User 870ab5b546
08-08-2006 17:44:40
Hi folks,
We can't use Marvin 4.1 until we get a version of JChem that understands what are MRectanglePoints and MMidpoints and that has some methods for handling them. (See the discussion at
http://www.chemaxon.com/forum/ftopic1725.html.) Can you provide one? (Szilard should be back from vacation by now, no?)
-- Bob
ChemAxon 9c0afc9aaf
09-08-2006 09:35:18
Hi Bob,
Yes, I'm back from vacation.
Some parts of the code are being restructured, so probably you will have to wait until early next week for a test version of JChem.
Is a test version sufficient for you ?
The final release is still about one month away.
Best regards,
Szilard
User 870ab5b546
09-08-2006 11:45:13
Yes, a test version is sufficient, if it is reasonably stable. We will be using it on our development version of ACE.
Will JChem have the methods that I requested in the other post?
ChemAxon 9c0afc9aaf
17-08-2006 21:42:31
User 870ab5b546
17-08-2006 21:49:16
Thanks!
Someone said something in another post about the new JChem not being very stable yet. Will that be a concern for us?
-- Bob
ChemAxon 9c0afc9aaf
18-08-2006 06:12:16
Hi Bob,
You are probably referring to this comment of Szabolcs:
http://www.chemaxon.com/forum/viewpost7389.html#7389
In general, test releases are built from code under development, and they are not tested so rigorously as official releases (if tested at all).
So we do not recommend to use our test versions in live systems.
(Or if it is a must, extensive client-side testing should precede)
However these releases are suitable and recommended for development and early testing of new features.
In short: for development / testing it is sufficiently stable.
Best regards,
Szilard
User 870ab5b546
18-08-2006 10:57:29
OK, I understand. Let me be a bit more specific. In the near future, the only features of the new JChem that we will definitely need are those relating to MMidPoints and MRectanglePoints. Can we expect that the features of JChem that are carried over from prior versions will continue to enjoy the same stability as they did in the prior versions? That is, any instability will be associated only with new features?
ChemAxon 9c0afc9aaf
18-08-2006 12:22:05
In general there are more bugs concerning new features, than old ones.
As in the case of every complex software, there is always a small chance that the introduction of a new feature will cause a bug in one or more existing feature.
(even a bugfix can cause an other bug, although it's very rare)
Of course it depends on how isolated the improvements are (how deep the changes go).
There have been numerous changes since the 3.1.x series apart from the API improvements you need.
Fortunately a set of constantly running automatic tests and other interim testing ensure that even the test releases are always reasonably stable.
And if a bug gets trough despite all of our efforts, shout and we provide a fix very soon (way faster than most other SW companies).
Best regards,
Szilard
ChemAxon 9c0afc9aaf
21-08-2006 11:31:13
Dear Bob,
Could you paste here the full stack trace, please ?
Thanks,
Szilard
User fa1369adab
21-08-2006 12:18:01
Here is the output of jcman u for the first of 4 structure tables. The others produce similar output.
| Code: |
Regenerating ACEORG15.MISC_MOLECULES_V1 ... Error at molecule 310
chemaxon.marvin.modules.LicenseException: No valid license key has been found.
Please contact sales _at_ chemaxon.com to obtain a license key.
Students and academic researchers can obtain license keys
for free through our Academic Package, for more information
please visit: http://www.chemaxon.com.
at chemaxon.enumeration.supergraph.Supergraph.<init>(Supergraph.java:134)
at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:826)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1758)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1737)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:75)
|
ChemAxon a3d59b832c
22-08-2006 12:09:44
Hi,
It seems that your table contains generic (Markush) structures.
Earlier these structures were not supported and could only be imported into the database by error. Now these can be imported and searched in the database. This requires extra license keys. (Although this feature is still under development, it is already functional.)
Can you explain how you use these structures? You may be eligible to use Markush database covered by the academic package.
Best regards,
Szabolcs
User 870ab5b546
22-08-2006 13:02:31
If we have Markush structures in the database, it is entirely by accident. We must be using a Markush tag for some purpose other than the one for which most of your customers use it.
We don't even search the database anymore. We merely use it to store structures. All JChem search functions in our code are direct comparisons of two structures.
User 870ab5b546
22-08-2006 17:54:57
Actually, we do need to regenerate the tables; JChem won't let us write to the tables anymore!
