Geometry option fails for (bastard) Claus Benzol

Hi,


the Geometry Plugin In Marvin 4.1.2 has problems with Claus Benzol,


SMILES C12C3C4C1C3C24 which is a probably non-existing C6H6 structure, however it will be generated by deterministic structure generators.





Claus Benzol (also Dewar, Kekule and others can be seen here)


http://books.google.com/books?vid=OCLC57642783&id=yCE_MoPOsHcC&pg=PA11&lpg=PA11&dq=dewar+benzol&num=100#PPA12,M1





IF you choose Geometry Options, Calcluate Lowest Energy Conformer Always --> JAVA EXCEPTION


It works if you use "Never"





-----------------


This is not the only molecule there are bunch of others, where this option


fails. I will report them later (some of the CDK SMILES are broken). This also affects JCHEM and Instant-JChem (this error with fallback option will render the molecule non-visible).


-----------------


Error output


java.lang.NullPointerException


at chemaxon.calculations.Geometry.get3DMolecule(Geometry.java:80)


at chemaxon.marvin.calculations.GeometryPlugin.getResultMolecule(GeometryPlugin.java:693)


at chemaxon.marvin.calculations.GeometryPlugin.getResultMolecules(GeometryPlugin.java:718)


at chemaxon.marvin.calculations.GeometryPluginDisplay.store(GeometryPluginDisplay.java:49)


at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:171)


at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:154)


at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:108)


at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:73)


at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:87)


at chemaxon.marvin.common.swing.MolPanel.run(MolPanel.java:2471)


[catch] at java.lang.Thread.run(Unknown Source)





-----------------------------------------------


217 C6H6 smiles (not unique unique)


c1ccccc1


C1=CC1C2C=C2


C1=CC2C=CC12


C1=CC2C3C1C23


C12C3C1C4C2C34


C13C2C4C1C2C34


C#CC=CC=C


C#CCC1C=C1


C#CC1C=CC1


C#CC1C2CC12


C1=CCC=C=C1


C=C=CC1C=C1


C=CC1C=C=C1


C=1=CC2CC2(C=1)


C=C1C=CC=C1


C=CC=1C=CC=1


C=CC=C1C=C1


C1=CC1C2=CC2


C1=CC2C=C2(C1)


C1=CC2=CC1C2


C1=CC2CC2(=C1)


C1=CC2=CCC12


C1=CC2=CC2(C1)


C=C1C2C=CC12


C=CC1C2C=C12


C1=C2CC3C1C23


C=2C1C3CC1C=23


C=1CC2C3C=1C23


C=1C2CC3C=1C23


C=1C2C=1C3CC23


C=C1C2C3C1C23


C1=CC2(C1)(C=C2)


C1C3C1C23(C=C2)


C1=CC23(CC3(C12))


C=CC23(C1C3(C12))


C1C2C3C4C1C234


C2C1C3C4C1C234


C2C3C1C4C1C234


C#CCCC#C


C=CC#CC=C


C1=CCCC#C1


C1=CCC#CC1


C=CC1C#CC1


C=CCC1C#C1


C1#CC1C2CC2


C1#CC2CCC12


C1#CC2CC2(C1)


C1#CC2CC1C2


C#CCC=C=C


C=CC=C=C=C


C=C=CC=C=C


C=1CCC=C=C=1


C#CC(=C)C=C


C#CC=C1CC1


C#CC1=CCC1


C#CCC1=CC1


C#CC1CC1(=C)


C=C=C1C=CC1


C=C=CC1=CC1


C=CC=1CC=C=1


C=CCC=1C=C=1


C=C1CC=C=C1


C1=C=C2CCC12


C1=C=C2CC1C2


C1=C=C1C2CC2


C=1CC2CC2(=C=1)


C=C=C1C2CC12


C=C1C=CC1(=C)


C=CC1=CC1(=C)


C1=CC1=C2CC2


C1=CC=2CCC1=2


C1=CC=2CC=2(C1)


C=1C=C2CCC=12


C=1C=C2CC=1C2


C1CC=2C=C1C=2


C1C=C2C=C2(C1)


C=1CC2=CC=1C2


C1C=C2CC2(=C1)


C=1CC=1C2=CC2


C=1CC2=CCC=12


C=C1CC2=CC12


C=CC1C=2CC1=2


C=C1CC2C=C12


C=C2C1C=C2(C1)


C=C1C=C2CC12


C=C1C2=CCC12


C=CC=1C2CC=12


C=C1C2C(=C)C12


C1CC=2C3C1C=23


C1C2CC3=C1C23


C1C=2CC3C1C=23


C1C2C1C=3CC2=3


C1C2C1=C3CC23


C2C1C3CC1=C23


C1CC2C=3C1C2=3


C1C2CC=3C1C2=3


C#CC12(CC2(C1))


C=1=CC2(C=1)(CC2)


C=C2CC12(C=C1)


C=CC12(C=C2(C1))


C1CC23(C=C3(C12))


C1C3=CC23(CC12)


C1=C2CC13(CC23)


C=1C3C=1C23(CC2)


C=1C3CC23(CC=12)


C=1CC23(CC3(C=12))


C1C2CC13(C=C23)


C=C1C3C2CC123


C1=CC23(CC13(C2))


C2C1C34(CC14(C23))


C1CC34(C2C4(C123))


C1C2C14(C3CC234)


C1C2C3C14(CC234)


C1C24(CC13(C4(C23)))


C=C1C#CCC1


C=C1CC#CC1


C=C=C=C1CC1


C=C=C1CC1(=C)


C1CC2=C=C2(C1)


C1CC=2CC1=C=2


C=C1C(=C)C1(=C)


