@PublicAPI public class StereoisomerSettings extends java.lang.Object
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);
Modifier and Type | Class and Description |
---|---|
static class |
StereoisomerSettings.StereoisomerType
Types of stereoisomers.
|
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.
|
public static StereoisomerSettings create()
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
StereoisomerSettings
objectpublic java.util.EnumSet<StereoisomerSettings.StereoisomerType> stereoisomerTypes()
EnumSet
which contains the stereoisomerism typesStereoisomerSettings.StereoisomerType
public boolean protectTetrahedralStereo()
public boolean protectDoubleBondStereo()
public com.google.common.base.Optional<java.lang.Integer> maxStereoisomerCount()
Optional.absent()
.Optional
object which contains the adjusted valuepublic boolean verify3d()
public boolean outputIn3d()
public StereoisomerSettings setStereoisomerType(java.util.EnumSet<StereoisomerSettings.StereoisomerType> types)
Available values:
StereoisomerSettings.StereoisomerType.TETRAHEDRAL
: tetrahedral stereoisomers are generated
StereoisomerSettings.StereoisomerType.CISTRANS
: double bond stereoisomers are generated
types
- are the stereoisomerism types (represented by an enumset)StereoisomerSettings
formed from this and the specified settingsStereoisomerSettings.StereoisomerType
public StereoisomerSettings setProtectTetrahedralStereo(boolean protectTetrahedralStereo)
If true
then stereo configuration of tetrahedral stereo centers with preset stereo information
will not be changed.
protectTetrahedralStereo
- is true
if preset tetrahedral stereo centers should be protectedStereoisomerSettings
formed from this and the specified settingspublic StereoisomerSettings setProtectDoubleBondStereo(boolean protectDoubleBondStereo)
If true
then the stereo configuration of double bonds with preset stereo information
will not be changed.
protectDoubleBondStereo
- is true
if preset double bond stereo information should be protectedStereoisomerSettings
formed from this and the specified settingspublic StereoisomerSettings setMaxStereoisomerCount(int maxStereoisomerCount)
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.
maxStereoisomerCount
- the number of stereoisomers to be generatedStereoisomerSettings
formed from this and the specified settingspublic StereoisomerSettings setVerify3d(boolean verify3d)
verify3d
- StereoisomerSettings
formed from this and the specified settingspublic StereoisomerSettings setOutputIn3d(boolean outputIn3d)
outputIn3d
- StereoisomerSettings
formed from this and the specified settingspublic java.lang.String toString()
toString
in class java.lang.Object