Merge pull request #15 from TieuLongPhan/main

v0.0.5

.gitignore

@@ -1,18 +1,168 @@
 .DS_Store
 *.pyc
 .vscode
-
-.DS_Store
 .jukit/
-
-
-venv/
 *.pdf
-.coverage
 tmp/
 out/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
 dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
 
-Data/Validation_set/validation_set_result.csv
-Data/Run/
+# Cython debug symbols
+cython_debug/
 
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

Docs/Paper_fig/figures.py

@@ -1,8 +1,8 @@
 import matplotlib.pyplot as plt
 
-from SynRBL.SynVis import ReactionVisualizer
-from SynRBL.rsmi_utils import load_database
-from SynRBL.SynUtils.chem_utils import remove_atom_mapping
+from synrbl.SynVis import ReactionVisualizer
+from synrbl.rsmi_utils import load_database
+from synrbl.SynUtils.chem_utils import remove_atom_mapping
 
 
 def clear_atom_nums(dataset):

README.md

@@ -90,13 +90,13 @@ To install and set up the SynRBL framework, follow these steps. Please ensure yo
   After installation, you can verify that SynRBL is correctly installed by running a simple test or checking the package version.
 
   ```python
-  python -c "import SynRBL; print(SynRBL.__version__)"
+  python -c "import synrbl; print(synrbl.__version__)"
   ```
 
 ## Usage
 
   ```python
-  from SynRBL import SynRBL
+  from synrbl import Balancer
   ```
 
 

Scripts/result_evaluation.py

@@ -6,9 +6,9 @@
 import rdkit.Chem.rdChemReactions as rdChemReactions
 import rdkit.Chem.Draw.rdMolDraw2D as rdMolDraw2D
 from PIL import Image
-from SynRBL.SynUtils.chem_utils import normalize_smiles, remove_atom_mapping
+from synrbl.SynUtils.chem_utils import normalize_smiles, remove_atom_mapping
 
-import Scripts.validation_set_interface as db
+import scripts.validation_set_interface as db
 
 
 def get_reaction_img(smiles):

synrbl_pilot.py → Scripts/synrbl_pilot.py

@@ -3,8 +3,8 @@
 import os
 import logging
 import traceback
-from SynRBL import Balancer
-from SynRBL.rsmi_utils import load_database, save_database
+from synrbl import Balancer
+from synrbl.rsmi_utils import load_database, save_database
 
 
 def setup_logging(log_file=None):

Scripts/validation_set_interface.py

@@ -2,7 +2,7 @@
 import json
 import pandas as pd
 
-from SynRBL.SynUtils.chem_utils import normalize_smiles
+from synrbl.SynUtils.chem_utils import normalize_smiles
 
 _FILE_NAME = "dataset"
 

Test/SynChemImputer/test_appeal_reaction.py

@@ -1,6 +1,6 @@
 import unittest
 
-from SynRBL.SynChemImputer.appel_reaction import (
+from synrbl.SynChemImputer.appel_reaction import (
     AppelReaction,
 )  # Make sure to import your class correctly
 

Test/SynChemImputer/test_peroxide_imputer.py

@@ -1,6 +1,6 @@
 import unittest
 
-from SynRBL.SynChemImputer.peroxide_imputer import (
+from synrbl.SynChemImputer.peroxide_imputer import (
     PeroxidGroupImputer,
 )  # Replace with the actual module name
 

Test/SynMCSImputer/MissingGraph/test_find_graph_dict.py

@@ -1,6 +1,6 @@
 import unittest
 from rdkit import Chem
-from SynRBL.SynMCSImputer.MissingGraph.find_graph_dict import (
+from synrbl.SynMCSImputer.MissingGraph.find_graph_dict import (
     find_single_graph,
     find_single_graph_parallel,
     convert_smiles_to_mols,

Test/SynMCSImputer/MissingGraph/test_find_missing_graphs.py

@@ -2,8 +2,8 @@
 import copy
 
 from rdkit import Chem
-from SynRBL.SynMCSImputer.SubStructure.substructure_analyzer import SubstructureAnalyzer
-from SynRBL.SynMCSImputer.MissingGraph.find_missing_graphs import FindMissingGraphs
+from synrbl.SynMCSImputer.SubStructure.substructure_analyzer import SubstructureAnalyzer
+from synrbl.SynMCSImputer.MissingGraph.find_missing_graphs import FindMissingGraphs
 
 
 class TestFindMissingGraphs(unittest.TestCase):

