Spencer Bliven
Spencer Bliven
This should limit one of the biggest reasons for slow prompts, mitigating #6. Set `$AGNOSTER_PROMPT_TIMEOUT` to limit the amount of time the git command can run. This requires GNU timeout,...
It would be nice to use the planner with older Factorio versions as well.
A discussion came up in PR #774 regarding the correct behavior when parsing an mmCif file without `auth_seq_id`. BioJava 4.2.11 requires the `auth_seq_id` column. This is a problem because it...
This addresses #1019 and was developed in parallel with @josemduarte's fix #1020. It has been rebased to remove duplicated effort, and now consists mostly of additional tests for the bug.
I think `Profile` was indended to be general enough to represent multiple sequence alignments. However `SimpleProfile` is the only current implementation and it only supports pairwise alignments. There is also...
What's the intended meaning of `PDBHeader.getDescription`? It is populated in mmCIF with the `_struct_keywords.pdbx_keywords` field, the same as `getClassification()` (e.g. lyase, oxidase, etc). It seems to be unused in PDB...
PDB and mmCIF files use symmetry operators to reduce the number of atoms which need to be specified. This is used with NCS to reconstruct the asymmetric unit (e.g. in...
CATH releases [daily snapshots](http://cathdb.info/wiki/doku/?id=index#cath_daily_snapshot). It would be very nice to be able to access these in BioJava. Currently it's not easy to work with these in `CathInstallation`. We should add...
Creating a new `contact.ResidueIdentifier` (not to be confused with `ResidueNumber`) requires that the Group have a valid alignedResIndex in the corresponding `Compound`. Is there a reasonable way to handle missing...
AtomCache doesn't fetch obsolete entries if configured to use MMTF. I believe that RCSB is not providing obsolete MMTF files. In this case we should fall back to mmcif. We...