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More robust iload.molecules() in case of NoSuchAtomTypeException #8
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I think there was an issue with catching Java exzceptions in R - I have to On Wed, Feb 22, 2012 at 10:38 AM, sneumann <
Rajarshi Guha |
Actually, with ## iterate over a large file
moliter <- iload.molecules(chebifile, type="sdf",
aromaticity = FALSE, typing = FALSE, skip=TRUE) the problem is not anymore in the iteration through the file, chebifp[i] <- get.fingerprint(mol, type = "standard") ## Exception with Se.2 I am using Yours, Steffen |
The latest version in github fixes this (if you want to see exceptions set verbose=TRUE in the call to get.fingerprint |
Hi,
another problem occurs for other exceptions:
Error in .jcall(.jnew("org/openscience/cdk/ChemObject"), "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;", :
org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType Se.2 could not be found
Can these be caught with rJava ? And an option added to iload.molecules()
to just jump over them, because we can't do anything with them anyway ?
Yours,
Steffen
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