remove
========================

.. contents::
  :local:

In this task, pdbtop will remove ions, waters, ligands, chains, etc. from the input molecule.

.. hint::

  All removing operations are done by **residue**. To delete a single atom, please refer to :doc:`modify`.

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 output will be written to ``x-remove.pdb``.

.. option:: --ions

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Default
      - False
  
  Remove ions from the input molecule, like Na\ :sup:`+`, Cl\ :sup:`-`, SO\ :sub:`4`\ :sup:`2-`, etc.

.. option:: --waters

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Default
      - False
  
  Remove waters from the input molecule.

.. option:: --ligands

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Default
      - False
  
  Remove ligands from the input molecule.

  Example:
  
  .. code-block:: bash

    $ # Remove ions, waters, and ligands from the input molecule 
    $ pdbtop remove -i 3kab.pdb --ions --waters --ligands -o 3kab-protein.pdb

.. option:: --chains

  .. list-table::
    :stub-columns: 1
       
    * - Mandatory
      - No
    * - Argument
      - 1 or more chain IDs, like  ``A`` or ``"B C"``
    * - Default
      - False
  
  Remove chains from the input molecule.

  Example:
  
  .. code-block:: bash

    $ pdbtop remove -i 3kab.pdb --chains "A B" # Remove chain A and B from the input molecule
    $ pdbtop remove -i 3kab.pdb --chains A     # Remove chain A from the input molecule