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View Code? Open in Web Editor NEWPolymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools
License: MIT License
Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools
License: MIT License
Would like to encapsulate and better document file extensions
Several refinements and additions planned for the rdutils.amalgamation.portlib module:
Currently, the maths.lattices.bravais.LatticeParameters class, while correctly implemented mathematically and supporting radians or degrees, does not provide support for OpenMM Quanity values for lattice parameters. Additionally, many legacy components of polymerist could be unified by reimplementation via LatticeParameters, rather than bespoke array methods as currently implemented. Namely:
More broadly, the use of OpenMM-style units as defaults throughout this project may in the future be replaced by OpenFF-style units for greater cross-compatibility. This would effect a number of changes including:
Several refinements and additions planned for the rdutils.amalgamation.bonding module:
Feel the need to strengthen typing and tyehints in a handful of places:
Certain polymerist modules are essentially clones of scripts found in openff/polymer_examples, written by Connor Davel. These scripts would be greatly improved by being made more consistent with the rest of polymerist, in terms of functionality, consistency, and readability. The most obvoius of such changes are:
Numerous feature expansion are planned for rdutils.reactions and the relatedrdutils.bonding, including:
Have documented a handful of issues with loading of serialized States and systems in the sequential openmm simulation runner that need to be resolved:
Currently, the only solvent defined in openfftools.solvation.solvents is TIP3P water; would like to expand this library in the future to include charged structural SDF files for many common small-molecule solvents (e.g. ethanol, DCM, toluene, etc)
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