get.volume giving error

[garimaloh]

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

[rajarshi]

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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#123>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAIMOPNVSIO3IVMMO6KLFLTVPLYJANCNFSM47TSBS3Q> .

-- Rajarshi Guha | http://blog.rguha.net | @rguha <https://twitter.com/rguha>

[garimaloh]

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

[garimaloh]

SMILES is a column name in a data table with value in 5th row

[rajarshi]

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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[garimaloh]

I was able to install from github. its= gives me same errors.

[garimaloh]

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

[rajarshi]

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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#123 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAIMOOXFDDMWD7HQY7GXXTTVZJ4TANCNFSM47TSBS3Q> .

-- Rajarshi Guha | http://blog.rguha.net | @rguha <https://twitter.com/rguha>

[rajarshi]

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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#123 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAIMOOXFDDMWD7HQY7GXXTTVZJ4TANCNFSM47TSBS3Q> .

-- Rajarshi Guha | http://blog.rguha.net | @rguha <https://twitter.com/rguha>