Update GuacaMol binding to work single threaded with default GuacaMol…

… implementation

evomol/guacamol_binding.py

@@ -138,23 +138,23 @@ def _get_benchmark_name(self, curr_benchmark_id):
         return benchmark_names_list[curr_benchmark_id]
 
     def generate_optimized_molecules(self, scoring_function: ScoringFunction, number_molecules: int,
-                                     starting_population: Optional[List[str]] = None, name=None) -> List[str]:
+                                     starting_population: Optional[List[str]] = None) -> List[str]:
 
         instance = self.pop_alg.copy_instance_with_parameters()
 
         # Updating benchmark id
         self.curr_benchmark_id += 1
 
         # Extracting benchmark name
-        # curr_benchmark_name = self._get_benchmark_name(self.curr_benchmark_id)
+        curr_benchmark_name = self._get_benchmark_name(self.curr_benchmark_id)
 
         # Setting folder to save the results
-        # instance.output_folder_path = join(self.output_save_path, curr_benchmark_name)
-        instance.output_folder_path = join(self.output_save_path, name)
+        instance.output_folder_path = join(self.output_save_path, curr_benchmark_name)
+        # instance.output_folder_path = join(self.output_save_path, name)
 
         # Extracting GuacaMol evaluation function
-        guacamol_evaluation_strategy = GuacamolEvaluationStrategy(scoring_function, name)
-        # guacamol_evaluation_strategy = GuacamolEvaluationStrategy(scoring_function, curr_benchmark_name)
+        # guacamol_evaluation_strategy = GuacamolEvaluationStrategy(scoring_function, name)
+        guacamol_evaluation_strategy = GuacamolEvaluationStrategy(scoring_function, curr_benchmark_name)
 
         # Merging the evaluation strategy of the PopAlg instance to the GuacaMol objective
         if isinstance(instance.evaluation_strategy, UndefinedGuacaMolEvaluationStrategy):
@@ -166,8 +166,8 @@ def generate_optimized_molecules(self, scoring_function: ScoringFunction, number
         instance.mutation_strategy.evaluation_strategy = instance.evaluation_strategy
 
         # Setting additional stop criterion, stopping the execution when best possible score is obtained
-        # instance.kth_score_to_record_key = curr_benchmark_name
-        instance.kth_score_to_record_key = name
+        instance.kth_score_to_record_key = curr_benchmark_name
+        # instance.kth_score_to_record_key = name
         additional_stop_criterion = KthScoreMaxValue(1, round=3)
         instance.stop_criterion_strategy.set_additional_strategy(additional_stop_criterion)
         instance.stop_criterion_strategy.set_pop_alg_instance(instance)

evomol/test/1_test_evaluation_functions/0_qed/errors.csv

@@ -1,6 +1,13 @@
 step,error
 0,No more individual to be mutated
+7,No improver found
 8,No improver found
+8,No improver found
+8,No improver found
+8,No improver found
+9,No improver found
+9,No improver found
+9,No improver found
 9,No improver found
 9,No improver found
 9,No improver found
@@ -12,9 +19,13 @@ step,error
 10,No improver found
 10,No improver found
 10,No improver found
+10,No improver found
+11,No improver found
+11,No improver found
+11,No improver found
+11,No improver found
 11,No improver found
 11,No improver found
-12,No improver found
 12,No improver found
 12,No improver found
 13,No improver found

evomol/test/1_test_evaluation_functions/0_qed/pop.csv

@@ -1,11 +1,11 @@
 smiles,n_success_mut,n_failures_mut,qed,total,history_data
-CC(P)CC1(P)CCNCC(P)OC1C(F)P,0,0,0.8041986616768374,0.8041986616768374,C
-CC(P)CC1(P)C(C(F)P)CCNN1P,0,0,0.7991116063365711,0.7991116063365711,
-CC(P)CC1(P)C(P)NCCCC1C(F)P,3,0,0.7902886802816198,0.7902886802816198,
-CC(P)CC1(C(F)PP)CCCNN(P)C1,0,0,0.8034416419846797,0.8034416419846797,
-CC(P)CC1(C(F)P)CCCNN(P)C1P,2,0,0.8054178782221852,0.8054178782221852,
-CC(P)CC1C(C(F)PP)CCCNN1P,0,0,0.803440939217587,0.803440939217587,
-CC(P)CC1(C(P)CF)CCCNN(P)C1P,0,0,0.8016037613062327,0.8016037613062327,
-CC(P)CC1(P)CNCC(P)OC1C(F)P,1,0,0.8000467663981665,0.8000467663981665,
-CC(P)CC1(P)C(C(F)CP)CCCNN1P,0,0,0.8016037613062327,0.8016037613062327,
-CC(P)CC1(P)C(C(F)P)CCCNN1P,4,0,0.8054178782221852,0.8054178782221852,
+CC1CC2COCC1C2C1(CC(O)CP)PC1F,3,0,0.8054397332661329,0.8054397332661329,C
+OCCC1(C(CP)C2CCCCOC2)PC1F,4,0,0.7836245688754945,0.7836245688754945,
+CC1COCCC(C2(CC(O)CP)CP2)C1,0,0,0.7862322704733017,0.7862322704733017,
+CC1(C2(CC(O)CP)PC2F)C2CCC1COC2,0,0,0.8063275495325761,0.8063275495325761,
+OC(CP)CC1(C2CC3CCC2COC3)PC1F,1,0,0.806327549532576,0.806327549532576,
+CC(O)C1(C2C3COCC2C(C)(P)C3)PC1F,0,0,0.7829783965622259,0.7829783965622259,
+OCCC1(C(CP)C2CCCCCOC2)PC1F,1,0,0.7901287439413213,0.7901287439413213,
+OC(CP)CC1(C2C3CCC2COC3)PC1F,3,0,0.7971491942494499,0.7971491942494499,
+OCCC1CCCCOCC1C(OP)C1PC1F,0,0,0.7914549818740849,0.7914549818740849,
+OCCC1CC(F)CCOCC1C(CP)C1PC1F,1,0,0.7908670554197845,0.7908670554197845,