User 677b9c22ff
14-11-2006 21:50:59
Hi,
if I call cxcalc CC12CCCC1\C3=C(/CC2)C4(C)CCC(=O)CC4CC3 dreidingenergy
CC12CCCC1C3=C(CC2)C4(C)CCC(=O)CC4CC3
O=C1CCC2(C)C=3CCC4(C)CCCC4C=3CCC2C1
[H]C([H])([H])C12C([H])([H])C([H])([H])C([H])([H])C1([H])C3=C(C([H])([H])C2([H])[H])C4(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C([H])([H])C4([H])C([H])([H])C3([H])[H]
CC12CCCC1\C3=C(/CC2)C4(C)CCC(=O)CC4CC3
I get an error also for these (same) smiles, however in Marvin it works
90-95 kcal/mol:
Exception in thread "main" java.io.IOException: Unmatched ring closure number 2 in SMILES string
at chemaxon.marvin.modules.SmilesImport.readMol0(SmilesImport.java:893)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:528)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:457)
at chemaxon.formats.MolImporter.readMol(MolImporter.java:763)
at chemaxon.formats.MolImporter.read(MolImporter.java:595)
at chemaxon.formats.MolImporter.read(MolImporter.java:561)
at chemaxon.marvin.Calculator.readMol(Calculator.java:674)
at chemaxon.marvin.Calculator.run(Calculator.java:852)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
--------------------------
Marvin can read it, cxcalc + dreidingenergy
CC1=CC(=[N+]=N1)c2ccccc2
Invalid state in BuildCommand.
No regular build due to fallback.
Error at molecule: 1249 ID = 1249
java.lang.ArrayIndexOutOfBoundsException: 0
java.lang.ArrayIndexOutOfBoundsException: 0
at chemaxon.marvin.modelling.struc.MultiConformerImpl$1.isGreater(MultiConformerImpl.java:144)
at chemaxon.marvin.modules.Optimization.quickSort(Optimization.java:5039)
at chemaxon.marvin.modules.Optimization.quickSort(Optimization.java:5022)
at chemaxon.marvin.modelling.struc.MultiConformerImpl.sortByEnergy(MultiConformerImpl.java:141)
at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:676)
at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)
at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)
at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3114)
at chemaxon.struc.Molecule.clean(Molecule.java:598)
at chemaxon.calculations.Geometry.calculateLowestEnergyConformer(Geometry.java:110)
at chemaxon.marvin.calculations.GeometryPlugin.calculateLowestEnergyConformer(GeometryPlugin.java:310)
at chemaxon.marvin.calculations.GeometryPlugin.run(GeometryPlugin.java:515)
at chemaxon.marvin.plugin.CalculatorPluginOutput.getResult(CalculatorPluginOutput.java:208)
at chemaxon.marvin.Calculator.run(Calculator.java:880)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
'em' is not recognized as an internal or external command,
-------------------------
working example with Iron atom.
Z:\>cxcalc Fe dreidingenergy
id Dreiding energy
1 58.43
non-working example from smiles file (put Fe into iron.smi)
Z:\>cxcalc iron.smi dreidingenergy
Exception in thread "main" java.io.IOException: Unrecognized element type "e"
at chemaxon.marvin.modules.SmilesImport.readSymbolAndAddAtom(SmilesImport.java:1124)
at chemaxon.marvin.modules.SmilesImport.readMol0(SmilesImport.java:633)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:528)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:457)
at chemaxon.formats.MolImporter.readMol(MolImporter.java:763)
at chemaxon.formats.MolImporter.read(MolImporter.java:595)
at chemaxon.formats.MolImporter.read(MolImporter.java:561)
at chemaxon.marvin.Calculator.readMol(Calculator.java:674)
at chemaxon.marvin.Calculator.run(Calculator.java:852)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
--------------------------
The same problem with Fe in a smiles file refers to molconvert
Hence put Fe into iron.smi (on line) and run:
molconvert smiles -3:EP iron.smi -T Energy
ERROR:
error: Unrecognized element type "e"
If you put oxygen in, it works.
So I guess all the metals throw an exception.
