Class StereoisomerSettings
java.lang.Object
com.chemaxon.calculations.stereoisomers.StereoisomerSettings
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
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Nested Class Summary
Modifier and TypeClassDescriptionstatic enum
Types of stereoisomers. -
Method Summary
Modifier and TypeMethodDescriptionstatic StereoisomerSettings
create()
Constructs a newStereoisomerSettings
object with default settings.Returns the adjusted maximum number of generated stereoisomers orOptional#absent()
.boolean
Returns true if 3D structures will be generated.boolean
Returns the adjusted double bond stereo protection flag.boolean
Returns the adjusted tetrahedral stereo protection flag.setMaxStereoisomerCount
(int maxStereoisomerCount) Sets the maxinum number of stereoisomers to be generated.setOutputIn3d
(boolean outputIn3d) 3D structures are generated (invalid 3D structure are filtered)setProtectDoubleBondStereo
(boolean protectDoubleBondStereo) Sets double bond stereo protection.setProtectTetrahedralStereo
(boolean protectTetrahedralStereo) Sets the protection of tetrahedral stereo centers.Sets which types of stereoisomers should be generated.setVerify3d
(boolean verify3d) Invalid 3D structures of generated stereoisomers are filtered.Returns the type of generated stereoisomers.toString()
boolean
verify3d()
Returns true if 3D structure will be checked for a valid stereo conformation.
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Method Details
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create
Constructs a newStereoisomerSettings
object with default settings.Defaults:
Types: EnumSet.allOf(StereoisomerType.class) Protect tetrahedral stereo: false Protect double bond stereo: false Max stereoisomer count: Optional.empty() 3D verify: false 3D output: false
- Returns:
- a new
StereoisomerSettings
object
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stereoisomerTypes
Returns the type of generated stereoisomers.- Returns:
- an
EnumSet
which contains the stereoisomerism types - See Also:
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protectTetrahedralStereo
public boolean protectTetrahedralStereo()Returns the adjusted tetrahedral stereo protection flag.- Returns:
- true if protects the tetrahedral stereo centers
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protectDoubleBondStereo
public boolean protectDoubleBondStereo()Returns the adjusted double bond stereo protection flag.- Returns:
- true if protects the double bond stereo centers
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maxStereoisomerCount
Returns the adjusted maximum number of generated stereoisomers orOptional#absent()
.- Returns:
- an
Optional
object which contains the adjusted value
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verify3d
public boolean verify3d()Returns true if 3D structure will be checked for a valid stereo conformation.- Returns:
- the adjusted value
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outputIn3d
public boolean outputIn3d()Returns true if 3D structures will be generated.- Returns:
- the adjusted value
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setStereoisomerType
public StereoisomerSettings setStereoisomerType(EnumSet<StereoisomerSettings.StereoisomerType> types) Sets which types of stereoisomers should be generated.Available values:
StereoisomerSettings.StereoisomerType.TETRAHEDRAL
: tetrahedral stereoisomers are generatedStereoisomerSettings.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:
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setProtectTetrahedralStereo
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
- istrue
if preset tetrahedral stereo centers should be protected- Returns:
- a
StereoisomerSettings
formed from this and the specified settings
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setProtectDoubleBondStereo
Sets double bond stereo protection.If
true
then the stereo configuration of double bonds with preset stereo information will not be changed.- Parameters:
protectDoubleBondStereo
- istrue
if preset double bond stereo information should be protected- Returns:
- a
StereoisomerSettings
formed from this and the specified settings
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setMaxStereoisomerCount
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
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setVerify3d
Invalid 3D structures of generated stereoisomers are filtered.- Returns:
- a
StereoisomerSettings
formed from this and the specified settings
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setOutputIn3d
3D structures are generated (invalid 3D structure are filtered)- Returns:
- a
StereoisomerSettings
formed from this and the specified settings
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toString
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