ChemAxon 9c0afc9aaf
22-08-2006 18:11:29
Dear Bob,
You can still regenerate the table.
Regeneration will not stop on problematic structures, it will just print the stack trace.
All other rows will be updated normally.
Please let if finish, and then you can import again.
Best regards,
Szilard
User 870ab5b546
22-08-2006 22:53:53
We are sometimes able to save again, but not always. When I try to save the Molecule below, I get this in the log:
DBTables: delete from answers_v2 where pb_id=2675 and major_id not in ( 0,1,2,3)
DBTables: delete from references_v4 where pb_id=2675 and id not in ( 0)
MolTable.java:importMol: mol name is --; table name is misc_molecules_v1
chemaxon.jchem.db.TransferException: MultiFaceAtom does not have any visible face
at com.prenhall.epoch.db.chem.MolTable.importMol(MolTable.java:185)
at com.prenhall.epoch.db.chem.MolTable.addMol(MolTable.java:269)
at com.prenhall.epoch.db.ProblemStoreWriter.setProblem(ProblemStoreWriter.java:278)
at com.prenhall.epoch.db.ProblemStoreWriter.setProblem(ProblemStoreWriter.java:55)
at com.prenhall.epoch.session.ProblemSet.setProblem(ProblemSet.java:256)
at org.apache.jsp.authortool.dbactions_jsp._jspService(dbactions_jsp.java:111)
Rafi tells me he was getting the same error when he was regenerating the table.
The Molecule is:
| Code: |
<?xml version="1.0" ?>
<MDocument>
<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"
elementType="C C O H H C H C C C O Br Br C C O H C H Br O R O R"
formalCharge="0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 -1 0 0 0"
sgroupRef="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 sg1 0 sg2"
x2="-8.808333396911621 -7.474654275083585 -7.474654275083585 -5.370975153255549 -4.60097515325555 -6.14097515325555 -5.742393823797667 1.8083332777023315 3.1420123995303673 4.475691521358403 3.1420123995303673 6.241666793823242 7.781666793823242 -2.1755294110849475 -0.8418502892569117 -0.8418502892569117 2.031828832571124 0.491828832571124 0.8904101620290064 1.2618288325711242 -4.025000095367432 -2.4850000953674316 7.4666666984558105 9.00666669845581"
y2="4.550000190734863 5.320000190734863 6.860000190734863 5.883679312562899 4.550000190734863 4.550000190734863 3.062474418249698 4.608333110809326 5.378333110809326 4.608333110809325 6.918333110809326 6.883333206176758 6.883333206176758 -2.284688581662934 -1.5146885816629343 0.02531141833706485 -2.284688581662934 -2.284688581662934 -3.7722143541480992 -0.9510094598348986 7.875 7.875 3.383333444595337 3.383333444595337"
/>
<bondArray>
<bond atomRefs2="a1 a2" order="1" />
<bond atomRefs2="a2 a3" order="2" />
<bond atomRefs2="a2 a6" order="1" />
<bond atomRefs2="a6 a4" order="1" />
<bond atomRefs2="a6 a5" order="1" />
<bond atomRefs2="a6 a7" order="1" />
<bond atomRefs2="a8 a9" order="1" />
<bond atomRefs2="a9 a11" order="1" />
<bond atomRefs2="a9 a10" order="2" />
<bond atomRefs2="a12 a13" order="1" />
<bond atomRefs2="a14 a15" order="1" />
<bond atomRefs2="a15 a16" order="2" />
<bond atomRefs2="a15 a18" order="1" />
<bond atomRefs2="a18 a20" order="1" />
<bond atomRefs2="a18 a17" order="1" />
<bond atomRefs2="a18 a19" order="1" />
<bond atomRefs2="a23 a24" order="1" />
<bond atomRefs2="a21 a22" order="1" />
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="Et" molID="m2">
<atomArray
atomID="a25 a26"
elementType="C C"
attachmentPoint="1 0"
x2="-1.4233333492279052 -2.9633333492279053"
y2="7.991666793823242 7.991666793823242"
