CDK-R
get.volume giving error
am trying to use get.volume to get the molecular volume. But i am getting error. Please would you help me to resolve the issue.
Here is my code:
mols <- parse.smiles(pep[4,SMILES])[[1]] convert.implicit.to.explicit(mols) get.tpsa(mols) [1] 624.96 get.volume(mols) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found
What is the SMILES string? And does this fail with the latest version from Github?
On Wed, Jun 30, 2021 at 11:07 PM Garima @.***> wrote:
am trying to use get.volume to get the molecular volume. But i am getting error. Please would you help me to resolve the issue.
Here is my code:
mols <- parse.smiles(pep[4,SMILES])[[1]] convert.implicit.to.explicit(mols) get.tpsa(mols) [1] 624.96 get.volume(mols) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found
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-- Rajarshi Guha | http://blog.rguha.net | @rguha https://twitter.com/rguha
install_github("https://github.com/CDK-R/rcdklibs") install_github("https://github.com/CDK-R/cdkr", subdir="rcdk")
They dont work for me. How to install this tool from github
What is the error?
Sent from my iPhone
On Jul 2, 2021, at 7:58 PM, Garima @.***> wrote:
SMILES is a column name in a data table with value in 5th row
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mols2 <- parse.smiles(pep[2,SMILES])[[1]] class(mols2) [1] "jobjRef" attr(,"package") [1] "rJava" kk=view.molecule.2d(mols2) Error in view.molecule.2d(mols2) : java.lang.NoSuchMethodError:
get.volume(mols2) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found
What is the SMILES you're trying to parse?
On Fri, Jul 2, 2021 at 8:22 PM Garima @.***> wrote:
mols2 <- parse.smiles(pep[2,SMILES])[[1]] class(mols2) [1] "jobjRef" attr(,"package") [1] "rJava" kk=view.molecule.2d(mols2) Error in view.molecule.2d(mols2) : java.lang.NoSuchMethodError: get.volume(mols2) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found
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The following works for me on OS X (10.15.7), R 4.0.2
m <- parse.smiles('CCC')[[1]]
view.molecule.2d(m)
set.atom.types(mol=m)
get.volume(m)
[1] 60.44441
On Fri, Jul 2, 2021 at 8:22 PM Garima @.***> wrote:
mols2 <- parse.smiles(pep[2,SMILES])[[1]] class(mols2) [1] "jobjRef" attr(,"package") [1] "rJava" kk=view.molecule.2d(mols2) Error in view.molecule.2d(mols2) : java.lang.NoSuchMethodError: get.volume(mols2) Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : org.openscience.cdk.exception.NoSuchAtomTypeException: The AtomType null could not be found
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-- Rajarshi Guha | http://blog.rguha.net | @rguha https://twitter.com/rguha