Some cxcalc terms fail even with fallback option on

Hi,


the following terms calculations fail (due to the claus benzene?),


cxcalc -g hindrance C6H6-CDK.smi


cxcalc -g dreidingenergy C6H6-CDK.smi


cxcalc -g distance C6H6-CDK.smi


cxcalc -g dihedral C6H6-CDK.smi


cxcalc -g angle C6H6-CDK.smi


All others are OK!





For Instant-JChem:


Some of these SMILES also make problems during the calculation of


stericHindrance(1) to (6). Some of them are calculated some of them


not (around 40), after using the Standardizer or molconvert the number


of failed compounds is random <30-40 (which means values can be calculated). This is within I-JChem.





On the commandline (evaluate has no fallback) it looks like


evaluate -e "stericHindrance(1)" C6H6-CDK.smi





I think thats also the stupid thing about SMILES codes,


everybody invented his own SMILES format, leading to some


nasty interconversion errors and blaiming the other one


not to use "Standard" SMILES :-)





But I am happy with MOLCONVERT which I consider the


best interpreter, at least it can handle also bastard SMILES


from most of the other companies...





Tobias


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


C6H6-CDK.smi





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 following terms calculations fail (due to the claus benzene?), cxcalc -g hindrance C6H6-CDK.smi cxcalc -g dreidingenergy C6H6-CDK.smi cxcalc -g distance C6H6-CDK.smi cxcalc -g dihedral C6H6-CDK.smi cxcalc -g angle C6H6-CDK.smi All others are OK! For Instant-JChem: Some of these SMILES also make problems during the calculation of stericHindrance(1) to (6). Some of them are calculated some of them not (around 40), after using the Standardizer or molconvert the number of failed compounds is random <30-40 (which means values can be calculated). This is within I-JChem. On the commandline (evaluate has no fallback) it looks like evaluate -e "stericHindrance(1)" C6H6-CDK.smi

All these calculations are implemented in Geometry plugin, and their default setting is to generate the lowest energy conformer, if the input structure is not a 3D structure (you can change this behaviour with "-l" command line option, see e.g. "cxcalc hindrance -h" help message for details). Our conformer generator can not generate conformations for non-existing structures (see this topic for details), that's why these calculations fail.

Quote:

I think thats also the stupid thing about SMILES codes, everybody invented his own SMILES format, leading to some nasty interconversion errors and blaiming the other one not to use "Standard" SMILES :-) But I am happy with MOLCONVERT which I consider the best interpreter, at least it can handle also bastard SMILES from most of the other companies...

We are happy to hear this :)





Best regards,


Zsolt