Difference between revisions of "Bump Filter"

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Orientations and grow steps may be filtered prior to scoring to discard those in which the molecule significantly overlaps receptor atoms. This feature is enabled with the bump_filter flag. At the time of construction of the bump filter, the amount of atom VDW overlap is defined with the bump_overlap parameter (see Grid). At the time of bump evaluation the number of allowed bumps is defined with the max_bump parameter. If score optimization is being performed, then a few number of bumps should be allowed, since the minimizer can recover from such clashes. In addition, a few bumps often indicate an orientation that interacts intimately with the site and often leads to a strongly favorable orientation after minimization.
  
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NOTE: The following parameter definitions will use the format below:
  
    Orientations and grow steps may be filtered prior to scoring to discard those in which the molecule significantly overlaps receptor atoms. This feature is enabled with the bump_filter flag. At the time of construction of the bump filter, the amount of atom VDW overlap is defined with the bump_overlap parameter (see Grid). At the time of bump evaluation the number of allowed bumps is defined with the max_bump parameter. If score optimization is being performed, then a few number of bumps should be allowed, since the minimizer can recover from such clashes. In addition, a few bumps often indicate an orientation that interacts intimately with the site and often leads to a strongly favorable orientation after minimization.
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parameter_name [default] (value):
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#description
  
    NOTE: The following parameter definitions will use the format below:
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In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.
  
        parameter_name [default] (value):
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Bump Filter Parameters
        #description
 
  
    In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.
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* bump_filter [yes] (yes, no):
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#Flag to perform bump filtering
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* bump_grid_prefix [grid] (string):
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#The prefix to the grid file containing the desired bump grid
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* max_bumps [2] (int):
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#The maximum allowed number of bumps for a molecule to pass #the filter
  
    Bump Filter Parameters
 
  
        * bump_filter [yes] (yes, no):
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[[Category:DOCK:Sampling problem]]
          #Flag to perform bump filtering
 
        * bump_grid_prefix [grid] (string):
 
          #The prefix to the grid file containing the desired bump grid
 
        * max_bumps [2] (int):
 
          #The maximum allowed number of bumps for a molecule to pass #the filter
 

Latest revision as of 18:10, 8 October 2012

Orientations and grow steps may be filtered prior to scoring to discard those in which the molecule significantly overlaps receptor atoms. This feature is enabled with the bump_filter flag. At the time of construction of the bump filter, the amount of atom VDW overlap is defined with the bump_overlap parameter (see Grid). At the time of bump evaluation the number of allowed bumps is defined with the max_bump parameter. If score optimization is being performed, then a few number of bumps should be allowed, since the minimizer can recover from such clashes. In addition, a few bumps often indicate an orientation that interacts intimately with the site and often leads to a strongly favorable orientation after minimization.

NOTE: The following parameter definitions will use the format below:

parameter_name [default] (value):

  1. description

In some cases, parameters are only needed (questions will only be asked) if the parameter above is enforced. These parameters are indicated below by additional indentation.

Bump Filter Parameters

  • bump_filter [yes] (yes, no):
  1. Flag to perform bump filtering
  • bump_grid_prefix [grid] (string):
  1. The prefix to the grid file containing the desired bump grid
  • max_bumps [2] (int):
  1. The maximum allowed number of bumps for a molecule to pass #the filter