SMIRKSTransformation (Ambit 2 4.0.1-SNAPSHOT API)

java.lang.Object
- ambit2.smarts.processors.SMIRKSTransformation

All Implemented Interfaces:

Comparable<SMIRKSTransformation>
```
public class SMIRKSTransformation
extends Object
implements Comparable<SMIRKSTransformation>
```
Placeholder for set of SMIRKS with additional options

Author:

nina

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`applicable`
`protected boolean`	`enabled`
`protected String`	`example`
`protected int`	`id`
`protected SmartsConst.SSM_MODE`	`mode`
`protected String`	`name`
`protected int`	`order`
`protected Set<String>`	`precondition_atom`
`protected Set<String>`	`precondition_atomtype`
`protected String`	`reactionClass`
`protected String`	`smirks`
`protected SMIRKSReaction`	`smirksReaction`

Constructor Summary

Constructors
Constructor and Description

SMIRKSTransformation()

Constructors
Constructor and Description
`SMIRKSTransformation()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addPreconditionAtom(String atomSymbol)`
`void`	`addPreconditionAtomtype(String atomtype)`
`boolean`	`applyTransformation(SMIRKSManager smrkMan, org.openscience.cdk.interfaces.IAtomContainer target)`
`int`	`compareTo(SMIRKSTransformation o)`
`void`	`configure(SMIRKSManager smrkMan)`
`boolean`	`equals(Object obj)`
`String`	`getExample()`
`int`	`getId()`
`SmartsConst.SSM_MODE`	`getMode()`
`String`	`getName()`
`int`	`getOrder()`
`String`	`getReactionClass()`
`String`	`getSMIRKS()`
`int`	`hashCode()`
`Boolean`	`hasPreconditionAtom(String atomSymbol)`
`Boolean`	`hasPreconditionAtomDefined()`
`Boolean`	`hasPreconditionAtomtype(String atomtype)`
`Boolean`	`hasPreconditionAtomTypeDefined()`
`boolean`	`isApplicable()`
`boolean`	`isEnabled()`
`void`	`setApplicable(boolean applicable)`
`void`	`setEnabled(boolean enabled)`
`void`	`setExample(String example)`
`void`	`setId(int id)`
`void`	`setMode(SmartsConst.SSM_MODE mode)`
`void`	`setName(String name)`
`void`	`setOrder(int order)`
`void`	`setReactionClass(String reactionClass)`
`void`	`setSMIRKS(String smirks)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

enabled
```
protected boolean enabled
```

smirks
```
protected String smirks
```

id
```
protected int id
```

mode
```
protected SmartsConst.SSM_MODE mode
```

precondition_atom

protected Set<String> precondition_atom

precondition_atomtype

protected Set<String> precondition_atomtype

applicable
```
protected boolean applicable
```

example
```
protected transient String example
```

order
```
protected int order
```

name
```
protected String name
```

reactionClass
```
protected String reactionClass
```

smirksReaction

protected transient SMIRKSReaction smirksReaction

Constructor Detail
- SMIRKSTransformation
```
public SMIRKSTransformation()
```

Method Detail

getOrder
```
public int getOrder()
```

setOrder
```
public void setOrder(int order)
```

getExample
```
public String getExample()
```

setExample

public void setExample(String example)

isApplicable
```
public boolean isApplicable()
```

setApplicable

public void setApplicable(boolean applicable)

getMode
```
public SmartsConst.SSM_MODE getMode()
```

setMode

public void setMode(SmartsConst.SSM_MODE mode)

isEnabled
```
public boolean isEnabled()
```

setEnabled

public void setEnabled(boolean enabled)

getSMIRKS
```
public String getSMIRKS()
```

setSMIRKS
```
public void setSMIRKS(String smirks)
```

getId
```
public int getId()
```

setId
```
public void setId(int id)
```

getName
```
public String getName()
```

setName
```
public void setName(String name)
```

getReactionClass
```
public String getReactionClass()
```

setReactionClass

public void setReactionClass(String reactionClass)

addPreconditionAtom

public void addPreconditionAtom(String atomSymbol)

addPreconditionAtomtype

public void addPreconditionAtomtype(String atomtype)

hasPreconditionAtomtype

public Boolean hasPreconditionAtomtype(String atomtype)

hasPreconditionAtomDefined

public Boolean hasPreconditionAtomDefined()

hasPreconditionAtomTypeDefined

public Boolean hasPreconditionAtomTypeDefined()

hasPreconditionAtom

public Boolean hasPreconditionAtom(String atomSymbol)

configure

public void configure(SMIRKSManager smrkMan)
               throws Exception

Throws:: Exception

applyTransformation

public boolean applyTransformation(SMIRKSManager smrkMan,
                                   org.openscience.cdk.interfaces.IAtomContainer target)
                            throws Exception

Throws:: Exception

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class Object

compareTo
```
public int compareTo(SMIRKSTransformation o)
```
Specified by:

compareTo in interface Comparable<SMIRKSTransformation>

equals
```
public boolean equals(Object obj)
```
Overrides:

equals in class Object

toString
```
public String toString()
```
Overrides:

toString in class Object

Class SMIRKSTransformation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

enabled

smirks

id

mode

precondition_atom

precondition_atomtype

applicable

example

order

name

reactionClass

smirksReaction

Constructor Detail

SMIRKSTransformation

Method Detail

getOrder

setOrder

getExample

setExample

isApplicable

setApplicable

getMode

setMode

isEnabled

setEnabled

getSMIRKS

setSMIRKS

getId

setId

getName

setName

getReactionClass

setReactionClass

addPreconditionAtom

addPreconditionAtomtype

hasPreconditionAtomtype

hasPreconditionAtomDefined

hasPreconditionAtomTypeDefined

hasPreconditionAtom

configure

applyTransformation

hashCode

compareTo

equals

toString