diff --git a/synrbl/SynMCSImputer/SubStructure/mcs_graph_detector.py b/synrbl/SynMCSImputer/SubStructure/mcs_graph_detector.py index 98345fb..7c429b5 100644 --- 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 index 4774cf9..6b63dab 100644 --- 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 index 8111efe..6a036a3 100644 --- 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)