Polymerist

Latest version: v0.1.5rc1

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0.1.5rc1

Minor feature cleanup and improvements to kekulization handling and chemical database query services
* Greatly expanded robustness of smileslib.chemdbqueries:
* Reimplemented core via Strategy pattern and provided concrete implementations for
* [NIH CACTUS CIR](https://cactus.nci.nih.gov/chemical/structure)
* [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
* Added capability to check is services are online prior to attempting query
* Compiled comprehensive lists of queryable chemical properties and namespaces for each implementations
* Added service-agnostic get_chemical_property() wrapper for convenience
*Provided greater control over Kekulization in RDKit-derived functionality
* Added enable_kekulized_drawing() and disble_kekulized_drawing() config methods to rdutils.rdkdraw
-* Made rdkdraw imported at toplevel rdutils
* Added flag to disable Kekulization in SMILES string expansion (polymers.monomers.specification.expanded_SMILES(...))
* Added procrustean_string(...) function to genutils.textual.prettyprint (related to PROCRUSTES algorithm implemented in .polymers for copolymer sequencing)

0.1.4rc1

Minor fixes to README and optional dependencies

What's changed
* Fixed issue with accidental file redirect in NAGL install command in README
* Corrected typos in README
* Added missing `pubchempy` requirement to "chemdb" optional dependency category

0.1.3rc1

Overhaul of README and improvements to dependency management

What's changed
* Front-facing README completely rewritten to provide:
* Details on compatible OS and package managers
* More specific installation instruction
* Pip-compatible installation instructions
* Details on installing peripheral AM1-BCC toolkits
* Simplified dependencies
* Espaloma_charge is no longer required OR optional in pyproject.toml
* espaloma_charge dependency in release-build.yml changed from pip-based to conda-based
* Pre-import checks for [cirpy](https://cirpy.readthedocs.io/en/latest/) and [pubchempy](https://pubchempy.readthedocs.io/en/latest/) added to [smileslib.chemdbqueries](https://github.com/timbernat/polymerist/blob/main/polymerist/smileslib/chemdbqueries.py)
* Fixed str.capitalize() call in use_case arg to MissingPrerequisitePackage, as this was causing unintended lowercasing later in the string
* Former "jupyter" and "visuals" optional dependency categories consolidated into single "interactive" category
* Made "rich" a required dependency

0.1.1rc1

Minor tweaks to Python build files to get documentation and package index uploads working. No changes to code, only affects:
* pyproject.toml: Added pip dependencies
* readthedocs.yaml: Added pip install directive
* devtools/conda-envs/release-build.yml: Added Sphinx theme requirement to nudge ReadTheDocs build along

0.1.0

Initial commit of example scripts

0.1.0rc1

Release candidate in-transition from beta to official release

What's changed
* Added new `molfiles` subpackage for handling molecule file writing
* Consolidated dynamic imports and dependency checking into genutils.importutils subpackage
* Added dependency check for non-pip installable dependencies (namely OpenFF stack, mBuild, OpenBabel, and OpenEye)
* Added generic tree-like data structure interface, used to reimplement file and directory trees
* Deprecated unintuitive "DOP" keyword in polymer builder in favor of explicit number of monomers
* Added Validation, end group auto-generation, and several convencience methods to MonomerGroup
* Added robust copolymer sequence checking and fitting ("PROCRUSTEAN sequence alignment"), including support for fractional base sequence repeats
* Updated OpenFF NAGL models
* Simplified OpenFF partial charge method and toolkit registration
* Increased test coverage throughout (particularly for new features)

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