autosphere.readme

最经典的分子对结软件

                       README file for AutoSphere:

            A program to form a sphere set for docking from the 
                  0 cluster spheres generated by SPHGEN.

      Authors:  Scott Pegg (Kuntz Group, Dept. of Pharm. Chem., UCSF)
                Jim Arnold (Kuntz Group, Dept. of Pharm. Chem., UCSF)
                Ken Foreman and Michelle Lamb gave good constructive criticism.


Overview
--------

The spheres in "cluster 0" of the SPHGEN output file are selected with the following 
procedure:

     1. Remove spheres not within one of the following specifications for volume:
           a box, a large sphere, or close to a designated protein residue with
           a defined radius.
     2. Remove spheres distant from the protein surface.
     3. Remove spheres too close to other spheres, as such:
           x = sphere closest to the center of the enclosed space
           loop (until all spheres visited or removed):
              remove all spheres closer than given filt_cut to x
              x = next closest remaining sphere

Currently, the algorithm will execute all three steps.


Usage
-----

The parameters for AutoSphere are read from an input file that should be
specified on the command line. For example, if the parameters are in the file
"foo.in", AutoSphere should be called as 

      AutoSphere foo.in



INPUT FILE  The input file will look like this (each parameter is described further below):
----------

residue          1
res_num          25
residue_cutoff   10.0
sphere           0
sphere_center    0.0 0.0 0.0
radius           1.0
box              0
box_center       0.0 0.0 0.0
filter_cutoff    1.4
surface_cutoff   6.0
receptor_file    /idk1/people/arnold/fulcrum/SitePrint/TestSet/hivpr/site/4phv_align_neg.pdb
sph_file         /idk1/people/arnold/fulcrum/SitePrint/TestSet/hivpr/spheres/4phv0.sph
output_file      /idk1/people/arnold/fulcrum/SitePrint/TestSet/hivpr/spheres/4phv0_ts


Format Notes:

   - You can only have one argument per line.
   - Absolute path names must be specified, i.e.  
       
       "/idk1/people/arnold/fulcrum..."    NOT    "~arnold/fulcrum..."

   - You must remove TERs from the input pdb file so that all chains will be read
     (the dock 4.0.1 code is used to read the input pdb).


Parameters
----------

The parameters are specified in a separate text file, and have the format:

      <parameter>   <type> [<type2> ... ]

Some parameters are required, and are denoted with a <req> after the <type>
shown below.  The <req> field does NOT go into the .in file and is just shown
here to help you put together a good input file.  There is also error checking 
in the program to let you know if anything is left out.


The following are the allowed parameters:

  residue  <int> <req:  must specify either residue, sphere, or box>

    If true, spheres will be filtered by distance to a defined residue.

  res_num  <int> <req:  if residue is specified>

    Number of the residue used to define center of binding site for 
    sphere filtering.

  residue_cutoff  <float> <req:  if residue is specified>

    Max distance a sphere may be from a heavy atom of a residue used to 
    designate the binding site.

  sphere  <int> <req:  must specify either residue, sphere, or box>

    True if a spherical volume is being used to decide which spheres to keep.

  sphere_center  <float> <float> <float> <req:  if sphere is true>

    This parameter specifies the center of the sphere.
    The three floating point values should be the X, Y, and Z coordinates.

  radius  <float> <req if sphere is true>

    This parameter specifies the radius of the spherical enclosed space. The
    value should be a floating point distance in angstroms.

  box  <int> <req:  must specify either residue, sphere, or box>

    This parameter specifies that the enclosed space used to select spheres to
    keep is a box.
    The three floating point values specifiy the length of each dimension of
    the box, in X, Y, Z order. 

  box_center  <float> <float> <float> <req if box is true>

    This parameter specifies the center of the rectalinear enclosed space.
    The three floating point values specifiy the X, Y, and Z coordinates of
    the center of the box.

  filter_cutoff  <float>

    Min distance between spheres when filtering out spheres that "bump"
    other spheres.

  surface_cutoff  <float>

    Max distance a sphere may be from a heavy atom on the receptor molecule
    and still be retained.

  lig_sph_file  <filename.pdb> 

    Specifies a pdb format file containing a ligand bound in the site of
    interest.  Spheres from the ligand heavy atoms will be added to the
    list of spheres.

  receptor_file  <filename.pdb> <req>

    Specifies a pdb format file containing the binding site molecule.

  sph_file  <SPHGEN output file> <req>

    This parameter specifies the name of the SPHGEN output file that 
    contains the spheres you want to choose from. The AutoSphere program
    uses "cluster 0" from this file, so make sure you've got that cluster
    labelled as such.

  output_file	<filename> <req>

    This parameter specifies a name for the output of the thinned spheres
    in SPHGEN output format. This file is readable by DOCK.

    ** Both .pdb and .sph output files will be written, so you can also
       look at the spheres.

  


Errors
------

There are a fair amount of GUARDS in the program to prevent it from crashing
due to problems like beginning with 0 spheres.  If you find an error, please
email Scott and Jim with details about how you produced it.  

The debug (.dbf) file contains flags that you can turn on to see diagnostic
messages without recompiling the program.  Look in the code to see which flags 
you want to have on.


Programmer's Notes
------------------

There are a few programming notes as comments in AutoSphere.c and a bit more
in AutoSphere.h.

Bugs and gripes go to: [e-mail] or [e-mail]