loos::DensityTools::BulkedWaterFilter Class Reference

Add bulk water back into the mask/map. More...

#include <internal-water-filter.hpp>

Inheritance diagram for loos::DensityTools::BulkedWaterFilter:

Collaboration diagram for loos::DensityTools::BulkedWaterFilter:

Public Member Functions
	BulkedWaterFilter (WaterFilterBase *p, const double pad, const double zmin, const double zmax)
std::string	name (void) const
	Just states the name of the filter/picker.
std::vector< int >	filter (const loos::AtomicGroup &, const loos::AtomicGroup &)
	Given a molecule and a set of waters, pick which waters are inside.
std::vector< loos::GCoord >	boundingBox (const loos::AtomicGroup &)
	Calculate the appropriate bounding box (given the molecule)
double	volume (void)
	Calculate the volume of the region we can pick waters from...
Public Member Functions inherited from loos::DensityTools::WaterFilterDecorator
	WaterFilterDecorator (WaterFilterBase *p)

Additional Inherited Members
Protected Attributes inherited from loos::DensityTools::WaterFilterBase
std::vector< loos::GCoord >	bdd_

Detailed Description

Add bulk water back into the mask/map.

When using a water filter, particularly with the ZClipped decorator, you will end up with internal waters that don't necessarily connect to bulk (for pore-like proteins). You will also not get bulk water layers if you're simulating a membrane system. To make it obvious that you've got water in there, use the Bulked decorator. This decorator examines waters not picked by the internal filters. If the water lies within the molecule's bounding box (plus pad), and is higher or lower than the given z-bounds, it is accepted as an "internal" water. This will give you a nice plane of bulk water over your protein/membrane.

Member Function Documentation

boundingBox()

vector< GCoord > loos::DensityTools::BulkedWaterFilter::boundingBox ( const loos::AtomicGroup & )

virtual

Calculate the appropriate bounding box (given the molecule)

Reimplemented from loos::DensityTools::WaterFilterDecorator.

filter()

vector< int > loos::DensityTools::BulkedWaterFilter::filter ( const loos::AtomicGroup & , const loos::AtomicGroup &  )

virtual

Given a molecule and a set of waters, pick which waters are inside.

The result is a map of which waters are inside (1 = inside, 0 = not)

Reimplemented from loos::DensityTools::WaterFilterDecorator.

name()

string loos::DensityTools::BulkedWaterFilter::name ( void ) const

virtual

Just states the name of the filter/picker.

Reimplemented from loos::DensityTools::WaterFilterDecorator.

volume()

double loos::DensityTools::BulkedWaterFilter::volume ( void )

inlinevirtual

Calculate the volume of the region we can pick waters from...

Reimplemented from loos::DensityTools::WaterFilterDecorator.

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The documentation for this class was generated from the following files:

• Packages/DensityTools/internal-water-filter.hpp
• Packages/DensityTools/internal-water-filter.cpp