MultiFaceAtom does not have any visible fa

User 870ab5b546

09-12-2006 04:36:36

We have this code:

Code:

studentMolecule = getSearchMolecule(studentXml, true); // hydrogenize

authorMolecule = getSearchMolecule(authorXml, false); // don't hydro.

if (studentMolecule == null || authorMolecule == null) {

return false;

} // if missing data

print("hasSubstructure: got student molecule");

print("hasSubstructure: student molecule is:\n"

+ studentMolecule.toFormat("mrv"));

print("hasSubstructure: author molecule is:\n"

+ authorMolecule.toFormat("mrv"));

...

public Molecule getSearchMolecule(String xml, boolean hydrogenizeIt)

throws MolFormatException {

MolImporter importer = new MolImporter();

Molecule molecule = importer.importMol(xml);

molecule.ungroupSgroups();

molecule.aromatize();

if (hydrogenizeIt)

molecule = ChemUtils.addImplicitHnoClone(molecule);

molecule = MechSet.normalizeRadicals(molecule);

molecule = MolFunctions.replaceHnoClone(molecule);

return molecule;

} // getStudentData()

We submit this molecule:

Code:

<?xml version="1.0" ?>

<MDocument>

<MPolyline id="o1" color="#000000" headLength="0.8" headWidth="0.5">

<MRectanglePoint pos="6" rectRef="o7" />

<MRectanglePoint pos="4" rectRef="o6" />

</MPolyline>

<MPolyline id="o2" color="#000000" headLength="0.8" headWidth="0.5">

<MPoint x="1.3970290422439575" y="-7.937664985656738" />

<MRectanglePoint pos="5" rectRef="o7" />

</MPolyline>

<MPolyline id="o3" color="#000000" headLength="0.8" headWidth="0.5">

<MRectanglePoint pos="6" rectRef="o9" />

<MRectanglePoint pos="4" rectRef="o8" />

</MPolyline>

<MPolyline id="o4" color="#000000" headLength="0.8" headWidth="0.5">

<MPoint x="-1.2065250873565674" y="0.0" />

<MRectanglePoint pos="7" rectRef="o9" />

</MPolyline>

<MPolyline id="o5" color="#000000" headLength="0.8" headWidth="0.5">

<MPoint x="-5.016603946685791" y="4.8261003494262695" />

<MRectanglePoint pos="4" rectRef="o10" />

</MPolyline>

<MRectangle id="o6" color="#000000">

<MPoint x="-10.033207893371582" y="-12.636762619018555" />

<MPoint x="0.6350131630897522" y="-12.636762619018555" />

<MPoint x="0.6350131630897522" y="-18.478883743286133" />

<MPoint x="-10.033207893371582" y="-18.478883743286133" />

</MRectangle>

<MRectangle id="o7" color="#000000">

<MPoint x="-10.223711967468262" y="-4.8261003494262695" />

<MPoint x="0.0" y="-4.8261003494262695" />

<MPoint x="0.0" y="-9.969706535339355" />

<MPoint x="-10.223711967468262" y="-9.969706535339355" />

</MRectangle>

<MRectangle id="o8" color="#000000">

<MPoint x="1.3970290422439575" y="-4.699097633361816" />

<MPoint x="10.160210609436035" y="-4.699097633361816" />

<MPoint x="10.160210609436035" y="-11.049229621887207" />

<MPoint x="1.3970290422439575" y="-11.049229621887207" />

</MRectangle>

<MRectangle id="o9" color="#000000">

<MPoint x="1.6510342359542847" y="4.1275858879089355" />

<MPoint x="10.287213325500488" y="4.1275858879089355" />

<MPoint x="10.287213325500488" y="-3.492572546005249" />

<MPoint x="1.6510342359542847" y="-3.492572546005249" />

</MRectangle>

<MRectangle id="o10" color="#000000">

<MPoint x="-10.160210609436035" y="3.4290711879730225" />

<MPoint x="-1.2065250873565674" y="3.4290711879730225" />

<MPoint x="-1.2065250873565674" y="-3.3020684719085693" />

<MPoint x="-10.160210609436035" y="-3.3020684719085693" />

</MRectangle>

<MRectangle id="o11" color="#000000">

<MPoint x="-10.096709251403809" y="10.541218757629395" />

<MPoint x="0.12700264155864716" y="10.541218757629395" />

<MPoint x="0.12700264155864716" y="4.8261003494262695" />

<MPoint x="-10.096709251403809" y="4.8261003494262695" />

</MRectangle>

<MEFlow id="o12" color="#000000" arcAngle="-254.995522631729"

headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.15">

<MAtomSetPoint atomRefs="m1.a57 m1.a60" />

<MAtomSetPoint atomRefs="m1.a57" />

</MEFlow>

<MEFlow id="o13" color="#000000" arcAngle="248.39738999999997"

headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.15">

<MAtomSetPoint atomRefs="m1.a44 m1.a46" />

<MAtomSetPoint atomRefs="m1.a46" />

</MEFlow>

<MEFlow id="o14" color="#000000" arcAngle="-254.995522631729"

headSkip="0.15" headLength="0.5" headWidth="0.4" tailSkip="0.25">

<MAtomSetPoint atomRefs="m1.a45" />

<MAtomSetPoint atomRefs="m1.a44 m1.a45" />

</MEFlow>

<MEFlow id="o15" color="#000000" arcAngle="248.39738999999997"

headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.15">

<MAtomSetPoint atomRefs="m1.a35 m1.a36" />

<MAtomSetPoint atomRefs="m1.a35" />

</MEFlow>

<MEFlow id="o16" color="#000000" arcAngle="150.0" headSkip="0.15"

headLength="0.5" headWidth="0.4" tailSkip="0.25">

<MAtomSetPoint atomRefs="m1.a33" />

<MAtomSetPoint atomRefs="m1.a33 m1.a36" weights="0.25 0.75" />

</MEFlow>

<MEFlow id="o17" color="#000000" arcAngle="248.39738999999997"

headSkip="0.25" headLength="0.5" headWidth="0.4" tailSkip="0.15">

<MAtomSetPoint atomRefs="m1.a19 m1.a20" />

<MAtomSetPoint atomRefs="m1.a20" />

</MEFlow>

<MEFlow id="o18" color="#000000" arcAngle="-150.0" headSkip="0.15"

headLength="0.5" headWidth="0.4" tailSkip="0.25">

<MAtomSetPoint atomRefs="m1.a23" />

<MAtomSetPoint atomRefs="m1.a23 m1.a19" weights="0.25 0.75" />

</MEFlow>

<MEFlow id="o19" color="#000000" arcAngle="150.0" headSkip="0.15"

headLength="0.5" headWidth="0.4" tailSkip="0.25">

<MAtomSetPoint atomRefs="m1.a9" />

<MAtomSetPoint atomRefs="m1.a9 m1.a11" weights="0.25 0.75" />

</MEFlow>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55 a56 a57 a58 a59 a60 a61 a62 a63 a64 a65 a66 a67 a68 a69 a70 a71"

elementType="C C C C C C C C O O H C C C C C C C C O O C O C C C C C C C C O O C O H C C C C C C C C O O C O C C C C C C C C O O C H C C C C C C C C O O C"

formalCharge="0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0"

x2="-7.940625190734863 -9.274294531783122 -9.274294531783122 -7.940625190734863 -6.606955849686605 -6.606955849686605 -5.273276727858569 -3.9395976060305333 -3.9395976060305333 -2.6059184842024976 -0.721875011920929 -7.80853614832265 -9.142205489370909 -9.142205489370909 -7.80853614832265 -6.474866807274392 -6.474866807274392 -5.141187685446356 -3.8075085636183204 -3.8075085636183204 -2.4738294417902846 -5.823124885559082 -4.283124885559082 3.3790980628858165 2.045428721837558 2.045428721837558 3.3790980628858165 4.712767403934075 4.712767403934075 6.046446525762111 7.380125647590146 7.380125647590146 8.713804769418182 5.364509325649385 6.904509325649385 8.23818844747742 3.361228847336668 2.0275595062884095 2.0275595062884095 3.361228847336668 4.694898188384927 4.694898188384927 6.028577310212962 7.362256432040997 7.362256432040997 8.695935553869035 5.346640110100236 6.886640110100236 -8.04916120554311 -9.382830546591368 -9.382830546591368 -8.04916120554311 -6.715491864494851 -6.715491864494851 -5.381812742666815 -4.0481336208387795 -4.0481336208387795 -2.7144544990107438 -1.380775377182708 -2.7144544990107438 -7.435183744470551 -8.76885308551881 -8.76885308551881 -7.435183744470551 -6.101514403422293 -6.101514403422293 -4.767835281594257 -3.4341561597662214 -3.4341561597662214 -2.1004770379381856 -0.7667979161101499"

