Re: [Ambit-users] [Urgent] problem with smirks

[Yannick .D. <y.d...@gm...>]

require 'java'
require 'lib/cdk/cdk-1.4.19.jar'
require 'lib/ambit2/ambit2-core-2.5.4-20140227.134038-19.jar'
require 'lib/ambit2/ambit2-base-2.5.4-20140227.134038-19.jar'
require 'lib/ambit2/ambit2-smarts-2.5.4-20140104.083219-2.jar'

import java.util.Vector
import 'ambit2.smarts.SMIRKSManager'
import 'ambit2.smarts.SMIRKSReaction'
import 'ambit2.smarts.SMIRKSTransform'
import 'ambit2.smarts.query.SmartsPatternCDK'
import 'org.openscience.cdk.AtomContainer'
import 'org.openscience.cdk.smiles.SmilesParser'
import 'org.openscience.cdk.smiles.SmilesGenerator'
import 'org.openscience.cdk.smiles.smarts.SMARTSQueryTool'
import 'org.openscience.cdk.silent.SilentChemObjectBuilder'
import 'org.openscience.cdk.tools.manipulator.AtomContainerManipulator'
import 'org.openscience.cdk.interfaces.IChemObjectBuilder'
 
builder = SilentChemObjectBuilder.getInstance()
sg = SmilesGenerator.new
sp = SmilesParser.new(builder)
cob = IChemObjectBuilder.new()
smrkMan = SMIRKSManager.new(cob)

reaction = smrkMan.parse(a given SMIRKS string)
molecule = sp.parseSmiles(the query smiles)

if smrkMan.applyTransformation(molecule, reaction)
  return target
end


Example 1
	#SMIRKS / SMILES
		[*;#6:1][C:2]#[C:3][*;#6:4]>>[*:1]/[C:2](/[H])=[*:3](/[H])[C:4]
		COCCCC#CCCC

	Error: 
	Vector.java:744:in `get': java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 0
		from SMIRKSManager.java:512:in `applyTransformAtLocation'
		from SMIRKSManager.java:286:in `applyTransformation'
		from SMIRKSManager.java:194:in `applyTransformation'
		from NativeMethodAccessorImpl.java:-2:in `invoke0'
		from NativeMethodAccessorImpl.java:57:in `invoke'
		from DelegatingMethodAccessorImpl.java:43:in `invoke'
		from Method.java:606:in `invoke'
		from JavaMethod.java:470:in `invokeDirectWithExceptionHandling'
		from JavaMethod.java:328:in `invokeDirect'
		from InstanceMethodInvoker.java:71:in `call'
		from CachingCallSite.java:346:in `cacheAndCall'
		from CachingCallSite.java:204:in `call'
	

Example 2
	#SMIRKS / SMILES	
		[*;#6:1][C:2]=[O:3]>>[*;#6:1][C:2]-[O:3][*;#6]
		CCC=O
	
	Error: No error


Example 3

	#SMIRKS / SMILES
		[C:1]=O>>[C:1]1OCCO1   # Taken from the Daylight SMIRKS examples page
		CCCCCCC=O
	
	Error:
		NoMethodError: undefined method `newInstance' for #<#<Class:0xfb0d6fe>:0x22f2c5be>
		newInstance at org/jruby/gen/InterfaceImpl765047607.gen:13
		   (root) at metabolize-with-ambit-cdk.jrb: xxx ==> This refers to the line 29 "if smrkMan.applyTransformation(molecule, reaction)"

Example 4

	#SMIRKS / SMILES
		[*:1]C(=O)O>>[*:1]C(N)=O   # Taken from the Daylight SMIRKS examples page
		CCCCCCC(=O)O
		
	Error:
		NoMethodError: undefined method `newInstance' for #<#<Class:0xfb0d6fe>:0x22f2c5be>
		newInstance at org/jruby/gen/InterfaceImpl765047607.gen:13
		   (root) at metabolize-with-ambit-cdk.jrb: xxx ==> This refers to the line 29 "if smrkMan.applyTransformation(molecule, reaction)"

   
    It looks like the smirks is wrong but I do not think so. I have tried many others but I get a lot of these errors.