Molconvert also throws an exception on this one.
CC1=[N+]=NC(C)=C1C=Cc2ccccc2
-------------------------
I think it would be nice if cxcalc is called from the batch file would
put an "error" in the list, instead of thrwoing an JAVA exception to the console. Especially if thousands of molecules are calculated and then
in the very middle it throws an exception.
So, after running some samples, it does actually what I suggested :-)
For Marvin no problem
CC(=O)N(Nc1ccc(cc1)-c2ccc(cc2)[N+]([O-])=O)c3ccccc3
For cxcalc, it says error but calculates further (good).
ERROR! Exception: 0 >= 0
This build will report FAIL, exception not thrown.
java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at java.util.Vector.elementAt(Unknown Source)
at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:971)
at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)
at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)
at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)
at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)
at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1484)
at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:770)
at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)
at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)
at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)
at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)
at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:664)
at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)
at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)
at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3114)
at chemaxon.struc.Molecule.clean(Molecule.java:598)
at chemaxon.calculations.Geometry.calculateLowestEnergyConformer(Geometry.java:110)
at chemaxon.marvin.calculations.GeometryPlugin.calculateLowestEnergyConformer(GeometryPlugin.java:310)
at chemaxon.marvin.calculations.GeometryPlugin.run(GeometryPlugin.java:515)
at chemaxon.marvin.plugin.CalculatorPluginOutput.getResult(CalculatorPluginOutput.java:208)
at chemaxon.marvin.Calculator.run(Calculator.java:880)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
Tobias
if I call cxcalc CC12CCCC1\C3=C(/CC2)C4(C)CCC(=O)CC4CC3 dreidingenergy
CC12CCCC1C3=C(CC2)C4(C)CCC(=O)CC4CC3
O=C1CCC2(C)C=3CCC4(C)CCCC4C=3CCC2C1
[H]C([H])([H])C12C([H])([H])C([H])([H])C([H])([H])C1([H])C3=C(C([H])([H])C2([H])[H])C4(C([H])([H])[H])C([H])([H])C([H])([H])C(=O)C([H])([H])C4([H])C([H])([H])C3([H])[H]
CC12CCCC1\C3=C(/CC2)C4(C)CCC(=O)CC4CC3
I get an error also for these (same) smiles, however in Marvin it works
90-95 kcal/mol:
Exception in thread "main" java.io.IOException: Unmatched ring closure number 2 in SMILES string
at chemaxon.marvin.modules.SmilesImport.readMol0(SmilesImport.java:893)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:528)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:457)
at chemaxon.formats.MolImporter.readMol(MolImporter.java:763)
at chemaxon.formats.MolImporter.read(MolImporter.java:595)
at chemaxon.formats.MolImporter.read(MolImporter.java:561)
at chemaxon.marvin.Calculator.readMol(Calculator.java:674)
at chemaxon.marvin.Calculator.run(Calculator.java:852)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
--------------------------
Marvin can read it, cxcalc + dreidingenergy
CC1=CC(=[N+]=N1)c2ccccc2
Invalid state in BuildCommand.
No regular build due to fallback.
Error at molecule: 1249 ID = 1249
java.lang.ArrayIndexOutOfBoundsException: 0
java.lang.ArrayIndexOutOfBoundsException: 0
at chemaxon.marvin.modelling.struc.MultiConformerImpl$1.isGreater(MultiConformerImpl.java:144)
at chemaxon.marvin.modules.Optimization.quickSort(Optimization.java:5039)
at chemaxon.marvin.modules.Optimization.quickSort(Optimization.java:5022)
at chemaxon.marvin.modelling.struc.MultiConformerImpl.sortByEnergy(MultiConformerImpl.java:141)
at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:676)
at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)
at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)
at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3114)
at chemaxon.struc.Molecule.clean(Molecule.java:598)
at chemaxon.calculations.Geometry.calculateLowestEnergyConformer(Geometry.java:110)
at chemaxon.marvin.calculations.GeometryPlugin.calculateLowestEnergyConformer(GeometryPlugin.java:310)
at chemaxon.marvin.calculations.GeometryPlugin.run(GeometryPlugin.java:515)
at chemaxon.marvin.plugin.CalculatorPluginOutput.getResult(CalculatorPluginOutput.java:208)
at chemaxon.marvin.Calculator.run(Calculator.java:880)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
'em' is not recognized as an internal or external command,
-------------------------
working example with Iron atom.
