Home / Browse / The Chemistry Development Kit / Mail / Archive

The Chemistry Development Kit

Email Archive: cdk-devel (read-only)

2001:	_Jan	_Feb	_Mar	_Apr	_May	_Jun	_Jul	_Aug	_Sep	_Oct (28)	_Nov (13)	_Dec (25)
2002:	_Jan (14)	_Feb (30)	_Mar (8)	_Apr (24)	_May (13)	_Jun (8)	_Jul (12)	_Aug (46)	_Sep (30)	_Oct (40)	_Nov (68)	_Dec (15)
2003:	_Jan (20)	_Feb (93)	_Mar (56)	_Apr (21)	_May (28)	_Jun (78)	_Jul (58)	_Aug (54)	_Sep (213)	_Oct (162)	_Nov (81)	_Dec (54)
2004:	_Jan (139)	_Feb (227)	_Mar (87)	_Apr (150)	_May (107)	_Jun (70)	_Jul (42)	_Aug (87)	_Sep (17)	_Oct (34)	_Nov (60)	_Dec (93)
2005:	_Jan (45)	_Feb (76)	_Mar (67)	_Apr (109)	_May (90)	_Jun (46)	_Jul (39)	_Aug (78)	_Sep (67)	_Oct (32)	_Nov (81)	_Dec (86)
2006:	_Jan (85)	_Feb (76)	_Mar (85)	_Apr (84)	_May (144)	_Jun (78)	_Jul (55)	_Aug (55)	_Sep (85)	_Oct (71)	_Nov (60)	_Dec (30)
2007:	_Jan (27)	_Feb (74)	_Mar (48)	_Apr (183)	_May (33)	_Jun (50)	_Jul (83)	_Aug (37)	_Sep (110)	_Oct (109)	_Nov (78)	_Dec (126)
2008:	_Jan (112)	_Feb (81)	_Mar (58)	_Apr (38)	_May (167)	_Jun (115)	_Jul (143)	_Aug (164)	_Sep (173)	_Oct (143)	_Nov (98)	_Dec (134)
2009:	_Jan (185)	_Feb (116)	_Mar (125)	_Apr (201)	_May (59)	_Jun (110)	_Jul (56)	_Aug (85)	_Sep (109)	_Oct (129)	_Nov (315)	_Dec (93)
2010:	_Jan (49)	_Feb (93)	_Mar (207)	_Apr (123)	_May (114)	_Jun (63)	_Jul (111)	_Aug (160)	_Sep (70)	_Oct (254)	_Nov (11)	_Dec (91)
2011:	_Jan (34)	_Feb (155)	_Mar (92)	_Apr (15)	_May (82)	_Jun (191)	_Jul (102)	_Aug (71)	_Sep (113)	_Oct (44)	_Nov (66)	_Dec (84)
2012:	_Jan (51)	_Feb (95)	_Mar (31)	_Apr (100)	_May (133)	_Jun (73)	_Jul (103)	_Aug (90)	_Sep (84)	_Oct (217)	_Nov (113)	_Dec (30)
2013:	_Jan (9)	_Feb (18)	_Mar (10)	_Apr (17)	_May (22)	_Jun	_Jul	_Aug	_Sep	_Oct	_Nov	_Dec


S	M	T	W	T	F	S
			1	2	3	4
			(2)	(1)		(2)
5	6	7	8	9	10	11
	(3)	(5)	(10)	(9)	(4)	(3)
12	13	14	15	16	17	18
	(8)		(6)	(5)
19	20	21	22	23	24	25
(3)			(3)	(2)	(2)	(3)
26	27	28
	(4)	(1)

[Cdk-devel] online pdf generation from sdf

From: Stefan Kuhn <stefan.kuhn@un...> - 2006-02-22 14:38

Hi all,
there is a new function on cdk.org (Tab "Miscellaneous"), which generates=
 a=20
pdf table from an sdf file. The code comes from Rajarshi (thanks!).
Stefan
--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Cdk-devel] Problem with Jmol on cdk.org

From: Noel O'Boyle <no228@ca...> - 2006-02-22 14:55

Hello all,

The Jmol applet on cdk.org appears to have a problem with the following
molecule:
CC(CCC2CCC1C(=3DCCS1)C2)CC(=3DO)CCS
(taken from the Open Molecule Database)

When I import the SMILES string, the 2D structure is shown fine. But
when I then click on "Render the current structure in 3D", I get the
following error messages:

RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be
layout.Sorry java.io.IOException: RingAtomLayoutError: Not every ring
atom is placed! Molecule cannot be layout.Sorry at
org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordinates=
(ModelBuilder3D.java:219) at org.openscience.cdkweb.modules.actions.portlet=
s.Render3DAction.doRender(Render3DAction.java:85) at sun.reflect.NativeMeth=
odAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorIm=
pl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethod=
AccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.refl=
ect.Method.invoke(Method.java:585) at org.apache.jetspeed.modules.actions.p=
ortlets.PortletActionEvent.fireEvent(PortletActionEvent.java:176) at org.ap=
ache.jetspeed.modules.actions.portlets.PortletActionEvent.executeEvents(Por=
tletActionEvent.java:133) at org.apache.jetspeed.modules.actions.portlets.G=
enericMVCAction.perform(GenericMVCAction.java:105) at org.apache.turbine.mo=
dules.ActionLoader.exec(ActionLoader.java:122) at org.apache.jetspeed.porta=
l.portlets.GenericMVCPortlet.buildContent(GenericMVCPortlet.java:276) at or=
g.apache.jetspeed.portal.portlets.GenericMVCPortlet.getContent(GenericMVCPo=
rtlet.java:207) at org.apache.jetspeed.portal.security.portlets.PortletWrap=
per.getContent(PortletWrapper.java:119) at sun.reflect.GeneratedMethodAcces=
sor115.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.i=
nvoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.inv=
oke(Method.java:585) at org.apache.velocity.runtime.parser.node.ASTMethod.e=
xecute(ASTMethod.java:260) at org.apache.velocity.runtime.parser.node.ASTRe=
ference.execute(ASTReference.java:207) at org.apache.velocity.runtime.parse=
r.node.ASTReference.render(ASTReference.java:250) at org.apache.velocity.ru=
ntime.parser.node.ASTBlock.render(ASTBlock.java:94) at org.apache.velocity.=
runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:109) at org.a=
pache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:94) at org=
.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.j=
ava:109) at org.apache.velocity.runtime.parser.node.SimpleNode.render(Simpl=
eNode.java:271) at org.apache.velocity.Template.merge(Template.java:296) at=
 org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at org.a=
pache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at org.apache.=
turbine.services.velocity.TurbineVelocityService.decodeRequest(TurbineVeloc=
ityService.java:494) at org.apache.turbine.services.velocity.TurbineVelocit=
yService.handleRequest(TurbineVelocityService.java:336) at org.apache.turbi=
ne.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:143=
) at org.apache.jetspeed.portal.controls.VelocityPortletControl.getContent(=
VelocityPortletControl.java:155) at sun.reflect.GeneratedMethodAccessor108.=
invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(D=
elegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Met=
hod.java:585) at org.apache.velocity.runtime.parser.node.ASTMethod.execute(=
ASTMethod.java:260) at org.apache.velocity.runtime.parser.node.ASTReference=
.execute(ASTReference.java:207) at org.apache.velocity.runtime.parser.node.=
ASTReference.render(ASTReference.java:250) at org.apache.velocity.runtime.p=
arser.node.ASTBlock.render(ASTBlock.java:94) at org.apache.velocity.runtime=
.directive.Foreach.render(Foreach.java:344) at org.apache.velocity.runtime.=
parser.node.ASTDirective.render(ASTDirective.java:153) at org.apache.veloci=
ty.runtime.parser.node.ASTBlock.render(ASTBlock.java:94) at org.apache.velo=
city.runtime.directive.Foreach.render(Foreach.java:344) at org.apache.veloc=
ity.runtime.parser.node.ASTDirective.render(ASTDirective.java:153) at org.a=
pache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:271) a=
t org.apache.velocity.Template.merge(Template.java:296) at org.apache.veloc=
ity.app.Velocity.mergeTemplate(Velocity.java:492) at org.apache.velocity.ap=
p.Velocity.mergeTemplate(Velocity.java:461) at org.apache.turbine.services.=
velocity.TurbineVelocityService.decodeRequest(TurbineVelocityService.java:4=
94) at org.apache.turbine.services.velocity.TurbineVelocityService.handleRe=