/>
<bondArray>
<bond atomRefs2="a26 a25" order="1" />
</bondArray>
</molecule>
<molecule id="sg2" role="SuperatomSgroup" title="Et" molID="m3">
<atomArray
atomID="a27 a28"
elementType="C C"
attachmentPoint="1 0"
x2="9.71833330154419 8.178333301544189"
y2="3.674999952316284 3.674999952316284"
/>
<bondArray>
<bond atomRefs2="a28 a27" order="1" />
</bondArray>
</molecule>
</molecule>
</MChemicalStruct>
<MEFlow id="o2" arcAngle="-215.96093639468995" headSkip="0.15"
headLength="0.5" headWidth="0.4" tailSkip="0.15">
<MAtomSetPoint atomRefs="m1.a6 m1.a4" />
<MAtomSetPoint atomRefs="m1.a2 m1.a6" />
</MEFlow>
<MEFlow id="o3" arcAngle="248.39738999999997" headSkip="0.25"
headLength="0.5" headWidth="0.4" tailSkip="0.15">
<MAtomSetPoint atomRefs="m1.a2 m1.a3" />
<MAtomSetPoint atomRefs="m1.a3" />
</MEFlow>
<MEFlow id="o4" arcAngle="248.39738999999997" headSkip="0.25"
headLength="0.5" headWidth="0.4" tailSkip="0.15">
<MAtomSetPoint atomRefs="m1.a12 m1.a13" />
<MAtomSetPoint atomRefs="m1.a13" />
</MEFlow>
<MEFlow id="o5" arcAngle="150.0" headSkip="0.15" headLength="0.5"
headWidth="0.4" tailSkip="0.15">
<MAtomSetPoint atomRefs="m1.a9 m1.a10" />
<MAtomSetPoint atomRefs="m1.a10 m1.a12" />
</MEFlow>
<MEFlow id="o6" arcAngle="-254.995522631729" headSkip="0.15"
headLength="0.5" headWidth="0.4" tailSkip="0.25">
<MAtomSetPoint atomRefs="m1.a11" />
<MAtomSetPoint atomRefs="m1.a9 m1.a11" />
</MEFlow>
<MRectangle id="o7">
<MPoint x="-10.149999618530273" y="9.449999809265137" />
<MPoint x="-1.6333332061767578" y="9.449999809265137" />
<MPoint x="-1.6333332061767578" y="2.0999999046325684" />
<MPoint x="-10.149999618530273" y="2.0999999046325684" />
</MRectangle>
<MRectangle id="o8">
<MPoint x="0.6416666507720947" y="9.158333778381348" />
<MPoint x="9.975000381469727" y="9.158333778381348" />
<MPoint x="9.975000381469727" y="2.3333332538604736" />
<MPoint x="0.6416666507720947" y="2.3333332538604736" />
</MRectangle>
<MRectangle id="o9">
<MPoint x="-4.7833333015441895" y="0.9916666746139526" />
<MPoint x="3.0333333015441895" y="0.9916666746139526" />
<MPoint x="3.0333333015441895" y="-4.433333396911621" />
<MPoint x="-4.7833333015441895" y="-4.433333396911621" />
</MRectangle>
<MPolyline id="o10" headLength="0.8" headWidth="0.5">
<MPoint x="-1.6333332061767578" y="5.7749998569488525" />
<MPoint x="0.6416666507720947" y="5.745833516120911" />
</MPolyline>
<MPolyline id="o11" headLength="0.8" headWidth="0.5">
<MPoint x="0.6416666507720947" y="2.3333332538604736" />
<MPoint x="-0.875" y="0.9916666746139526" />
</MPolyline>
<MEFlow id="o12" arcAngle="-199.95659599409996" headSkip="0.15"
headLength="0.5" headWidth="0.4" tailSkip="0.25">
<MAtomSetPoint atomRefs="m1.a21" />
<MAtomSetPoint atomRefs="m1.a21 m1.a4" />
</MEFlow>
</MDocument> |
Could it have to do with the shortcut groups?
User 870ab5b546
22-08-2006 23:17:10
More information: The bug appears to be associated with saving structures that contain an electron-flow arrow that involves an explicit H. Make the H into an SiMe3, and there's no problem. Get rid of the electron-flow arrow making a bond to H and the electron-flow arrow breaking the C-H bond, and there's no problem.
!?!?
ChemAxon 9c0afc9aaf
24-08-2006 06:28:38
Hi,
We have fixed the problem, this bug will not be present in the next (test) release.
Best regards,
Szilard
User 870ab5b546
24-08-2006 10:42:58
And when will that be available?
ChemAxon 9c0afc9aaf
25-08-2006 14:39:31