aamutils 0.0.1__tar.gz → 0.0.3__tar.gz

{aamutils-0.0.1 → aamutils-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: aamutils
-Version: 0.0.1
+Version: 0.0.3
 Summary: Collection of atom-atom-mapping utility functions.
 Project-URL: homepage, https://github.com/klausweinbauer/AAMUtils
 Project-URL: source, https://github.com/klausweinbauer/AAMUtils
@@ -26,7 +26,12 @@ A collection of atom-atom-mapping utility functions.
 
 ## Installation
 
-TODO
+The easiest way to use AAMUtils is by installing the PyPI package
+[aamutils](https://pypi.org/project/aamutils/).
+
+```
+pip install aamutils
+```
 
 ## Usage
 
@@ -43,7 +48,7 @@ echo "CCC[Cl:1].[N:2]>>CCC[N:2].[Cl:1]" > testinput.txt
 Next, run AAMUtils to expand the partial AAM. 
 
 ```bash 
-python3 ./aamutils/__main__.py expand testinput.txt
+python3 -m aamutils expand testinput.txt
 ```
 
 The output is written to 'testinput_extended.json'. 
@@ -56,17 +61,40 @@ cat testinput_extended.json
 [
     {
         "input": "CCC[Cl:1].[N:2]>>CCC[N:2].[Cl:1]",
-        "expanded_aam": "[Cl:1][CH2:5][CH2:4][CH3:3].[NH3:2]>>[ClH:1].[NH2:2][CH2:5][CH2:4][CH3:3]",
+        "expanded_aam": "[Cl:1][CH2:5][CH2:4][CH3:3].[NH3:2]>>[ClH:1].[NH2:2][CH2:3][CH2:4][CH3:5]",
         "ilp_status": "Optimal",
-        "optimization_result": 2.0,
+        "optimization_result": 4.0,
         "invalid_reaction_center": false,
-        "reaction_edges": 3
+        "reaction_edges": 4
     }
 ]
 ```
 
+## Benchmark
+
+To rerun the benchmarks from the paper use the ``benchmark.py`` script. The
+reported results can be reproduced by running the following commands:
+
+### (1) Extend partial reaction center (50%, 75% and 100% missing atoms)  
+
+```
+python3 benchmark.py --remove-mode rc --remove-ratio 0.5
+```
+```
+python3 benchmark.py --remove-mode rc --remove-ratio 0.75
+```
+```
+python3 benchmark.py --remove-mode rc --remove-ratio 1
+```
+
+### (2) Extend partial AAM with fully mapped RC 
+```
+python3 benchmark.py --remove-mode keep_rc --remove-ratio 1
+```
+
+
 ## Functionality
-Here is an overview of implemented functionallity:
+Here is an overview of implemented functionality:
 
 - SMILES to graph and graph to SMILES parsing
 - Reaction center validity checks

{aamutils-0.0.1 → aamutils-0.0.3}/README.md

@@ -4,7 +4,12 @@ A collection of atom-atom-mapping utility functions.
 
 ## Installation
 
-TODO
+The easiest way to use AAMUtils is by installing the PyPI package
+[aamutils](https://pypi.org/project/aamutils/).
+
+```
+pip install aamutils
+```
 
 ## Usage
 
@@ -21,7 +26,7 @@ echo "CCC[Cl:1].[N:2]>>CCC[N:2].[Cl:1]" > testinput.txt
 Next, run AAMUtils to expand the partial AAM. 
 