quest(TurbineVelocityService.java:336) at org.apache.turbine.services.veloc=
ity.TurbineVelocity.handleRequest(TurbineVelocity.java:143) at org.apache.j=
etspeed.portal.controllers.VelocityPortletController.getContent(VelocityPor=
tletController.java:105) at org.apache.jetspeed.portal.BasePortletSet.getCo=
ntent(BasePortletSet.java:353) at sun.reflect.GeneratedMethodAccessor128.in=
voke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Del=
egatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Metho=
d.java:585) at org.apache.velocity.runtime.parser.node.ASTMethod.execute(AS=
TMethod.java:260) at org.apache.velocity.runtime.parser.node.ASTReference.e=
xecute(ASTReference.java:207) at org.apache.velocity.runtime.parser.node.AS=
TReference.render(ASTReference.java:250) at org.apache.velocity.runtime.par=
ser.node.SimpleNode.render(SimpleNode.java:271) at org.apache.velocity.Temp=
late.merge(Template.java:296) at org.apache.velocity.app.Velocity.mergeTemp=
late(Velocity.java:492) at org.apache.velocity.app.Velocity.mergeTemplate(V=
elocity.java:461) at org.apache.turbine.services.velocity.TurbineVelocitySe=
rvice.decodeRequest(TurbineVelocityService.java:494) at org.apache.turbine.=
services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityServi=
ce.java:336) at org.apache.turbine.services.velocity.TurbineVelocity.handle=
Request(TurbineVelocity.java:143) at org.apache.jetspeed.portal.controllers=
.VelocityPortletController.getContent(VelocityPortletController.java:105) a=
t org.apache.jetspeed.portal.BasePortletSet.getContent(BasePortletSet.java:=
353) at sun.reflect.GeneratedMethodAccessor128.invoke(Unknown Source) at su=
n.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.=
java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.apache.=
velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:260) at org.a=
pache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:2=
07) at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTRefer=
ence.java:250) at org.apache.velocity.runtime.parser.node.ASTBlock.render(A=
STBlock.java:94) at org.apache.velocity.runtime.parser.node.SimpleNode.rend=
er(SimpleNode.java:271) at org.apache.velocity.runtime.parser.node.ASTIfSta=
tement.render(ASTIfStatement.java:128) at org.apache.velocity.runtime.parse=
r.node.ASTBlock.render(ASTBlock.java:94) at org.apache.velocity.runtime.par=
ser.node.ASTIfStatement.render(ASTIfStatement.java:109) at org.apache.veloc=
ity.runtime.parser.node.SimpleNode.render(SimpleNode.java:271) at org.apach=
e.velocity.Template.merge(Template.java:296) at org.apache.velocity.app.Vel=
ocity.mergeTemplate(Velocity.java:492) at org.apache.velocity.app.Velocity.=
mergeTemplate(Velocity.java:461) at org.apache.turbine.services.velocity.Tu=
rbineVelocityService.decodeRequest(TurbineVelocityService.java:494) at org.=
apache.turbine.services.velocity.TurbineVelocityService.handleRequest(Turbi=
neVelocityService.java:336) at org.apache.turbine.services.velocity.Turbine=
Velocity.handleRequest(TurbineVelocity.java:143) at org.apache.jetspeed.por=
tal.controls.VelocityPortletControl.getContent(VelocityPortletControl.java:=
155) at org.apache.jetspeed.util.template.JetspeedTool.getPane(JetspeedTool=
.java:154) at sun.reflect.GeneratedMethodAccessor144.invoke(Unknown Source)=
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.a=
pache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:260) at=
 org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.=
java:207) at org.apache.velocity.runtime.parser.node.ASTReference.render(AS=
TReference.java:250) at org.apache.velocity.runtime.parser.node.ASTBlock.re=
nder(ASTBlock.java:94) at org.apache.velocity.runtime.parser.node.SimpleNod=
e.render(SimpleNode.java:271) at org.apache.velocity.runtime.parser.node.AS=
TIfStatement.render(ASTIfStatement.java:128) at org.apache.velocity.runtime=
.parser.node.SimpleNode.render(SimpleNode.java:271) at org.apache.velocity.=
Template.merge(Template.java:296) at org.apache.velocity.app.Velocity.merge=
Template(Velocity.java:492) at org.apache.velocity.app.Velocity.mergeTempla=
