Metadata-Version: 2.1
Name: scipion-em-atomstructutils
Version: 3.0.3
Summary: A Scipion plugin to manipulate atomic structure files (PDB/MMCIF)
Home-page: https://github.com/scipion-em/scipion-em-atomstructutils
Author: Roberto Marabini and Marta Martinez
Author-email: scipion@cnb.csic.es
License: UNKNOWN
Keywords: scipion pdb  scipion-3
Platform: UNKNOWN
Requires-Dist: scipion-em-chimera (>=3.0.0)

================================
Atom_struct_utils scipion plugin
================================

Utilities for handling PDB/mmcif atomic structure files:

Current plugin protocols:

* operate (option extract): extract a chain from an atom structure (pdb/cif file).
* operate (option add): perform union of several atomic structures.
* convert_sym: takes an atomStruct in any icosahedric symemtry and rotates it to another.

===================
Install this plugin
===================

**READ** The "Binary file" section before installing this package


You will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion to run these protocols.

- **Stable version**  

.. code-block:: 

      scipion installp -p scipion-em-atom_struct_utils

OR

  - through the plugin manager GUI by launching Scipion and following **Configuration** >> **Plugins**

- **Developer's version** 

1. Download repository: 

.. code-block::

            git clone https://github.com/scipion-em/scipion-em-atom_struct_utils.git

2. Install:


.. code-block::

            scipion installp -p path_to_scipion-em-atom_struct_utils --devel

- **Binary files** 

Atom_struct_utils plugin is a pure Python module but uses the program "maxit"
for conversion of pdb/cif files with atomic coordinates. If not available maxit will be
instaled. Prerequisites for maxit are  **bison**, **flex**, **csh** and **tcsh**

.. code-block::

      sudo apt install bison  (command valid for ubuntu/debian and similar OS)
      sudo apt install felx   (command valid for ubuntu/debian and similar OS) 
      sudo apt install csh   (command valid for ubuntu/debian and similar OS) 


- **Tests**

To check the installation, simply run the following Scipion test:
    * `scipion test --grep TestOperate --run`
    * `scipion test --grep TestConvertSymmetry --run`

========
Examples
========

See `Model Building Tutorial <https://github.com/I2PC/scipion/wiki/tutorials/tutorial_model_building_basic.pdf>`_



===============
Buildbot status
===============

Status devel version: 

.. image:: http://scipion-test.cnb.csic.es:9980/badges/atomstructutils_devel.svg

Status production version: 

.. image:: http://scipion-test.cnb.csic.es:9980/badges/atomstructutils_prod.svg