Test/SynMCSImputer/MissingGraph/test_molcurator.py

@@ -1,7 +1,7 @@
 import unittest
 from rdkit import Chem
 
-from SynRBL.SynMCSImputer.MissingGraph.molcurator import MoleculeCurator
+from synrbl.SynMCSImputer.MissingGraph.molcurator import MoleculeCurator
 
 
 class TestMoleculeCurator(unittest.TestCase):

Test/SynMCSImputer/MissingGraph/test_uncertainty_graph.py

@@ -1,6 +1,6 @@
 import unittest
 
-from SynRBL.SynMCSImputer.MissingGraph.uncertainty_graph import GraphMissingUncertainty
+from synrbl.SynMCSImputer.MissingGraph.uncertainty_graph import GraphMissingUncertainty
 
 
 class TestGraphMissingUncertainty(unittest.TestCase):

Test/SynMCSImputer/SubStructure/test_extract_common_mcs.py

@@ -1,6 +1,6 @@
 import unittest
 
-from SynRBL.SynMCSImputer.SubStructure.extract_common_mcs import ExtractMCS
+from synrbl.SynMCSImputer.SubStructure.extract_common_mcs import ExtractMCS
 
 
 class TestExtractMCS(unittest.TestCase):

Test/SynMCSImputer/SubStructure/test_mcs_graph_detector.py

@@ -2,7 +2,7 @@
 
 from rdkit import Chem
 
-from SynRBL.SynMCSImputer.SubStructure.mcs_graph_detector import MCSMissingGraphAnalyzer
+from synrbl.SynMCSImputer.SubStructure.mcs_graph_detector import MCSMissingGraphAnalyzer
 
 
 class TestMCSMissingGraphAnalyzer(unittest.TestCase):

Test/SynMCSImputer/SubStructure/test_mcs_process.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from unittest.mock import patch
-from SynRBL.SynMCSImputer.SubStructure.mcs_process import single_mcs
+from synrbl.SynMCSImputer.SubStructure.mcs_process import single_mcs
 
 
 class TestMCSFunctions(unittest.TestCase):
@@ -26,7 +26,7 @@ def setUp(self):
         ]
 
     @patch(
-        "SynRBL.SynMCSImputer.SubStructure.mcs_graph_detector.MCSMissingGraphAnalyzer.fit"
+        "synrbl.SynMCSImputer.SubStructure.mcs_graph_detector.MCSMissingGraphAnalyzer.fit"
     )
     def test_single_mcs(self, mock_fit):
         # Mocking MCSMissingGraphAnalyzer.fit to return predefined values

Test/SynMCSImputer/SubStructure/test_substructure_analyzer.py

@@ -1,6 +1,6 @@
 import unittest
 
-from SynRBL.SynMCSImputer.SubStructure.substructure_analyzer import SubstructureAnalyzer
+from synrbl.SynMCSImputer.SubStructure.substructure_analyzer import SubstructureAnalyzer
 from rdkit import Chem
 
 

Test/SynMCSImputer/test_merge.py

@@ -1,8 +1,8 @@
 import unittest
 import unittest.mock as mock
 
-import SynRBL.SynMCSImputer.merge as merge
-from SynRBL.SynMCSImputer.structure import Compound, CompoundSet
+import synrbl.SynMCSImputer.merge as merge
+from synrbl.SynMCSImputer.structure import Compound, CompoundSet
 
 
 class DummyMergeRule:
@@ -28,7 +28,7 @@ def apply(self):
 
 
 class TestMergeBoundary(unittest.TestCase):
-    @mock.patch("SynRBL.SynMCSImputer.merge.MergeRule")
+    @mock.patch("synrbl.SynMCSImputer.merge.MergeRule")
     def test_no_rule_found(self, m_MergeRule):
         rule = mock.MagicMock()
         rule.can_apply.return_value = False
@@ -89,7 +89,7 @@ def test_phosphor_bond3(self):
 
 
 class TestExpansion(unittest.TestCase):
-    @mock.patch("SynRBL.SynMCSImputer.merge.ExpandRule")
+    @mock.patch("synrbl.SynMCSImputer.merge.ExpandRule")
     def test_simple_expansion(self, m_ExpandRule):
         m_ExpandRule.get_all = mock.MagicMock(return_value=[DummyExpandRule()])
         c = Compound("C")
@@ -98,7 +98,7 @@ def test_simple_expansion(self, m_ExpandRule):
         self.assertEqual("O", cm.smiles)  # type: ignore
         self.assertEqual(1, len(cm.boundaries))  # type: ignore
 
-    @mock.patch("SynRBL.SynMCSImputer.merge.ExpandRule")
+    @mock.patch("synrbl.SynMCSImputer.merge.ExpandRule")
     def test_rule_apply_check(self, m_ExpandRule):
         m_ExpandRule.get_all = mock.MagicMock(
             return_value=[