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Re: [Cdk-user] substract substructure
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From: Tobias G. <tob...@gm...> - 2010-10-26 12:47:58
|
Thanks for the reply and the code Asad, but as replied to Rajarshi I would
like to prevent using MCS if possible.
On Tue, Oct 26, 2010 at 2:37 PM, Syed Asad Rahman <as...@eb...> wrote:
> Sorry for the cross posting, just updated the header for sake of the topic relevance.
>
> Here is my suggestion...
>
>
> 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
>
>
>
> On 26 Oct 2010, at 12:42, cdk...@li... wrote:
>
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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 <tob...@gm...>
> Subject: [Cdk-user] substract substructure
> To: cdk...@li...
> Message-ID:
> <AAN...@ma...>
> 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: tob...@gm...
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 Oct 2010 10:59:21 +0200
> From: Tobias Girschick <tob...@gm...>
>
> Subject: Re: [Cdk-user] substract substructure
> To: cdk...@li...
> Message-ID:
> <AAN...@ma...<AANLkTimcDybgo0vvMBAybJD4tPsyNQQ%2BU...@ma...>
> >
> 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 <
>
> tob...@gm...> 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: tob...@gm...
>
>
>
>
>
> --
> Tobias Girschick
> mailto: tob...@gm...
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 Oct 2010 07:42:06 -0400
> From: Rajarshi Guha <raj...@gm...>
>
> Subject: Re: [Cdk-user] substract substructure
> To: Tobias Girschick <tob...@gm...>
> Cc: cdk...@li...
> Message-ID: <0A9...@gm...>
> 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 <
> tob...@gm...
>
> 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: tob...@gm...
>
>
>
>
> --
>
> Tobias Girschick
>
> mailto: tob...@gm...
>
>
> ------------------------------------------------------------------------------
>
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>
> http://p.sf.net/sfu/nokia-dev2dev_______________________________________________
>
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>
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>
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>
>
> ----------------------------------------------------
> 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
>
> ------------------------------
>
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>
>
> End of Cdk-user Digest, Vol 53, Issue 21
> ****************************************
>
>
>
--
Tobias Girschick
mailto: tob...@gm...
|