iphasimulator.parameterization_gaff2
====================================

.. py:module:: iphasimulator.parameterization_gaff2

.. autoapi-nested-parse::

   GAFF2 parameterisation workflow using AmberTools.



Exceptions
----------

.. autoapisummary::

   iphasimulator.parameterization_gaff2.AmberToolsError


Classes
-------

.. autoapisummary::

   iphasimulator.parameterization_gaff2.Gaff2Outputs


Functions
---------

.. autoapisummary::

   iphasimulator.parameterization_gaff2.ambertools_available
   iphasimulator.parameterization_gaff2.require_ambertools
   iphasimulator.parameterization_gaff2.parameterize_gaff2


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

.. py:class:: Gaff2Outputs

   Files produced by the GAFF2/AmberTools workflow.


   .. py:attribute:: output_dir
      :type:  pathlib.Path


   .. py:attribute:: mol2_path
      :type:  pathlib.Path


   .. py:attribute:: frcmod_path
      :type:  pathlib.Path


   .. py:attribute:: tleap_input_path
      :type:  pathlib.Path


   .. py:attribute:: prmtop_path
      :type:  pathlib.Path


   .. py:attribute:: inpcrd_path
      :type:  pathlib.Path


   .. py:attribute:: pdb_path
      :type:  pathlib.Path


   .. py:attribute:: antechamber_log
      :type:  pathlib.Path


   .. py:attribute:: raw_antechamber_log
      :type:  pathlib.Path


   .. py:attribute:: sqm_log
      :type:  pathlib.Path


   .. py:attribute:: parmchk2_log
      :type:  pathlib.Path


   .. py:attribute:: tleap_log
      :type:  pathlib.Path


   .. py:attribute:: timing_log
      :type:  pathlib.Path


   .. py:attribute:: antechamber_seconds
      :type:  float


   .. py:attribute:: parmchk2_seconds
      :type:  float


   .. py:attribute:: tleap_seconds
      :type:  float


.. py:exception:: AmberToolsError



   Raised when AmberTools is unavailable or a command fails.


.. py:function:: ambertools_available() -> bool

   Return True when the required AmberTools executables are on PATH.


.. py:function:: require_ambertools() -> None

   Raise a clear error if AmberTools executables are not available.


.. py:function:: parameterize_gaff2(input_sdf: str | pathlib.Path, output_dir: str | pathlib.Path, *, name: str | None = None, net_charge: int = 0, residue_name: str = 'MOL', charge_method: str = 'abcg2', atom_count_warning_threshold: int | None = 120, verbose: bool = False, runner=subprocess.run, check_tools: bool = True) -> Gaff2Outputs

   Create GAFF2 AMBER topology files from an input SDF.

   The workflow runs AmberTools in three steps:
   antechamber -> parmchk2 -> tleap.