Strip whitespaces from atom/element names
Opened this issue · 1 comments
babaid commented
When looking at an atom record I discovered that the whitespaces do not get stripped from the atom/element names when they are parsed.
An example: Dict{String, AbstractAtom}(" CA " => Atom CA with serial ,.....
As you can see, CA is sorrounded by spaces, which is kind of inconvenient. I suggest changing the function parseatomname in pdb.jl to the following:
function parseatomname(line::String, line_n::Integer=1)
try
return strip(line[13:16])
catch
throw(PDBParseError("could not read atom name", line_n, line))
end
end
And the same for parseelement.
jgreener64 commented
atomname
and similar functions strip the white space, and you can index into residues without the white space.
It does need to be kept though, since different spacings are used to indicate e.g. C-alpha vs calcium, and this should be preserved on writing out.