C=C1C=2CCC1=2


C=C1CC=2CC1=2


C1CC2(C1)(C#C2)


C1#CC2(C1)(CC2)


C1CC23(CC3(=C12))


C1C3=C1C23(CC2)


C1C=2CC13(CC=23)


C=C2C13(CC23(C1))


C1C24(CC34(CC123))


C#CC(C)C#C


CC#CC1C=C1


CC=CC1C#C1


CC1C=CC#C1


CC1C2C#CC12


C#CC=C=CC


CC1C=C=C=C1


C#CC1C=C1(C)


C#CC1=CC1(C)


CC=1C=CC=C=1


CC=C=C1C=C1


CC=CC=1C=C=1


CC1=CC=C=C1


CC=C1C=C=C1


CC1C2C=C=C12


CC1=CC2C=C12


CC=1C2C=CC=12


CC1=CC2=CC12


CC=C1C2C=C12


CC1C=C2C=C12


CC1C=2C=CC1=2


CC1C2=CC=C12


CC2C1=CC2(=C1)


CC=1C2C3C=1C23


CC1C2C3C1=C23


CC1C2C=3C1C2=3


C#CC1(C)(C=C1)


CC2=CC12(C=C1)


CC12(C=CC2(=C1))


CC1C3C2=CC123


CC23(C=C1C3(C12))


CC23(C1C=C3(C12))


CC2C14(C3C1C234)


CC14(C3C2C1C234)


C#CC#CCC


C#CCC#CC


C=C=CC#CC


C=C=C=C=CC


CCC1=CC#C1


CC1=CC#CC1


CCC=C1C#C1


CC=1C#CCC=1


CC#CC1=CC1


CC=C1C#CC1


C=C(C)C1C#C1


C=C1C#CC1(C)


C#CC(C)=C=C


CCC=1C=C=C=1


CC=1CC=C=C=1


C#CC=1CC=1(C)


C=C=C1C=C1(C)


C=CC1=C=C1(C)


C=C1C=C=C1(C)


C=C(C)C=1C=C=1


CCC1C2=C=C12


CC1=C=C2CC12


CC2C=1CC2(=C=1)


CC1CC2=C=C12


CCC=1C2=CC=12


CC=1CC2=CC=12


CC=2C1=CC=2(C1)


CC=1C=C2CC=12


CC1=CC=2CC1=2


CC=1C2=CCC=12


CC=C1C=2CC1=2


C=C1C2C(C)=C12


C=C1C=2C(C)C1=2


C=CC1(C)(C#C1)


CC2CC12(C#C1)


CC12(C#CC2(C1))


CC12(C=C=C2(C1))


C=C1C2=CC12(C)


CCC23(C1C3(=C12))


CC1=C3C2CC123


CC1C3=C2CC123


CC23(C1CC3(=C12))


CC23(CC=1C3(C=12))


CC23(CC1C3(=C12))


CC13(CC23(C=C12))


CC24(C1C34(CC123))


CC#CC#CC


CC(C)=C1C#C1


CC=1C#CC=1(C)


CC1=C=C=C1(C)


CC1=C2C(C)=C12


CC2(C)(C1=C=C12)


CC13(C2=C1C23(C))

Hi,

TobiasKind wrote:

Hi, the Geometry Plugin In Marvin 4.1.2 has problems with Claus Benzol, SMILES C12C3C4C1C3C24 which is a probably non-existing C6H6 structure, however it will be generated by deterministic structure generators. Claus Benzol (also Dewar, Kekule and others can be seen here) http://books.google.com/books?vid=OCLC57642783&id=yCE_MoPOsHcC&pg=PA11&lpg=PA11&dq=dewar+benzol&num=100#PPA12,M1

This molecule has no valid conformers (it is a non-existing structure), that's why our conformer generator (Clean3D) does not generate its lowest energy conformer.

Quote:

IF you choose Geometry Options, Calcluate Lowest Energy Conformer Always --> JAVA EXCEPTION It works if you use "Never"

The "Never" option means: take the input structure and calculate the Deriding energy and steric hindrance for this structure. It is useful if you already have a 3D structure and you want to calculate the properties of this input structure. If the input is a 2D structure, then (with "Never" option) it will be treated as a 3D structure with z=0 coordinates.





The "Always" options means: always generate the lowest energy conformer of the input molecule (even if it's a 3D structure).

Quote:

This is not the only molecule there are bunch of others, where this option fails. I will report them later (some of the CDK SMILES are broken). This also affects JCHEM and Instant-JChem (this error with fallback option will render the molecule non-visible). ----------------- Error output java.lang.NullPointerException at chemaxon.calculations.Geometry.get3DMolecule(Geometry.java:80) at chemaxon.marvin.calculations.GeometryPlugin.getResultMolecule(GeometryPlugin.java:693) at chemaxon.marvin.calculations.GeometryPlugin.getResultMolecules(GeometryPlugin.java:718) at chemaxon.marvin.calculations.GeometryPluginDisplay.store(GeometryPluginDisplay.java:49) at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:171) at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:154) at chemaxon.marvin.plugin.CalculatorPluginManager.runPlugin(CalculatorPluginManager.java:108) at chemaxon.marvin.plugin.CalculatorPluginManager.callback(CalculatorPluginManager.java:73) at chemaxon.marvin.plugin.PluginManager.callback(PluginManager.java:87) at chemaxon.marvin.common.swing.MolPanel.run(MolPanel.java:2471) [catch] at java.lang.Thread.run(Unknown Source)

We will replace the exception message with an error message, like in conformer plugin ("No valid conformer or structure generation failed.").





Best regards,


Zsolt