Try this:
import java.io.IOException;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import org.junit.Test;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.SMILESWriter;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.smsd.Isomorphism;
public class Mcs {
public static IAtomContainer getMcsAsNewContainer(IAtomContainer mol1,
IAtomContainer mol2) throws CDKException, CloneNotSupportedException,
IOException {
Isomorphism mcs = new
Isomorphism(org.openscience.cdk.smsd.interfaces.Algorithm.DEFAULT, true);
mcs.init(mol1, mol2, true, true);
mcs.setChemFilters(true, true, true);
System.out.println("MCS Size: " + mcs.getTanimotoAtomSimilarity());
System.out.println("MCS First Map: " + mcs.getFirstMapping());
System.out.println("MCS First size: " +
mcs.getFirstAtomMapping().size());
mol1 = mcs.getReactantMolecule();
mol2 = mcs.getProductMolecule();
IMolecule mcsmolecule =
DefaultChemObjectBuilder.getInstance().newInstance(IMolecule.class, mol1);
List<IAtom> atomsToBeRemoved = new ArrayList<IAtom>();
for (IAtom atom : mcsmolecule.atoms()) {
int index = mcsmolecule.getAtomNumber(atom);
// System.out.println("index: " +index);
if (!mcs.getFirstMapping().containsKey(index)) {
atomsToBeRemoved.add(atom);
}
}
for (IAtom atom : atomsToBeRemoved) {
mcsmolecule.removeAtomAndConnectedElectronContainers(atom);
}
StringWriter stringWriter = new StringWriter();
SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
smilesWriter.write(mcsmolecule);
smilesWriter.close();
System.out.println("MCS SMILES: " + stringWriter.toString());
return (IAtomContainer) mcsmolecule.clone();
}
@Test
public static void main(String[] args) throws CDKException,
CloneNotSupportedException, IOException {
SmilesParser sp = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
// Men_12
IAtomContainer A1 =
sp.parseSmiles("c1cccc(COC(=O)NC(CC(C)C)C(=O)NC(CCc2ccccc2)C(=O)COC)c1");
// Tri_06
IAtomContainer A2 =
sp.parseSmiles("c1cccc(COC(=O)NC(CC(C)C)C(=O)NCC#N)c1");
getMcsAsNewContainer(A2, A1);
getMcsAsNewContainer(A1, A2);
}
}
Best,
Asad
************************************************
Syed Asad Rahman (PhD, PG, B.Engg)
Research Scientist
EMBL-EBI
WTGC,
Hinxton CB10 1SD
Cambridge, UK
Phone: +44- (0)1223 492537
Fax: +44- (0)1223 494486
[email protected]
www.ebi.ac.uk /~asad
*************************************************
On 26 Oct 2010, at 12:42, [email protected] wrote:
> Send Cdk-user mailing list submissions to
> [email protected]
>
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>
>
> Today's Topics:
>
> 1. substract substructure (Tobias Girschick)
> 2. Re: substract substructure (Tobias Girschick)
> 3. Re: substract substructure (Rajarshi Guha)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 26 Oct 2010 10:56:35 +0200
> From: Tobias Girschick <[email protected]>
> Subject: [Cdk-user] substract substructure
> To: [email protected]
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I would like to substract a substructure from a structure and keep the
> remaining parts. There was a similar post in the mailing list history:
>
> http://sourceforge.net/mailarchive/message.php?msg_id=200702050602.05302.e.willighagen%40science.ru.nl
>
> The difference (is it a difference?) is, that I don't calculate the
> substructure with CDK code but get it from somewhere else. My code looks
