+Introduction

+************

+

+This package provides a mechanism to describe the generation of a

+theoretical model (for example, via comparative or homology model)

+a set of Python objects. This includes, if applicable

+

+ - the templates(s) used for the modeling;

+ - the alignment between the template(s) and target sequence;

+ - the protocol used to generate models, such as template search, modeling,

+ and model selection;

+ - the actual coordinates of output models;

+ - grouping of multiple models;

+ - quality scores for models and/or alignments.

+

+Once created, this set of Python objects can be written to an mmCIF file

+that is compliant with the

+`ModelCIF extension <https://github.com/ihmwg/ModelCIF>`_

+to the `PDBx/mmCIF dictionary <http://mmcif.wwpdb.org/>`_,

+suitable for deposition in a repository such as

+`ModelArchive <https://modelarchive.org/>`_. The files can be viewed in any

+regular PDBx mmCIF viewer, such as

+`UCSF ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_ (although most viewers

+to date will only show the model coordinates, not the ModelCIF-specific

+metadata).

+

+This package leverages functionality provided by the

+`python-ihm <https://github.com/ihmwg/python-ihm>`_ package, which functions

+similarly, building a Python hierarchy and then reading/writing mmCIF files.

+(However, python-ihm is used for integrative models, and reads or writes files

+compliant with the `integrative/hybrid modeling <https://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/>`_ extension dictionary.)

+In particular, many python-ihm classes and modules are used in this library,

+for example the :class:`ihm.Grant` and :class:`ihm.Citation` classes for

+handling grant or citation information, or the :mod:`ihm.dictionary` module

+for validating files against the mmCIF dictionary itself.