y2="8.951283995558999 8.181267054999958 6.6412331738818775 5.871216233322837 6.6412331738818775 8.181267054999958 5.871233173881878 6.6412331738818775 8.181233173881878 5.871233173881878 9.48062515258789 2.906790690720298 2.1367737501612574 0.5967398690431764 -0.17327707151586402 0.5967398690431764 2.1367737501612574 -0.17326013095682313 0.5967398690431764 2.1367398690431774 -0.17326013095682313 -2.2618749141693115 -2.2618749141693115 3.2248213271312753 2.454804386572235 0.914770505454154 0.14475356489511348 0.914770505454154 2.454804386572235 0.14477050545415437 0.914770505454154 2.454770505454155 0.14477050545415437 -1.943844277758334 -1.943844277758334 -2.713844277758334 -4.930180737490621 -5.700197678049661 -7.240231559167742 -8.010248499726782 -7.240231559167742 -5.700197678049661 -8.010231559167742 -7.240231559167742 -5.700231559167741 -8.010231559167742 -10.09884634238023 -10.09884634238023 -5.900084156691811 -6.670101097250852 -8.210134978368933 -8.980151918927973 -8.210134978368933 -6.670101097250852 -8.980134978368932 -8.210134978368933 -6.670134978368932 -8.980134978368932 -8.210134978368933 -5.900134978368932 -13.523082419720563 -14.293099360279605 -15.833133241397686 -16.603150181956725 -15.833133241397686 -14.293099360279605 -16.603133241397686 -15.833133241397686 -14.293133241397683 -16.603133241397686 -15.833133241397686"

