1.0.2

Minor improvements to docs and local-but-important bugfixes:

• Bugfixes

  • Fixed sporadic stereochemistry inversion in some calls to rdcoords.tiling.tile_lattice_with_rdmol() (caused by bug in Jacobi rotation implementation in RDKit's ComputeCanonicalTransform; see related Issue)

  • Added support for arbitrary names to polymer repeat units from sequences passed to polymers.building.build_linear_polymer()

  • Added SetSerializer to fileutils.jsonio.serialize

  • Greatly extended test coverage, particularly for OpenMM runners and polymer build/sequencing

• Docs
  • Included logo onto Docs page
  • Fixed malformatted and outdated links

What's Changed

• Maintenance cleanup by @timbernat in #51
• CI tweaks by @timbernat in #52
• 1.0.2 patches by @timbernat in #53

Full Changelog: v1.0.1...v1.0.2

1.0.1

Minor fixes after 1.0.0 release:

• Documentation improvements
  • Fix errors on documentation examples page
    • Fixed broken links in section 3 ("workflows")
    • Corrected "miscellanous" typo
  • Improved docstrings in several modules:
    • polymers.specification
    • polymers.estimation
    • polymers.building.mbconvert
    • openfftools.topology
    • openfftools.boxvectors
• Bugfixes
  • Fixed bug combine_mols call in ReactionAssembler.reactants, error no longer raised when a number of reactive groups other than 2 is input
  • Improve typing and robustness of importutils.pkgiter module trees
    • Added explicit Error + logging for ImportError
    • Fixed typehint on "blacklist" arg (from List to Container)
• Packaging
  • Fix erroneous install of rdutils.rdconvert (deprecated on 2025/01/31 but 1.0.0 distribution was built incorrectly and included it anyway)

1.0.0

First major release, following several large-scale changes!

Updates

• Implemented new PINPRICS ring piercing detection algorithm and interfaces
• General utilities (genutils)
  • fileutils
    • Added empty dir/file checkers
    • Added context manager for temporarily changing the current working directory
    • Moved allow_string_paths/allow_pathlib_paths decorators from decorators.functional to fileutils.pathutils to avoid
  • jsonio
    • Added TypeSerializer for numpy arrays to jsonio (NDArraySerializer)
    • Allowed make_jsonifiable to act on dataclasses with Optional[...] fields by fixing KEYWORD_ONLY signature detection
• Added PDB atom labeller for polymer export
  • Provided virtual ("EP") site support for OpenMM PDB export
• RDKit functionality:
  • Enhanced sanitization utilities
  • Enhanced atom/bond search by conditional queries
  • Added basic functionality for producing chemical graphs from RDKit Mols
  • Added calculation of effective radius of RDMol with one or more Conformer
    • Made calculation agnostic of RDKit-specific coordinate operations
• Reactions:
  • Moved react/valid_reactant_ordering etc. from Reactor directly into AnnotatedReaction
  • Added detailed traces for following atom and bond provenance through a reaction
• Fragment enumeration:
  • Generalized Reactor fragment search to iterative expand pool, rather than piping fragment directly through reaction; can now handle much broader classes of reactions
  • Included bond-weighted fragment strategy which given more chemically-reasonable cut choices
    • Deprecated ReseparateRGroups as default fragment strategy
  • Allowed fragment propagation to "resample" reactants, enabling autopolymerization modelling and detection
  • Added option to randomize rxn tree traversal
  • Expanded logging options when showing steps of reaction assembly
• Polymer building:
  • Fixed conversion of charged atoms in spec SMARTS translator (non-neutral molecules are converted faithfully now)
    • Propagated awareness of charged into mBuild interface
  • Updated list of valid property queries to NIH CACTUS / PubChem
• Molecular dynamics APIs
  • OpenFF
    • Dropped unnecessary "exclusion" parameter from pack_topology_with_solvent()
    • Added function to check if the unit cell defined by one set of box vectors is entirely contained in that of another
  • OpenMM
    • Added option to select thermostat/barostat, rather than using prescribed LangevinMiddle thermostat and MC barostat as before
      • Added new parameter sets for thermostat and barostat
      • Added auto-detection of named ensemble (e.g. NVE, NVT, NPT) rather than requiring user to provide this
  • LAMMPS
    • Reimplemented purely in terms of pylammps API calls (no more bespoke regex parsing)

Deprecations

• Deprecated SANITIZE_AS_KEKULE throughout for Mol sanitization
• Deprecated .analysis
• Deprecated maths.statistics
• Deprecated typetools.numpytypes.parametric
• Deprecated graphics.named_colors
• Deprecated openfftools.omminter and openfftools.mdobjects
• Merged several submodules of mdtools.openmmtools into .serialization and .forces submodules

Bugfixes

• Fixed long-standing barostat bleedover issue in OpenMM schedule runner - barostats will no longer persist from earlier simulations in a schedule
• Fixed lammps single-point energy test failures due to misguided exact float comparison
• Installation
  • Fixed slow lammps solver import
    • Removed need to perform mixed install via pip in devtools/conda-envs
  • Updated OpenFF stack version pins
  • Added helpful PrerequisitePackageErrors throughout to guide user through install of missing-but-essential packages

What's Changed

• Pre-commit of release updates by @timbernat in #45
• Release cleanup by @timbernat in #46
• Polymerist 1.0.0. release by @timbernat in #47

Full Changelog: v0.1.5rc1...v1.0.0

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
    • PubChem
  • 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 and pubchempy added to smileslib.chemdbqueries
  • 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

0.1.0rc1

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)

0.0.1 Beta version

Pre-release version of polymerist.

Intended to:

• Checkpoint this version of polymerist prior to planned 1.0.0
• Allow reversion to pre-release build for dependent code
• Enable building of documentation for ReadTheDocs
• Enable testing of pip-installable version

Full Changelog: https://github.com/timbernat/polymerist/commits/v0.0.1-beta