polymerist.polymers.monomers
For representing, generating, and modifying information about groups of monomer fragments
Submodules
Attributes
Classes
Stores collections of residue-labelled monomer SMARTS |
Functions
|
Convert a generic SMARTS string into a monomer specification-compliant one |
Package Contents
- class polymerist.polymers.monomers.MonomerGroup[source]
Stores collections of residue-labelled monomer SMARTS
- monomers: dict[str, polymerist.smileslib.Smarts | list[polymerist.smileslib.Smarts]]
- term_orient: dict[str, str]
- add_monomer(resname: str, smarts: polymerist.smileslib.Smarts | Iterable[polymerist.smileslib.Smarts]) None[source]
Register new monomers, either directly from SMARTS or from a container of SMARTS
- static is_terminal(monomer: rdkit.Chem.Mol) bool[source]
Determine whether or not a monomer is terminal
- property SMARTS: dict[str, list[polymerist.smileslib.Smarts]]
Alias of legacy “monomers” attribute
- iter_rdmols(term_only: bool | None = None) Generator[tuple[str, rdkit.Chem.Mol], None, None][source]
Generate (residue name, RDKit Mol) pairs of all monomers present Simplifies iteration over internal lists of monomer Mols
- Can optionally filter by monomer termination:
term_only=True -> only terminal monomers term_only=False -> only middle monomers term_only=None -> all monomers
- rdmols(term_only: bool | None = None) dict[str, list[rdkit.Chem.Mol]][source]
Returns dict of RDKit Mol lists keyed by residue name
- Can optionally filter by monomer termination:
term_only=True -> only terminal monomers term_only=False -> only middle monomers term_only=None -> all monomers
- contributions(term_only: bool | None = None) dict[str, list[int]][source]
Returns dict of the number of real (i.e. non-linker) atoms in each residue list
- property n_monomers: int
Returns number of distinct monomer templates present Distinct monomers under the same residue name are counted separately
- linear_end_groups() dict[str, tuple[str, rdkit.Chem.Mol]][source]
Returns head-and-tail end group residue names and Mol objects as defined by term_orient
If term orient is undefined, will automatically take then first <= 2 terminal groups available to be the end groups
- Returns:
end_groups – A dict whose keys are any of {‘head’, ‘tail’} and whose values are 2-tuples of residue names and Mols for the corresponding monomer
- Return type:
dict[str, tuple[str, Chem.Mol]]
- is_homopolymer() bool[source]
Identify if a polymer is a homopolymer (i.e. only 1 type of middle monomer)
- property is_branchable: bool
Whether it is possible to generate a branched polymer from this set of monomers
- property is_linear: bool
Whether a group of monomers can ONLY be assembled into a linear chain
- property is_linear_homopolymer: bool
Identify if a polymer is a linear homopolymer
- property num_mid_and_term: tuple[int, int]
Counts of how many of the monomers are middle vs terminal, respectively
- polymerist.polymers.monomers.PE_FRAGMENTS: dict[str, list[str]]
- polymerist.polymers.monomers.MPD_TMC_FRAGMENTS: dict[str, list[str]]
- polymerist.polymers.monomers.PEG_PLGA_FRAGMENTS: dict[str, list[str]]
- polymerist.polymers.monomers.compliant_mol_SMARTS(smarts: polymerist.smileslib.cleanup.Smiles | polymerist.smileslib.cleanup.Smarts) str[source]
Convert a generic SMARTS string into a monomer specification-compliant one For details on specification, see https://doi-org.colorado.idm.oclc.org/10.1021/acs.jcim.3c01691
- Parameters:
smarts (Union[Smiles, Smarts]) – The SMARTS (or, by virtue of superset, SMILES) string to convert
- Returns:
compliant_smarts – The structurally-correspondent monomer specification-compliant SMARTS string
- Return type:
Smarts