oqp.utils.geometry
==================

.. py:module:: oqp.utils.geometry

.. autoapi-nested-parse::

   .. code-block:: text

      Geometry helpers for OpenQP Python inputs.



Exceptions
----------

.. autoapisummary::

   oqp.utils.geometry.GeometryLookupError


Functions
---------

.. autoapisummary::

   oqp.utils.geometry.builtin_geometry
   oqp.utils.geometry.pubchem_geometry
   oqp.utils.geometry.get_geometry
   oqp.utils.geometry.geometry_from_sdf
   oqp.utils.geometry.normalize_system


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

.. py:exception:: GeometryLookupError

   Bases: :py:obj:`ValueError`


   .. code-block:: text

      Raised when a named geometry cannot be resolved.


.. py:function:: builtin_geometry(query)

   .. code-block:: text

      Return a built-in approximate Angstrom geometry for common small molecules.


.. py:function:: pubchem_geometry(query, timeout=10)

   .. code-block:: text

      Fetch a 3D conformer from PubChem PUG-REST and return OpenQP geometry text.


.. py:function:: get_geometry(query, source='auto', timeout=10)

   .. code-block:: text

      Resolve a named molecular geometry to OpenQP inline geometry text.

      source="auto" tries OpenQP's small built-in table first, then PubChem.
      source="builtin" only uses the local table.
      source="pubchem" only uses PubChem PUG-REST.


.. py:function:: geometry_from_sdf(sdf, query)

   .. code-block:: text

      Convert a PubChem-style V2000 SDF string to OpenQP inline geometry text.


.. py:function:: normalize_system(system, unit='Angstrom')

   .. code-block:: text

      Normalize inline molecular geometries for OpenQP input.system.

      Coordinates are written in Angstrom because the OpenQP input reader converts
      the text geometry into its internal Bohr representation. Bohr inputs can be
      passed with unit="Bohr".