iphasimulator.amber_complex
===========================

.. py:module:: iphasimulator.amber_complex

.. autoapi-nested-parse::

   Inputs for an Amber/OpenMM enzyme + polymer system built from a docked complex.

   The same complex PDB used for CHARMM-GUI (protein + polymer pose, e.g. from
   docking) is split into a protein PDB for ``tleap``/ff19SB and a posed copy of the
   05A GAFF2 polymer mol2, so both force-field routes start from the same structure.
   Nothing here runs tleap or OpenMM.



Attributes
----------

.. autoapisummary::

   iphasimulator.amber_complex.CHARMM_TO_AMBER_HISTIDINE
   iphasimulator.amber_complex.HISTIDINE_NAMES
   iphasimulator.amber_complex.SOLVENT_AND_IONS


Classes
-------

.. autoapisummary::

   iphasimulator.amber_complex.ProteinPdbSummary
   iphasimulator.amber_complex.PoseTransferResult


Functions
---------

.. autoapisummary::

   iphasimulator.amber_complex.read_charmm_histidine_states
   iphasimulator.amber_complex.write_protein_pdb
   iphasimulator.amber_complex.pose_polymer_mol2


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

.. py:data:: CHARMM_TO_AMBER_HISTIDINE

.. py:data:: HISTIDINE_NAMES
   :value: ('HIS', 'HSD', 'HSE', 'HSP', 'HID', 'HIE', 'HIP')


.. py:data:: SOLVENT_AND_IONS
   :value: ('HOH', 'WAT', 'TIP3', 'SOL', 'SOD', 'CLA', 'NA', 'CL', 'POT', 'K')


.. py:class:: ProteinPdbSummary

   .. py:attribute:: output_path
      :type:  pathlib.Path


   .. py:attribute:: residues
      :type:  int


   .. py:attribute:: removed_hydrogens
      :type:  int


   .. py:attribute:: histidines
      :type:  dict[int, str]


.. py:class:: PoseTransferResult

   .. py:attribute:: output_mol2
      :type:  pathlib.Path


   .. py:attribute:: heavy_atoms
      :type:  int


   .. py:attribute:: hydrogens_placed
      :type:  int


   .. py:attribute:: stereocentres
      :type:  list[tuple[str, str]]


.. py:function:: read_charmm_histidine_states(protein_itp: str | pathlib.Path) -> dict[int, str]

   Residue number -> Amber histidine name (HID/HIE/HIP) from a CHARMM-GUI ``PROA.itp``.


.. py:function:: write_protein_pdb(complex_pdb: str | pathlib.Path, output_pdb: str | pathlib.Path, *, ligand_resname: str = 'LIG', histidine_states: dict[int, str] | None = None) -> ProteinPdbSummary

   Write the protein part of a complex PDB for ``tleap`` (ff19SB).

   Drops the ligand, water, ions and hydrogens (tleap adds hydrogens), and renames
   histidines to HID/HIE/HIP from ``histidine_states`` (residue number -> name).
   Histidines without a state stay ``HIS``, which tleap treats as HIE.


.. py:function:: pose_polymer_mol2(mol2_path: str | pathlib.Path, template_sdf: str | pathlib.Path, complex_pdb: str | pathlib.Path, output_mol2: str | pathlib.Path, *, ligand_resname: str = 'LIG') -> PoseTransferResult

   Copy the docked polymer pose onto the 05A GAFF2 mol2.

   ``template_sdf`` is the antechamber input written by 05A (same atom order as the
   mol2; it carries bond orders and stereochemistry). Heavy atoms are matched to the
   pose by element and connectivity; hydrogens are placed from the posed heavy
   atoms. Atom names, types and charges in the mol2 are unchanged.