue_col=issue_col,
                 **condition,
-                Timeout=Timeout,
+                timeout=timeout,
             )
             for data_dict in data
         )

diff --git a/synrbl/mcs_search.py b/synrbl/mcs_search.py
@@ -80,7 +80,6 @@ def find(self, reactions):
             id_col=self.id_col,
             issue_col=self.issue_col,
             n_jobs=self.n_jobs,
-            Timeout=60,
         )
 
         largest_conditions = ExtractMCS.get_largest_condition(*condition_results)