te(Velocity.java:461) at org.apache.turbine.services.velocity.TurbineVeloci=
tyService.decodeRequest(TurbineVelocityService.java:494) at org.apache.turb=
ine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityS=
ervice.java:336) at org.apache.turbine.services.velocity.TurbineVelocity.ha=
ndleRequest(TurbineVelocity.java:143) at org.apache.turbine.modules.screens=
.VelocityDirectScreen.buildTemplate(VelocityDirectScreen.java:123) at org.a=
pache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:13=
0) at org.apache.turbine.modules.Screen.build(Screen.java:99) at org.apache=
.turbine.modules.ScreenLoader.eval(ScreenLoader.java:129) at org.apache.tur=
bine.util.template.TemplateScreen.toString(TemplateScreen.java:126) at org.=
apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:3=
21) at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode=
.java:271) at org.apache.velocity.Template.merge(Template.java:296) at org.=
apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at org.apache=
.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at org.apache.turbi=
ne.services.velocity.TurbineVelocityService.decodeRequest(TurbineVelocitySe=
rvice.java:494) at org.apache.turbine.services.velocity.TurbineVelocityServ=
ice.handleRequest(TurbineVelocityService.java:336) at org.apache.turbine.se=
rvices.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:143) at =
org.apache.turbine.modules.layouts.VelocityDirectLayout.doBuild(VelocityDir=
ectLayout.java:106) at org.apache.turbine.modules.Layout.build(Layout.java:=
91) at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:123) =
at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:16=
9) at org.apache.turbine.modules.Page.build(Page.java:90) at org.apache.tur=
bine.modules.PageLoader.exec(PageLoader.java:123) at org.apache.turbine.Tur=
bine.doGet(Turbine.java:563) at org.apache.turbine.Turbine.doPost(Turbine.j=
ava:658) at javax.servlet.http.HttpServlet.service(HttpServlet.java:763) at=
 javax.servlet.http.HttpServlet.service(HttpServlet.java:856) at org.apache=
.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterCha=
in.java:237) at org.apache.catalina.core.ApplicationFilterChain.doFilter(Ap=
plicationFilterChain.java:157) at org.apache.catalina.core.StandardWrapperV=
alve.invoke(StandardWrapperValve.java:214) at org.apache.catalina.core.Stan=
dardValveContext.invokeNext(StandardValveContext.java:104) at org.apache.ca=
talina.core.StandardPipeline.invoke(StandardPipeline.java:520) at org.apach=
e.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.ja=
va:198) at org.apache.catalina.core.StandardContextValve.invoke(StandardCon=
textValve.java:152) at org.apache.catalina.core.StandardValveContext.invoke=
Next(StandardValveContext.java:104) at org.apache.catalina.core.StandardPip=
eline.invoke(StandardPipeline.java:520) at org.apache.catalina.core.Standar=
dHostValve.invoke(StandardHostValve.java:137) at org.apache.catalina.core.S=
tandardValveContext.invokeNext(StandardValveContext.java:104) at org.apache=
.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.=
apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.j=
ava:102) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeli=
ne.java:520) at org.apache.catalina.core.StandardEngineValve.invoke(Standar=
dEngineValve.java:109) at org.apache.catalina.core.StandardValveContext.inv=
okeNext(StandardValveContext.java:104) at org.apache.catalina.core.Standard=
Pipeline.invoke(StandardPipeline.java:520) at org.apache.catalina.core.Cont=
ainerBase.invoke(ContainerBase.java:929) at org.apache.coyote.tomcat5.Coyot=
eAdapter.service(CoyoteAdapter.java:160) at org.apache.jk.server.JkCoyoteHa=
ndler.invoke(JkCoyoteHandler.java:300) at org.apache.jk.common.HandlerReque=
st.invoke(HandlerRequest.java:374) at org.apache.jk.common.ChannelSocket.in=
voke(ChannelSocket.java:743) at org.apache.jk.common.ChannelSocket.processC=
onnection(ChannelSocket.java:675) at org.apache.jk.common.SocketConnection.=
runIt(ChannelSocket.java:866) at org.apache.tomcat.util.threads.ThreadPool$=
ControlRunnable.run(ThreadPool.java:683) at java.lang.Thread.run(Thread.jav=
a:595)

