[Biojava-l] How to find Pubmed ID

[Enrico Morelli]

On Tue, 28 May 2024 10:36:12 -0700
Jose Duarte <jose.duarte at 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 <morelli at 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 at 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
------------------------------------------------------------