#1172 Strange bug parsing SDF file and SMARTS matching

[Rajarshi Guha]

If I try and match [NH2]c1ncncc1 against the molecule read in from the attached SDF file, I get no hits. But if I convert the file to SMILES and then match it works. Hereis example code:

    String filename = "/Users/guhar/src/cdkpcore/ligand3BIY.sdf";
    InputStream ins = new FileInputStream(new File(filename));
    DefaultChemObjectReader reader = new MDLV2000Reader(ins);
    ChemFile content;
    content = (ChemFile) reader.read((ChemObject) new ChemFile());
    List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content);
    IAtomContainer atomContainer = cList.get(0);

    CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()).addImplicitHydrogens(atomContainer);
    AtomContainerManipulator.convertImplicitToExplicitHydrogens(atomContainer);

// SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
// IAtomContainer atomContainer = sp.parseSmiles("O=P(=O)(OP(=O)(=O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSCC(=O)NCCCCC(NC(=O)C)C(=O)N)OCC1C(C(C(O1)n2c3c(nc2)c(ncn3)N)O)OP(=O)(=O)=O");
SMARTSQueryTool sqt = new SMARTSQueryTool("[NH2]c1ncncc1");
boolean status = sqt.matches(atomContainer);
Assert.assertEquals(true, status);

    int nmatch = sqt.countMatches();
    int nqmatch = sqt.getUniqueMatchingAtoms().size();

    Assert.assertEquals(1, nmatch);
    Assert.assertEquals(1, nqmatch);

[Rajarshi Guha]

[John May]

Probably an aromaticity problem.

Regards,
John W May
john.wilkinsonmay@gmail.com

On 11 August 2016 at 12:15, Egon Willighagen egonw@users.sf.net wrote:

• assigned_to: Egon Willighagen --> Rajarshi Guha
• Comment:

Rajarshi, can you check if this bug still exists? It probably is fixed...

• [bugs:#1172] https://sourceforge.net/p/cdk/bugs/1172/ Strange bug
  parsing SDF file and SMARTS matching*

Status: open
Group: cdk-1.4.x
Labels: cdk-smarts module
Created: Tue Aug 30, 2011 10:47 PM UTC by Rajarshi Guha
Last Updated: Sat Nov 03, 2012 07:32 AM UTC
Owner: Rajarshi Guha

If I try and match [NH2]c1ncncc1 against the molecule read in from the
attached SDF file, I get no hits. But if I convert the file to SMILES and
then match it works. Hereis example code:

String filename = "/Users/guhar/src/cdkpcore/ligand3BIY.sdf";
InputStream ins = new FileInputStream(new File(filename));
DefaultChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content;
content = (ChemFile) reader.read((ChemObject) new ChemFile());
List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content);
IAtomContainer atomContainer = cList.get(0);

CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()).addImplicitHydrogens(atomContainer);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(atomContainer);

// SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.
getInstance());
// IAtomContainer atomContainer = sp.parseSmiles("O=P(=O)(OP(=O)
(=O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSCC(=O)NCCCCC(NC(=O)C)C(=O)
N)OCC1C(C(C(O1)n2c3c(nc2)c(ncn3)N)O)OP(=O)(=O)=O");
SMARTSQueryTool sqt = new SMARTSQueryTool("[NH2]c1ncncc1");
boolean status = sqt.matches(atomContainer);
Assert.assertEquals(true, status);

int nmatch = sqt.countMatches();
int nqmatch = sqt.getUniqueMatchingAtoms().size();

Assert.assertEquals(1, nmatch);
Assert.assertEquals(1, nqmatch);

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[Rajarshi Guha]

The problem is resolved in master.

Unfortunately I can't remember nmy sf.net login to go and close the bug.
Can you close it for me?

On Thu, Aug 11, 2016 at 7:15 AM, Egon Willighagen egonw@users.sf.net
wrote:

• assigned_to: Egon Willighagen --> Rajarshi Guha
• Comment:

Rajarshi, can you check if this bug still exists? It probably is fixed...

• [bugs:#1172] https://sourceforge.net/p/cdk/bugs/1172/ Strange bug
  parsing SDF file and SMARTS matching*

Status: open
Group: cdk-1.4.x
Labels: cdk-smarts module
Created: Tue Aug 30, 2011 10:47 PM UTC by Rajarshi Guha
Last Updated: Sat Nov 03, 2012 07:32 AM UTC
Owner: Rajarshi Guha

If I try and match [NH2]c1ncncc1 against the molecule read in from the
attached SDF file, I get no hits. But if I convert the file to SMILES and
then match it works. Hereis example code:

String filename = "/Users/guhar/src/cdkpcore/ligand3BIY.sdf";
InputStream ins = new FileInputStream(new File(filename));
DefaultChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content;
content = (ChemFile) reader.read((ChemObject) new ChemFile());
List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content);
IAtomContainer atomContainer = cList.get(0);

CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()).addImplicitHydrogens(atomContainer);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(atomContainer);

// SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.
getInstance());
// IAtomContainer atomContainer = sp.parseSmiles("O=P(=O)(OP(=O)
(=O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSCC(=O)NCCCCC(NC(=O)C)C(=O)
N)OCC1C(C(C(O1)n2c3c(nc2)c(ncn3)N)O)OP(=O)(=O)=O");
SMARTSQueryTool sqt = new SMARTSQueryTool("[NH2]c1ncncc1");
boolean status = sqt.matches(atomContainer);
Assert.assertEquals(true, status);

int nmatch = sqt.countMatches();
int nqmatch = sqt.getUniqueMatchingAtoms().size();

Assert.assertEquals(1, nmatch);
Assert.assertEquals(1, nqmatch);

---

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NIH Center for Advancing Translational Science

[Egon Willighagen]

Rajarshi, can you check if this bug still exists? It probably is fixed...