iphasimulator.naming
====================

.. py:module:: iphasimulator.naming

.. autoapi-nested-parse::

   Canonical PHA naming helpers.



Attributes
----------

.. autoapisummary::

   iphasimulator.naming.ResidueRole
   iphasimulator.naming.MONOMER_TO_POLYMER
   iphasimulator.naming.POLYMER_TO_MONOMER
   iphasimulator.naming.LEGACY_MONOMER_ALIASES
   iphasimulator.naming.RESIDUE_ROLE_SUFFIXES


Functions
---------

.. autoapisummary::

   iphasimulator.naming.canonical_monomer_code
   iphasimulator.naming.validate_monomer_code
   iphasimulator.naming.monomer_to_polymer_code
   iphasimulator.naming.validate_polymer_code
   iphasimulator.naming.oligomer_name
   iphasimulator.naming.validate_oligomer_name
   iphasimulator.naming.multi_chain_system_name
   iphasimulator.naming.validate_system_name
   iphasimulator.naming.residue_variant_name
   iphasimulator.naming.residue_variant_names
   iphasimulator.naming.validate_pha_name


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

.. py:data:: ResidueRole

.. py:data:: MONOMER_TO_POLYMER
   :type:  dict[str, str]

.. py:data:: POLYMER_TO_MONOMER
   :type:  dict[str, str]

.. py:data:: LEGACY_MONOMER_ALIASES
   :type:  dict[str, str]

.. py:data:: RESIDUE_ROLE_SUFFIXES
   :type:  tuple[str, str, str]
   :value: ('H', 'M', 'T')


.. py:function:: canonical_monomer_code(code: str) -> str

   Return the canonical monomer/residue code, accepting legacy aliases.


.. py:function:: validate_monomer_code(code: str) -> str

   Validate and return a canonical monomer/residue code such as ``3HB``.


.. py:function:: monomer_to_polymer_code(monomer_code: str) -> str

   Convert a monomer/residue code such as ``3HB`` to ``P3HB``.


.. py:function:: validate_polymer_code(code: str) -> str

   Validate and return a polymer code such as ``P3HB``.


.. py:function:: oligomer_name(monomer_code: str, repeat_units: int) -> str

   Return a single-chain oligomer name such as ``P3HB_4``.


.. py:function:: validate_oligomer_name(name: str) -> str

   Validate and return a single-chain oligomer name such as ``P3HO_8``.


.. py:function:: multi_chain_system_name(chain_count: int, monomer_code: str | None = None, repeat_units: int | None = None, *, oligomer: str | None = None) -> str

   Return a multi-chain system name such as ``25_P3HB_3``.


.. py:function:: validate_system_name(name: str) -> str

   Validate and return a multi-chain system name such as ``25_P3HB_3``.


.. py:function:: residue_variant_name(monomer_code: str, role: ResidueRole) -> str

   Return a head/main/tail residue name such as ``3HB_H``.


.. py:function:: residue_variant_names(monomer_code: str) -> tuple[str, str, str]

   Return head, main, and tail residue names for one monomer code.


.. py:function:: validate_pha_name(name: str) -> str

   Validate any canonical PHA monomer, polymer, oligomer, or system name.