Paul Pillot

RCSB is deprecating MMTF file format and will stop serve it in July 2024

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https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c Recommended way would be to support BinaryMMCIF instead.

Compression efficiency: some mmCIF files are smaller than their BinaryCIF counterparts when not gzipped

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This is a question rather than an issue report. I have downloaded the BinaryCIF file for structure 5z6y from RCSB and the corresponding mmCIF file. | format | size |...

1015 binary cif support

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This PR adds support for Binary Cif files parsing and changes the RCSB data source provider to use this new format instead of the deprecated MMTF format. ### Changes made...

Take into account explicit hydrogens when creating and representing Hydrogen bonds (regular and weak)

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# Description Fixes #1163 This PR refines the way Hydrogen bonds are created and represented when explicit hydrogen atoms atoms are present: - Donors: the angle between H-Donor-Acceptor must be...

Hydrogen bonds perceived between polar hydrogens

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Hi team! I was looking at PDB 1GJ5 and noticed that the hydrogens from a water molecules had Hbonds interactions perceived with other polar hydrogens (from hydroxyl or amine groups)....

Interactions: Charge and H donor perceived on neutral Nitrogen when residue is protonated

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I've noticed the following interactions with the PDB structure 6KNR that has all hydrogens defined on its ligand DL9: notice the highlighted Nitrogen which has 3 covalent single bonds (hence...

**Is your feature request related to a problem? Please describe.** I would like to use the MCSS functions which were recently made available in MinimalLib, but the RDKitModule object generated...

Auto-bonding from PDB file generates covalent bonds around metals instead of coordination

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When loading 7RPZ from a PDB file and focusing the Mg ion, we can see that 6 covalent bonds have been created: When loading the same model from mmCIF, these...