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Polymer builder overhaul #34

Merged
merged 78 commits into from
Dec 12, 2024
Merged

Polymer builder overhaul #34

merged 78 commits into from
Dec 12, 2024

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timbernat
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@timbernat timbernat commented Dec 10, 2024 •
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Description

Enhancements to monomer processing and linear polymer builder

Todos

Notable points that this PR has either accomplished or will accomplish.

  • Adds automatic dependency checks for mbuild/openbabel
  • Addresses De-jankify implementation of DOP in polymer building #24
    • Replaces DOP - 2 hard-code
    • Adds explicit specification for target number of repeat units in polymer
    • Adds extensive validation of periodic copolymer sequences (the PROCRUSTEAN algorithm)
  • Strengthens MonomerGroup
    • Adds add_monomer() method, with validation pre-checks
    • Adds dict-like syntax to directly access contents of .monomers dict
    • Absorbs end group determination (previously done by linear polymer builder)
  • Adds RDKit compatibility to mbuild-generated polymers (with correct PDB residue info)
    • Provides shared interface for implementing Compounds converters/serializers
  • Provides test coverage for MonomerGroup, polymer builders, and copolymer sequencer

Status

  • Check merge compatibility
  • Wait for CI checks to pass

@timbernat
Added typehints for SMILES and SMARTS strings
1adc0b4
@timbernat
Exposed Smiles and Smarts typehints at subpackage level
5919913
@timbernat
Added function for uniquifying strings (which can preserve character …
d5cd8fc 
…order)
@timbernat
Updated DOP calculation to check for and yield correct number of mono…
9a6278e 
…mers regardless of block sequence length
@timbernat
Established placeholder file + sample fragments for polymer building …
c18d394 
…unit tests
@timbernat
Added internal used-monomer-only MonomerGroup which improves accuracy…
4cc360d 
… of n_atoms estimate
@timbernat
Deprecated DOP alias for n_monomers property
173990c
@timbernat
Expunged all references to "DOP" in favor of clearer terminology
8eb7267
@timbernat
Deprecated filter_text_by_condition()
88f8b6b
@timbernat
Renamed textual.strsearch to textual.substrings, updated docstring
98cec89
@timbernat
Implemented function for repeating a string a (possibly fractional) n…
de314e7 
…umber of times
@timbernat
Added argument for indicating separator between string repeats
3685b39
@timbernat
Renamed uniquify_str() to unique_string()
497791e
@timbernat
Renamed "join_indicator" to "joiner" for brevity
3c7448e
@timbernat
Fixed bug with parenthesization vs tuplification
13c9db7
@timbernat
Wrote unit tests for textual.substrings
d3c8be7
@timbernat
Delayed monomer linearity check to only be on the monomer fragments s…
487ae6a 
…elected for building
@timbernat
Added range and int typing checks to target_length
ddc20bc
@timbernat
Added option to register residue names when converting a spec SMARTS …
8714eb8 
…fragment into an mBuild Compound
@timbernat
Renamed "resname_repl" to "resname_map" throughout
0fe10e9
@timbernat
Implemented mBuild Compound to RDKit converter which preserves confor…
0bd4355 
…mer and residue info
@timbernat
Deprecated irrelevant custom Exceptions, pared down use of "Error" su…
d947336 
…ffix on Exception names
@timbernat
Implemented support for fractional sequence repeats, with informative…
7d4b5a1 
… Exceptions for invalid inputs
@timbernat
Added new custom Exception for end-group dominated chains
3797c64
@timbernat
Separated procrustean sequence determination into dedicated helper fu…
8c96e48 
…nction
@timbernat
Switched order of residue name and head/tail identifier in MonomerGro…
f7422bb 
…up.term_orient (head/tail is now key, and residue name is value)
@timbernat
Added __post_init__ check for listification of bare SMARTS and for SM…
e2be34d 
…ARTS string validity
@timbernat
Added module-level logger
56b4144
@timbernat
Added internal method for producing end groups for linear polymer bui…
d852ed3 
…lding (with dynamic fallback)
@timbernat
Changed MonomerGroup.linear_end_groups from property to vanilla metho…
9903dd1 
…d to emphasize that calculation being done is non-trivial
@timbernat timbernat changed the title polymerist.polymers overhaul Polymer builder overhaul Dec 10, 2024
@timbernat
Fixed indent on openff_topology_to_openmm() arguments
4e31488
@timbernat
Removed deprecated local TKREGS import
051d128
@timbernat
Moved unitsys outside of omminter to resolve circular import
e0cdfc5
@timbernat
Moved sample monomer fragment sets from unit tests to polymerist proper
f416a32
@timbernat
Corrected typo in end group autogen warning
a770906
@timbernat
Fixed indent on serialize_openmm_pdb() arguments
c991c17
@timbernat
Fixed accidental duplication of 3-functional TMC monomer fragment
040a718
@timbernat
Added new subpackage for molecule file I/O
bbd1b85
@timbernat
Froze SerialAtomLabeller dataclass to avoid unintentional label forma…
34d1a7b 
…t mutation
@timbernat
Switched PDB atom labelled to dependency-injection based model
d9afdc4
@timbernat
Renamed "chain" to "polymer" where it occurs to avoid confusion with …
668c3f9 
…the related-but-distinct OpenMM notion of a Chain
@timbernat
Added placeholder unit tests for newly-created molfiles subpackage
a5cc442
@timbernat
Added residue info injection into mbmol_to_openmm_pdb (PDB outputs ar…
4d128e3 
…e now totally consistent with RDKit PDB output)
@timbernat
Renamed "atom_label_size" to "atom_label_length" for clarity
f1f8039
@timbernat
Renamed once more to atom_label_width
370dc3a
@timbernat
Fixed non-attribute value in atom_label_width Exception message
c61f16a
@timbernat
Added string type check for atom element symbols
e40600e
@timbernat
Wrote unit tests for molfiles.pdb.SerialAtomLabeller
5c282d7
@timbernat timbernat merged commit ce9e052 into dev Dec 12, 2024
2 checks passed
@timbernat timbernat deleted the DOP-hotfix branch December 12, 2024 00:57
This was referenced Dec 12, 2024
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@timbernat