Calculating X-ray scattering profiles from large number of atoms using GPU
(Last Updated: 09/02/2019, Merged to SWAXS.jl, Archived 09/14/2020)
- ArrayFire
- Microsoft Visual Studio Community
Run gpuswaxs --help
********************************************************************************
********** gpuswaxs.exe: version 1.0.0 **********
********** A GPU-accelerated computation of the small-wide-angle **********
********** X-ray scattering (SWAXS) profile (.dat) from .binvox **********
********** or .pdb file(s). Require: ArrayFire Library **********
********** **********
********** AUTHOR: Yen-Lin Chen @ Cornell **********
********** DATE: Sept. 2 2019 **********
********************************************************************************
GPU implementation of SWAXS profile calculation.
Usage:
GPUSWAXS [OPTION...] [ARGS...]
-B, --binvox arg The shape file of dummy voxels: .binvox (default: )
-P, --pdb arg The single PDB mode for atomic coordinates: .pdb (default: )
-T, --solute arg The solute.pdb file (default: )
-V, --solvent arg The solvent.pdb file (default: )
-d, --density arg The electron density averaged on a voxel, in e/A^3 (default: 0.50)
-v, --voxdim arg The voxel size in A (default: 2.0)
-J, arg The number of orientations (default: 1800)
--qmin arg The minimum q in 1/A
--qspacing arg The spacing in q axis
--qmax arg The maximum q reached
-h, --help Print this help message and exit
Run the following
gpuswaxs --binvox por.binvox 0.0 0.01 1.0
The command line output should look like this:
********************************************************************************
********** gpuswaxs.exe: version 1.0.0 **********
********** A GPU-accelerated computation of the small-wide-angle **********
********** X-ray scattering (SWAXS) profile (.dat) from .binvox **********
********** or .pdb file(s). Require: ArrayFire Library **********
********** **********
********** AUTHOR: Yen-Lin Chen @ Cornell **********
********** DATE: Sept. 2 2019 **********
********************************************************************************
GPUSWAXS: Operating in binvox shape mode ...
GPUSWAXS: binvox file = por.binvox with J = 1800 and q = 0:0.01:1 density = 0.5 voxdim = 2
Voxel INFO: [#binvox]
Voxel INFO: Reading binvox version: 1
Voxel INFO: Keyword [translate], ignored.
Voxel INFO: Keyword [scale], ignored.
Voxel INFO: Success, read 4083 voxels
Voxel INFO: por.binvox read-in successfully.
Voxel INFO: Start to calculate swaxs curves with J = 1800 and q = 0:0.01:1 density = 4e/A^3
100% completed: |||||||||||||||||||||||||||||||||||||||||||||||||
Voxel INFO: Elapsed time: 3.95272 seconds
Voxel INFO: Writing q, and intensity to the file: por.dat .
Voxel INFO: Writing completed successfully.
The SWAXS profile is then saved as por.dat file.
Run the following
gpuswaxs --pdb rna.pdb 0.0 0.01 1.0
The output should look like
********************************************************************************
********** gpuswaxs.exe: version 1.0.0 **********
********** A GPU-accelerated computation of the small-wide-angle **********
********** X-ray scattering (SWAXS) profile (.dat) from .binvox **********
********** or .pdb file(s). Require: ArrayFire Library **********
********** **********
********** AUTHOR: Yen-Lin Chen @ Cornell **********
********** DATE: Sept. 2 2019 **********
********************************************************************************
GPUSWAXS: Operating in single pdb mode ...
GPUSWAXS: pdb file = rna.pdb with J = 1800 and q = 0:0.01:1
PDB INFO: Detected 8998 atoms in the file: rna.pdb.
PDB INFO: Processing all atomic coordinates ...
PDB INFO: Finished processing all atomic coordinates.
PDB INFO: Start to calculate swaxs curves...
100% completed: |||||||||||||||||||||||||||||||||||||||||||||||||
PDB INFO: Elapsed time: 8.91705 seconds
PDB INFO: Writing q, and intensity profile to the file: rna.dat .
PDB INFO: Writing completed successfully.
The SWAXS profile is saved as rna.dat file.
Run
gpuswaxs --solute solute.pdb --solvent solvent.pdb 0.0 0.01 1.0
The output is then
********************************************************************************
********** gpuswaxs.exe: version 1.0.0 **********
********** A GPU-accelerated computation of the small-wide-angle **********
********** X-ray scattering (SWAXS) profile (.dat) from .binvox **********
********** or .pdb file(s). Require: ArrayFire Library **********
********** **********
********** AUTHOR: Yen-Lin Chen @ Cornell **********
********** DATE: Sept. 2 2019 **********
********************************************************************************
GPUSWAXS: Operating in pair pdb mode ...
GPUSWAXS: solute file = solute.pdb solvent file = solvent.pdb with J = 1800 and q = 0:0.01:1
PDB INFO: Detected 8998 atoms in the file: solute.pdb.
PDB INFO: Processing all atomic coordinates ...
PDB INFO: Finished processing all atomic coordinates.
PDB INFO: Detected 8230 atoms in the file: solvent.pdb.
PDB INFO: Processing all atomic coordinates ...
PDB INFO: Finished processing all atomic coordinates.
PDB INFO: Start to calculate swaxs curves...
100% completed: |||||||||||||||||||||||||||||||||||||||||||||||||
PDB INFO: Elapsed time: 13.8732 seconds
PDB INFO: Writing q, and intensity to the file: solute_buffer_subtracted.dat .
PDB INFO: Writing completed successfully.
The result will have a postfix of _buffer_subtracted. The SWAXS file is saved as solute_buffer_subtracted.dat.
- Regarding PDB errors, please format your
.pdbfile(s). - Not sure if I will maintain this in the future ...