There's a call to get alt locs, e.g. something like this:
if (g.hasAltLoc()) {
System.out.println("## alt locs");
System.out.println(g.getAltLocs().size());
for (Group altLoc: g.getAltLocs()) {
for (Atom a : altLoc.getAtoms()) {
System.out.println(a);
}
}
}
Also do note the javadoc for getAltLocs to see what the exact behaviour is:
https://github.com/biojava/biojava/blob/5a699eb6465509b853463ae34ec04c4d90bc2a54/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java#L344-L364
On Wed, 7 May 2025 at 03:40, Enrico Morelli <more...@cerm.unifi.it> wrote:
> Dear all,
>
> we are trying to read the HETATM of the following cif
> https://files.rcsb.org/view/4KL8.cif with this code:
>
> for (Chain c : structure.getChains()) {
> for (Group g : c.getAtomGroups(GroupType.HETATM)) {
> for (Atom a : g.getAtoms()) {
> System.out.println(a);
>
> }
> }
> }
>
> But we realized that your methods doesn't read all the alternative
> conformation of some of the hetatm in the structure.
> For instance it reads FE 12360 but not FE 12361_
>
> HETATM 12360 FE FE A FCO W 7 . ? 27.605 -32.546 26.346 0.33 9.74
> ? 501 FCO M FE 1
> HETATM 12361 FE FE B FCO W 7 . ? 27.573 -32.629 26.079 0.67 10.53
> ? 501 FCO M FE 1
>
>
> Is it possible to read both or at least the one with the higher occupancy?
>
> Thank you very much in advance
>
> Regards
> --
> -----------------------------------------------------------
> Enrico Morelli
> System Administrator | Programmer | Web Developer
>
> CERM - Polo Scientifico
> via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
> ------------------------------------------------------------
> _______________________________________________
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> https://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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