PDataCollector Class Reference

#include <PDataCollector.h>

List of all members.

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Detailed Description

User interface to collect information about loop conformations and output the results to a CS2 file.

Public Member Functions
	PDataCollector (const string &cs2FileName, const string &pdbFileName, int loopStartResIndex, int loopEndResIndex)
	PDataCollector (const string &cs2FileName, PProtein *loop)
	PDataCollector (const string &cs2FileName)
void	Clone (const string &newActivecs2Filename)
void	FindConformations (int amt, bool shouldBeCollisionFree)
void	FindConformations (int amt, LoopConfFunction FindOneConformation)
void	VisualizeLoop ()
void	VisualizeConformationSpace ()

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Constructor & Destructor Documentation

PDataCollector::PDataCollector	(	const string &	cs2FileName,
		const string &	pdbFileName,
		int	loopStartResIndex,
		int	loopEndResIndex
	)

Creates or overwrites the .cs2 file cs2FileName with the loop in pdbFileName from the residue indices given as parameters. The .cs2 file will have only one conformation inside, that from the pdb file.

PDataCollector::PDataCollector	(	const string &	cs2FileName,
		PProtein *	loop
	)

Creates or overwrites the .cs2 file cs2FileName with loop. loop should be a sub-loop of a protein.

PDataCollector::PDataCollector

(

const string &

cs2FileName

)

Creates a data collector that will append to the given file.

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Member Function Documentation

void PDataCollector::Clone

(

const string &

newActivecs2Filename

)

Clones the data collector and makes it layer off of the new file given.

void PDataCollector::FindConformations	(	int	amt,
		bool	shouldBeCollisionFree
	)

Finds the requested amount of conformations with the collision status necessary for a valid conformation given as a parameter. Behind the scenes, this function uses Cyclic Coordinate Descent (CCD) followed by an analytical exact IK solver. If the resulting conformation does not match the collision status necessary, it is discarded.

void PDataCollector::FindConformations	(	int	amt,
		LoopConfFunction	FindOneConformation
	)

Finds the requested amount of conformations using a user-provided function to find a conformation (which is given as a parameter a loop with randomized degrees of freedom).

void PDataCollector::VisualizeLoop

(

)

Visualizes a conformation and allows the user to manipulate it by hand. This function never returns.

void PDataCollector::VisualizeConformationSpace

(

)

Visualizes the conformation space. This function never returns.

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

• src/core/PDataCollector.h
• src/core/PDataCollector.cc

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