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 to the PDBx/mmCIF dictionary, suitable for deposition in a repository such as ModelArchive. The files can be viewed in any regular PDBx mmCIF viewer, such as UCSF 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 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 extension dictionary.) In particular, many python-ihm classes and modules are used in this library, for example the ihm.Grant and ihm.Citation classes for handling grant or citation information, or the ihm.dictionary module for validating files against the mmCIF dictionary itself.