Comments (3)
I think there was an issue with catching Java exzceptions in R - I have to
revisit that. Can you send an example file to test on?
On Wed, Feb 22, 2012 at 10:38 AM, sneumann <
[email protected]
wrote:
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 foundCan 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
Reply to this email directly or view it on GitHub:
#8
Rajarshi Guha
NIH Chemical Genomics Center
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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,
but I get them further down in my script when trying to obtain the fingerprint.
chebifp[i] <- get.fingerprint(mol, type = "standard") ## Exception with Se.2
I am using
ftp://ftp.ebi.ac.uk/pub/databases/chebi/SDF/ChEBI_complete.sdf.gz
(unzipped first, of course)
Yours, Steffen
from cdkr.
The latest version in github fixes this (if you want to see exceptions set verbose=TRUE in the call to get.fingerprint
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