Z:\>cxcalc Fe dreidingenergy
id Dreiding energy
1 58.43
non-working example from smiles file (put Fe into iron.smi)
Z:\>cxcalc iron.smi dreidingenergy
Exception in thread "main" java.io.IOException: Unrecognized element type "e"
at chemaxon.marvin.modules.SmilesImport.readSymbolAndAddAtom(SmilesImport.java:1124)
at chemaxon.marvin.modules.SmilesImport.readMol0(SmilesImport.java:633)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:528)
at chemaxon.marvin.modules.SmilesImport.readMol(SmilesImport.java:457)
at chemaxon.formats.MolImporter.readMol(MolImporter.java:763)
at chemaxon.formats.MolImporter.read(MolImporter.java:595)
at chemaxon.formats.MolImporter.read(MolImporter.java:561)
at chemaxon.marvin.Calculator.readMol(Calculator.java:674)
at chemaxon.marvin.Calculator.run(Calculator.java:852)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
--------------------------
The same problem with Fe in a smiles file refers to molconvert
Hence put Fe into iron.smi (on line) and run:
molconvert smiles -3:EP iron.smi -T Energy
ERROR:
error: Unrecognized element type "e"
If you put oxygen in, it works.
So I guess all the metals throw an exception.
Molconvert also throws an exception on this one.
CC1=[N+]=NC(C)=C1C=Cc2ccccc2
-------------------------
I think it would be nice if cxcalc is called from the batch file would
put an "error" in the list, instead of thrwoing an JAVA exception to the console. Especially if thousands of molecules are calculated and then
in the very middle it throws an exception.
So, after running some samples, it does actually what I suggested :-)
For Marvin no problem
CC(=O)N(Nc1ccc(cc1)-c2ccc(cc2)[N+]([O-])=O)c3ccccc3
For cxcalc, it says error but calculates further (good).
ERROR! Exception: 0 >= 0
This build will report FAIL, exception not thrown.
java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
at java.util.Vector.elementAt(Unknown Source)
at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:971)
at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)
at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)
at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)
at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)
at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1484)
at chemaxon.marvin.modelling.build.FragFragFuser.nextFuse(FragFragFuser.java:770)
at chemaxon.marvin.modelling.build.FragFragFuser.invokeBuild(FragFragFuser.java:410)
at chemaxon.marvin.modelling.build.FragClean$FragFragFuseBuildCommand.invokeBuild(FragClean.java:289)
at chemaxon.marvin.modelling.build.BuildCommand.fetchCoordinates(BuildCommand.java:936)
at chemaxon.marvin.modelling.build.BuildCommand.build(BuildCommand.java:1778)
at chemaxon.marvin.modelling.build.FragClean$MultiFragBuildCommand.build(FragClean.java:664)
at chemaxon.marvin.modelling.build.FragClean.startClean(FragClean.java:98)
at chemaxon.marvin.modules.Clean3D.modfunc_0(Clean3D.java:1438)
at chemaxon.marvin.modules.Clean3D.modfunc(Clean3D.java:491)
at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:3114)
at chemaxon.struc.Molecule.clean(Molecule.java:598)
at chemaxon.calculations.Geometry.calculateLowestEnergyConformer(Geometry.java:110)
at chemaxon.marvin.calculations.GeometryPlugin.calculateLowestEnergyConformer(GeometryPlugin.java:310)
at chemaxon.marvin.calculations.GeometryPlugin.run(GeometryPlugin.java:515)
at chemaxon.marvin.plugin.CalculatorPluginOutput.getResult(CalculatorPluginOutput.java:208)
at chemaxon.marvin.Calculator.run(Calculator.java:880)
at chemaxon.marvin.Calculator.main(Calculator.java:1076)
Tobias