iphasimulator.build
===================

.. py:module:: iphasimulator.build

.. autoapi-nested-parse::

   RDKit-based PHA chain builder.



Attributes
----------

.. autoapisummary::

   iphasimulator.build.ESTER_BOND


Functions
---------

.. autoapisummary::

   iphasimulator.build.validate_pha_chain
   iphasimulator.build.build_pha_chain
   iphasimulator.build.build_pha_by_sidechain
   iphasimulator.build.build_custom_pha


Module Contents
---------------

.. py:data:: ESTER_BOND

.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.