Solvent Accessible Surface Area

General Usage
2

Update:

After the help from you, now we are in a different ballpark here.

For small structures the SASA here implemented takes similar time than Gromacs and VMD.

For large structures, it is much faster than Gromacs, and similar to VMD without the julia startup time (6co8.pdb is a ~700k virus capsid):

Gromacs:

$ time gmx sasa -s ./6co8.pdb -o sasa_output.xvg -ndots 100
real    1m15,536s
user    1m15,412s
sys     0m0,123s

VMD:

$ time vmd -dispdev text -e sasa_big.vmd
real    0m3,941s
user    0m3,716s
sys     0m0,543s

SASA from PDBTools.jl:

$ time julia --project -e "using PDBTools; sasa(atomic_sasa(read_pdb(\"6co8.pdb\")))"
real    0m7,134s
user    0m8,000s
sys     0m0,400s

#or
julia> @b sasa(atomic_sasa(pdb; parallel=false))
3.635 s (40045204 allocs: 1.186 GiB, 17.71% gc time, without a warmup)

To be released soon in PDBTools.jl 3.5.2

(all these are single-threaded, I’m not sure if VMD is using the GPU)

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