Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Use CIF format instead of discontinued MMTF #548

Merged
merged 1 commit into from
Aug 16, 2024
Merged

Use CIF format instead of discontinued MMTF #548

merged 1 commit into from
Aug 16, 2024

Conversation

paulsmirnov
Copy link
Member

Description

Resolves #539

As of July 2, 2024, RCSB PDB no longer serves PDB data in the MMTF compression format. So, this PR:

  • Changes the Gallery and examples to use CIF instead of MMTF,
  • Removes the "mmtf:" prefix support from the load function,
  • Keeps the MMTF file format support for backward compatibility.

Type of changes

  • Bug fix (non-breaking change that fixes an issue)

Note that the external source ceased to work, so we shouldn't mark it as a breaking change even if it removes the old (non-working) functionality.

Checklist

  • I have read CONTRIBUTING and CODE_OF_CONDUCT guides.
  • I have followed the code style of this project.
  • I have run yarn run ci: lint and tests pass locally with my changes.
  • I have updated tests that prove my fix/feature works.
  • I have updated the necessary documentation.

@paulsmirnov
Use CIF format instead of discontinued MMTF
8af17a2 
As of July 2, 2024, RCSB PDB will no longer serve PDB data in the MMTF
compression format. Users are strongly encouraged to switch to
accessing the data files offered in the compressed BinaryCIF (BCIF)
format.
@paulsmirnov paulsmirnov self-assigned this Aug 16, 2024
@paulsmirnov paulsmirnov linked an issue Aug 16, 2024 that may be closed by this pull request
Cannot load an MMTF file #539
Closed
NataliaDSmirnova
NataliaDSmirnova approved these changes Aug 16, 2024
View reviewed changes
Copy link
Collaborator

@NataliaDSmirnova NataliaDSmirnova left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It's a good time to update the format support declaration👍

@paulsmirnov paulsmirnov merged commit 6acff3d into main Aug 16, 2024
4 checks passed
@paulsmirnov paulsmirnov deleted the 539-cannot-load-mmtf branch August 16, 2024 02:29
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@NataliaDSmirnova NataliaDSmirnova NataliaDSmirnova approved these changes

Assignees

@paulsmirnov paulsmirnov

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Cannot load an MMTF file
2 participants
@paulsmirnov @NataliaDSmirnova