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Code and Scripts



pdb_broken_dock_mol_using_clustering_varinglenth.py "This code will loop through dock 3.6 and topdock output and remove broken molecules."
db2_to_mol2.py This code will convert a db2 file to a multi mol2 file. A version of this script is also distrbuted with DOCK3.7. Needs mol2.py.
mol2.py This python library is for reading in, writting out, and processing mol2 files. A version of this library is also distrbuted with DOCK3.7. This library was written by Trent Balius and Sudipto Mukherjee.
mol2_center_of_mass.py calculates the center of mass of a mol2 file using the python library mol2 files. Written by Trent Balius.
pdb_lib.py This python library is for reading in, writting out, and processing pdb files.
sph_lib.py This python library is for reading in, writting out, and processing sph files (files produced by sphgen which is an program avalible with DOCK).
close_sph.py This python program that is for reading in sphere file and a pdb file and writes out all sphere close to the pdb file (square of 5 from any atom of the pdb). This program uses both pdb_lib.py and sph_lib.py.
mol2toSPH_radius.py This python program that converts a mol2 file to a sphere file. This program uses the library mol2.py.
volume_cal_sph.py This python program reads in a sphere file and will calculate the volume displaced by the spheres. It does this by performing the following: (1) laying a grid over the spheres (Ng is the size of the grid, Vg is the volume of the grid box). (2) idenifing those point contained in the spheres (Ns). The volume of spheres is calculated by the following:
Vs ~= Vg * (Ns/Ng).
This method was used in Pottel et al. ACS Chem. Biol., 2018, 13 (9), pp 2522-2533. See Wiki page on how to run it.
GIST_scripts.zip Scripts for combining and processing GIST grids. The code is avalible on github here.
heme parms The heme force field was downloaded from Bryce's AMBER parameter database The heme parameters were adapted for Cytochrome c Peroxidases by adding a positive charge to the iron (iron Fe III has a 1.25 charge). Amber preparation (prep and frcmod) files for the heme are here.
tarball for rescoring Here is what is in the tarball:


This scripts suport the bkslab wiki page:

The script convert_anyMol2_to_dockMol2.py is contributed by Ying Yang.

modified: 2018/09/26