> like this (but doesn't work):
>
> while (sdfreader.hasNext()) {
> /*
> Substructure: O=Cc1ccccc1
> A: OC(=O)c1cccc(c1)Cl
> B: CC(=O)c1cccc(F)c1
> C: Nc1cccc(c1)C(O)=O
> */
>
> IMolecule mol2store = (IMolecule)sdfreader.next();
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2store);
> CDKHueckelAromaticityDetector.detectAromaticity(mol2store);
>
> FileInputStream fes = new FileInputStream(f_bb);
> IteratingMDLReader sdreader = new IteratingMDLReader(fes,
> DefaultChemObjectBuilder.getInstance());
> IMolecule mol = null;
> while (sdreader.hasNext()) {
> mol = (IMolecule) sdreader.next();
> }
> sdreader.close();
> fes.close();
>
> String smiles = sg.createSMILES(mol);
> System.out.println("S: " + smiles);
> smiles = sg.createSMILES(mol2store);
> System.out.println("A: " + smiles);
>
> Iterable<IAtom> i = mol.atoms();
> Iterator<IAtom> atoms = i.iterator();
> while(atoms.hasNext()){
> IAtom a = atoms.next();
> mol2store.removeAtomAndConnectedElectronContainers(a);
> }
> smiles = sg.createSMILES(mol2store);
> System.out.println("B: " + smiles);
> smiles = sg.createSMILES(mol);
> System.out.println("S: " + smiles);
> System.out.println("-------------");
> }
>
> --
> Tobias Girschick
> mailto: [email protected]
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 Oct 2010 10:59:21 +0200
> From: Tobias Girschick <[email protected]>
> Subject: Re: [Cdk-user] substract substructure
> To: [email protected]
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> sorry, I sent the message before it was ready....here the complete version
>
> Hi,
>
> I would like to substract a substructure from a structure and keep the
> remaining parts. There was a similar post in the mailing list history:
>
> http://sourceforge.net/mailarchive/message.php?msg_id=200702050602.05302.e.willighagen%40science.ru.nl
>
> The difference (is it a difference?) is, that I don't calculate the
> substructure with CDK code but get it from somewhere else. My code looks
> like this (but doesn't work):
>
> while (sdfreader.hasNext()) {
> /*
> Substructure: O=Cc1ccccc1
> A: OC(=O)c1cccc(c1)Cl
> B: CC(=O)c1cccc(F)c1
> C: Nc1cccc(c1)C(O)=O
> */
>
> // read the molecules A, B, C
> IMolecule mol2store = (IMolecule)sdfreader.next();
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2store);
> CDKHueckelAromaticityDetector.detectAromaticity(mol2store);
>
> // read the substructure
> FileInputStream fes = new FileInputStream(f_bb);
> IteratingMDLReader sdreader = new IteratingMDLReader(fes,
> DefaultChemObjectBuilder.getInstance());
> IMolecule mol = null;
> while (sdreader.hasNext()) {
> mol = (IMolecule) sdreader.next();
> }
> sdreader.close();
> fes.close();
>
> String smiles = sg.createSMILES(mol);
> System.out.println("S: " + smiles);
> smiles = sg.createSMILES(mol2store);
> System.out.println("A: " + smiles);
>
> Iterable<IAtom> i = mol.atoms();
> Iterator<IAtom> atoms = i.iterator();
> while(atoms.hasNext()){
> IAtom a = atoms.next();
> mol2store.removeAtomAndConnectedElectronContainers(a);
> }
> smiles = sg.createSMILES(mol2store);
> System.out.println("B: " + smiles);
> smiles = sg.createSMILES(mol);
> System.out.println("S: " + smiles);
> System.out.println("-------------");
> }
>
> Considering the SMILES output, the atoms haven't been substracted from the
> molecules ABC. Any thoughts?
