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timbernat merged 170 commits intodevtimbernat/polymerist:devfrom maintimbernat/polymerist:mainCopy head branch name to clipboardJul 17, 2024

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Commits on Mar 14, 2024

• Merge pull request #10 from timbernat/dev

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• Merge pull request #11 from timbernat/dev

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• This is a test commit to check that GitHub sync is working properly

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• Initial commit with MolSSI Cookiecutter template

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Commits on Mar 15, 2024

• Deleted now-redundant internal .gitignore

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• Removed manual author/version dunders

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Commits on Mar 19, 2024

• Merge pull request #12 from timbernat/cookiecutter

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• Consolidated and renamed conda env requirements files

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• Reinstated test_env.tml

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• Removed unneccesary detail from canonical conda requirements YAML

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• Updated conda reqs

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• Update README.md

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• Update README.md

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• Update README.md

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• Added dirty install instructions to README

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• Added TOC graphic to static docs files

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• Added graphical abstract and links to publication

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• Corrected typos and improved aesthetics

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Commits on Mar 20, 2024

• Added reaction name attr transfer in ReactionAssembler.assemble_rxn()

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• Merge remote-tracking branch 'refs/remotes/origin/main'

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• Added functions for labelling and unlabelling bond indices

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• Changed IBIS passing to Polymerizationreactor.propagate() from class-based to instance-based (allows for custom init args)

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• Disabled Mol sanitization in IBIS.produce_fragments(), implemented uniquified version of ReseparateRGroups IBIS

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• Changed default PolymerizationReactor IBIS from ReseparateRGroups to ReseparateRGroupsUnique

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• Fixed typos in README

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Commits on Apr 4, 2024

• Converted "textual" into module with dedicated submodules for specific functionality

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• Added module-wide references to ASCII character subsets

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• Added function for identifying minimal repeating substrings of strings

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• Added dedicated module for parsing and validating parenthetical delimiters

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• Implemented translation between monomer graphs and in-line strings (simplified SMILES-like format)

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• Formatted descriptive comments for string encoding/decoding algorithms

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Commits on Apr 8, 2024

• Added support for multiple connected components via dot (".") separation in monomer strings

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• Added regex-based substring delimitation

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• Added visualization and name alias ("MonoGraph") to MonomerGraph class

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Commits on Apr 9, 2024

• Implemented MonoGraph JSON TypeSerializer, added references to SMIDGE ("SMILES-like Monomer Interconnectivity & Degree Graph Encoding") strings

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• Added port-agnostic linker counting function

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• Added submodule for representing and manipulating rational numbers and general ratios

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• Expanded and automated definition of dictionaries of SMILES+SMARTS bond primitives

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Commits on Apr 10, 2024

• Added registries for reverse lookup by SMILES+SMARTS

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Commits on Apr 11, 2024

• Added regex-compatible bond primitives index

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• Outsourced SMIDGE string tranlation to externally-implemented readers and writers

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• Created new module specific to SMIDGE string parsing and validation

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• Added compact representation class for MID graph bond info

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• Implemented SMIDGE string reader and writer (with bond info) as finite-state register machines

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• Added chevrons ("<>") to common delimiters registry

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• Added generator property for terminal monomers

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• Added convenience methods for looking up named node attributes

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Commits on Apr 12, 2024

• Added dataclass field init checker and signature updates to jsonifiable_serializer_factory

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• Improved typechecking on MultiTypeSerializer init

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Commits on Apr 13, 2024

• Made methods specific to dataclasses, added serializability recogition of init args, removed redundant boilerplate code

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• Removed TypeSerializer boilerplate made redundant by jsonio updates

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Commits on Apr 15, 2024

• Converted SMIDGE bond delimiters from curly braces "{}" to chevrons "<>" to make f-string formatting less annoying

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Commits on Apr 19, 2024

• Added typehints for numpy array dimensions

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• Removed debug print statement

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• Added left and right matrix pseudo-inverse calculations

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• Added representation class for converting between lattice parameter and lattice vector representations of a unit cell

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• Separated genutils.typetools into dedicated submodules

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• Updated genutils.typetools imports

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• Added registry of common unit cell vectors

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Commits on Apr 22, 2024

• Added dynamic registration for common lattice parameter classmethod constructors

