Is there a package that can compute the molecular mass based on an amino acid sequence?
MolecularGraph has the machinery, but that appears to be focused on small molecules.
I can’t find a method in BioSequences
Probably not what you want, but from the PDB file you can do this:
julia> using PDBTools
julia> pdb = wget("1LBD")
Array{Atoms,1} with 1870 atoms with fields:
index name resname chain resnum residue x y z beta occup model segname index_pdb
1 N SER A 225 1 45.228 84.358 70.638 67.05 1.00 1 - 1
2 CA SER A 225 1 46.080 83.165 70.327 68.73 1.00 1 - 2
3 C SER A 225 1 45.257 81.872 70.236 67.90 1.00 1 - 3
⋮
1868 OG1 THR A 462 238 -27.462 74.325 48.885 79.98 1.00 1 - 1868
1869 CG2 THR A 462 238 -27.063 71.965 49.222 78.62 1.00 1 - 1869
1870 OXT THR A 462 238 -25.379 71.816 51.613 84.35 1.00 1 - 1870
julia> mass(pdb)
24719.768399999957
julia> formula(pdb)
C₁₁₉₂N₃₂₀O₃₄₆S₁₂
Thanks for the link. I was not aware of PDBTools. I looked in BioStructures.jl, but did not find anything,
I love the formula 
I don’t normally have a PDB-file, but now we have alphafold, so maybe 
It’s not in BioStructures.jl - PRs welcome of course.
Well, that was really easy (not surprisingly) to implement in PDBTools. Now you can do (with version 0.12.12, which will be available at any moment):
julia> using PDBTools
julia> seq = "ATVR"
"ATVR"
julia> mass(Sequence(seq))
427.4986
julia> seq = ["ARG", "THR", "GLU"]
3-element Vector{String}:
"ARG"
"THR"
"GLU"
julia> mass(Sequence(seq))
386.4036
It does not handle terminals in any sense, it is just the sum of the average mass (isopically speaking) of the amino acid residues in the sequence.
Thank you so much @lmiq . This is exactly what I need!
How I just love this community!