chemaxon.marvin.alignment

Enum AlignmentProperties.FlexibilityMode

java.lang.Object

java.lang.Enum<AlignmentProperties.FlexibilityMode>

chemaxon.marvin.alignment.AlignmentProperties.FlexibilityMode

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<AlignmentProperties.FlexibilityMode>

Enclosing class:

AlignmentProperties

public static enum AlignmentProperties.FlexibilityMode
extends java.lang.Enum<AlignmentProperties.FlexibilityMode>

Conformational flexibility treatment during the alignment for a pair of a molecule. If the reference molecule is set as rigid its coordinates remains intact, while if it is set for the second molecule, that will translate and rotate as a rigid body. If any molecule is set flexible it will translate and rotate and also, and if it has rotatable bonds, the dihedral angles around these bonds are tweaked in a continuous manner enabling the conformation to change to maximize the overlay.

Enum Constant Summary

Enum Constants

Enum Constant and Description
KEEP_BOTH_FLEXIBLE Keep both structures flexible during the alignment.
KEEP_BOTH_RIGID Keep both structures conformationally rigid during the alignment.
KEEP_FIRST_RIGID_SECOND_FLEXIBLE Keep the first reference structure rigid, and the second as flexible during the alignment.
KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA As of KEEP_FIRST_RIGID_SECOND_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds).

Method Summary

Modifier and Type	Method and Description
AlignmentProperties.DegreeOfFreedomType	getDf1()
AlignmentProperties.DegreeOfFreedomType	getDf2()
static AlignmentProperties.FlexibilityMode	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static AlignmentProperties.FlexibilityMode[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

KEEP_BOTH_RIGID

public static final AlignmentProperties.FlexibilityMode KEEP_BOTH_RIGID

Keep both structures conformationally rigid during the alignment.

KEEP_BOTH_FLEXIBLE

public static final AlignmentProperties.FlexibilityMode KEEP_BOTH_FLEXIBLE

Keep both structures flexible during the alignment.

KEEP_FIRST_RIGID_SECOND_FLEXIBLE

public static final AlignmentProperties.FlexibilityMode KEEP_FIRST_RIGID_SECOND_FLEXIBLE

Keep the first reference structure rigid, and the second as flexible during the alignment.

KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA

public static final AlignmentProperties.FlexibilityMode KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA

As of KEEP_FIRST_RIGID_SECOND_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds). So the cis amide in second molecule can be tweaked to trans if it is favored by the alignment.

Method Detail

values

public static AlignmentProperties.FlexibilityMode[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (AlignmentProperties.FlexibilityMode c : AlignmentProperties.FlexibilityMode.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static AlignmentProperties.FlexibilityMode valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

getDf1

public AlignmentProperties.DegreeOfFreedomType getDf1()

Returns:

the df1

getDf2

public AlignmentProperties.DegreeOfFreedomType getDf2()

Returns:

the df2