Package ffx.algorithms.misc

Class GenerateRotamers

java.lang.Object

ffx.algorithms.misc.GenerateRotamers

public class GenerateRotamers
extends Object

The GenerateRotamers class helps generate a rotamer library (particularly for nonstandard amino acids) for a Residue.

Author:

Jacob M. Litman, Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener)	Intended to create rotamer sets for nonstandard amino acids.
GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener, RotamerLibrary library)	Intended to create rotamer sets for nonstandard amino acids.

Method Summary

Modifier and Type	Method	Description
void	applyAndSaveTorsions(String[] torSets)	Accessory method for more simplistic saving of specific torsion states.
void	setBaselineAARes(AminoAcidUtils.AminoAcid3 aa3)	Sets a standard amino acid to be the baseline for rotamer generation.
void	setDepth(int start, int end)	Set which torsions to work on.
void	setElectrostatics(String electrostatics)	Inactivates electrostatics for atom sets defined by 'start-end,start-end,...'.
void	setInactiveAtoms(String iatoms)	Inactivates atom sets defined by 'start-end,start-end,...'.
void	setIncrement(double incr)	Sets the angle to change torsions by.
void	setPrint(boolean print)	Sets algorithm to log all torsions/energies (not just to file).
void	setSearchWidth(double width)	Sets the width around each torsion to search (+/-, so 10 degree width will search a 20 degree arc).
void	setVideo(String videoFile)	Null file indicates to not write a video.
void	tryRotamers()	Main driver method; spins torsions, evaluates energy, and prints to file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GenerateRotamers

public GenerateRotamers(MolecularAssembly molecularAssembly,
 Potential potential,
 Residue residue,
 File file,
 int nChi,
 AlgorithmListener listener)

Intended to create rotamer sets for nonstandard amino acids.

Parameters:

molecularAssembly - a MolecularAssembly object.

potential - a Potential object.

residue - a Residue object.

file - Output file

nChi - Number of rotameric torsions in the residue

listener - a AlgorithmListener object.

GenerateRotamers

public GenerateRotamers(MolecularAssembly molecularAssembly,
 Potential potential,
 Residue residue,
 File file,
 int nChi,
 AlgorithmListener listener,
 RotamerLibrary library)

Intended to create rotamer sets for nonstandard amino acids.

Parameters:

molecularAssembly - a MolecularAssembly object.

potential - a Potential object.

residue - a Residue object.

file - Output file

nChi - Number of rotameric torsions in the residue

listener - a AlgorithmListener object.

library - Rotamer library to use

Method Details

applyAndSaveTorsions

public void applyAndSaveTorsions(String[] torSets)

Accessory method for more simplistic saving of specific torsion states.

Parameters:

torSets - an array of String objects.

setBaselineAARes

public void setBaselineAARes(AminoAcidUtils.AminoAcid3 aa3)

Sets a standard amino acid to be the baseline for rotamer generation. For example, use TYR as a baseline for phospho-tyrosine.

Parameters:

aa3 - a AminoAcidUtils.AminoAcid3 object.

setDepth

public void setDepth(int start,
 int end)

Set which torsions to work on. Negative end values set the final depth to be the total number of torsions.

Parameters:

start - The first torsion to work on.

end - The last torsion to work on.

setElectrostatics

public void setElectrostatics(String electrostatics)

Inactivates electrostatics for atom sets defined by 'start-end,start-end,...'.

Parameters:

electrostatics - Input string

setInactiveAtoms

public void setInactiveAtoms(String iatoms)

Inactivates atom sets defined by 'start-end,start-end,...'.

Parameters:

iatoms - Input string

setIncrement

public void setIncrement(double incr)

Sets the angle to change torsions by.

Parameters:

incr - a double.

setPrint

public void setPrint(boolean print)

Sets algorithm to log all torsions/energies (not just to file).

Parameters:

print - a boolean.

setSearchWidth

public void setSearchWidth(double width)

Sets the width around each torsion to search (+/-, so 10 degree width will search a 20 degree arc).

Parameters:

width - a double.

setVideo

public void setVideo(String videoFile)

Null file indicates to not write a video.

Parameters:

videoFile - Filename for video or null

tryRotamers

public void tryRotamers()

Main driver method; spins torsions, evaluates energy, and prints to file.