Note that there is no problem with my test molecule "CCCC".

Regards,
 Noel

Re: [Cdk-devel] Problem with Jmol on cdk.org

From: Stefan Kuhn <stefan.kuhn@un...> - 2006-02-22 15:38

Hi,
this is the well known bug in modelbuilder3d not to work with rings. When=
 I=20
did the last cdk update on cdk.org, I warned that this bug would show up.=
 The=20
update was needed to get other features.
This bug is due to a problem with the UniversalIsomorphismTester. See=20
testItself() in UniversalIsomorphismTesterTest. This is how far I got.
Stefan

Am Wednesday 22 February 2006 15:55 schrieb Noel O'Boyle:
> Hello all,
>
> The Jmol applet on cdk.org appears to have a problem with the following
> molecule:
> CC(CCC2CCC1C(=3DCCS1)C2)CC(=3DO)CCS
> (taken from the Open Molecule Database)
>
> When I import the SMILES string, the 2D structure is shown fine. But
> when I then click on "Render the current structure in 3D", I get the
> following error messages:
>
> RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be
> layout.Sorry java.io.IOException: RingAtomLayoutError: Not every ring
> atom is placed! Molecule cannot be layout.Sorry at
> org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordin=
ates
>(ModelBuilder3D.java:219) at
> org.openscience.cdkweb.modules.actions.portlets.Render3DAction.doRender=
(Ren
>der3DAction.java:85) at sun.reflect.NativeMethodAccessorImpl.invoke0(Nat=
ive
> Method) at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.ja=
va:3
>9) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImp
>l.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at
> org.apache.jetspeed.modules.actions.portlets.PortletActionEvent.fireEve=
nt(P
>ortletActionEvent.java:176) at
> org.apache.jetspeed.modules.actions.portlets.PortletActionEvent.execute=
Even
>ts(PortletActionEvent.java:133) at
> org.apache.jetspeed.modules.actions.portlets.GenericMVCAction.perform(G=
ener
>icMVCAction.java:105) at
> org.apache.turbine.modules.ActionLoader.exec(ActionLoader.java:122) at
> org.apache.jetspeed.portal.portlets.GenericMVCPortlet.buildContent(Gene=
ricM
>VCPortlet.java:276) at
> org.apache.jetspeed.portal.portlets.GenericMVCPortlet.getContent(Generi=
cMVC
>Portlet.java:207) at
> org.apache.jetspeed.portal.security.portlets.PortletWrapper.getContent(=
Port
>letWrapper.java:119) at
> sun.reflect.GeneratedMethodAccessor115.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImp
>l.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.jav=
a:26
>0) at
> org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReferen=
ce.j
>ava:207) at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReferenc=
e.ja
>va:250) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStat=
emen
>t.java:109) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStat=
emen
>t.java:109) at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at org.apache.velocity.Template.merge(Template.java:296) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at
> org.apache.turbine.services.velocity.TurbineVelocityService.decodeReque=
st(T
>urbineVelocityService.java:494) at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleReque=
st(T
>urbineVelocityService.java:336) at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(Turb=
ineV
>elocity.java:143) at
> org.apache.jetspeed.portal.controls.VelocityPortletControl.getContent(V=
eloc
>ityPortletControl.java:155) at
> sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImp
>l.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.jav=
a:26
>0) at
> org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReferen=
ce.j
>ava:207) at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReferenc=
e.ja
>va:250) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at org.apache.velocity.runtime.directive.Foreach.render(Foreach.java:34=
4)
> at
> org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirectiv=
e.ja
>va:153) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at org.apache.velocity.runtime.directive.Foreach.render(Foreach.java:34=
4)
> at
> org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirectiv=
e.ja
>va:153) at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at org.apache.velocity.Template.merge(Template.java:296) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at
> org.apache.turbine.services.velocity.TurbineVelocityService.decodeReque=
st(T
>urbineVelocityService.java:494) at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleReque=
st(T
>urbineVelocityService.java:336) at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(Turb=
ineV
>elocity.java:143) at
> org.apache.jetspeed.portal.controllers.VelocityPortletController.getCon=
tent
>(VelocityPortletController.java:105) at
> org.apache.jetspeed.portal.BasePortletSet.getContent(BasePortletSet.jav=
a:35
>3) at sun.reflect.GeneratedMethodAccessor128.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImp
>l.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.jav=
a:26
>0) at
> org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReferen=
ce.j
>ava:207) at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReferenc=
e.ja
>va:250) at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at org.apache.velocity.Template.merge(Template.java:296) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at
> org.apache.turbine.services.velocity.TurbineVelocityService.decodeReque=
st(T
>urbineVelocityService.java:494) at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleReque=
st(T
>urbineVelocityService.java:336) at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(Turb=
ineV
>elocity.java:143) at
> org.apache.jetspeed.portal.controllers.VelocityPortletController.getCon=
tent
>(VelocityPortletController.java:105) at
> org.apache.jetspeed.portal.BasePortletSet.getContent(BasePortletSet.jav=
a:35
>3) at sun.reflect.GeneratedMethodAccessor128.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImp
>l.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.jav=
a:26
>0) at
