Merging branch before publication (#5)

* fix bug * change rule writing format Mg++ to Mg2+ * update uncertain hydrogen handling * fix * update source * update source * clean repo * clean notebook * clean notebook
TieuLongPhan · Sep 17, 2024 · b609e33 · b609e33
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diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,6 @@
 *.gml
 .pytest_cache
 __pycache__
-*pdf
 
 
 *.tar.gz

diff --git a/Data/AAM/balance/aam_processing.log b/Data/AAM/balance/aam_processing.log
diff --git a/Data/AAM/balance/ecoli/ecoli_aam_reactions.json.gz b/Data/AAM/balance/ecoli/ecoli_aam_reactions.json.gz
diff --git a/Data/AAM/balance/ecoli/ecoli_reactions.json.gz b/Data/AAM/balance/ecoli/ecoli_reactions.json.gz
diff --git a/Data/AAM/balance/ecoli_reactions.json.gz b/Data/AAM/balance/ecoli_reactions.json.gz
diff --git a/Data/AAM/balance/golden/golden_aam_reactions.json.gz b/Data/AAM/balance/golden/golden_aam_reactions.json.gz
diff --git a/Data/AAM/balance/golden/golden_reactions.json.gz b/Data/AAM/balance/golden/golden_reactions.json.gz
diff --git a/Data/AAM/balance/golden_reactions.json.gz b/Data/AAM/balance/golden_reactions.json.gz
diff --git a/Data/AAM/balance/mapping_times.csv b/Data/AAM/balance/mapping_times.csv
diff --git a/Data/AAM/balance/natcomm/natcomm_aam_reactions.json.gz b/Data/AAM/balance/natcomm/natcomm_aam_reactions.json.gz
diff --git a/Data/AAM/balance/natcomm/natcomm_reactions.json.gz b/Data/AAM/balance/natcomm/natcomm_reactions.json.gz
diff --git a/Data/AAM/balance/natcomm_reactions.json.gz b/Data/AAM/balance/natcomm_reactions.json.gz
diff --git a/Data/AAM/balance/recon3d/recon3d_aam_reactions.json.gz b/Data/AAM/balance/recon3d/recon3d_aam_reactions.json.gz
diff --git a/Data/AAM/balance/recon3d/recon3d_reactions.json.gz b/Data/AAM/balance/recon3d/recon3d_reactions.json.gz
diff --git a/Data/AAM/balance/recon3d_reactions.json.gz b/Data/AAM/balance/recon3d_reactions.json.gz
diff --git a/Data/AAM/balance/uspto_3k/uspto_3k_aam_reactions.json.gz b/Data/AAM/balance/uspto_3k/uspto_3k_aam_reactions.json.gz
diff --git a/Data/AAM/balance/uspto_3k/uspto_3k_reactions.json.gz b/Data/AAM/balance/uspto_3k/uspto_3k_reactions.json.gz
diff --git a/Data/AAM/balance/uspto_3k_reactions.json.gz b/Data/AAM/balance/uspto_3k_reactions.json.gz
diff --git a/Data/AAM/unbalance/aam_processing.log → .../AAM/results_benchmark/aam_processing.log b/Data/AAM/unbalance/aam_processing.log → .../AAM/results_benchmark/aam_processing.log
diff --git a/...M/unbalance/ecoli/ecoli_aam_reactions.csv → ...s_benchmark/ecoli/ecoli_aam_reactions.csv b/...M/unbalance/ecoli/ecoli_aam_reactions.csv → ...s_benchmark/ecoli/ecoli_aam_reactions.csv
diff --git a/Data/AAM/unbalance/golden/golden.csv → Data/AAM/results_benchmark/golden/golden.csv b/Data/AAM/unbalance/golden/golden.csv → Data/AAM/results_benchmark/golden/golden.csv
diff --git a/Data/AAM/unbalance/mapping_times.csv → Data/AAM/results_benchmark/mapping_times.csv b/Data/AAM/unbalance/mapping_times.csv → Data/AAM/results_benchmark/mapping_times.csv
diff --git a/Data/AAM/unbalance/natcomm/natcomm.csv → ...AAM/results_benchmark/natcomm/natcomm.csv b/Data/AAM/unbalance/natcomm/natcomm.csv → ...AAM/results_benchmark/natcomm/natcomm.csv
diff --git a/...balance/recon3d/Recon3D_aam_reactions.csv → ...nchmark/recon3d/Recon3D_aam_reactions.csv b/...balance/recon3d/Recon3D_aam_reactions.csv → ...nchmark/recon3d/Recon3D_aam_reactions.csv
diff --git a/Data/AAM/unbalance/uspto_3k/uspto_3k.csv → ...M/results_benchmark/uspto_3k/uspto_3k.csv b/Data/AAM/unbalance/uspto_3k/uspto_3k.csv → ...M/results_benchmark/uspto_3k/uspto_3k.csv
diff --git a/Data/AAM/unbalance/aam_benchmark.json.gz b/Data/AAM/unbalance/aam_benchmark.json.gz
diff --git a/Data/AAM/unbalance/ecoli/ecoli_aam_reactions.json.gz b/Data/AAM/unbalance/ecoli/ecoli_aam_reactions.json.gz
diff --git a/Data/AAM/unbalance/ecoli/ecoli_reactions.json.gz b/Data/AAM/unbalance/ecoli/ecoli_reactions.json.gz
diff --git a/Data/AAM/unbalance/golden/golden_aam_reactions.json.gz b/Data/AAM/unbalance/golden/golden_aam_reactions.json.gz
diff --git a/Data/AAM/unbalance/golden/golden_aam_reactions_old.json.gz b/Data/AAM/unbalance/golden/golden_aam_reactions_old.json.gz
diff --git a/Data/AAM/unbalance/golden/golden_reactions.json.gz b/Data/AAM/unbalance/golden/golden_reactions.json.gz
diff --git a/Data/AAM/unbalance/natcomm/natcomm_aam_reactions.json.gz b/Data/AAM/unbalance/natcomm/natcomm_aam_reactions.json.gz
diff --git a/Data/AAM/unbalance/natcomm/natcomm_reactions.json.gz b/Data/AAM/unbalance/natcomm/natcomm_reactions.json.gz
diff --git a/Data/AAM/unbalance/recon3d/recon3d_aam_reactions.json.gz b/Data/AAM/unbalance/recon3d/recon3d_aam_reactions.json.gz
diff --git a/Data/AAM/unbalance/recon3d/recon3d_reactions.json.gz b/Data/AAM/unbalance/recon3d/recon3d_reactions.json.gz
diff --git a/Data/AAM/unbalance/uspto_3k/uspto_3k_aam_reactions.json.gz b/Data/AAM/unbalance/uspto_3k/uspto_3k_aam_reactions.json.gz
diff --git a/Data/AAM/unbalance/uspto_3k/uspto_3k_reactions.json.gz b/Data/AAM/unbalance/uspto_3k/uspto_3k_reactions.json.gz
diff --git a/Data/Temp/Benchmark/raw_results.json b/Data/Temp/Benchmark/raw_results.json
@@ -2,24 +2,24 @@
     "Valid": {
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@@ -41,47 +41,48 @@
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@@ -103,25 +104,151 @@
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     }
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,6 @@ @@
     *.gml
     .pytest_cache
     __pycache__
-    *pdf
     *.tar.gz
@@ Expand Down @@