/>

<bondArray>

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a1 a6" order="2" />

<bond atomRefs2="a2 a3" order="2" />

<bond atomRefs2="a3 a4" order="1" />

<bond atomRefs2="a4 a5" order="2" />

<bond atomRefs2="a5 a6" order="1" />

<bond atomRefs2="a5 a7" order="1" />

<bond atomRefs2="a7 a8" order="1" />

<bond atomRefs2="a8 a9" order="2" />

<bond atomRefs2="a8 a10" order="1" />

<bond atomRefs2="a12 a13" order="1" />

<bond atomRefs2="a12 a17" order="2" />

<bond atomRefs2="a13 a14" order="2" />

<bond atomRefs2="a14 a15" order="1" />

<bond atomRefs2="a15 a16" order="2" />

<bond atomRefs2="a16 a18" order="1" />

<bond atomRefs2="a16 a17" order="1" />

<bond atomRefs2="a18 a19" order="1" />

<bond atomRefs2="a19 a21" order="1" />

<bond atomRefs2="a19 a20" order="2" />

<bond atomRefs2="a22 a23" order="1" />

<bond atomRefs2="a24 a25" order="1" />

<bond atomRefs2="a24 a29" order="2" />

<bond atomRefs2="a25 a26" order="2" />

<bond atomRefs2="a26 a27" order="1" />

<bond atomRefs2="a27 a28" order="2" />

<bond atomRefs2="a28 a30" order="1" />

<bond atomRefs2="a28 a29" order="1" />

<bond atomRefs2="a30 a31" order="1" />

<bond atomRefs2="a31 a33" order="1" />

<bond atomRefs2="a31 a32" order="1" />

<bond atomRefs2="a34 a35" order="1" />

<bond atomRefs2="a31 a35" order="1" />

<bond atomRefs2="a35 a36" order="1" />

<bond atomRefs2="a37 a38" order="1" />

<bond atomRefs2="a37 a42" order="2" />

<bond atomRefs2="a38 a39" order="2" />

<bond atomRefs2="a39 a40" order="1" />

<bond atomRefs2="a40 a41" order="2" />

<bond atomRefs2="a41 a43" order="1" />

<bond atomRefs2="a41 a42" order="1" />

<bond atomRefs2="a43 a44" order="1" />

<bond atomRefs2="a44 a46" order="1" />

<bond atomRefs2="a44 a45" order="1" />

<bond atomRefs2="a44 a48" order="1" />

<bond atomRefs2="a47 a48" order="1" />

<bond atomRefs2="a49 a50" order="1" />

<bond atomRefs2="a49 a54" order="2" />

<bond atomRefs2="a50 a51" order="2" />

<bond atomRefs2="a51 a52" order="1" />

<bond atomRefs2="a52 a53" order="2" />

<bond atomRefs2="a53 a55" order="1" />

<bond atomRefs2="a53 a54" order="1" />

<bond atomRefs2="a55 a56" order="1" />

<bond atomRefs2="a56 a58" order="1" />

<bond atomRefs2="a56 a57" order="2" />

<bond atomRefs2="a58 a59" order="1" />

<bond atomRefs2="a57 a60" order="1" />

<bond atomRefs2="a61 a62" order="1" />

<bond atomRefs2="a61 a66" order="2" />

<bond atomRefs2="a62 a63" order="2" />

<bond atomRefs2="a63 a64" order="1" />

<bond atomRefs2="a64 a65" order="2" />

<bond atomRefs2="a65 a67" order="1" />

<bond atomRefs2="a65 a66" order="1" />

<bond atomRefs2="a67 a68" order="1" />

<bond atomRefs2="a68 a70" order="1" />

<bond atomRefs2="a68 a69" order="2" />

<bond atomRefs2="a70 a71" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

We get a weird exception from Molecule.toFormat():

Code:

MechSubStructSearch::hasSubstructure: got student molecule

MechSubstructure: exception thrown, msg = MultiFaceAtom does not have any visible face

java.lang.RuntimeException: MultiFaceAtom does not have any visible face

at chemaxon.struc.graphics.MAtomSetPoint$MultiFaceAtom.getVisible(MAtomSetPoint.java:65)

at chemaxon.struc.graphics.MAtomSetPoint.getAtoms(MAtomSetPoint.java:242)

at chemaxon.marvin.modules.MrvExport.appendPoint(MrvExport.java:139)

at chemaxon.marvin.modules.MrvExport.convert(MrvExport.java:112)

at chemaxon.struc.Molecule.exportToObject(Molecule.java:1141)

at chemaxon.struc.Molecule.exportToObject(Molecule.java:1106)

at chemaxon.struc.Molecule.exportToFormat(Molecule.java:955)

at chemaxon.struc.Molecule.toFormat(Molecule.java:933)

at com.prenhall.epoch.mechanisms.MechSubStructSearch.hasSubstructure(MechSubStructSearch.java:63)

What might be causing this exception? I've never before seen anything like it from toFormat().

So I put in a try statement to catch the exception. But later, we call this method:

Code:

public static int getFlowType(MEFlow flow) {

Object source = flow.getMolObject(MEFlow.E_SOURCE);

Object sink = flow.getMolObject(MEFlow.E_SINK);

int theSStype = SSTypeOf(source)*10 + SSTypeOf(sink);

if (flow.getNumElectrons() == 2) // flow types for 2-electron flows

theSStype *= -1; // are negative.

return theSStype;

} // flowType()

And then we get the same weird exception:

Code:

java.lang.RuntimeException: MultiFaceAtom does not have any visible face

at chemaxon.struc.graphics.MAtomSetPoint$MultiFaceAtom.getVisible(MAtomSetPoint.java:65)

at chemaxon.struc.graphics.MAtomSetPoint.getAtoms(MAtomSetPoint.java:242)

at chemaxon.struc.graphics.MEFlow.getMolObject(MEFlow.java:106)

at com.prenhall.epoch.mechanisms.MechSubStructSearch.getFlowType(MechSubStructSearch.java:359)

What's going on here? We're using JChem 3.2.1.

ChemAxon 9c0afc9aaf

09-12-2006 08:14:24

Hi Bob,

I have moved this topic here, because I think it better suits this forum.

My colleagues will answer soon.

Best regards,

Szilard

User 870ab5b546

11-12-2006 03:47:20

Further information: A Google search reveals that the same error, MultiFaceAtom has no visible face, appeared in a previous discussion. In that discussion, the bug was elicited by the presence of an electron-flow arrow pointing to an incipient bond to an H atom. Indeed, this structural feature is now present in the structure that is generating the errors new MultiFaceAtom error messages. Previously, the problem involved storing such structures; now, we can store them, but we get the error when processing them in other ways, such as converting them to MRV format or getting the MEFlow sinks and sources.