>
> On Tue, Oct 26, 2010 at 10:56 AM, Tobias Girschick <
> [email protected]> wrote:
>
>> Hi,
>>
>> I would like to substract a substructure from a structure and keep the
>> remaining parts. There was a similar post in the mailing list history:
>>
>>
>> http://sourceforge.net/mailarchive/message.php?msg_id=200702050602.05302.e.willighagen%40science.ru.nl
>>
>> The difference (is it a difference?) is, that I don't calculate the
>> substructure with CDK code but get it from somewhere else. My code looks
>> like this (but doesn't work):
>>
>> while (sdfreader.hasNext()) {
>> /*
>> Substructure: O=Cc1ccccc1
>> A: OC(=O)c1cccc(c1)Cl
>> B: CC(=O)c1cccc(F)c1
>> C: Nc1cccc(c1)C(O)=O
>> */
>>
>> IMolecule mol2store = (IMolecule)sdfreader.next();
>>
>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2store);
>> CDKHueckelAromaticityDetector.detectAromaticity(mol2store);
>>
>> FileInputStream fes = new FileInputStream(f_bb);
>> IteratingMDLReader sdreader = new IteratingMDLReader(fes,
>> DefaultChemObjectBuilder.getInstance());
>> IMolecule mol = null;
>> while (sdreader.hasNext()) {
>> mol = (IMolecule) sdreader.next();
>> }
>> sdreader.close();
>> fes.close();
>>
>> String smiles = sg.createSMILES(mol);
>> System.out.println("S: " + smiles);
>> smiles = sg.createSMILES(mol2store);
>> System.out.println("A: " + smiles);
>>
>> Iterable<IAtom> i = mol.atoms();
>> Iterator<IAtom> atoms = i.iterator();
>> while(atoms.hasNext()){
>> IAtom a = atoms.next();
>> mol2store.removeAtomAndConnectedElectronContainers(a);
>> }
>> smiles = sg.createSMILES(mol2store);
>> System.out.println("B: " + smiles);
>> smiles = sg.createSMILES(mol);
>> System.out.println("S: " + smiles);
>> System.out.println("-------------");
>> }
>>
>> --
>> Tobias Girschick
>> mailto: [email protected]
>>
>
>
>
> --
> Tobias Girschick
> mailto: [email protected]
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 Oct 2010 07:42:06 -0400
> From: Rajarshi Guha <[email protected]>
> Subject: Re: [Cdk-user] substract substructure
> To: Tobias Girschick <[email protected]>
> Cc: [email protected]
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> This cannot work since the atom from mol is a different instance from
> the atom in mol2store, so that
> mol2store.removeAtomAndConnectedElectronContainers(a) will never
> remove any atoms.
>
> In fact, given the substructure you must perform a substructure search
> to get the mapping of the target atoms to the substructure atoms and
> use that mapping to remove the target atoms.
>
> See http://rguha.net/code/java/#umcss for an example - most likely it
> won't work with the latest CDK as it was written a long time ago, but
> should point you in the direction
>
> On Oct 26, 2010, at 4:59 AM, Tobias Girschick wrote:
>
>> sorry, I sent the message before it was ready....here the complete
>> version
>>
>> Hi,
>>
>> I would like to substract a substructure from a structure and keep
>> the remaining parts. There was a similar post in the mailing list
>> history:
>>
>> http://sourceforge.net/mailarchive/message.php?msg_id=200702050602.05302.e.willighagen%40science.ru.nl
>>
>> The difference (is it a difference?) is, that I don't calculate the
>> substructure with CDK code but get it from somewhere else. My code
>> looks like this (but doesn't work):
>>
>> while (sdfreader.hasNext()) {
>> /*
>> Substructure: O=Cc1ccccc1
>> A: OC(=O)c1cccc(c1)Cl
>> B: CC(=O)c1cccc(F)c1
>> C: Nc1cccc(c1)C(O)=O
>> */
>>
>> // read the molecules A, B, C
>> IMolecule mol2store = (IMolecule)sdfreader.next();
>>
>> AtomContainerManipulator
>> .percieveAtomTypesAndConfigureAtoms(mol2store);
>>
>> CDKHueckelAromaticityDetector.detectAromaticity(mol2store);
>>
>> // read the substructure
>> FileInputStream fes = new FileInputStream(f_bb);
>> IteratingMDLReader sdreader = new
>> IteratingMDLReader(fes, DefaultChemObjectBuilder.getInstance());
>> IMolecule mol = null;
>> while (sdreader.hasNext()) {
>> mol = (IMolecule) sdreader.next();
>> }
>> sdreader.close();
>> fes.close();
>>
>> String smiles = sg.createSMILES(mol);
>> System.out.println("S: " + smiles);
>> smiles = sg.createSMILES(mol2store);
>> System.out.println("A: " + smiles);
>>
>> Iterable<IAtom> i = mol.atoms();
>> Iterator<IAtom> atoms = i.iterator();
>> while(atoms.hasNext()){
>> IAtom a = atoms.next();
>> mol2store.removeAtomAndConnectedElectronContainers(a);
>> }
>> smiles = sg.createSMILES(mol2store);
>> System.out.println("B: " + smiles);
>> smiles = sg.createSMILES(mol);
>> System.out.println("S: " + smiles);
>> System.out.println("-------------");
>> }
>>
>> Considering the SMILES output, the atoms haven't been substracted
>> from the molecules ABC. Any thoughts?