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• Added dynamic lookup dicts of builtin types, removed ArrayLike check

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• Improved dynamic signatures on _union_member_factory

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• Added decorator to allow functions which expect a single tuple (or list) to accept starred non-keyword arguments

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Commits on Apr 24, 2024

• Added decorator signature transfer to AdaptedDecorator meta-decorator class

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• Added Union definition for "ListLike" types

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• Implemented support for output type casting in flexible_listlike_input

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• Temporarily removed as-of-now redundant maths.lattices import

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• Added basic coordinate array distance geometry methods

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• Implemented function to determine the corner points of the tight bounding box of coordinate array

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• Implemented core representation class for orthogonal integer-values lattices

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• Broke maths.lattices into submodules

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• Added lattice vectors for rhombohedral and hexagonal cells

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• Consolidated redundant rhombohedral cell definition

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• Implemented affine transformation method

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• Corrected "tranformation" -> "transformation" typo

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• Added checker function for determining which coordinates are within a bounding box

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• Added optional weighting to centroid calculation

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Commits on Apr 25, 2024

• changed np.product() call to np.prod() to avoid deprecation warning

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• Implemented calculation for nearest integer-valued point in a given normal direction relative to a control point

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• Grouped bounding box operations into single encapsulation class

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• Added clone method for bounding boxes

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Commits on Apr 26, 2024

• Implemented method for finding which Bravais lattice points lie within a bounding box in n-dimensions

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• Implemented core Coordinates representation class and BoundingBox subclass

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• Migrated class definitions to lattices.coordinates

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• Implemented lexicographic ordering methods in base Coordinates class

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• Rewrote CubicIntegerLattice as subclass of Coordinates

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• Renamed ".integers" to ".integral"

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• Added dimensioality and Numeric-like Generic typehint

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• Tweaked numpy array typehinting

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• Renamed ".unitcell" to ".bravais"

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• Dismantled coordops, distributed functionality amongst .integral and .bravais

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• Fixed CubicIntegerLattice super() init bug, renamed integer box sizes variable from "sidelens" to "counts_along_dims" to avoid confusion

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• Replaced generic __class__.__init__() call with Coordinates.__init__() call to avoid inheritance issues when using "as_coords=True" flag

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• Added registries of all OpenFF OFFXML directories and files (not just from "openforcefields")

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• Corrected typo in validate_point() (changed "_point_is_valid()" to correct "_point_is_compat()")

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• Fixed missing transpose bug in lattice vector inversion, improved variable naming

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• Downgrade c-blosc2 req from v2.13.2 to v2.12.0 to fix pytables install dependency error

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• Added BoundingBox properties for generating hypervolume face-forming point groupings

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Commits on May 1, 2024

• Fixed annoying tuple outputs on odd and even sublattice indices

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• Removed unnecessary property decorators

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Commits on May 2, 2024

• Separated lattice scaling from RDMol population

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• Improved imput signature to topology_from_molecule_onto_lattice()

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• Added new string encoding submodule to genutils.textual

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Commits on May 9, 2024

• Renamed smileslib.queries to smileslib.substructures

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• Added submodule for querying info by SMILES from chemical databases

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• Updated smileslib.queries -> smileslib.substructures import

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• Replaced absolute polymerist imports with relative ones

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• Promoted "smileslib" from rdutils submodule to polymerist module in its own right

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• Updated relative smileslib imports

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Commits on May 10, 2024

• Renamed has_string_urlsafe() to hash_to_alphanumeric()

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• Added methods and properties for exporting AnnotatedReactions to SMILES/SMARTS (wrappers around rdChemReactions converters)

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Commits on May 11, 2024

• Renamed from "hash_to_alphanumeric()" to "hash_as_alphanumeric()" to avoid confusing connotation

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• Added missing parens on to_smiles/to_smarts decorator calls

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• Changed NIH CACTUS query to take first result, rather than last

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Commits on May 13, 2024

• Added support for command line argument passing when imitializing lammps.lammps() objects

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• Created new "digits" submodule of mahs to handle digits of numbers in positional notations

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• Moved factoradic number utils to maths.digits

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Commits on May 14, 2024

• Implemented greedy algorithm for the change-making problem

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Commits on May 15, 2024

• Renamed "maths.digits" to "maths.positional"