 ```bash 
-python3 ./aamutils/__main__.py expand testinput.txt
+python3 -m aamutils expand testinput.txt
 ```
 
 The output is written to 'testinput_extended.json'. 
@@ -34,17 +39,40 @@ cat testinput_extended.json
 [
     {
         "input": "CCC[Cl:1].[N:2]>>CCC[N:2].[Cl:1]",
-        "expanded_aam": "[Cl:1][CH2:5][CH2:4][CH3:3].[NH3:2]>>[ClH:1].[NH2:2][CH2:5][CH2:4][CH3:3]",
+        "expanded_aam": "[Cl:1][CH2:5][CH2:4][CH3:3].[NH3:2]>>[ClH:1].[NH2:2][CH2:3][CH2:4][CH3:5]",
         "ilp_status": "Optimal",
-        "optimization_result": 2.0,
+        "optimization_result": 4.0,
         "invalid_reaction_center": false,
-        "reaction_edges": 3
+        "reaction_edges": 4
     }
 ]
 ```
 
+## Benchmark
+
+To rerun the benchmarks from the paper use the ``benchmark.py`` script. The
+reported results can be reproduced by running the following commands:
+
+### (1) Extend partial reaction center (50%, 75% and 100% missing atoms)  
+
+```
+python3 benchmark.py --remove-mode rc --remove-ratio 0.5
+```
+```
+python3 benchmark.py --remove-mode rc --remove-ratio 0.75
+```
+```
+python3 benchmark.py --remove-mode rc --remove-ratio 1
+```
+
+### (2) Extend partial AAM with fully mapped RC 
+```
+python3 benchmark.py --remove-mode keep_rc --remove-ratio 1
+```
+
+
 ## Functionality
-Here is an overview of implemented functionallity:
+Here is an overview of implemented functionality:
 
 - SMILES to graph and graph to SMILES parsing
 - Reaction center validity checks

{aamutils-0.0.1 → aamutils-0.0.3}/aamutils/__main__.py

@@ -15,4 +15,7 @@ if __name__ == "__main__":
 
     parser = setup_argparser()
     args = parser.parse_args()
-    args.func(args)
+    try:
+        args.func(args)
+    except Exception:
+        parser.print_help()

{aamutils-0.0.1 → aamutils-0.0.3}/aamutils/cmd/expanding.py

@@ -4,9 +4,9 @@ import logging
 import rdkit.Chem.rdmolfiles as rdmolfiles
 import rdkit.Chem.rdmolops as rdmolops
 
-from utils import mol_to_graph, set_aam, graph_to_mol, is_valid_rxn_smiles
-from algorithm.ilp import expand_partial_aam_balanced
-from algorithm.aaming import get_its, get_rc, is_rc_valid
+from aamutils.utils import mol_to_graph, set_aam, graph_to_mol, is_valid_rxn_smiles
+from aamutils.algorithm.ilp import expand_partial_aam_balanced
+from aamutils.algorithm.aaming import get_its, get_rc, is_rc_valid
 
 logger = logging.getLogger("aamutils")
 

aamutils-0.0.1/benchmarking.py → aamutils-0.0.3/benchmark.py

@@ -50,7 +50,9 @@ def load_data():
     return data
 
 
-def run(n, remove_mode, remove_ratio):
+def run(n, remove_mode, remove_ratio, seed=None):
+    if seed is not None:
+        random.seed(seed)
     data = load_data()
     testcase_cnt = 0
     success_cnt = 0
@@ -136,6 +138,7 @@ if __name__ == "__main__":
     default_rm_mode = "rc"
     default_rm_ratio = 0.5
     default_n = 1000
+    default_seed = None
 
     parser = argparse.ArgumentParser(
         prog="benchmarks.py",
@@ -171,6 +174,13 @@ if __name__ == "__main__":
             + " Default: {}"
         ).format(default_rm_ratio),
     )
+    parser.add_argument(
+        "--seed",
+        default=default_seed,
+        help=(
+            "The seed used to initialize random number generation. " + "Default: {}"
+        ).format(default_seed),
+    )
 
     args = parser.parse_args()
-    run(args.n, args.remove_mode, args.remove_ratio)
+    run(args.n, args.remove_mode, args.remove_ratio, args.seed)

{aamutils-0.0.1 → aamutils-0.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "aamutils"
-version = "0.0.1"
+version = "0.0.3"
 authors = [
 	{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}
 	]