topol
========================

.. contents::
  :local:

This task is used to add missing atoms and build the topology of the input molecule.

.. hint::

  It is strongly **recommended** to use ``check`` to correct the molecules before generating topology.

Arguments
-------------

.. option:: -i, --in

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - Yes
    * - Argument
      - PDB filename or XYZ filename
    * - Default
      - None
  
  Give the input molecule.

.. option:: -o, --out

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - A filename prefix
    * - Default
      - None
  
  Give the output filename prefix. If not given, the molecule and topology will be written to ``x-topol.pdb`` and ``x-topol.psf``, respectively.

  Example:

  .. code-block:: bash

    # Add hydrogen atoms, then build the topology.
    $ pdbtop topol -i 3kab-protein.pdb -o 3kab-topol

.. option:: --add-rtfs

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - Additional residue topology files.
    * - Default
      - None
  
  Give additional residue topology files (RTF), path can be included.

  By default, pdbtop will load RTF files in ``data/``. If you want to add your own ones, you can use this option.

  Example:

  .. code-block:: bash

    # Add 2 topology files: ``my-topology1.rtf`` and ``/usr/data/my-topology2.rtf``.
    $ pdbtop topol -i 3kab-protein.pdb -o 3kab-topol --add-rtfs "my-topology1.rtf /usr/data/my-topology2.rtf"

.. option:: --no-patching-terminus

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Default
      - False
  
  By defulat, pdbtop will add N- and C-terminus for each protein chain. But if ``--no-patching-terminus`` is given, this will not be done.

  .. hint::

    It you want to do some modifications on the terminal resiudes, you'd better use ``--no-patching-terminus`` at this stage. After modifications, you can patch terminus again.