com.chemaxon.calculations.stereoisomers

Class StereoisomerSettings

java.lang.Object

com.chemaxon.calculations.stereoisomers.StereoisomerSettings

@PublicAPI
public class StereoisomerSettings
extends java.lang.Object

Settings class for StereoisomerEnumeration.

Usage example:

 // create and set a new instance
 StereoisomerSettings settings = StereoisomerSettings.create()
         .setStereoisomerType(EnumSet.of(StereoisomerType.CISTRANS))   // only double bond stereoisomers are generated
         .setProtectTetrahedralStereo(true)                            // protect tetrahedral stereocenters
         .setVerify3d(true);                                           // invalid 3D structures are fitered
 
 // use these settings when a new enumeration is constructed
 StereoisomerEnumeration enumeration = new StereoisomerEnumeration(molecule, settings);
 

Since:

Marvin 14.12.15

Author:

Laszlo Antal

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StereoisomerSettings.StereoisomerType Types of stereoisomers.

Method Summary

Modifier and Type	Method and Description
static StereoisomerSettings	create() Constructs a new StereoisomerSettings object with default settings.
com.google.common.base.Optional<java.lang.Integer>	maxStereoisomerCount() Returns the adjusted maximum number of generated stereoisomers or Optional.absent().
boolean	outputIn3d() Returns true if 3D structures will be generated.
boolean	protectDoubleBondStereo() Returns the adjusted double bond stereo protection flag.
boolean	protectTetrahedralStereo() Returns the adjusted tetrahedral stereo protection flag.
StereoisomerSettings	setMaxStereoisomerCount(int maxStereoisomerCount) Sets the maxinum number of stereoisomers to be generated.
StereoisomerSettings	setOutputIn3d(boolean outputIn3d) 3D structures are generated (invalid 3D structure are filtered)
StereoisomerSettings	setProtectDoubleBondStereo(boolean protectDoubleBondStereo) Sets double bond stereo protection.
StereoisomerSettings	setProtectTetrahedralStereo(boolean protectTetrahedralStereo) Sets the protection of tetrahedral stereo centers.
StereoisomerSettings	setStereoisomerType(java.util.EnumSet<StereoisomerSettings.StereoisomerType> types) Sets which types of stereoisomers should be generated.
StereoisomerSettings	setVerify3d(boolean verify3d) Invalid 3D structures of generated stereoisomers are filtered.
java.util.EnumSet<StereoisomerSettings.StereoisomerType>	stereoisomerTypes() Returns the type of generated stereoisomers.
java.lang.String	toString()
boolean	verify3d() Returns true if 3D structure will be checked for a valid stereo conformation.

Methods inherited from class java.lang.Object

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

Method Detail

create

public static StereoisomerSettings create()

Constructs a new StereoisomerSettings object with default settings.

Defaults:

 Types:                        EnumSet.allOf(StereoisomerType.class)
 Protect tetrahedral stereo:   false
 Protect double bond stereo:   false
 Max stereoisomer count:       Optional.absent()
 3D verify:                    false
 3D output:                    false
 

Returns:

a new StereoisomerSettings object

stereoisomerTypes

public java.util.EnumSet<StereoisomerSettings.StereoisomerType> stereoisomerTypes()

Returns the type of generated stereoisomers.

Returns:

an EnumSet which contains the stereoisomerism types

See Also:

StereoisomerSettings.StereoisomerType

protectTetrahedralStereo

public boolean protectTetrahedralStereo()

Returns the adjusted tetrahedral stereo protection flag.

Returns:

true if protects the tetrahedral stereo centers

protectDoubleBondStereo

public boolean protectDoubleBondStereo()

Returns the adjusted double bond stereo protection flag.

Returns:

true if protects the double bond stereo centers

maxStereoisomerCount

public com.google.common.base.Optional<java.lang.Integer> maxStereoisomerCount()

Returns the adjusted maximum number of generated stereoisomers or Optional.absent().

Returns:

an Optional object which contains the adjusted value

verify3d

public boolean verify3d()

Returns true if 3D structure will be checked for a valid stereo conformation.

Returns:

the adjusted value

outputIn3d

public boolean outputIn3d()

Returns true if 3D structures will be generated.

Returns:

the adjusted value

setStereoisomerType

public StereoisomerSettings setStereoisomerType(java.util.EnumSet<StereoisomerSettings.StereoisomerType> types)

Sets which types of stereoisomers should be generated.

Available values:

• StereoisomerSettings.StereoisomerType.TETRAHEDRAL : tetrahedral stereoisomers are generated
• StereoisomerSettings.StereoisomerType.CISTRANS : double bond stereoisomers are generated

Parameters:

types - are the stereoisomerism types (represented by an enumset)

Returns:

a StereoisomerSettings formed from this and the specified settings

See Also:

StereoisomerSettings.StereoisomerType

setProtectTetrahedralStereo

public StereoisomerSettings setProtectTetrahedralStereo(boolean protectTetrahedralStereo)

Sets the protection of tetrahedral stereo centers.

If true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed.

Parameters:

protectTetrahedralStereo - is true if preset tetrahedral stereo centers should be protected

Returns:

a StereoisomerSettings formed from this and the specified settings

setProtectDoubleBondStereo

public StereoisomerSettings setProtectDoubleBondStereo(boolean protectDoubleBondStereo)

Sets double bond stereo protection.

If true then the stereo configuration of double bonds with preset stereo information will not be changed.

Parameters:

protectDoubleBondStereo - is true if preset double bond stereo information should be protected

Returns:

a StereoisomerSettings formed from this and the specified settings

setMaxStereoisomerCount

public StereoisomerSettings setMaxStereoisomerCount(int maxStereoisomerCount)

Sets the maxinum number of stereoisomers to be generated.

If not set the StereoisomerEnumeration generates all stereoisomers of the molecule. It is recommended to use when there are too much stereoisomers to fit to the memory.

Parameters:

maxStereoisomerCount - the number of stereoisomers to be generated

Returns:

a StereoisomerSettings formed from this and the specified settings

setVerify3d

public StereoisomerSettings setVerify3d(boolean verify3d)

Invalid 3D structures of generated stereoisomers are filtered.

Parameters:

verify3d -

Returns:

a StereoisomerSettings formed from this and the specified settings

setOutputIn3d

public StereoisomerSettings setOutputIn3d(boolean outputIn3d)

3D structures are generated (invalid 3D structure are filtered)

Parameters:

outputIn3d -

Returns:

a StereoisomerSettings formed from this and the specified settings

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object