ChemAxon 7c2d26e5cf

11-12-2006 16:12:13

Hi Bob,

This part of your code is not clear for me. What did you do exactly here with the molecule?

Code:

if (hydrogenizeIt)

molecule = ChemUtils.addImplicitHnoClone(molecule);

molecule = MechSet.normalizeRadicals(molecule);

molecule = MolFunctions.replaceHnoClone(molecule);

Did you clone the molecule? Probably an inconsistent molecule is created after these operations.

This information can help us in debugging.

User 870ab5b546

11-12-2006 16:33:54

It doesn't seem to me that we clone the molecule. Although a clone is created in addImplicitHnoClone(), the original (but modified) Molecule is returned.

Code:

public static Molecule addImplicitHnoClone(Molecule mol) {

// System.out.println("ChemUtils.addImplicitH: starting with \n"

// + mol.toFormat("mrv"));

int MOLBOND_WAVY = 24; // taken from MolFunctions.java

int origNumBonds = mol.getBondCount();

Molecule origMol = (Molecule) mol.clone();

mol.hydrogenize(true); // modifies the given molecule

for (int bIndex = 0; bIndex<origNumBonds; bIndex++) {

MolBond mb = (MolBond) mol.getEdge(bIndex);

int type = mb.getType();

MolBond origmb = (MolBond) origMol.getEdge(bIndex);

int origType = origmb.getType();

if (type != origType) {

System.out.println("ChemUtils.addImplicitH: "

+ "resetting a " + mb.getAtom1().getSymbol()

+ "-" + mb.getAtom2().getSymbol()

+ " bond from type " + type

+ " back to original type " + origType);

mb.setType(origType);

} // if stereo has been changed by hydrogenizing

} // for each original bond in mol

for (int bIndex = origNumBonds; bIndex<mol.getBondCount(); bIndex++) {

MolBond mb = (MolBond) mol.getEdge(bIndex);

int stereo = mb.getFlags() & MolBond.STEREO_MASK;

if (stereo == MOLBOND_WAVY) {

System.out.println("ChemUtils.addImplicitH: "

+ "straightening a new wavy bond to H...");

mb.setType(1);

} // if the new bond (to H) is wavy

} // for each new bond in mol

// System.out.println("ChemUtils.addImplicitH: returning \n"

// + mol.toFormat("mrv"));

return mol;

} // addImplictHnoClone(Molecule)

Code:

public static Molecule normalizeRadicals(Molecule mol) {

for (int atomIndex = 0; atomIndex < mol.getAtomCount(); atomIndex++) {

MolAtom atom = mol.getAtom(atomIndex);

int rad = atom.getRadical();

if (rad==MolAtom.RAD2_SINGLET || rad==MolAtom.RAD2_TRIPLET) {

System.out.println("MechSet::normalizeRadicals: "

+ atom.getSymbol() + " normalized to RAD2");

atom.setRadical(MolAtom.RAD2);

}

else if (rad==MolAtom.RAD3_DOUBLET || rad==MolAtom.RAD3_QUARTET) {

System.out.println("MechSet::normalizeRadicals: "

+ atom.getSymbol() + " normalized to RAD3");

atom.setRadical(MolAtom.RAD3);

}

} // for each atom

return mol;

} // normalizeRadicals()

Code:

public static Molecule replaceHnoClone(Molecule mol) {

String hydrogenLabel = "H";

int franciumNum = 87;

for (int i=0; i<mol.getNodeCount(); i++) {

MolAtom atom = (MolAtom) mol.getNode(i);

if (atom.getSymbol().equalsIgnoreCase(hydrogenLabel)) {

//MolAtom npAtom = new MolAtom(franciumNum,

// atom.getX(), atom.getY(), atom.getZ());

atom.setAtno(franciumNum);

mol.setNode(i, atom);

}

} // for each node (atom)

return mol;

} // replaceHnoClone(Molecule)

ChemAxon 7c2d26e5cf

11-12-2006 17:54:15

Thanks for the code.

I have managed to reproduce the error with it.

We will debug it.

ChemAxon a3d59b832c

14-12-2006 13:28:13

I think the problem here may also relate to method replaceHnoClone(). See the other topic below.

http://www.chemaxon.com/forum/viewpost9565.html#9565

ChemAxon 7c2d26e5cf

08-01-2007 17:45:56

The bugfix will be available in the next release (4.1.5).