iphasimulator.build

RDKit-based PHA chain builder.

Attributes

ESTER_BOND

Functions

validate_pha_chain(→ rdkit.Chem.Mol)	Validate core chemistry invariants for a generated PHA oligomer.
build_pha_chain(→ rdkit.Chem.Mol)	Build a minimal RDKit molecule for a homopolymeric PHA oligomer.
build_pha_by_sidechain(→ rdkit.Chem.Mol)	Build a linear R-PHA oligomer from an alkyl side-chain length.
build_custom_pha(→ rdkit.Chem.Mol)	Build an R-PHA oligomer from a user-defined 3-hydroxy acid monomer.

Module Contents

iphasimulator.build.ESTER_BOND

iphasimulator.build.validate_pha_chain(mol: rdkit.Chem.Mol | None, monomer: iphasimulator.monomers.Monomer, n: int, stereochemistry: str) → rdkit.Chem.Mol

Validate core chemistry invariants for a generated PHA oligomer.

iphasimulator.build.build_pha_chain(monomer: str, n: int, stereochemistry: str = 'R') → rdkit.Chem.Mol

Build a minimal RDKit molecule for a homopolymeric PHA oligomer.

The returned molecule is capped as the linear hydroxy acid oligomer: HO-[CH(R)-CH2-C(=O)-O]n-H, represented with implicit hydrogens.

iphasimulator.build.build_pha_by_sidechain(side_chain_carbons: int, degree: int) → rdkit.Chem.Mol

Build a linear R-PHA oligomer from an alkyl side-chain length.

iphasimulator.build.build_custom_pha(monomer_smiles: str, degree: int, name: str) → rdkit.Chem.Mol

Build an R-PHA oligomer from a user-defined 3-hydroxy acid monomer.