Sam Ireland

CD-Hit Precompiled Binaries

2

Would it be possible for precompiled binaries for the usual platforms to be provided through some means? In the same way that the NCBI provide binaries for blast+? I managed...

Select atom by location in biological assemblies with duplicate chains

5

Currently the atom selection language lets you specify chain/residue/name etc. to determine which atom you are talking about, and is quite comprehensive. When dealing with the raw asymmetric unit coordinates,...

If a post links to a imgur.com/gallery post, they are currently just skipped. Ideally this would be handled, but it's not a priority.

Issue raised via Twitter. Difficult currently as atoms are returned as just set objects - this would need to be changed, but doing so would open up other possibilities too....

Add option for offline mirror of PDB

1

Using an environment variable, user should be able to specify a directory that atomium will look in first before fetching a file over the internet.

Two examples are 6SG9 and 6SGA. The zinc atoms have no chain associated because the two columns seem to have swapped meaning in these structures. It is unclear if this...

For some reason, the .cif files for specific assemblies that you can download for assemblies don't have a `struct_asym` table. atomium needs this table because there is no other way...

Implement parallel processing

3

The multiprocessing library could speed up parts of the PDB parsing process - especially those parts that are just processing thousands of records.

As in: https://github.com/samirelanduk/atomium/blob/b2bcc432eff035e1dd5803204ecbdd348289c5b8/atomium/structures/molecules.py#L267

'Invalid database read for database data' on running expandaln

6

The `expandaln` command fails to properly read index, producing an '`Invalid database read for database data`' error ## Expected Behavior Command to run without error messages. ## Current Behavior Command...