Package ffx.potential

Class Utilities

java.lang.Object

ffx.potential.Utilities

public final class Utilities
extends Object

The Utilities class provides methods to locate functional units of an organic system.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	Utilities.FileType	An enumeration of recognized file types.
static enum	Utilities.PolymerType	An enumeration of recognized organic polymers.

Constructor Summary

Constructors

Constructor	Description
Utilities()

Method Summary

Modifier and Type	Method	Description
static void	biochemistry(MolecularAssembly molecularAssembly, List<Atom> atoms)	This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.
static Atom	findSeed(Atom end, Atom other)	Returns an atom bonded to the "end" atom, which is not equal to "other".
static Character	getChainID(int i)	Determine chainID for a given polymer number.
static double	RMSCoordDev(MolecularAssembly m1, MolecularAssembly m2)	Finds the RMS deviation between the atoms of MolecularAssembly m1 and m2 provided they have the same number of atoms.
static String	stackTraceToString(Throwable ex)	Gets the stack trace for an exception and converts it to a String.

Methods inherited from class java.lang.Object

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

Constructor Details

Utilities

public Utilities()

Method Details

RMSCoordDev

public static double RMSCoordDev(MolecularAssembly m1,
 MolecularAssembly m2)

Finds the RMS deviation between the atoms of MolecularAssembly m1 and m2 provided they have the same number of atoms.

Parameters:

m1 - a MolecularAssembly object.

m2 - a MolecularAssembly object.

Returns:

a double.

biochemistry

public static void biochemistry(MolecularAssembly molecularAssembly,
 List<Atom> atoms)

This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.

Parameters:

molecularAssembly - a MolecularAssembly object.

atoms - a List object.

findSeed

public static Atom findSeed(Atom end,
 Atom other)

Returns an atom bonded to the "end" atom, which is not equal to "other".

Parameters:

end - Atom

other - Atom

Returns:

Atom

getChainID

public static Character getChainID(int i)

Determine chainID for a given polymer number.

Parameters:

i - int

Returns:

Character

stackTraceToString

public static String stackTraceToString(Throwable ex)

Gets the stack trace for an exception and converts it to a String.

Parameters:

ex - An exception.

Returns:

A String of its stack trace.