>>
>> On Tue, Oct 26, 2010 at 10:56 AM, Tobias Girschick
>> <[email protected]
>>> wrote:
>> Hi,
>>
>> I would like to substract a substructure from a structure and keep
>> the remaining parts. There was a similar post in the mailing list
>> history:
>>
>> http://sourceforge.net/mailarchive/message.php?msg_id=200702050602.05302.e.willighagen%40science.ru.nl
>>
>> The difference (is it a difference?) is, that I don't calculate the
>> substructure with CDK code but get it from somewhere else. My code
>> looks like this (but doesn't work):
>>
>> while (sdfreader.hasNext()) {
>> /*
>> Substructure: O=Cc1ccccc1
>> A: OC(=O)c1cccc(c1)Cl
>> B: CC(=O)c1cccc(F)c1
>> C: Nc1cccc(c1)C(O)=O
>> */
>>
>> IMolecule mol2store = (IMolecule)sdfreader.next();
>>
>> AtomContainerManipulator
>> .percieveAtomTypesAndConfigureAtoms(mol2store);
>>
>> CDKHueckelAromaticityDetector.detectAromaticity(mol2store);
>>
>> FileInputStream fes = new FileInputStream(f_bb);
>> IteratingMDLReader sdreader = new
>> IteratingMDLReader(fes, DefaultChemObjectBuilder.getInstance());
>> IMolecule mol = null;
>> while (sdreader.hasNext()) {
>> mol = (IMolecule) sdreader.next();
>> }
>> sdreader.close();
>> fes.close();
>>
>> String smiles = sg.createSMILES(mol);
>> System.out.println("S: " + smiles);
>> smiles = sg.createSMILES(mol2store);
>> System.out.println("A: " + smiles);
>>
>> Iterable<IAtom> i = mol.atoms();
>> Iterator<IAtom> atoms = i.iterator();
>> while(atoms.hasNext()){
>> IAtom a = atoms.next();
>> mol2store.removeAtomAndConnectedElectronContainers(a);
>> }
>> smiles = sg.createSMILES(mol2store);
>> System.out.println("B: " + smiles);
>> smiles = sg.createSMILES(mol);
>> System.out.println("S: " + smiles);
>> System.out.println("-------------");
>> }
>>
>> --
>> Tobias Girschick
>> mailto: [email protected]
>>
>>
>>
>> --
>> Tobias Girschick
>> mailto: [email protected]
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America
>> contest
>> Create new apps & games for the Nokia N8 for consumers in U.S. and
>> Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>> marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi
>> Store
>> http://p.sf.net/sfu/nokia-dev2dev_______________________________________________
>> Cdk-user mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
> ----------------------------------------------------
> Rajarshi Guha | NIH Chemical Genomics Center
> http://www.rguha.net | http://ncgc.nih.gov
> ----------------------------------------------------
> A committee is a group that keeps the minutes and loses hours.
> -- Milton Berle
>
>
>
>
>
> ------------------------------
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
>
> ------------------------------
>
> _______________________________________________
> Cdk-user mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
> End of Cdk-user Digest, Vol 53, Issue 21
> ****************************************
------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
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