Package org.openscience.cdk.smirks
Enum SmirksOption
- java.lang.Object
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- java.lang.Enum<SmirksOption>
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- org.openscience.cdk.smirks.SmirksOption
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- All Implemented Interfaces:
Serializable
,Comparable<SmirksOption>
public enum SmirksOption extends Enum<SmirksOption>
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Enum Constant Summary
Enum Constants Enum Constant Description DIFF_PART
Do not allow '[*:1].[*:2]' to match the same fragment.EXPAND_HYDROGENS
Preprocessing - Automatically convert implicit hydrogens to explicit hydrogens when the pattern contains a '*'.IGNORE_IMPL_H
Do not allow the implicit hydrogen count to be set.IGNORE_SET_ELEM
Do not allow the atomic number to be changed.IGNORE_TOTAL_H
Do not allow the total hydrogen count to be set.IGNORE_TOTAL_H0
Do not allow the total hydrogen count to be set if it is 0.OVERWRITE_BOND
If a bond already exists where a new one is to be created update the bond order as required.PEDANTIC
Additional check and warnings when parsing SMIRKS.RECOMPUTE_HYDROGENS
Postprocessing - Recompute the implicit hydrogen count on changed atoms that has not had its hydrogen count explicitly set.REMOVE_UNMAPPED_FRAGMENTS
Postprocessing - Remove any disconnected fragments that were not matched by the transformed.REVERSE
Run the reaction backwards (retro synthesis).
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Field Summary
Fields Modifier and Type Field Description static Set<SmirksOption>
DAYLIGHT
static Set<SmirksOption>
RDKIT
Align closer with RDKit's "Reaction SMARTS" semantics.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static SmirksOption
valueOf(String name)
Returns the enum constant of this type with the specified name.static SmirksOption[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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PEDANTIC
public static final SmirksOption PEDANTIC
Additional check and warnings when parsing SMIRKS.
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REVERSE
public static final SmirksOption REVERSE
Run the reaction backwards (retro synthesis). The right-hand-side is now matched as a query. Note that not all SMIRKS are reversible and good form is usually write separate forward/backwards transformations.
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DIFF_PART
public static final SmirksOption DIFF_PART
Do not allow '[*:1].[*:2]' to match the same fragment. The preferred way to do this component grouping '([*:1]).([*:2])' but if you are only performing reactions it is reasonable that you expect the parts to be different and some toolkits only have this as an option.
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IGNORE_SET_ELEM
public static final SmirksOption IGNORE_SET_ELEM
Do not allow the atomic number to be changed.[Pb:1]>>[Au:1]
will do nothing.
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IGNORE_IMPL_H
public static final SmirksOption IGNORE_IMPL_H
Do not allow the implicit hydrogen count to be set.[Ch4:1]>>[Ch3:1]
does nothing.
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IGNORE_TOTAL_H
public static final SmirksOption IGNORE_TOTAL_H
Do not allow the total hydrogen count to be set.[CH4:1]>>[CH3:1]
does nothing.
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IGNORE_TOTAL_H0
public static final SmirksOption IGNORE_TOTAL_H0
Do not allow the total hydrogen count to be set if it is 0.[CH4:1]>>[CH3:1]
works but[CH4:1]>>[CH0:1]
does not.
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OVERWRITE_BOND
public static final SmirksOption OVERWRITE_BOND
If a bond already exists where a new one is to be created update the bond order as required.
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REMOVE_UNMAPPED_FRAGMENTS
public static final SmirksOption REMOVE_UNMAPPED_FRAGMENTS
Postprocessing - Remove any disconnected fragments that were not matched by the transformed.
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RECOMPUTE_HYDROGENS
public static final SmirksOption RECOMPUTE_HYDROGENS
Postprocessing - Recompute the implicit hydrogen count on changed atoms that has not had its hydrogen count explicitly set.
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EXPAND_HYDROGENS
public static final SmirksOption EXPAND_HYDROGENS
Preprocessing - Automatically convert implicit hydrogens to explicit hydrogens when the pattern contains a '*'.
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Field Detail
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RDKIT
public static final Set<SmirksOption> RDKIT
Align closer with RDKit's "Reaction SMARTS" semantics.
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DAYLIGHT
public static final Set<SmirksOption> DAYLIGHT
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Method Detail
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values
public static SmirksOption[] 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 (SmirksOption c : SmirksOption.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static SmirksOption valueOf(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:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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