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Provenance
**********
The IHM dictionary is designed to capture all aspects of integrative modeling,
from the original deposited experimental data to the final validated models.
This allows for maximum reproducibility and resuability. However, many
modeling packages are only concerned with the conversion of their own inputs
to output models (for example, a model of a complex may be generated by
docking comparative models guided by some experimental data of the
entire complex). If only this last step of the procedure is captured in the
output mmCIF file (in this case, without any information on how the comparative
models were themselves obtained) the chain is broken and the outputs cannot
be reproduced.
One solution to this problem is to diligently ensure that every input to
the modeling has been deposited in an appropriate database and always refer
to inputs using :class:`ihm.location.DatabaseLocation`. In cases where this
is not possible, the library provides some metadata parsers in the
:mod:`ihm.metadata` module. These will make a best effort to extract any
metadata from files available on the local hard drive to better describe their
provenance. For example, if the file contains headers or other information that
shows that it is merely a copy of a file deposited in an official database,
the metadata parsers will return a suitable
:class:`~ihm.location.DatabaseLocation` for the dataset. Other information,
such as the software used to generate the file, may be available in the
metadata.
For more details, see :class:`ihm.metadata.MRCParser` for electron microscopy
density maps (MRC files) or
:class:`ihm.metadata.PDBParser` for coordinate files in PDB format.
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