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• Implemented unified framework for handling fixed- and mixed-radix number systems

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• Deprecated custom generic "Numeric" Union type in favor of builtin numbers.Number, which behaves the same

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• Added support for Generic type parameterization of Coordinates

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• Replaced numeric type with numbers.Number, renamed dimension var N -> D and len var M -> N

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• Merged duplicate BondOrderModificationError into rdutils.rderrors

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• Edited all comments and docstrings which feature rdtypes classes (e.g. RDMol, RDBond, RDAtom, or RWMol) in preparation for mass-rename

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Commits on May 16, 2024

• Encapsulated ratios in new maths.fractions submodule

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• Initialzed submodule for working with continued fractions

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• Broke apart maths.positional into separate submodules, under the new "numbersys" maths module

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• Comartmentalized maths.greek into separate alphabet and prefix submodules

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• Implemented dynamic systematic Greek numerical prefix generation

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• Deprecated rdutils.rdtypes in favor of direct references to rdkit.Chem.rdchem classes

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• Generalized and condensed rdprops.detailed_atom_info to any RDKit core object using genutils.importlib gettable attribute compile method

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Commits on May 17, 2024

• Added new openmm submodule for handling force group labeling

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• Added new openmm submoudle for describing OpenMM objects

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• Added new OpenMM submodule for evaluating properties from Contexts

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• Migrated get_simulation_positions() to .evaluation as get_context_positions()

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• Fixed bug in simulation_from_thermo where provided states were not being applied to Simulation objects

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• Consolidated openfftools, openmmtool, and lammpstools as submodules of master "mdtools" core module

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• Moved "monomers" into "polymers" core module

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• Renamed maths.combinatorics.core to .numbers for clarity, absorbing .graphenum in the process

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• Added function for computing the Bernoulli numbers

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• Switched integer type from unsigned to signed (i.e. np.uint64 -> np.int64) to support negative reals

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Commits on May 18, 2024

• Added dynamic Union registration for numpy float and int types

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• Implemented the extended Euclidean algorithm, strengthened typing

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• Updated section header

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Commits on May 20, 2024

• Removed "_numbers" suffix from Catalan and Bell number functions for consistency with module

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• Updated relative imports in polymers.monomers

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Commits on May 21, 2024

• Updated relative imports in mdtools

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• Fixed Simulation state loading, with support for both State objects and file-like inputs (or None)

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Commits on May 22, 2024

• Imported OpenFF Quantities, corrected typos

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• Added molecular mass calculations methods for OpenFF Molecule and Topology objects

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• Deprecated RDKit conversion in packmol number density mass calculation

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Commits on Jun 14, 2024

• Migrated product() from seuquences.py to iteration.py (incuding in dependencies)

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• Expanded genutils.sequences into full module (with prior functionality moved into seqops.py submodule), updated dependencies

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• Updated seqops docstring, made core utils importable thru toplevel module

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• Added new genutils.bits package for bitwise operations

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Commits on Jun 17, 2024

• Added sort_dict_by_keys() counterpart function to sort_dict_by_values()

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• Created new sequence similarity submodule which implements Levenshtein distance-related functionality (among other things)

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Commits on Jun 18, 2024

• Migrated bin_ids_forming_sequence from sequences.seqops to new sequences.choices, updating dependencies

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Commits on Jun 19, 2024

• Corrected typo in imports (containers -> collections)

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Commits on Jul 4, 2024

• Craeted new module for solving the generalized ransom note index enumeration problem

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• Implemented representation class for manipulations on ordered sequences of symbol multisets

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• Implemented base solution interface and cartesian, recursive, and stack-based concrete solution algorithms

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• Implemented front-facing solver interface class

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• Wrote unit tests to ensure consistency between DISCERNMENT algorithm implementations

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• Deprecated sequences.choices in favor of sequences.discernment, updated dependent co-modules

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Commits on Jul 5, 2024

• Made num_automorphisms() more secure by removing possibility of conflicting "uniquify" kwargs values

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• Cleaned up naming on full_builtin() (now called "full_arr_builtin()") for clarity

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• Made valid_reactant_ordering() implementation more explicit (clearer typing and variable names, more re-use of calculations)

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• Fixed relative imports from genutils and unitutils (remnants of move into mdtools)

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