- Add Python 3.9 support.
- Single-chain models are now assigned the chain ID 'A'. This differs
from older versions of Modeller, which assigned a blank ID. To get
the old behavior, set AutoModel.blank_single_chain to True, or set the
same argument for Alignment.append_sequence(),
Model.generate_topology(), or Model.build_sequence().
- All Modeller classes are now named using CamelCase (e.g. Model,
Alignment, AutoModel) for consistency with other Python packages.
The Modeller 9 class names (e.g. model, alignment, automodel)
are still provided for backwards compatibility. Using one of the old names
will trigger a warning. To report an error instead, set the
MODELLER_DEPRECATION environment variable to the string 'ERROR'.
- All classes in the modeller.parallel module for handling remote
processes now derive from the Worker class (e.g. LocalWorker,
SSHWorker). As above, the old class names are retained for backwards
- The default file format for Model.read() has changed from 'PDB' to
'PDB_OR_MMCIF', i.e. a file with a .cif extension will now be read as an
mmCIF file while all other files will be read as PDB (as before).
- Residue numbers >= 10000 are now supported in PDB format files, using
hybrid-36 notation. This can be disabled by setting env.io.hybrid36
- 2-character chain IDs are now supported in PDB format files, by using
the otherwise-unused column 21. This can be disabled by
setting env.io.two_char_chain to False.
- Bundled version of HDF5 updated to 1.10.6.