> org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReferen=
ce.j
>ava:207) at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReferenc=
e.ja
>va:250) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStat=
emen
>t.java:128) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStat=
emen
>t.java:109) at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at org.apache.velocity.Template.merge(Template.java:296) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at
> org.apache.turbine.services.velocity.TurbineVelocityService.decodeReque=
st(T
>urbineVelocityService.java:494) at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleReque=
st(T
>urbineVelocityService.java:336) at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(Turb=
ineV
>elocity.java:143) at
> org.apache.jetspeed.portal.controls.VelocityPortletControl.getContent(V=
eloc
>ityPortletControl.java:155) at
> org.apache.jetspeed.util.template.JetspeedTool.getPane(JetspeedTool.jav=
a:15
>4) at sun.reflect.GeneratedMethodAccessor144.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso=
rImp
>l.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.jav=
a:26
>0) at
> org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReferen=
ce.j
>ava:207) at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReferenc=
e.ja
>va:250) at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:9=
4)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStat=
emen
>t.java:128) at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at org.apache.velocity.Template.merge(Template.java:296) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at
> org.apache.turbine.services.velocity.TurbineVelocityService.decodeReque=
st(T
>urbineVelocityService.java:494) at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleReque=
st(T
>urbineVelocityService.java:336) at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(Turb=
ineV
>elocity.java:143) at
> org.apache.turbine.modules.screens.VelocityDirectScreen.buildTemplate(V=
eloc
>ityDirectScreen.java:123) at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScree=
n.ja
>va:130) at org.apache.turbine.modules.Screen.build(Screen.java:99) at
> org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:129) at
> org.apache.turbine.util.template.TemplateScreen.toString(TemplateScreen=
.jav
>a:126) at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReferenc=
e.ja
>va:321) at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.ja=
va:2
>71) at org.apache.velocity.Template.merge(Template.java:296) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492) at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461) at
> org.apache.turbine.services.velocity.TurbineVelocityService.decodeReque=
st(T
>urbineVelocityService.java:494) at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleReque=
st(T
>urbineVelocityService.java:336) at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(Turb=
ineV
>elocity.java:143) at
> org.apache.turbine.modules.layouts.VelocityDirectLayout.doBuild(Velocit=
yDir
>ectLayout.java:106) at
> org.apache.turbine.modules.Layout.build(Layout.java:91) at
> org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:123) at
> org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:1=
69)
> at org.apache.turbine.modules.Page.build(Page.java:90) at
> org.apache.turbine.modules.PageLoader.exec(PageLoader.java:123) at
> org.apache.turbine.Turbine.doGet(Turbine.java:563) at
> org.apache.turbine.Turbine.doPost(Turbine.java:658) at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:763) at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:856) at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applic=
atio
>nFilterChain.java:237) at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFil=
terC
>hain.java:157) at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVal=
ve.j
>ava:214) at
> org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveC=
onte
>xt.java:104) at
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:=
520)
> at
> org.apache.catalina.core.StandardContextValve.invokeInternal(StandardCo=
ntex
>tValve.java:198) at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextVal=
ve.j
>ava:152) at
> org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveC=
onte
>xt.java:104) at
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:=
520)
> at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.jav=
a:13
>7) at
> org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveC=
onte
>xt.java:104) at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.jav=
a:11
>7) at
> org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveC=
onte
>xt.java:102) at
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:=
520)
> at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve=
.jav
>a:109) at
> org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveC=
onte
>xt.java:104) at
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:=
520)
> at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:929=
) at
> org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:160)=
 at
> org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:300) a=
t
> org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:374) at
> org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:743) at
> org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java=
:675
>) at org.apache.jk.common.SocketConnection.runIt(ChannelSocket.java:866)=
 at
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPoo=
l.ja
>va:683) at java.lang.Thread.run(Thread.java:595)
>
> Note that there is no problem with my test molecule "CCCC".
>
> Regards,
>  Noel
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files for problems?  Stop!  Download the new AJAX search engine that ma=
kes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=103432&bid#0486&dat=12164=
2
> _______________________________________________
> Cdk-devel mailing list
> Cdk-devel@...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu