Python
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CDPKit - CONFORT: High-Quality Conformer Generation (standalone).
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Chython: Library for processing molecules and reactions in python way.
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ODDT: Open Drug Discovery Toolkit, toolkit for drug discovery (standalone)
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OpenBabel: toolkit for drug discovery, file format etc (standalone)
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RDKit: Scopy: an integrated negative design python library for desirable HTS/VS database design
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cinfony:
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rdkit-scripts: rdkit scripts making life easier (standalone)