Difference between revisions of "Matching Sphere Scan"

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Usage:
 
Usage:
  
     python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py {YOUR_DOCK_DIR} {#DIRECTORIES} {MAX_DIST_TO_PERTURB}
+
     python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py -p {YOUR_DOCK_DIR}
  
So if you wanted to generate 100 new docking directories with 100 different perturbed matching sphere setups (randomly differing from the original matching spheres by at maximum 0.5 Å), use the command:
+
By default, it will create 10 directories with perturbed matching spheres (randomly differing from the original matching spheres by at maximum 0.5 Å)
  
     python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py DOCK_DIR/ 100 0.5
+
If you want to change the number of directories or distance from the original matching spheres, use the -n and -d flags:
 +
 
 +
     python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py -p {YOUR_DOCK_DIR} -n 100 -d 0.5
  
 
Trent's original script, which makes use of his "sph_lib.py" is located here, and can be run on a single set of matching spheres:
 
Trent's original script, which makes use of his "sph_lib.py" is located here, and can be run on a single set of matching spheres:

Revision as of 12:18, 21 May 2020

This script generates some number of directories with perturbed matching spheres. This will randomly perturb non-crystallographic spheres generated by SPHGEN during blastermaster.

The original script was written by Trent Balius. Wrapper script is written by Reed Stein.

Usage:

   python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py -p {YOUR_DOCK_DIR}

By default, it will create 10 directories with perturbed matching spheres (randomly differing from the original matching spheres by at maximum 0.5 Å)

If you want to change the number of directories or distance from the original matching spheres, use the -n and -d flags:

   python ~rstein/zzz.scripts/sphere_sets_scripts/generate_non_xtal_spheres_dirs.py -p {YOUR_DOCK_DIR} -n 100 -d 0.5

Trent's original script, which makes use of his "sph_lib.py" is located here, and can be run on a single set of matching spheres:

   python ~tbalius/zzz.scripts/make_random_sph_non_ligand.py {INPUT_SPHERE_FILE} {MAX_DISTANCE_TO_PERTURB} {OUTPUT_SPHERE_NAME}

Note that the non-crystallographic spheres in the original matching_spheres.sph file have a "0.000" in the fifth column. This is changed to "0.500" after perturbing the matching spheres. If you would like to perturb the matching spheres again after you have already run it, the fifth column with "0.500" needs to be changed back to "0.000"


If you would like to perturb all matching spheres, and not just the non-crystallographic spheres generated from SPHGEN, run the following command:

   python ~tbalius/zzz.scripts/make_random_sph.py {INPUT_SPHERE_FILE} {MAX_DISTANCE_TO_PERTURB} {OUTPUT_SPHERE_NAME}