polymerist.molfiles.pdb
=======================

.. py:module:: polymerist.molfiles.pdb

.. autoapi-nested-parse::

   PDB file atom line formatting tools



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/polymerist/molfiles/pdb/pdbatoms/index


Classes
-------

.. autoapisummary::

   polymerist.molfiles.pdb.SerialAtomLabeller


Package Contents
----------------

.. py:class:: SerialAtomLabeller

   For assigning unique numbered atom names based on their
   order of appearance within a molecule and elemental class

   Useful, for example, in generating unique atom names for a PDB file

   :Parameters: * **atom_label_width** (*int , default 4*) -- Exact length alloted for any generated atom label
                  Labels shorter than this are right-padded with spaces,
                  while labels longer than this are truncated

                  Default of 4 is the chosen to be compatible with the PDB specification ("Atom name: lines 13-16, left-justified")
                  https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
                * **include_elem_idx** (*bool, default True*) -- Whether to attach a numerical element-index postfix to atom labels

                  E.g. with atom_label_width=4, the fifth carbon in a topology
                  will be labelled as "C004" with include_elem_idx=True,
                  while labelled as "C   " with include_elem_idx=False,
                * **default_elem_idx** (*int, default 0*) -- Starting index for each element category
                  By default, is 0-indexed; MUST BE POSITIVE


   .. py:attribute:: atom_label_width
      :type:  int
      :value: 4



   .. py:attribute:: include_elem_idx
      :type:  bool
      :value: True



   .. py:attribute:: default_elem_idx
      :type:  int
      :value: 0



   .. py:attribute:: element_counter
      :type:  collections.Counter


   .. py:method:: get_atom_label(elem_symbol: str) -> str

      Obtain a numbered atom label for an atom based on its element,
      updating the underlying element context in the process