initial commit

.gitignore

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+# secrets detector
+.secrets.baseline
+
+# mac files
+.DS_Store
+
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+__pycache__/
+*.py[cod]
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+
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+docs_source/_modules/
+
+.vscode

DOCUMENTATION.md

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+# Documentation
+
+## Development instructions
+
+Documentation can be automatically generated with Sphinx.
+
+Make sure the dependencies are installed:
+
+```console
+pip install -r dev_requirements.txt
+```
+
+Afterwards, compile the documentation in the preferred format:
+
+```console
+cd docs_source/
+sh generate_modules_rst.sh
+# html
+make html
+# latex
+make latex
+make latexpdf
+# GitHub pages
+make github
+```

LICENSE

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+Copyright 2020 RXN for Chemistry team.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MANIFEST.in

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+include rxnmapper/models/transformers/*

README.md

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+# Unsupervised attention-guided atom-mapping
+
+## Install
+
+```console
+conda create -n rxnmapper python=3.6 -y
+conda activate rxnmapper
+conda install -c rdkit rdkit
+pip install git+https://github.ibm.com/PHS/rxnmapper.git
+```
+
+## For development
+You can install the environment for local development using the following:
+
+```console
+conda env create -f environment.yml
+conda activate rxnmapper
+pip install -e .
+pip install -r requirements.txt
+```
+
+## Usage
+
+### Basic usage
+
+```
+from rxnmapper import RXNMapper
+rxn_mapper = RXNMapper()
+rxns = ['CC(C)S.CN(C)C=O.Fc1cccnc1F.O=C([O-])[O-].[K+].[K+]>>CC(C)Sc1ncccc1F', 'C1COCCO1.CC(C)(C)OC(=O)CONC(=O)NCc1cccc2ccccc12.Cl>>O=C(O)CONC(=O)NCc1cccc2ccccc12']
+results = rxn_mapper.get_attention_guided_atom_maps(rxns)
+```
+The results contain the mapped reactions and confidence scores:
+```
+[{'mapped_rxn': 'CN(C)C=O.F[c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11].O=C([O-])[O-].[CH3:1][CH:2]([CH3:3])[SH:4].[K+].[K+]>>[CH3:1][CH:2]([CH3:3])[S:4][c:5]1[n:6][cH:7][cH:8][cH:9][c:10]1[F:11]',
+  'confidence': 0.9565619900376546},
+ {'mapped_rxn': 'C1COCCO1.CC(C)(C)[O:3][C:2](=[O:1])[CH2:4][O:5][NH:6][C:7](=[O:8])[NH:9][CH2:10][c:11]1[cH:12][cH:13][cH:14][c:15]2[cH:16][cH:17][cH:18][cH:19][c:20]12.Cl>>[O:1]=[C:2]([OH:3])[CH2:4][O:5][NH:6][C:7](=[O:8])[NH:9][CH2:10][c:11]1[cH:12][cH:13][cH:14][c:15]2[cH:16][cH:17][cH:18][cH:19][c:20]12',
+  'confidence': 0.9704424331552834}]
+```
+
+### Testing
+
+You can run the examples above with the test suite as well:
+
+1. `pip install -r dev_requirements.txt` 
+2. `pytest tests` from the root 
+
+## Examples
+
+To learn more see the [examples](./examples).
+

dev_requirements.txt

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+yapf==0.29.0
+flake8==3.7.9
+sphinx==2.2.1
+sphinx-rtd-theme==0.4.3
+twine==3.1.1
+pytest>=5.4.1