pdb_dataframe: inconsistent calpha pointer

[Lars Skjærven]

For branch feature_pdb_dataframe:

pdb = read.pdb("1cdk")
inds = atom.select(pdb, "calpha")$atom

identical(inds, which(pdb$calpha))
[1] FALSE

For branch master:

pdb = read.pdb("1cdk")
inds = atom.select(pdb, "calpha")$atom

identical(inds, which(pdb$calpha))
[1] TRUE

[Lars Skjærven]

proposing to replace the following in read.pdb():

calpha = (atom[,"elety"]=="CA") & (atom[,"resid"]!="CA") & (atom[,"type"]=="ATOM")

with

output$calpha <- seq(1, nrow(atom)) %in% atom.select(output, "calpha")$atom

the latter will include calphas also for residues of type TPO, SEP, etc, while the current implementation will not.

[Barry Grant]

I agree - This will keep all potentially funny calcium containing residue as Calpha issues to one function, atom.select()

[Lars Skjærven]

included in previous commit on the data-frame branch