Comments (2)
If you like, you could certainly make your own Alphabet
subclass for ligands. But you're supposed to pass ChemComp
objects for each ligand directly to the Entity
constructor. That being said, you'll run into problems later on (since the dumpers assume all entities are polymeric) but I'll work on that and update this issue accordingly.
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The library should now have basic support for writing out structures containing nonpolymers, although there are still a few loose ends. See the ligands_water.py
example, and open issues for any further problems you run into.
from python-ihm.
Related Issues (20)
- Don't ever treat read-in objects as identical
- Warn on output, don't fail, if one or more empty Entities are present
- Read entity.type from input files
- Better handle seq_id for waters, branched entities HOT 2
- CifCheck validation fails on files with non-ASCII characters HOT 1
- Support for chemical component dictionary HOT 3
- Handle duplicate save frames HOT 1
- Add `make-mmcif.py` to the python package
- Add support for database_2 and pdbx_database_status tables
- Installation doesn't copy ihm/util
- Add support for updates in IHMCIF required for unification with PDB
- Allow for float ihm_external_files.file_size_bytes
- Improve reading of ihm_external_files category
- Error while parsing sequence information in entry PDBDEV_00000030 HOT 3
- Add case- and whitespace-preserving tokenizers HOT 3
- make_mmcif.py does not handle some of the IHMCIF tables
- Make sure all unused objects are preserved by read-write cycle HOT 3
- `make-mmcif.py` does not support certain IHMCIF data items HOT 2
- Preserve alt locs in atom_site table
- Disallow empty sequence in ResidueFeature constructor
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