Bump Filter - Revision history

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2012-10-08T18:10:28Z

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JohnIrwin at 17:54, 27 September 2007

2007-09-27T17:54:18Z

← Older revision		Revision as of 17:54, 27 September 2007
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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.

	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:

	~~NOTE: The following parameter definitions will use the format below~~:		parameter_name [default] (value):
			#description

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


	[[Category:DOCK:Sampling problem]]		[[Category:DOCK:Sampling problem]]

JohnIrwin at 22:32, 13 September 2007

2007-09-13T22:32:18Z

← Older revision		Revision as of 22:32, 13 September 2007
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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.		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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	* max_bumps [2] (int):		* max_bumps [2] (int):
	#The maximum allowed number of bumps for a molecule to pass #the filter		#The maximum allowed number of bumps for a molecule to pass #the filter


			[[Category:DOCK:Sampling problem]]

JohnIrwin at 22:52, 19 September 2006

2006-09-19T22:52:26Z

New page

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):
#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):
#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