#999 cif parsing - Githubissues

nglviewer / ngl

WebGL protein viewer

http://nglviewer.org/ngl/

MIT License

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#999 cif parsing #1001

Closed ppillot closed 7 months ago

ppillot commented 7 months ago

This PR fixes 2 bugs in relation with CIF files parsing:

999 chem_comp can be set for macromolecular cif files and contain vectors of entities. In the case of mmCIF files the block of code that parses files containing only one entity (such as PDB het cif files) must not be reached.
950 core cif files often define charges as part of the atom type symbol. In that case, the element symbol must be stripped of the charge.

hainm commented 7 months ago

@ppillot are you able to reproduce the bug without your change and see if the change actually fixes the issue?

hainm commented 7 months ago

Also, do you have any idea why nglview fails to show 3pqr recently, althought it has been working well for years (because we have been showing it as example in our nglview website)

Here is the code in nglview: https://github.com/nglviewer/nglview/blob/d9e7740100b586b1e73cc51d247d16b6dc8d0914/nglview/adaptor.py#L123-L125

hainm commented 7 months ago

Thank you. Hopefully there will be a release soon.

ppillot commented 7 months ago

@hainm release done and available on npm

hainm commented 7 months ago

Beautiful. Thank you very much.

nglviewer / ngl

#999 cif parsing #1001

999 chem_comp can be set for macromolecular cif files and contain vectors of entities. In the case of mmCIF files the block of code that parses files containing only one entity (such as PDB het cif files) must not be reached.

950 core cif files often define charges as part of the atom type symbol. In that case, the element symbol must be stripped of the charge.