On Tue, 28 May 2024 10:36:12 -0700 Jose Duarte <jose.dua...@rcsb.org> wrote:
> Biojava doesn't parse pubmed ids by default. However you can do it > with the cif parser that Biojava uses underneath: ciftools-java . See > the README providing very clear examples on how to extract CIF fields: > > https://github.com/rcsb/ciftools-java > > Note that ciftools-java can also use the BinaryCIF format, which makes > parsing much faster. > Many thanks, this is very useful. Is there a way to loop over _atom_site entries? What I would like is to loop over the entries, check that there is, for example, a ZN atom and take its coordinates. Is it possible, or to do that is better to use BioJava? > Alternatively, you can avoid parsing CIF altogether and instead use > the RCSB PDB Data API for this (via the GraphQL interface). See this > example in the Data API tutorial: https://data.rcsb.org/#gql-example-2 Thanks, I'll check how to create GraphQl query in Spring boot. > > Jose > > > On Mon, 27 May 2024 at 07:39, Enrico Morelli <more...@cerm.unifi.it> > wrote: > > > Dear, > > > > is there a way to get PubMed ID from a CIF file downloaded from > > rscb.org site? > > > > In the CIF file is the line "citation.pdbx_database_id_PubMed > > 1910042". > > > > Thanks > > > > -- > > ----------------------------------------------------------- > > Enrico Morelli > > System Administrator | Programmer | Web Developer > > > > CERM - Polo Scientifico > > via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY > > ------------------------------------------------------------ > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > https://mailman.open-bio.org/mailman/listinfo/biojava-l > > -- ----------------------------------------------------------- Enrico Morelli System Administrator | Programmer | Web Developer CERM - Polo Scientifico via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY ------------------------------------------------------------ _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org https://mailman.open-bio.org/mailman/listinfo/biojava-l
