[Cdk-devel] [Cdk-user] Generating 3D coordinates from 2D molfile

[Mas K. <mas...@gm...>]

Hi,

I have just started learning CDK, and I made this Java code:
http://dl.dropbox.com/u/17348116/CDK/Cdk-user/Molfile2Dto3D.java
I intended to convert 2D molfiles into 3D molfiles.

When I input this compound (caffeine),
http://dl.dropbox.com/u/17348116/CDK/Cdk-user/ChEBI_27732.mol
my Java code generates 3D coordinates,
although there appear the following error messages:

  WARNING: Maybe RingTemplateError!
  KEYError: Unknown distance key in pSet: O=;Csp2 take default bond length:
1.5
  KEYError: Unknown distance key in pSet: O=;Csp2 take default bond length:
1.5
  KEYError: Unknown distance key in pSet: C;NPYL take default bond length:
1.5

I am curious what is going on, but this does not seem so serious.

What seems serious is the following.
When I input another compound (ATP),
http://dl.dropbox.com/u/17348116/CDK/Cdk-user/ChEBI_15422.mol
my Java code failed to generate 3D coordinates,
and showed the following messages:

  Could not final configure atom 18 due to
org.openscience.cdk.exception.NoSuchAtomTypeException: Atom is unkown:
Symbol:O does not MATCH AtomType. HoseCode:O-1;=P(OOO/P,C,/)
org.openscience.cdk.exception.CDKException: Could not final configure atom
due to problems with force field
at
org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.assignAtomTyps(ForceFieldConfigurator.java:296)
at
org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordinates(ModelBuilder3D.java:196)
at jp.kegg.sample.Molfile2Dto3D.main(Molfile2Dto3D.java:61)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:120)
Caused by: org.openscience.cdk.exception.NoSuchAtomTypeException: Atom is
unkown: Symbol:O does not MATCH AtomType. HoseCode:O-1;=P(OOO/P,C,/)
at
org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.configureMM2BasedAtom(ForceFieldConfigurator.java:542)
at
org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.configureAtom(ForceFieldConfigurator.java:391)
at
org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.assignAtomTyps(ForceFieldConfigurator.java:293)
... 7 more


Could someone tell me what is going on? I can not find anything to solve
this problem.

Best wishes,
Masaaki KOTERA
mas...@gm... | ko...@ku...
Ph.D Science, Assistant Professor at Kyoto University, Japan.
Laboratory of Chemical Life Science (Goto Laboratory)
Bioinformatics Centre, Institute for Chemical Research, Kyoto University.
http://web.kuicr.kyoto-u.ac.jp/~kot/