iphasimulator.docking_inputs
============================

.. py:module:: iphasimulator.docking_inputs

.. autoapi-nested-parse::

   Polymer-only PDB for docking, from a GROMACS ``.gro`` and its topology (notebook 11).

   Only the polymer is written: the atoms with one residue name, ``PHA`` for systems
   built with 06A (and the polymer benchmark) or ``LIG`` for CHARMM-GUI systems. Before
   writing, the polymer must be whole: a molecule split across the periodic box would
   give the docking program a broken structure.



Attributes
----------

.. autoapisummary::

   iphasimulator.docking_inputs.MAX_BOND_NM
   iphasimulator.docking_inputs.HYDROGEN_MAX_MASS
   iphasimulator.docking_inputs.WHOLE_MOLECULE_ADVICE


Classes
-------

.. autoapisummary::

   iphasimulator.docking_inputs.PolymerWholeCheck
   iphasimulator.docking_inputs.PolymerPdbExport


Functions
---------

.. autoapisummary::

   iphasimulator.docking_inputs.check_polymer_whole
   iphasimulator.docking_inputs.export_polymer_pdb


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

.. py:data:: MAX_BOND_NM
   :value: 0.3


.. py:data:: HYDROGEN_MAX_MASS
   :value: 4.0


.. py:data:: WHOLE_MOLECULE_ADVICE
   :value: 'Use a whole-molecule frame instead, e.g. the representative frame from notebook 08 or a frame...


.. py:class:: PolymerWholeCheck

   Bonded heavy-atom distances of the polymer (nm).


   .. py:attribute:: residue_name
      :type:  str


   .. py:attribute:: atoms
      :type:  int


   .. py:attribute:: heavy_bonds
      :type:  int


   .. py:attribute:: longest_bond
      :type:  tuple[str, str, float]


   .. py:attribute:: broken_bonds
      :type:  tuple[tuple[str, str, float], ...]


   .. py:attribute:: max_bond_nm
      :type:  float
      :value: 0.3



   .. py:property:: is_whole
      :type: bool



.. py:class:: PolymerPdbExport

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


   .. py:attribute:: atoms
      :type:  int


   .. py:attribute:: check
      :type:  PolymerWholeCheck


.. py:function:: check_polymer_whole(gro_path: str | pathlib.Path, topology_path: str | pathlib.Path, residue_name: str = 'PHA', max_bond_nm: float = MAX_BOND_NM) -> PolymerWholeCheck

   Measure every bonded heavy-atom pair of the polymer; whole if all are < ``max_bond_nm``.

   Bonds come from the polymer's ``[ moleculetype ]`` (named like its residue) in the
   topology or its ``#include`` files; coordinates come from the ``.gro`` file.


.. py:function:: export_polymer_pdb(gro_path: str | pathlib.Path, topology_path: str | pathlib.Path, pdb_path: str | pathlib.Path, *, residue_name: str = 'PHA', max_bond_nm: float = MAX_BOND_NM) -> PolymerPdbExport

   Write the polymer only (``residue_name``) as a PDB, after checking it is whole.

   Raises ``ValueError`` without writing anything when a bonded heavy-atom pair is
   ``max_bond_nm`` or longer. Atoms and residues are renumbered from 1, in chain A;
   coordinates are converted from nm to Å; no box (CRYST1) record is written.